AU2015203111B2 - Use of microvesicles in diagnosis, prognosis and treatment of medical diseases and conditions - Google Patents

Abstract

The presently disclosed subject matter is directed to methods of aiding diagnosis, prognosis, monitoring and evaluation of a disease or other medical condition in a' subject by detecting a biomarker in microvesicles isolated from a biological, sample from the subject. Moreover, disclosed subject matter is directed to methods of diagnosis, monitoring a disease by determining the concentration of microvesicles within a biological sample; methods of delivering a nucleic acid or protein to a target all by administering microvesicles that contain said nucleic acid or protein; methods for performing a body fluid transfusion by introducing a microvesicle-free or microvesicle enriched fluid fraction into a patient.

Description

PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

USE OF MICROVESICLES IN DIAGNOSIS, PROGNOSIS AND TREATMENT OF MEDICAL DISEASES AND CONDITIONS

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application claims priority to US provisional applications 61/025,536, filed February 1, 2008 and 61/100,293, filed September 26, 2008, each of which is incorporated herein by reference in its entirety.

GOVERNMENTAL SUPPORT

[0002] This invention was made with Government support under grants NCI CA86355 and NCI CA69246 awarded by the National Cancer Institute. The Government has certain rights in the invention.

FIELD OF THE INVENTION

[0003] The present invention relates to the fields of medical diagnosis, patient monitoring, treatment efficacy evaluation, nucleic acid and protein delivery, and blood transfusion.

BACKGROUND OF THE INVENTION

[0004] Glioblastomas are highly malignant brain tumors with a poor prognosis despite intensive research and clinical efforts (Louis et al., 2007). The invasive nature of this tumor makes complete surgical resection impossible and the median survival time is only about 15 months (Stupp et al., 2005). Glioblastoma cells as well as many other tumor cells have a remarkable ability to mold their stromal environment to their own advantage. Tumor cells directly alter surrounding normal cells to facilitate tumor cell growth, invasion, chemo-resistance, immune-evasion and metastasis (Mazzocca et al., 2005; Muerkoster et al., 2004; Singer et al., 2007). The tumor cells also hijack the normal vasculature and stimulate rapid formation of new blood vessels to supply the tumor with nutrition (Carmeliet and Jain, 2000). Although the immune system can initially suppress tumor growth, it is often progressively blunted by tumor activation of immunosuppressive pathways (Gabrilovich, 2007).

[0005] Small microvesicles shed by cells are known as exosomes (Thery et al., 2002). Exosomes are reported as having a diameter of approximately 30-100 nm and are shed from many different cell types under both normal and pathological conditions (Thery et al., 2002). These microvesicles were first described as a mechanism to discard transferrin-receptors 1 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 from the cell surface of maturing reticulocytes (Pan and Johnstone, 1983). Exosomes are formed through inward budding of endosomal membranes giving rise to intracellular multivesicular bodies (MVB) that later fuse with the plasma membrane, releasing the exosomes to the exterior (Thery et al., 2002). However, there is now evidence for a more direct release of exosomes. Certain cells, such as Jurkat T-cells, are said to shed exosomes directly by outward budding of the plasma membrane (Booth et al., 2006). All membrane vesicles shed by cells are referred to herein collectively as microvesicles.

[0006] Microvesicles in Drosophila melanogaster, so called argosomes, are said to contain morphogens such as Wingless protein and to move over large distances through the imaginal disc epithelium in developing Drosophila melanogaster embryos (Greco et al., 2001). Microvesicles found in semen, known as prostasomes, are stated to have a wide range of functions including the promotion of sperm motility, the stabilization of the acrosome reaction, the facilitation of immunosuppression and the inhibition of angiogenesis (Delves et al., 2007). On the other hand, prostasomes released by malignant prostate cells are said to promote angiogenesis. Microvesicles are said to transfer proteins (Mack et al., 2000) and recent studies state that microvesicles isolated from different cell lines can also contain messenger RNA (mRNA) and microRNA (miRNA) and can transfer mRNA to other cell types (Baj-Krzyworzeka et al., 2006; Valadi et al., 2007).

[0007] Microvesicles derived from B-cells and dendritic cells are stated to have potent immuno-stimulatory and antitumor effects in vivo and have been used as antitumor vaccines (Chaput et al., 2005). Dendritic cell-derived microvesicles are stated to contain the costimulatory proteins necessary for T-cell activation, whereas most tumor cell-derived microvesicles do not (Wieckowski and Whiteside, 2006). Microvesicles isolated from tumor cells may act to suppress the immune response and accelerate tumor growth (Clayton et al., 2007; Liu et al., 2006a). Breast cancer microvesicles may stimulate angiogenesis, and platelet-derived micro vesicles may promote tumor progression and metastasis of lung cancer cells (Janowska-Wieczorek et al., 2005; Millimaggi et al., 2007).

[0008] Cancers arise through accumulation of genetic alterations that promote unrestricted cell growth. It has been stated that each tumor harbors, on average, around 50-80 mutations that are absent in non-tumor cells (Jones et al., 2008; Parsons et al., 2008; Wood et al., 2007). Current techniques to detect these mutation profiles include the analysis of biopsy samples and the non-invasive analysis of mutant tumor DNA fragments circulating in bodily fluids such as blood (Diehl et al., 2008). The former method is invasive, complicated and 2 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 possibly harmful to subjects. The latter method inherently lacks sensitivity due to the extremely low copy number of mutant cancer DNA in bodily fluid (Gormally et al., 2007). Therefore, one challenge facing cancer diagnosis is to develop a diagnostic method that can detect tumor cells at different stages non-invasively, yet with high sensitivity and specificity. It has also been stated that gene expression profiles (encoding mRNA or microRNA) can distinguish cancerous and non-cancerous tissue (Jones et al., 2008; Parsons et al., 2008; Schetter et al., 2008). However, current diagnostic techniques to detect gene expression profiles require intrusive biopsy of tissues. Some biopsy procedures cause high risk and are potentially harmful. Moreover, in a biopsy procedure, tissue samples are taken from a limited area and may give false positives or false negatives, especially in tumors which are heterogeneous and/or dispersed within normal tissue. Therefore, a non-intrusive and sensitive diagnostic method for detecting biomarkers would be highly desirable.

SUMMARY OF THE INVENTION

[0009] In general, the invention is a novel method for detecting in a subject the presence or absence of a variety of biomarkers contained in micro vesicles, thereby aiding the diagnosis, monitoring and evaluation of diseases, other medical conditions, and treatment efficacy associated with microvesicle biomarkers.

[0010] One aspect of the invention are methods for aiding in the diagnosis or monitoring of a disease or other medical condition in a subject, comprising the steps of: a) isolating a microvesicle fraction from a biological sample from the subject; and b) detecting the presence or absence of a biomarker within the microvesicle fraction, wherein the biomarker is associated with the disease or other medical condition. The methods may further comprise the step or steps of comparing the result of the detection step to a control (e.g., comparing the amount of one or more biomarkers detected in the sample to one or more control levels), wherein the subject is diagnosed as having the disease or other medical condition (e.g., cancer) if there is a measurable difference in the result of the detection step as compared to a control.

[0011] Another aspect of the invention is a method for aiding in the evaluation of treatment efficacy in a subject, comprising the steps of: a) isolating a microvesicle fraction from a biological sample from the subject; and b) detecting the presence or absence of a biomarker within the microvesicle fraction, wherein the biomarker is associated with the treatment efficacy for a disease or other medical condition. The method may further 3 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 comprise the step of providing a series of a biological samples over a period of time from the subject. Additionally, the method may further comprise the step or steps of determining any measurable change in the results of the detection step (e.g., the amount of one or more detected biomarkers) in each of the biological samples from the series to thereby evaluate treatment efficacy for the disease or other medical condition.

[0012] In certain preferred embodiments of the foregoing aspects of the invention, the biological sample from the subject is a sample of bodily fluid. Particularly preferred body fluids are blood and urine.

[0013] In certain preferred embodiments of the foregoing aspects of the invention, the methods further comprise the isolation of a selective microvesicle fraction derived from cells of a specific type (e.g., cancer or tumor cells). Additionally, the selective microvesicle fraction may consist essentially of urinary micro vesicles.

[0014] In certain embodiments of the foregoing aspects of the invention, the biomarker associated with a disease or other medical condition is i) a species of nucleic acid; ii) a level of expression of one or more nucleic acids; iii) a nucleic acid variant; or iv) a combination of any of the foregoing. Preferred embodiments of such biomarkers include messenger RNA, microRNA, DNA, single stranded DNA, complementary DNA and noncoding DNA.

[0015] In certain embodiments of the foregoing aspects of the invention, the disease or other medical condition is a neoplastic disease or condition (e.g., glioblastoma, pancreatic cancer, breast cancer, melanoma and colorectal cancer), a metabolic disease or condition (e.g., diabetes, inflammation, perinatal conditions or a disease or condition associated with iron metabolism), a post transplantation condition, or a fetal condition.

[0016] Another aspect of the invention is a method for aiding in the diagnosis or monitoring of a disease or other medical condition in a subject, comprising the steps of a) obtaining a biological sample from the subject; and b) determining the concentration of microvesicles within the biological sample.

[0017] Yet another aspect of this invention is a method for delivering a nucleic acid or protein to a target cell in an individual comprising the steps of administering microvesicles which contain the nucleic acid or protein, or one or more cells that produce such microvesicles, to the individual such that the micro vesicles enter the target cell of the individual. In a preferred embodiment of this aspect of the invention, microvesicles are delivered to brain cells. 4 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 [0018] A further aspect of this invention is a method for performing bodily fluid transfusion (e.g., blood, serum or plasma), comprising the steps of obtaining a fraction of donor body fluid free of all or substantially all microvesicles, or free of all or substantially all microvesicles from a particular cell type (e.g., tumor cells), and introducing the microvesicle-free fraction to a patient. A related aspect of this invention is a composition of matter comprising a sample of body fluid (e.g., blood, serum or plasma) free of all or substantially all micro vesicles, or free of all or substantially all micro vesicles from a particular cell type.

[0019] Another aspect of this invention is a method for performing bodily fluid transfusion (e.g., blood, serum or plasma), comprising the steps of obtaining a microvesicle-enriched fraction of donor body fluid and introducing the microvesicle-enriched fraction to a patient. In a preferred embodiment, the fraction is enriched with micro vesicles derived from a particular cell type. A related aspect of this invention is a composition of matter comprising a sample of bodily fluid (e.g., blood, serum or plasma) enriched with micro vesicles.

[0020] A further aspect of this invention is a method for aiding in the identification of new biomarkers associated with a disease or other medical condition, comprising the steps of obtaining a biological sample from a subject; isolating a microvesicle fraction from the sample; and detecting within the microvesicle fraction species of nucleic acid; their respective expression levels or concentrations; nucleic acid variants; or combinations thereof.

[0021] Various aspects and embodiments of the invention will now be described in detail. It will be appreciated that modification of the details may be made without departing from the scope of the invention. Further, unless otherwise required by context, singular terms shall include pluralities and plural terms shall include the singular.

[0022] All patents, patent applications, and publications identified are expressly incorporated herein by reference for the purpose of describing and disclosing, for example, the methodologies described in such publications that might be used in connection with the present invention. These publications are provided solely for their disclosure prior to the filing date of the present application. Nothing in this regard should be construed as an admission that the inventors are not entitled to antedate such disclosure by virtue of prior invention or for any other reason. All statements as to the date or representations as to the contents of these documents are based on the information available to the applicants and do not constitute any admission as to the correctness of the dates or contents of these documents. 5 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

BRIEF DESCRIPTION OF THE DRAWINGS FIGURE 1. Glioblastoma cells produce microvesicles containing RNA. (a) Scanning electron microscopy image of a primary glioblastoma cell (bar = 10 pm), (b) Higher magnification showing the microvesicles on the cell surface. The vesicles vary in size with diameters between around 50 nm and around 500 nm (bar = 1 pm), (c) Graph showing the amount of total RNA extracted from microvesicles that were either treated or not treated with RNase A. The amounts are indicated as the absorption (Abs, y-axis) of 260nm wavelength (x-axis). The experiments were repeated 5 times and a representative graph is shown, (d) Bioanalyzer data showing the size distribution of total RNA extracted from primary glioblastoma cells and (e) Bioanalyzer data showing the size distribution of total RNA extracted from micro vesicles isolated from primary glioblastoma cells. The 25 nt peak represents an internal standard. The two prominent peaks in (d) (arrows) represent 18S (left arrow) and 28S (right arrow) ribosomal RNA. The ribosomal peaks are absent from RNA extracted from micro vesicles (e). (f) Transmission electron microscopy image of microvesicles secreted by primary glioblastoma cells (bar = 100 nm). FIGURE 2. Analysis of microvesicle RNA. FIGS. 2 (a) and 2 (b) are scatter plots of mRNA levels in microvesicles and mRNA levels in donor glioblastoma cells from two different experiments. Linear regressions show that mRNA levels in donor cells versus microvesicles were not well correlated. FIGS. 2 (c) and 2 (d) are mRNA levels in two different donor cells or two different micro vesicle preparations. In contrast to FIGS. 2 (a) and 2 (b), linear regressions show that mRNA levels between donor cells FIG 2 (c) or between microvesicles FIG 2 (d) were closely correlated. FIGURE 3. Analysis of microvesicle DNA. a) GAPDH gene amplification with DNA templates from exosomes treated with DNase prior to nucleic acid extraction. The lanes are identified as follows: 1. lOObp MW ladder 2. Negative control 3. Genomic DNA control from GBM 20/3 cells 4. DNA from normal serum exosomes (tumor cell-free control) 5. Exosome DNA from normal human fibroblasts (NHF19) 6. Exosome DNA from primary medulloblastoma cells (D425) 6 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 b) GAPDH gene amplification with DNA templates from exosomes without prior DNase treatment. The lanes are identified as follows: 1. lOObp MW ladder 2. DNA from primary melanoma cell 0105 3. Exosome DNA from melanoma 0105 4. Negative Control 5. cDNA from primary GBM 20/3 (positive control) c) Human Endogenous Retrovirus K gene amplification. The lanes are identified as follows: 1. 100 bp MW ladder 2. Exosome DNA from medulloblastoma D425 a 3. Exosome DNA from medulloblasotma D425 b 4. Exosome DNA from normal human fibroblasts (NHF19) 5. Exosome DNA from normal human serum 6. Genomic DNA from GBM 20/3. 7. Negative Control d) Tenascin C gene amplification. The lanes are listed identified follows: 1. lOObp MW ladder 2. Exosomes from normal human fibroblasts (NHF19) 3. Exosomes from serum (tumor cell free individual A) 4. Exosomes from serum (tumor cell free individual B) 5. Exosomes from primary medulloblastoma cell D425 e) Transposable Line 1 element amplification. The lanes are identified as follows: 1. lOObp MW ladder. 2. Exosome DNA from normal human serum. 3. Exosome DNA from normal human fibroblasts 4. Exosome DNA from medulloblastoma D425 a 7 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 5. Exosome DNA from medulloblastoma D425 b f) DNA is present in exosomes from D425 medulloblastoma cell. The lanes are identified as follows: 1. lOObp marker 2. D425 no DNase 3. D425 with DNase 4. lkb marker g) Single stranded nucleic acid analysis using a RNA pico chip. Upper panel: purified DNA was not treated with DNase; lower panel: purified DNA was treated with DNase. The arrow in the upper panel refers to the detected nucleic acids. The peak at 25 nt is an internal standard. h) Analysis of nucleic acids contained in exosomes from primary medulloblastoma D425. Upper panel: single stranded nucleic acids detected by a RNA pico chip. Lower panel: double stranded nucleic acids detected by a DNA 1000 chip. The arrow in the upper panel refers to the detected nucleic acids. The two peaks (15 and 1500 bp) are internal standards. i) Analysis of exosome DNA from different origins using a RNA pico chip. Upper panel: DNA was extracted from exosomes from glioblastoma cells. Lower panel: DNA was extracted from exosomes from normal human fibroblasts. FIGURE 4. Extracellular RNA extraction from serum is more efficient when a serum exosome isolation step is included, a) Exosome RNA from serum, b) Direct whole serum extraction, c) Empty well. Arrows refer to the detected RNA in the samples. FIGURE 5. Comparison of gene expression levels between microvesicles and cells of origin. 3426 genes were found to be more than 5-fold differentially distributed in the microvesicles as compared to the cells from which they were derived (p-value <0.01). FIGURE 6. Ontological analysis of microvesicular RNAs. (a) Pie chart displays the biological process ontology of the 500 most abundant mRNA species in the micro vesicles. (b) Graph showing the intensity of microvesicle RNAs belonging to ontologies related to tumor growth. The x-axis represents the number of mRNA transcripts present in the ontology. The median intensity levels on the arrays were 182. 8 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 FIGURE 7. Clustering diagram of mRNA levels. Microarray data on the mRNA expression profiles in cell lines and exosomes isolated from the culture media of these cell lines were analyzed and clusters of expression profiles were generated. The labels of the RNA species are as follows: 20/3C-1: Glioblastoma 20/3 Cell RNA, array replicate 1 20/3C-2: Glioblastoma 20/3 Cell RNA, array replicate 2

11/5C: Glioblastoma 11/5 Cell RNA

0105C: Melanoma 0105 Cell RNA

0664C: Melanoma 0664 Cell RNA 0664 E-l: Melanoma 0664 exosome RNA, array replicate 1 0664 E-2: Melanoma 0664 exosome RNA, array replicate 2

0105E: Melanoma 0105 Exosome RNA

20/3E: Glioblastoma 20/3 Exosome RNA 11/5E-1: Glioblastoma 11/5 Exosomes, array replicate 1 11/5E-2: Glioblastoma 11/5 Exosomes, array replicate 2 GBM: glioblastoma. The scale refers to the distance between clusters. FIGURE 8. Microvesicles from serum contain microRNAs. Levels of mature miRNAs extracted from microvesicles and from glioblastoma cells from two different patients (GBM1 and GBM2) were analysed using quantitative miRNA RT-PCR. The cycle threshold (Ct) value is presented as the mean + SEM (n = 4). FIGURE 9. Clustering diagram of microRNA levels. Microarray data on the microRNA expression profiles in cell lines and exosomes isolated from the culture media of these cell lines were analyzed and clusters of expression profiles were generated. The labels of the RNA species are as follows: 0664C-1: Melanoma 0664 Cell RNA, array replicate 1 0664C-2: Melanoma 0664 Cell RNA, array replicate 2 0105C-1: Melanoma 0105 Cell RNA, array replicate 1 0105C-2: Melanoma 0105 Cell RNA, array replicate 2 9 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 20/3C-1: Glioblastoma 20/3 Cell RNA, array replicate 1 20/3C-2: Glioblastoma 20/3 Cell RNA, array replicate 2 11/5C-1: Glioblastoma 11/5 Cell RNA, array replicate 1 11/5C-2: Glioblastoma 11/5 Cell RNA, array replicate 2 11/5E-1: Glioblastoma 11/5 Exosomes, array replicate 1 11/5E-2: Glioblastoma 11/5 Exosomes, array replicate 2 20/3E-1: Glioblastoma 20/3 Exosome RNA, array replicate 1 20/3E-2: Glioblastoma 20/3 Exosome RNA, array replicate 2

0664 E: Melanoma 0664 exosome RNA 0105E-1: Melanoma 0105 Exosome RNA, array replicate 1 0105E-2: Melanoma 0105 Exosome RNA, array replicate 2 GBM: Glioblastoma. The scale refers to the distance between clusters. FIGURE 10. The expression level of microRNA-21 in serum microvesicles is associated with glioma. Shown is a bar graph, normal control serum on the left, glioma serum on the right. Quantitative RT-PCR was used to measure the levels of microRNA-21 (miR-21) in exosomes from serum of glioblastoma patients as well as normal patient controls. Glioblastoma serum showed a 5.4 reduction of the Ct-value, corresponding to an approximately 40 (2ACt)-fold increase of miR21. The miR21 levels were normalized to GAPDH in each sample (n=3). FIGURE 11. Nested RT-PCR was used to detect EGFRvin mRNA in tumor samples and corresponding serum exosomes. The wild type EGFR PCR product appears as a band at 1153 bp and the EGFRvIII PCR product appears as a band at 352 bp. RT PCR of GAPDH mRNA was included as a positive control (226 bp). Samples considered as positive for EGFRvIII are indicated with an asterisk. Patients 11,12 and 14 showed only a weak amplification of EGFRvIII in the tumor sample, but it was evident when more samples were loaded. FIGURE 12. Nested RT PCR of EGFRvIII was performed on microvesicles from 52 normal control serums. EGFRvIII (352 bp) was never found in the normal control serums. PCR of GAPDH (226 bp) was included as a control. 10 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 FIGURE 13. Hepcidin mRNA can be detected within exosomes from human serum. A) Pseudo-gel generated by an Agilent Bioanalyzer. B) Raw plot generated by an Agilent Bioanalyser for the positive control (Sample 1). C) Raw plot generated by an Agilent Bioanalyser for the negative control (Sample 2). D) Raw plot generated by an Agilent Bioanalyser for the exosomes (Sample 3). FIGURE 14. Urinary exosome isolation and nucleic acid identification within urinary exosomes. (a) Electron microscopy image of a multivesicular body (MVB) containing many small “exosomes” in a kidney tubule cell, (b) Electron microscopy image of isolated urinary exosomes. (c) Analysis of RNA transcripts contained within urinary exosomes by an Agilent Bioanalyzer. A broad range of RNA species were identified but both 18S and 28S ribosomal RNAs were absent, (d) Identification of various RNA transcripts in urinary exosomes by PCR. The transcripts thus identified were: Aquaporin 1 (AQP1); Aquaporin 2 (AQP2); Cubulin (CUBN); Megalin (LRP2); Arginine Vasopressin Receptor 2 (AVPR2); Sodium/Hydrogen Exchanger 3 (SLC9A3); V-ATPase B1 subunit (ATP6V1B1); Nephrin (NPHS1); Podocin (NPHS2); and Chloride Channel 3 (CLCN3). From top to bottom, the five bands in the molecular weight (MW) lane correspond to 1000, 850, 650, 500, 400, 300 base pair fragments, (e) Bioanalyzer diagrams of exosomal nucleic acids from urine samples. The numbers refer to the numbering of human individuals, (f) Pseudogels depicting PCR products generated with different primer pairs using the nucleic acid extracts described in (e). House refers to actin gene and the actin primers were from Ambion (TX, USA). The +ve control refers to PCRs using human kidney cDNA from Ambion (TX, USA) as templates and the -ve control refers to PCRs without nucleic acid templates, (g) Pseudo-gel picture showing positive identification of actin gene cDNA via PCR with and without the DNase treatment of exosomes prior to nucleic acid extraction, (h) Bioanalyzer diagrams showing the amount of nucleic acids isolated from human urinary exosomes. FIGURE 15. Analysis of prostate cancer biomarkers in urinary exosomes. (a) Gel pictures showing PCR products of the TMPRSS2-ERG gene and digested fragments of the PCR products. PI and P2 refer to urine samples from patient 1 and patient 2, respectively.

For each sample, the undigested product is in the left lane and the digested product is in the right lane. MWM indicates lanes with MW markers. The sizes of the bands (both undigested and digested) are indicated on the right of the panel, (b) Gel pictures showing PCR products of the PCA3 gene and digested fragments of the PCR products. PI, P2, P3 and P4 refer to urine samples from patient 1, patient 2, patient 3 and patient 4, respectively. For each 11 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 sample, the undigested product is in the left lane and the digested product is in the right lane. MWM indicates lanes with MW markers. The sizes of the bands (both undigested and digested) are indicated on the right of the panel, (c) A summary of the information of the patients and the data presented in (a) and (b). TMERG refers to the TMPRSS2-ERG fusion gene. FIGURE 16. BRAF mRNA is contained within microvesicles shed by melanoma cells, (a) An electrophoresis gel picture showing RT-PCR products of BRAF gene amplification, (b) An electrophoresis gel picture showing RT-PCR products of GAPDH gene amplification. The lanes and their corresponding samples are as follows: Lane #1 - 100 bp Molecular Weight marker; Lane #2 - YUMEL-01-06 exo; Lane # 3 - YUMEL-01-06 cell; Lane # 4 YUMEL-06-64 exo; Lane # 5. YUMEL-06-64 cell; Lane # 6. M34 exo; Lane # 7 -M34 cell; Lane # 8 - Fibroblast cell; Lane # 9 - Negative control. The reference term “exo” means that the RNA was extracted from exosomes in the culture media. The reference term “cell” means that the RNA was extracted from the cultured cells. The numbers following YUMEL refers to the identification of a specific batch of YUMEL cell line, (c) Sequencing results of PCR products from YUMEL-01-06 exo. The results from YUMEL-01-06 cell, YUMEL-06-64 exo and YUMEL-06-64 cell are the same as those from YUMEL-01-06 exo. (d) Sequencing results of PCR products from M34 exo. The results from M34 cell are the same as those from M34 exo. FIGURE 17. Glioblastoma micro vesicles can deliver functional RNA to HBMVECs. (a) Purified microvesicles were labelled with membrane dye PKH67 (green) and added to HBMVECs. The microvesicles were internalised into endosome-like structures within an hour, (b) Microvesicles were isolated from glioblastoma cells stably expressing Glue. RNA extraction and RT-PCR of Glue and GAPDH mRNAs showed that both were incorporated into microvesicles, (c) Microvesicles were then added to HBMVECs and incubated for 24 hours. The Glue activity was measured in the medium at 0, 15 and 24 hours after micro vesicle addition and normalized to Glue activity in micro vesicles. The results are presented as the mean + SEM (n = 4). FIGURE 18. Glioblastoma microvesicles stimulate angiogenesis in vitro and contain angiogenic proteins, (a) HBMVECs were cultured on Matrigel™ in basal medium (EBM) alone, or supplemented with GBM microvesicles (EBM+MV) or angiogenic factors (EGM). Tubule formation was measured after 16 hours as average tubule length + SEM compared to cells grown in EBM (n = 6). (b) Total protein from primary glioblastoma cells and 12 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 microvesicles (MV) from these cells (1 mg each) were analysed on a human angiogenesis antibody array, (c) The arrays were scanned and the intensities analysed with the Image J software (n = 4). FIGURE 19. Microvesicles isolated from primary glioblastoma cells promote proliferation of the U87 glioblastoma cell line. 100,000 U87 cells were seeded in wells of a 24 well plate and allowed to grow for three days in (a) normal growth medium (DMEM-5% FBS) or (b) normal growth medium supplemented with 125 pg microvesicles. (c) After three days, the non-supplemented cells had expanded to 480,000 cells, whereas the microvesicle-supplemented cells had expanded to 810,000 cells. NC refers to cells grown in normal control medium and MV refers to cells grown in medium supplemented with microvesicles. The result is presented as the mean + SEM (n=6).

DETAILED DESCRIPTION OF THE INVENTION

[0023] Microvesicles are shed by eukaryotic cells, or budded off of the plasma membrane, to the exterior of the cell. These membrane vesicles are heterogeneous in size with diameters ranging from about lOnm to about 5000 nm. The small microvesicles (approximately 10 to lOOOnm, and more often 30 to 200 nm in diameter) that are released by exocytosis of intracellular multivesicular bodies are referred to in the art as “exosomes”. The methods and compositions described herein are equally applicable to microvesicles of all sizes; preferably 30 to 800 nm; and more preferably 30 to 200 nm.

[0024] In some of the literature, the term “exosome” also refers to protein complexes containing exoribonucleases which are involved in mRNA degradation and the processing of small nucleolar RNAs (snoRNAs), small nuclear RNAs (snRNAs) and ribosomal RNAs (rRNA) (Liu et al., 2006b; van Dijk et al., 2007). Such protein complexes do not have membranes and are not “microvesicles” or “exosomes” as those terms are used here in.

Exosomes As Diagnostic And/Or Prognostic Tools [0025] Certain aspects of the present invention are based on the surprising finding that glioblastoma derived microvesicles can be isolated from the serum of glioblastoma patients. This is the first discovery of microvesicles derived from cells in the brain, present in a bodily fluid of a subject. Prior to this discovery it was not known whether glioblastoma cells produced microvesicles or whether such microvesicles could cross the blood brain barrier into the rest of the body. These microvesicles were found to contain mutant mRNA associated with tumor cells. The microvesicles also contained microRNAs (miRNAs) which 13 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 were found to be abundant in glioblastomas. Glioblastoma-derived microvesicles were also found to potently promote angiogenic features in primary human brain microvascular endothelial cells (HBMVEC) in culture. This angiogenic effect was mediated at least in part through angiogenic proteins present in the microvesicles. The nucleic acids found within these microvesicles, as well as other contents of the microvesicles such as angiogenic proteins, can be used as valuable biomarkers for tumor diagnosis, characterization and prognosis by providing a genetic profile. Contents within these microvesicles can also be used to monitor tumor progression over time by analyzing if other mutations are acquired during tumor progression as well as if the levels of certain mutations are becoming increased or decreased over time or over a course of treatment [0026] Certain aspects of the present invention are based on the finding that microvesicles are secreted by tumor cells and circulating in bodily fluids. The number of microvesicles increases as the tumor grows. The concentration of the micro vesicles in bodily fluids is proportional to the corresponding tumor load. The bigger the tumor load, the higher the concentration of microvesicles in bodily fluids.

[0027] Certain aspects of the present invention are based on another surprising finding that most of the extracellular RNAs in bodily fluid of a subject are contained within microvesicles and thus protected from degradation by ribonucleases. As shown in Example 3, more than 90% of extracellular RNA in total serum can be recovered in micro vesicles.

[0028] One aspect of the present invention relates to methods for detecting, diagnosing, monitoring, treating or evaluating a disease or other medical condition in a subject by determining the concentration of microvesicles in a biological sample. The determination may be performed using the biological sample without first isolating the micro vesicles or by isolating the microvesicles first.

[0029] Another aspect of the present invention relates to methods for detecting, diagnosing, monitoring, treating or evaluating a disease or other medical condition in a subject comprising the steps of, isolating exosomes from a bodily fluid of a subject, and analyzing one or more nucleic acids contained within the exosomes. The nucleic acids are analyzed qualitatively and/or quantitatively, and the results are compared to results expected or obtained for one or more other subjects who have or do not have the disease or other medical condition. The presence of a difference in microvesicular nucleic acid content of the subject, as compared to that of one or more other individuals, can indicate the presence or 14 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 absence of, the progression of (e.g., changes of tumor size and tumor malignancy), or the susceptibility to a disease or other medical condition in the subject.

[0030] Indeed, the isolation methods and techniques described herein provide the following heretofore unrealized advantages: 1) the opportunity to selectively analyze disease-or tumor-specific nucleic acids, which may be realized by isolating disease- or tumor-specific microvesicles apart from other microvesicles within the fluid sample; 2) significantly higher yield of nucleic acid species with higher sequence integrity as compared to the yield/integrity obtained by extracting nucleic acids directly from the fluid sample; 3) scalability, e.g. to detect nucleic acids expressed at low levels, the sensitivity can be increased by pelleting more microvesicles from a larger volume of serum; 4) purer nucleic acids in that protein and lipids, debris from dead cells, and other potential contaminants and PCR inhibitors are excluded from the microvesicle pellets before the nucleic acid extraction step; and 5) more choices in nucleic acid extraction methods as microvesicle pellets are of much smaller volume than that of the starting serum, making it possible to extract nucleic acids from these microvesicle pellets using small volume column filters.

[0031] The microvesicles are preferably isolated from a sample taken of a bodily fluid from a subject. As used herein, a “bodily fluid” refers to a sample of fluid isolated from anywhere in the body of the subject, preferably a peripheral location, including but not limited to, for example, blood, plasma, serum, urine, sputum, spinal fluid, pleural fluid, nipple aspirates, lymph fluid, fluid of the respiratory, intestinal, and genitourinary tracts, tear fluid, saliva, breast milk, fluid from the lymphatic system, semen, cerebrospinal fluid, intraorgan system fluid, ascitic fluid, tumor cyst fluid, amniotic fluid and combinations thereof.

[0032] The term “subject” is intended to include all animals shown to or expected to have microvesicles. In particular embodiments, the subject is a mammal, a human or nonhuman primate, a dog, a cat, a horse, a cow, other farm animals, or a rodent (e.g. mice, rats, guinea pig. etc.). The term “subject” and “individual” are used interchangeably herein.

[0033] Methods of isolating microvesicles from a biological sample are known in the art. For example, a method of differential centrifugation is described in a paper by Raposo et al. (Raposo et al., 1996), and similar methods are detailed in the Examples section herein. Methods of anion exchange and/or gel permeation chromatography are described in US Patent Nos. 6,899,863 and 6,812,023. Methods of sucrose density gradients or organelle electrophoresis are described in U.S. Patent No. 7,198,923. A method of magnetic activated 15 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 cell sorting (MACS) is described in (Taylor and Gercel-Taylor, 2008). A method of nanomembrane ultrafiltration concentrator is described in (Cheruvanky et al., 2007). Preferably, microvesicles can be identified and isolated from bodily fluid of a subject by a newly developed microchip technology that uses a unique microfluidic platform to efficiently and selectively separate tumor derived micro vesicles. This technology, as described in a paper by Nagrath et al. (Nagrath et al., 2007), can be adapted to identify and separate microvesicles using similar principles of capture and separation as taught in the paper. Each of the foregoing references is incorporated by reference herein for its teaching of these methods.

[0034] In one embodiment, the microvesicles isolated from a bodily fluid are enriched for those originating from a specific cell type, for example, lung, pancreas, stomach, intestine, bladder, kidney, ovary, testis, skin, colorectal, breast, prostate, brain, esophagus, liver, placenta, fetus cells. Because the micro vesicles often carry surface molecules such as antigens from their donor cells, surface molecules may be used to identify, isolate and/or enrich for microvesicles from a specific donor cell type (Al-Nedawi et al., 2008; Taylor and Gercel-Taylor, 2008). In this way, microvesicles originating from distinct cell populations can be analyzed for their nucleic acid content. For example, tumor (malignant and non-malignant) micro vesicles carry tumor-associated surface antigens and may be detected, isolated and/or enriched via these specific tumor-associated surface antigens. In one example, the surface antigen is epithelial-cell-adhesion-molecule (EpCAM), which is specific to microvesicles from carcinomas of lung, colorectal, breast, prostate, head and neck, and hepatic origin, but not of hematological cell origin (Balzar et al., 1999; Went et al., 2004). In another example, the surface antigen is CD24, which is a glycoprotein specific to urine microvesicles (Keller et al., 2007). In yet another example, the surface antigen is selected from a group of molecules CD70, carcinoembryonic antigen (CEA), EGFR, EGFRvIII and other variants, Fas ligand, TRAIL, tranferrin receptor, p38.5, p97 and HSP72. Additionally, tumor specific microvesicles may be characterized by the lack of surface markers, such as CD80 and CD86.

[0035] The isolation of microvesicles from specific cell types can be accomplished, for example, by using antibodies, aptamers, aptamer analogs or molecularly imprinted polymers specific for a desired surface antigen. In one embodiment, the surface antigen is specific for a cancer type. In another embodiment, the surface antigen is specific for a cell type which is not necessarily cancerous. One example of a method of micro vesicle separation based on cell 16 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 surface antigen is provided in U.S. Patent No. 7,198,923. As described in, e.g., U.S. Patent Nos. 5,840,867 and 5,582,981, WO/2003/050290 and a publication by Johnson et al. (Johnson et al., 2008), aptamers and their analogs specifically bind surface molecules and can be used as a separation tool for retrieving cell type-specific microvesicles. Molecularly imprinted polymers also specifically recognize surface molecules as described in, e.g., US Patent Nos. 6,525,154, 7,332,553 and 7,384,589 and a publication by Bossi et al. (Bossi et al., 2007) and are a tool for retrieving and isolating cell type-specific microvesicles. Each of the foregoing reference is incorporated herein for its teaching of these methods.

[0036] It may be beneficial or otherwise desirable to extract the nucleic acid from the exosomes prior to the analysis. Nucleic acid molecules can be isolated from a microvesicle using any number of procedures, which are well-known in the art, the particular isolation procedure chosen being appropriate for the particular biological sample. Examples of methods for extraction are provided in the Examples section herein. In some instances, with some techniques, it may also be possible to analyze the nucleic acid without extraction from the microvesicle.

[0037] In one embodiment, the extracted nucleic acids, including DNA and/or RNA, are analyzed directly without an amplification step. Direct analysis may be performed with different methods including, but not limited to, the nanostring technology. NanoString technology enables identification and quantification of individual target molecules in a biological sample by attaching a color coded fluorescent reporter to each target molecule.

This approach is similar to the concept of measuring inventory by scanning barcodes. Reporters can be made with hundreds or even thousands of different codes allowing for highly multiplexed analysis. The technology is described in a publication by Geiss et al. (Geiss et al., 2008) and is incorporated herein by reference for this teaching.

[0038] In another embodiment, it may be beneficial or otherwise desirable to amplify the nucleic acid of the microvesicle prior to analyzing it. Methods of nucleic acid amplification are commonly used and generally known in the art, many examples of which are described herein. If desired, the amplification can be performed such that it is quantitative. Quantitative amplification will allow quantitative determination of relative amounts of the various nucleic acids, to generate a profile as described below.

[0039] In one embodiment, the extracted nucleic acid is RNA. RNAs are then preferably reverse-transcribed into complementary DNAs before further amplification. Such 17 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 reverse transcription may be performed alone or in combination with an amplification step. One example of a method combining reverse transcription and amplification steps is reverse transcription polymerase chain reaction (RT-PCR), which may be further modified to be quantitative, e.g., quantitative RT-PCR as described in US Patent No. 5,639,606, which is incorporated herein by reference for this teaching.

[0040] Nucleic acid amplification methods include, without limitation, polymerase chain reaction (PCR) (US Patent No. 5,219,727) and its variants such as in situ polymerase chain reaction (US Patent No. 5,538,871), quantitative polymerase chain reaction (US Patent No. 5,219,727), nested polymerase chain reaction (US Patent No. 5,556,773), self sustained sequence replication and its variants (Guatelli et al., 1990), transcriptional amplification system and its variants (Kwoh et al., 1989), Qb Replicase and its variants (Miele et al., 1983), cold-PCR (Li et al., 2008) or any other nucleic acid amplification methods, followed by the detection of the amplified molecules using techniques well known to those of skill in the art. Especially useful are those detection schemes designed for the detection of nucleic acid molecules if such molecules are present in very low numbers. The foregoing references are incorporated herein for their teachings of these methods.

[0041] The analysis of nucleic acids present in the microvesicles is quantitative and/or qualitative. For quantitative analysis, the amounts (expression levels), either relative or absolute, of specific nucleic acids of interest within the microvesicles are measured with methods known in the art (described below). For qualitative analysis, the species of specific nucleic acids of interest within the microvesicles, whether wild type or variants, are identified with methods known in the art (described below).

[0042] “Genetic aberrations” is used herein to refer to the nucleic acid amounts as well as nucleic acid variants within the microvesicles. Specifically, genetic aberrations include, without limitation, over-expression of a gene (e.g., oncogenes) or a panel of genes, underexpression of a gene (e.g., tumor suppressor genes such as p53 or RB) or a panel of genes, alternative production of splice variants of a gene or a panel of genes, gene copy number variants (CNV) (e.g. DNA double minutes) (Hahn, 1993), nucleic acid modifications (e.g., methylation, acetylation and phosphorylations), single nucleotide polymorphisms (SNPs), chromosomal rearrangements (e.g., inversions, deletions and duplications), and mutations (insertions, deletions, duplications, missense, nonsense, synonymous or any other nucleotide changes) of a gene or a panel of genes, which mutations, in many cases, ultimately affect the 18 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 activity and function of the gene products, lead to alternative transcriptional splicing variants and/or changes of gene expression level.

[0043] The determination of such genetic aberrations can be performed by a variety of techniques known to the skilled practitioner. For example, expression levels of nucleic acids, alternative splicing variants, chromosome rearrangement and gene copy numbers can be determined by microarray analysis (US Patent Nos. 6,913,879, 7,364,848, 7,378,245, 6,893,837 and 6,004,755) and quantitative PCR. Particularly, copy number changes may be detected with the Illumina Infinium II whole genome genotyping assay or Agilent Human Genome CGH Microarray (Steemers et al., 2006). Nucleic acid modifications can be assayed by methods described in, e.g., US Patent No. 7,186,512 and patent publication WO/2003/023065. Particularly, methylation profiles may be determined by Illumina DNA Methylation OMA003 Cancer Panel. SNPs and mutations can be detected by hybridization with allele-specific probes, enzymatic mutation detection, chemical cleavage of mismatched heteroduplex (Cotton et al., 1988), ribonuclease cleavage of mismatched bases (Myers et al., 1985), mass spectrometry (US Patent Nos. 6,994,960, 7,074,563, and 7,198,893), nucleic acid sequencing, single strand conformation polymorphism (SSCP) (Orita et al., 1989), denaturing gradient gel electrophoresis (DGGE)(Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), temperature gradient gel electrophoresis (TGGE) (Fischer and Lerman, 1979a; Fischer and Lerman, 1979b), restriction fragment length polymorphisms (RFLP) (Kan and Dozy, 1978a; Kan and Dozy, 1978b), oligonucleotide ligation assay (OLA), allele-specific PCR (ASPCR) (US Patent No. 5,639,611), ligation chain reaction (LCR) and its variants (Abravaya et al., 1995; Landegren et al., 1988; Nakazawa et al., 1994), flow-cytometric heteroduplex analysis (WO/2006/113590) and combinations/modifications thereof. Notably, gene expression levels may be determined by the serial analysis of gene expression (SAGE) technique (Velculescu et al., 1995). In general, the methods for analyzing genetic aberrations are reported in numerous publications, not limited to those cited herein, and are available to skilled practitioners. The appropriate method of analysis will depend upon the specific goals of the analysis, the condition/history of the patient, and the specific cancer(s), diseases or other medical conditions to be detected, monitored or treated. The forgoing references are incorporated herein for their teachings of these methods.

[0044] A variety of genetic aberrations have been identified to occur and/or contribute to the initial generation or progression of cancer. Examples of genes which are commonly up-regulated (i.e. over-expressed) in cancer are provided in Table 4 (cancers of different 19 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 types) and Table 6 (pancreatic cancer). Examples of microRNAs which are up-regulated in brain tumor are provided in Table 8. In one embodiment of the invention, there is an increase in the nucleic acid expression level of a gene listed in Table 4 and/or Table 6 and/or of a microRNA listed in Table 8. Examples of genes which are commonly down-regulated (e.g. under-expressed) in cancer are provided in Table 5 (cancers of different types) and Table 7 (pancreatic cancer). Examples of microRNAs which are down-regulated in brain tumor are provided in Table 9. In one embodiment of the invention, there is a decrease in the nucleic acid expression level of a gene listed in Table 5 and/or Table 7 and/or a microRNA listed in Table 9. Examples of genes which are commonly under expressed, or over expressed in brain tumors are reviewed in (Furnari et al., 2007), and this subject matter is incorporated herein by reference. With respect to the development of brain tumors, RB and p53 are often down-regulated to otherwise decrease their tumor suppressive activity. Therefore, in these embodiments, the presence or absence of an increase or decrease in the nucleic acid expression level of a gene(s) and/or a microRNA(s) whose disregulated expression level is specific to a type of cancer can be used to indicate the presence or absence of the type of cancer in the subject.

[0045] Likewise, nucleic acid variants, e.g., DNA or RNA modifications, single nucleotide polymorphisms (SNPs) and mutations (e.g., missense, nonsense, insertions, deletions, duplications) may also be analyzed within microvesicles from bodily fluid of a subject, including pregnant females where microvesicles derived from the fetus may be in serum as well as amniotic fluid. Non-limiting examples are provided in Table 3. In yet a further embodiment, the nucleotide variant is in the EGFR gene. In a still further embodiment, the nucleotide variant is the EGFRvIII mutation/variant. The terms “EGFR”,“epidermal growth factor receptor” and “ErbBl”are used interchangeably in the art, for example as described in a paper by Carpenter (Carpenter, 1987). With respect to the development of brain tumors, RB, PTEN, pi6, p21 and p53 are often mutated to otherwise decrease their tumor suppressive activity. Examples of specific mutations in specific forms of brain tumors are discussed in a paper by Furnari et al. (Furnari et al., 2007), and this subject matter is incorporated herein by reference.

[0046] In addition, more genetic aberrations associated with cancers have been identified recently in a few ongoing research projects. For example, the Cancer Genome Atlas (TCGA) program is exploring a spectrum of genomic changes involved in human cancers. The results of this project and other similar research efforts are published and 20 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 incorporated herein by reference (Jones et al., 2008; McLendon et al., 2008; Parsons et al., 2008; Wood et al., 2007). Specifically, these research projects have identified genetic aberrations, such as mutations (e.g., missense, nonsense, insertions, deletions and duplications), gene expression level variations (mRNA or microRNA), copy number variations and nucleic acid modification (e.g. methylation), in human glioblastoma, pancreatic cancer, breast cancer and/or colorectal cancer. The genes most frequently mutated in these cancers are listed in Table 11 and Table 12 (glioblastoma), Table 13 (pancreatic cancer), Table 14 (breast cancer) and Table 15 (colorectal cancer). The genetic aberrations in these genes, and in fact any genes which contain any genetic aberrations in a cancer, are targets that may be selected for use in diagnosing and/or monitoring cancer by the methods described herein.

[0047] Detection of one or more nucleotide variants can be accomplished by performing a nucleotide variant screen on the nucleic acids within the micro vesicles. Such a screen can be as wide or narrow as determined necessary or desirable by the skilled practitioner. It can be a wide screen (set up to detect all possible nucleotide variants in genes known to be associated with one or more cancers or disease states). Where one specific cancer or disease is suspected or known to exist, the screen can be specific to that cancer or disease. One example is a brain tumor/brain cancer screen (e.g., set up to detect all possible nucleotide variants in genes associated with various clinically distinct subtypes of brain cancer or known drug-resistant or drug-sensitive mutations of that cancer).

[0048] In one embodiment, the analysis is of a profile of the amounts (levels) of specific nucleic acids present in the microvesicle, herein referred to as a “quantitative nucleic acid profile” of the micro vesicles. In another embodiment, the analysis is of a profile of the species of specific nucleic acids present in the microvesicles (both wild type as well as variants), herein referred to as a “nucleic acid species profile.” A term used herein to refer to a combination of these types of profiles is “genetic profile” which refers to the determination of the presence or absence of nucleotide species, variants and also increases or decreases in nucleic acid levels.

[0049] Once generated, these genetic profiles of the microvesicles are compared to those expected in, or otherwise derived from a healthy normal individual. A profile can be a genome wide profile (set up to detect all possible expressed genes or DNA sequences). It can be narrower as well, such as a cancer wide profile (set up to detect all possible genes or nucleic acids derived therefrom, or known to be associated with one or more cancers). 21 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

Where one specific cancer is suspected or known to exist, the profile can be specific to that cancer (e.g., set up to detect all possible genes or nucleic acids derived therefrom, associated with various clinically distinct subtypes of that cancer or known drug-resistant or sensitive mutations of that cancer).

[0050] Which nucleic acids are to be amplified and/or analyzed can be selected by the skilled practitioner. The entire nucleic acid content of the exosomes or only a subset of specific nucleic acids which are likely or suspected of being influenced by the presence of a disease or other medical condition such as cancer, can be amplified and/or analyzed. The identification of a nucleic acid aberration(s) in the analyzed microvesicle nucleic acid can be used to diagnose the subject for the presence of a disease such as cancer, hereditary diseases or viral infection with which that aberration(s) is associated. For instance, analysis for the presence or absence of one or more nucleic acid variants of a gene specific to a cancer (e.g. the EGFRvIII mutation) can indicate the cancer’s presence in the individual. Alternatively, or in addition, analysis of nucleic acids for an increase or decrease in nucleic acid levels specific to a cancer can indicate the presence of the cancer in the individual (e.g., a relative increase in EGFR nucleic acid, or a relative decrease in a tumor suppressor gene such as p53).

[0051] In one embodiment, mutations of a gene which is associated with a disease such as cancer (e.g. via nucleotide variants, over-expression or under-expression) are detected by analysis of nucleic acids in micro vesicles, which nucleic acids are derived from the genome itself in the cell of origin or exogenous genes introduced through viruses. The nucleic acid sequences may be complete or partial, as both are expected to yield useful information in diagnosis and prognosis of a disease. The sequences may be sense or anti-sense to the actual gene or transcribed sequences. The skilled practitioner will be able to devise detection methods for a nucleotide variance from either the sense or anti-sense nucleic acids which may be present in a microvesicle. Many such methods involve the use of probes which are specific for the nucleotide sequences which directly flank, or contain the nucleotide variances. Such probes can be designed by the skilled practitioner given the knowledge of the gene sequences and the location of the nucleic acid variants within the gene. Such probes can be used to isolate, amplify, and/or actually hybridize to detect the nucleic acid variants, as described in the art and herein.

[0052] Determining the presence or absence of a particular nucleotide variant or plurality of variants in the nucleic acid within microvesicles from a subject can be performed 22 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 in a variety of ways. A variety of methods are available for such analysis, including, but not limited to, PCR, hybridization with allele-specific probes, enzymatic mutation detection, chemical cleavage of mismatches, mass spectrometry or DNA sequencing, including minisequencing. In particular embodiments, hybridization with allele specific probes can be conducted in two formats: 1) allele specific oligonucleotides bound to a solid phase (glass, silicon, nylon membranes) and the labeled sample in solution, as in many DNA chip applications, or 2) bound sample (often cloned DNA or PCR amplified DNA) and labeled oligonucleotides in solution (either allele specific or short so as to allow sequencing by hybridization). Diagnostic tests may involve a panel of variances, often on a solid support, which enables the simultaneous determination of more than one variance. In another embodiment, determining the presence of at least one nucleic acid variance in the microvesicle nucleic acid entails a haplotyping test. Methods of determining haplotypes are known to those of skill in the art, as for example, in WO 00/04194.

[0053] In one embodiment, the determination of the presence or absence of a nucleic acid variant(s) involves determining the sequence of the variant site or sites (the exact location within the sequence where the nucleic acid variation from the norm occurs) by methods such as polymerase chain reaction (PCR), chain terminating DNA sequencing (US Patent No. 5547859), minisequencing (Fiorentino et al., 2003), oligonucleotide hybridization, pyrosequencing, Illumina genome analyzer, deep sequencing, mass spectrometry or other nucleic acid sequence detection methods. Methods for detecting nucleic acid variants are well known in the art and disclosed in WO 00/04194, incorporated herein by reference. In an exemplary method, the diagnostic test comprises amplifying a segment of DNA or RNA (generally after converting the RNA to complementary DNA) spanning one or more known variants in the desired gene sequence. This amplified segment is then sequenced and/or subjected to electrophoresis in order to identify nucleotide variants in the amplified segment.

[0054] In one embodiment, the invention provides a method of screening for nucleotide variants in the nucleic acid of microvesicles isolated as described herein. This can be achieved, for example, by PCR or, alternatively, in a ligation chain reaction (LCR) (Abravaya et al., 1995; Landegren et al., 1988; Nakazawa et al., 1994). LCR can be particularly useful for detecting point mutations in a gene of interest (Abravaya et al., 1995). The LCR method comprises the steps of designing degenerate primers for amplifying the target sequence, the primers corresponding to one or more conserved regions of the nucleic acid corresponding to the gene of interest, amplifying PCR products with the primers using, as a template, a nucleic 23 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 acid obtained from a micro vesicle, and analyzing the PCR products. Comparison of the PCR products of the microvesicle nucleic acid to a control sample (either having the nucleotide variant or not) indicates variants in the microvesicle nucleic acid. The change can be either an absence or presence of a nucleotide variant in the microvesicle nucleic acid, depending upon the control.

[0055] Analysis of amplification products can be performed using any method capable of separating the amplification products according to their size, including automated and manual gel electrophoresis, mass spectrometry, and the like.

[0056] Alternatively, the amplification products can be analyzed based on sequence differences, using SSCP, DGGE, TGGE, chemical cleavage, OLA, restriction fragment length polymorphisms as well as hybridization, for example, nucleic acid microarrays.

[0057] The methods of nucleic acid isolation, amplification and analysis are routine for one skilled in the art and examples of protocols can be found, for example, in Molecular Cloning: A Laboratory Manual (3-Volume Set) Ed. Joseph Sambrook, David W. Russel, and Joe Sambrook, Cold Spring Harbor Laboratory, 3rd edition (January 15, 2001), ISBN: 0879695773. A particular useful protocol source for methods used in PCR amplification is PCR Basics: From Background to Bench by Springer Verlag; 1st edition (October 15, 2000), ISBN: 0387916008.

[0058] Many methods of diagnosis performed on a tumor biopsy sample can be performed with microvesicles since tumor cells, as well as some normal cells are known to shed microvesicles into bodily fluid and the genetic aberrations within these microvesicles reflect those within tumor cells as demonstrated herein. Furthermore, methods of diagnosis using microvesicles have characteristics that are absent in methods of diagnosis performed directly on a tumor biopsy sample. For example, one particular advantage of the analysis of microvesicular nucleic acids, as opposed to other forms of sampling of tumor/cancer nucleic acid, is the availability for analysis of tumor/cancer nucleic acids derived from all foci of a tumor or genetically heterogeneous tumors present in an individual. Biopsy samples are limited in that they provide information only about the specific focus of the tumor from which the biopsy is obtained. Different tumorous/cancerous foci found within the body, or even within a single tumor often have different genetic profiles and are not analyzed in a standard biopsy. However, analysis of the microvesicular nucleic acids from an individual presumably provides a sampling of all foci within an individual. This provides valuable 24 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 information with respect to recommended treatments, treatment effectiveness, disease prognosis, and analysis of disease recurrence, which cannot be provided by a simple biopsy.

[0059] Identification of genetic aberrations associated with specific diseases and/or medical conditions by the methods described herein can also be used for prognosis and treatment decisions of an individual diagnosed with a disease or other medical condition such as cancer. Identification of the genetic basis of a disease and/or medical condition provides useful information guiding the treatment of the disease and/or medical condition. For example, many forms of chemotherapy have been shown to be more effective on cancers with specific genetic abnormalities/aberrations. One example is the effectiveness of EGFR-targeting treatments with medicines, such as the kinase inhibitors gefitinib and erlotinib.

Such treatment have been shown to be more effective on cancer cells whose EGFR gene harbors specific nucleotide mutations in the kinase domain of EGFR protein (U.S. Patent publication 20060147959). In other words, the presence of at least one of the identified nucleotide variants in the kinase domain of EGFR nucleic acid message indicates that a patient will likely benefit from treatment with the EGFR-targeting compound gefitinib or erlotinib. Such nucleotide variants can be identified in nucleic acids present in micro vesicles by the methods described herein, as it has been demonstrated that EGFR transcripts of tumor origin are isolated from microvesicles in bodily fluid.

[0060] Genetic aberrations in other genes have also been found to influence the effectiveness of treatments. As disclosed in the publication by Fumari et al. (Furnari et al., 2007), mutations in a variety of genes affect the effectiveness of specific medicines used in chemotherapy for treating brain tumors. The identification of these genetic aberrations in the nucleic acids within microvesicles will guide the selection of proper treatment plans.

[0061] As such, aspects of the present invention relate to a method for monitoring disease (e.g. cancer) progression in a subject, and also to a method for monitoring disease recurrence in an individual. These methods comprise the steps of isolating microvesicles from a bodily fluid of an individual, as discussed herein, and analyzing nucleic acid within the micro vesicles as discussed herein (e.g. to create a genetic profile of the microvesicles). The presence/absence of a certain genetic aberration/profile is used to indicate the presence/absence of the disease (e.g. cancer) in the subject as discussed herein. The process is performed periodically over time, and the results reviewed, to monitor the progression or regression of the disease, or to determine recurrence of the disease. Put another way, a change in the genetic profile indicates a change in the disease state in the subject. The period 25 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 of time to elapse between sampling of microvesicles from the subject, for performance of the isolation and analysis of the microvesicle, will depend upon the circumstances of the subject, and is to be determined by the skilled practitioner. Such a method would prove extremely beneficial when analyzing a nucleic acid from a gene that is associated with the therapy undergone by the subject. For example, a gene which is targeted by the therapy can be monitored for the development of mutations which make it resistant to the therapy, upon which time the therapy can be modified accordingly. The monitored gene may also be one which indicates specific responsiveness to a specific therapy.

[0062] Aspects of the present invention also relate to the fact that a variety of noncancer diseases and/or medical conditions also have genetic links and/or causes, and such diseases and/or medical conditions can likewise be diagnosed and/or monitored by the methods described herein. Many such diseases are metabolic, infectious or degenerative in nature. One such disease is diabetes (e.g. diabetes insipidus) in which the vasopressin type 2 receptor (V2R) is modified. Another such disease is kidney fibrosis in which the genetic profiles for the genes of collagens, fibronectin and TGF-β are changed. Changes in the genetic profile due to substance abuse (e.g. a steroid or drug use), viral and/or bacterial infection, and hereditary disease states can likewise be detected by the methods described herein.

[0063] Diseases or other medical conditions for which the inventions described herein are applicable include, but are not limited to, nephropathy, diabetes insipidus, diabetes type I, diabetes II, renal disease glomerulonephritis, bacterial or viral glomerulonephritides, IgA nephropathy, Henoch-Schonlein Purpura, membranoproliferative glomerulonephritis, membranous nephropathy, Sjogren's syndrome, nephrotic syndrome minimal change disease, focal glomerulosclerosis and related disorders, acute renal failure, acute tubulointerstitial nephritis, pyelonephritis, GU tract inflammatory disease, Pre-clampsia, renal graft rejection, leprosy, reflux nephropathy, nephrolithiasis, genetic renal disease, medullary cystic, medullar sponge, polycystic kidney disease, autosomal dominant polycystic kidney disease, autosomal recessive polycystic kidney disease, tuberous sclerosis, von Hippel-Lindau disease, familial thin-glomerular basement membrane disease, collagen III glomerulopathy, fibronectin glomerulopathy, Alport's syndrome, Fabry's disease, Nail-Patella Syndrome, congenital urologic anomalies, monoclonal gammopathies, multiple myeloma, amyloidosis and related disorders, febrile illness, familial Mediterranean fever, HIV infection-AIDS, inflammatory disease, systemic vasculitides, polyarteritis nodosa, Wegener's granulomatosis, polyarteritis, 26 PCT/U S2009/032881 WO 2009/100029 2015203111 11 Jun2015 necrotizing and crecentic glomerulonephritis, polymyositis-dermatomyositis, pancreatitis, rheumatoid arthritis, systemic lupus erythematosus, gout, blood disorders, sickle cell disease, thrombotic thrombocytopenia purpura, Fanconi’s syndrome, transplantation, acute kidney injury, irritable bowel syndrome, hemolytic-uremic syndrome, acute corticol necrosis, renal thromboembolism, trauma and surgery, extensive injury, bums, abdominal and vascular surgery, induction of anesthesia, side effect of use of drugs or drug abuse, circulatory disease myocardial infarction, cardiac failure, peripheral vascular disease, hypertension, coronary heart disease, non-atherosclerotic cardiovascular disease, atherosclerotic cardiovascular disease, skin disease, soriasis, systemic sclerosis, respiratory disease, COPD, obstructive sleep apnoea, hypoia at high altitude or erdocrine disease, acromegaly, diabetes mellitus, or diabetes insipidus.

[0064] Selection of an individual from whom the microvesicles are isolated is performed by the skilled practitioner based upon analysis of one or more of a variety of factors. Such factors for consideration are whether the subject has a family history of a specific disease (e.g. a cancer), has a genetic predisposition for such a disease, has an increased risk for such a disease due to family history, genetic predisposition, other disease or physical symptoms which indicate a predisposition, or environmental reasons. Environmental reasons include lifestyle, exposure to agents which cause or contribute to the disease such as in the air, land, water or diet. In addition, having previously had the disease, being currently diagnosed with the disease prior to therapy or after therapy, being currently treated for the disease (undergoing therapy), being in remission or recovery from the disease, are other reasons to select an individual for performing the methods.

[0065] The methods described herein are optionally performed with the additional step of selecting a gene or nucleic acid for analysis, prior to the analysis step. This selection can be based on any predispositions of the subject, or any previous exposures or diagnosis, or therapeutic treatments experienced or concurrently undergone by the subject.

[0066] The cancer diagnosed, monitored or otherwise profiled, can be any kind of cancer. This includes, without limitation, epithelial cell cancers such as lung, ovarian, cervical, endometrial, breast, brain, colon and prostate cancers. Also included are gastrointestinal cancer, head and neck cancer, non-small cell lung cancer, cancer of the nervous system, kidney cancer, retina cancer, skin cancer, liver cancer, pancreatic cancer, genital-urinary cancer and bladder cancer, melanoma, and leukemia. In addition, the methods and compositions of the present invention are equally applicable to detection, diagnosis and 27 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 prognosis of non-malignant tumors in an individual (e.g. neurofibromas, meningiomas and schwannomas).

[0067] In one embodiment, the cancer is brain cancer. Types of brain tumors and cancer are well known in the art. Glioma is a general name for tumors that arise from the glial (supportive) tissue of the brain. Gliomas are the most common primary brain tumors. Astrocytomas, ependymomas, oligodendrogliomas, and tumors with mixtures of two or more cell types, called mixed gliomas, are the most common gliomas. The following are other common types of brain tumors: Acoustic Neuroma (Neurilemmoma, Schwannoma. Neurinoma), Adenoma, Astracytoma, Low-Grade Astrocytoma, giant cell astrocytomas, Mid-and High-Grade Astrocytoma, Recurrent tumors, Brain Stem Glioma, Chordoma, Choroid Plexus Papilloma, CNS Lymphoma (Primary Malignant Lymphoma), Cysts, Dermoid cysts, Epidermoid cysts, Craniopharyngioma, Ependymoma Anaplastic ependymoma, Gangliocytoma (Ganglioneuroma), Ganglioglioma, Glioblastoma Multiforme (GBM), Malignant Astracytoma, Glioma, Hemangioblastoma, Inoperable Brain Tumors, Lymphoma, Medulloblastoma (MDL), Meningioma, Metastatic Brain Tumors, Mixed Glioma, Neurofibromatosis, Oligodendroglioma. Optic Nerve Glioma, Pineal Region Tumors, Pituitary Adenoma, PNET (Primitive Neuroectodermal Tumor), Spinal Tumors, Subependymoma, and Tuberous Sclerosis (Boumeville’s Disease).

[0068] In addition to identifying previously known nucleic acid aberrations (as associated with diseases), the methods of the present invention can be used to identify previously unidentified nucleic acid sequences/modifications (e.g. post transcriptional modifications) whose aberrations are associated with a certain disease and/or medical condition. This is accomplished, for example, by analysis of the nucleic acid within microvesicles from a bodily fluid of one or more subjects with a given disease/medical condition (e.g. a clinical type or subtype of cancer) and comparison to the nucleic acid within microvesicles of one or more subjects without the given disease/medical condition, to identify differences in their nucleic acid content. The differences may be any genetic aberrations including, without limitation, expression level of the nucleic acid, alternative splice variants, gene copy number variants (CNV), modifications of the nucleic acid , single nucleotide polymorphisms (SNPs), and mutations (insertions, deletions or single nucleotide changes) of the nucleic acid. Once a difference in a genetic parameter of a particular nucleic acid is identified for a certain disease, further studies involving a clinically and statistically significant number of subjects may be carried out to establish the correlation between the 28 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 genetic aberration of the particular nucleic acid and the disease. The analysis of genetic aberrations can be done by one or more methods described herein, as determined appropriate by the skilled practitioner.

Exosomes As Delivery Vehicles [0069] Aspects of the present invention also relate to the actual microvesicles described herein. In one embodiment, the invention is an isolated microvesicle as described herein, isolated from an individual. In one embodiment, the microvesicle is produced by a cell within the brain of the individual (e.g. a tumor or non-tumor cell). In another embodiment, the microvesicle is isolated from a bodily fluid of an individual, as described herein.

Methods of isolation are described herein.

[0070] Another aspect of the invention relates to the finding that isolated microvesicles from human glioblastoma cells contain mRNAs, miRNAs and angiogenic proteins. Such glioblastoma microvesicles were taken up by primary human brain endothelial cells, likely via an endocytotic mechanism, and a reporter protein mRNA incorporated into the microvesicles was translated in those cells. This indicates that messages delivered by microvesicles can change the genetic and/or translational profile of a target cell (a cell which takes up a microvesicle). The microvesicles also contained miRNAs which are known to be abundant in glioblastomas (Krichevsky et al, manuscript in preparation). Thus microvesicles derived from glioblastoma tumors function as delivery vehicles for mRNA, miRNA and proteins which can change the translational state of other cells via delivery of specific mRNA species, promote angiogenesis of endothelial cells, and stimulate tumor growth.

[0071] In one embodiment, microvesicles are depleted from a bodily fluid from a donor subject before said bodily fluid is delivered to a recipient subject. The donor subject may be a subject with an undetectable tumor and the microvesicles in the bodily fluid are derived from the tumor. The tumor microvesicles in the donor bodily fluid, if unremoved, would be harmful since the genetic materials and proteins in the microvesicle may promote unrestricted growth of cells in the recipient subject.

[0072] As such, another aspect of the invention is the use of the microvesicles identified herein to deliver a nucleic acid to a cell. In one embodiment, the cell is within the body of an individual. The method comprises administering a microvesicle(s) which contains the nucleic acid, or a cell that produces such micro vesicles, to the individual such that the 29 PCT/U S2009/032881 WO 2009/100029 2015203111 11 Jun2015 microvesicles contacts and/or enters the cell of the individual. The cell to which the nucleic acid gets delivered is referred to as the target cell.

[0073] The microvesicle can be engineered to contain a nucleic acid that it would not naturally contain (i.e. which is exogenous to the normal content of the microvesicle). This can be accomplished by physically inserting the nucleic acid into the microvesicles. Alternatively, a cell (e.g. grown in culture) can be engineered to target one or more specific nucleic acid into the exosome, and the exosome can be isolated from the cell. Alternatively, the engineered cell itself can be administered to the individual.

[0074] In one embodiment, the cell which produces the exosome for administration is of the same or similar origin or location in the body as the target cell. That is to say, for delivery of a microvesicle to a brain cell, the cell which produces the microvesicle would be a brain cell (e.g. a primary cell grown in culture). In another embodiment, the cell which produces the exosome is of a different cell type than the target cell. In one embodiment, the cell which produces the exosome is a type that is located proximally in the body to the target cell.

[0075] A nucleic acid sequence which can be delivered to a cell via an exosome can be RNA or DNA, and can be single or double stranded, and can be selected from a group comprising: nucleic acid encoding a protein of interest, oligonucleotides, nucleic acid analogues, for example peptide-nucleic acid (PNA), pseudo-complementary PNA (pc-PNA), locked nucleic acid (LNA) etc. Such nucleic acid sequences include, for example, but are not limited to, nucleic acid sequences encoding proteins, for example that act as transcriptional repressors, antisense molecules, ribozymes, small inhibitory nucleic acid sequences, for example but are not limited to RNAi, shRNA, siRNA, miRNA, antisense oligonucleotides, and combinations thereof.

[0076] Microvesicles isolated from a cell type are delivered to a recipient subject. Said microvesicles may benefit the recipient subject medically. For example, the angiogenesis and pro-proliferation effects of tumor exosomes may help the regeneration of injured tissues in the recipient subject. In one embodiment, the delivery means is by bodily fluid transfusion wherein microvesicles are added into a bodily fluid from a donor subject before said bodily fluid is delivered to a recipient subject.

[0077] In another embodiment, the microvesicle is an ingredient (e.g. the active ingredient in a pharmaceutically acceptable formulation suitable for administration to the 30 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 subject (e.g. in the methods described herein). Generally this comprises a pharmaceutically acceptable carrier for the active ingredient. The specific carrier will depend upon a number of factors (e.g.. the route of administration).

[0078] The “pharmaceutically acceptable carrier” means any pharmaceutically acceptable means to mix and/or deliver the targeted delivery composition to a subject. This includes a pharmaceutically acceptable material, composition or vehicle, such as a liquid or solid filler, diluent, excipient, solvent or encapsulating material, involved in carrying or transporting the subject agents from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and is compatible with administration to a subject, for example a human.

[0079] Administration to the subject can be either systemic or localized. This includes, without limitation, dispensing, delivering or applying an active compound (e.g. in a pharmaceutical formulation) to the subject by any suitable route for delivery of the active compound to the desired location in the subject, including delivery by either the parenteral or oral route, intramuscular injection, subcutaneous/intradermal injection, intravenous injection, buccal administration, transdermal delivery and administration by the rectal, colonic, vaginal, intranasal or respiratory tract route.

[0080] It should be understood that this invention is not limited to the particular methodologies, protocols and reagents, described herein and as such may vary. The terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention, which is defined solely by the claims.

[0081] In one respect, the present invention relates to the herein described compositions, methods, and respective components thereof, as essential to the invention, yet open to the inclusion of unspecified elements, essential or not (“comprising”). In some embodiments, other elements to be included in the description of the composition, method or respective component thereof are limited to those that do not materially affect the basic and novel characteristic(s) of the invention (“consisting essentially of’). This applies equally to steps within a described method as well as compositions and components therein. In other embodiments, the inventions, compositions, methods, and respective components thereof, described herein are intended to be exclusive of any element not deemed an essential element to the component, composition or method (“consisting of’). 31 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

EXAMPLES

Examples 1-7. Tumor cells shed microvesicles, which contain RNAs, including mRNAs and microRNAs, and that microvesicles contain more than 90% of the extracellular RNA in bodily fluids.

Example 1: Microvesicles are shed from primary human glioblastoma cells.

[0082] Glioblastoma tissue was obtained from surgical resections and tumor cells were dissociated and cultured as monolayers. Specifically, brain tumor specimens from patients diagnosed by a neuropathologist as glioblastoma multiforme were taken directly from surgery and placed in cold sterile Neurobasal media (Invitrogen, Carlsbad, CA, USA). The specimens were dissociated into single cells within 1 hr from the time of surgery using a Neural Tissue Dissociation Kit (Miltenyi Biotech, Berisch Gladbach, Germany) and plated in DMEM 5% dFBS supplemented with penicillin-streptomycin (10IU ml'1 and 10 pg ml'1, respectively, Sigma-Aldrich, St Louis, MO, USA). Because microvesicles can be found in the fetal bovine serum (FBS) traditionally used to cultivate cells, and these microvesicles contain substantial amounts of mRNA and miRNA, it was important to grow the tumor cells in media containing micro vesicle-depleted FBS (dFBS). Cultured primary cells obtained from three glioblastoma tumors were found to produce microvesicles at both early and later passages (a passage is a cellular generation defined by the splitting of cells, which is a common cell culture technique and is necessary to keep the cells alive). The micro vesicles were able to be detected by scanning electronmicroscopy (FIGS la and lb) and transmission electronmicroscopy (FIG If). Briefly, human glioblastoma cells were placed on ornithine-coated cover-slips, fixed in 0.5x Kamovskys fixative and then washed 2x5min (2 times with 5 min each) with PBS. The cells were dehydrated in 35% EtOH 10 min, 50% EtOH 2x 10 min, 70% EtOH 2x 10 min, 95% EtOH 2x 10 min, and 100% EtOH 4 x 10 min. The cells were then transferred to critical point drying in a Tousimis SAMDR1-795 semi-automatic Critical Point Dryer followed by coating with chromium in a GATAN Model 681 High Resolution Ion Beam Coater. As shown in FIGS, la and lb, tumor cells were covered with microvesicles varying in size from about 50 - 500 nm.

Example 2: Glioblastoma microvesicles contain RNA.

[0083] To isolate microvesicles, glioblastoma cells at passage 1-15 were cultured in microvesicle-free media (DMEM containing 5% dFBS prepared by ultracentrifugation at 110,000 x g for 16 hours to remove bovine microvesicles). The conditioned medium from 40 32 PCT/U S2009/032881 WO 2009/100029 2015203111 11 Jun2015 million cells was harvested after 48 hours. The microvesicles were purified by differential centrifugation. Specifically, glioblastoma conditioned medium was centrifuged for 10 min at 300 x g to eliminate any cell contamination. Supernatants were further centrifuged for 20 min at 16,500 x g and filtered through a 0.22 pm filter. Microvesicles were then pelleted by ultracentrifugation at 110,000 x g for 70 min. The microvesicle pellets were washed in 13 ml PBS, pelleted again and resuspended in PBS.

[0084] Isolated microvesicles were measured for their total protein content using DC Protein Assay (Bio-Rad, Hercules, CA, USA).

[0085] For the extraction of RNA from microvesicles, RNase A (Fermentas, Glen Bumie, MD, USA) at a final concentration of 100 pg/ml was added to suspensions of microvesicles and incubated for 15 min at 37°C to get rid of RNA outside of the microvesicles and thus ensure that the extracted RNA would come from inside the microvesicles. Total RNA was then extracted from the microvesicles using the MirVana RNA isolation kit (Ambion, Austin TX, USA) according to the manufacturer’s protocol.

After treatment with DNAse according to the manufacturer’s protocol, the total RNA was quantified using a nanodrop ND-1000 instrument (Thermo Fischer Scientific, Wilmington, DE, USA).

[0086] Glioblastoma microvesicles were found to contain RNA and protein in a ratio of approximately 1:80 (pg RNA:pg protein). The average yield of proteins and RNAs isolated from microvesicles over a 48-hour period in culture was around 4 pg protein and 50 ng RNA/million cells.

[0087] To confirm that the RNA was contained inside the microvesicles, microvesicles were either exposed to RNase A or mock treatment before RNA extraction (FIG. lc). There was never more than a 7% decrease in RNA content following RNase treatment. Thus, it appears that almost all of the extracellular RNA from the media is contained within the microvesicles and is thereby protected from external RNases by the surrounding vesicular membrane.

[0088] Total RNA from microvesicles and their donor cells were analyzed with a Bioanalyzer, showing that the micro vesicles contain a broad range of RNA sizes consistent with a variety of mRNAs and miRNAs, but lack 18S and 28S the ribosomal RNA peaks characteristic of cellular RNA (FIGS. Id and le).

Example 3: Microvesicles contain DNA. 33 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 [0089] To test if microvesicles also contain DNA, exosomes were isolated as mentioned in Example 2 and then treated with DNase before being lysed to release contents. The DNase treatment step was to remove DNA outside of the exosomes so that only DNA residing inside the exosomes was extracted. Specifically, the DNase treatment was performed using the DNA-free kit from Ambion according to manufacturer’s recommendations (Catalog#AM1906). For the DNA purification step, an aliquot of isolated exosomes was lysed in 300pl lysis buffer that was part of the MirVana RNA isolation kit (Ambion) and the DNAs were purified from the lysed mixture using a DNA purification kit (Qiagen) according to the manufacturer’s recommendation.

[0090] To examine whether the extracted DNA contains common genes, PCRs were performed using primer pairs specific to GAPDH, Human endogenous retrovirus K, Tenascin-c and Line-1. For the GAPDH gene, the following primers were used: Forw3GAPDHnew (SEQ ID NO: 1) and Rev3GAPDHnew (SEQ ID NO: 2). The primer pair amplifies a 112bp amplicon if the template is a spliced GAPDH cDNA and a 216bp amplicon if the template is an un-spliced genomic GAPDH DNA. In one experiment, isolated exosomes were treated with DNase before being lysed for DNA extraction (FIG. 3a). The 112bp fragments were amplified as expected from the exosomes from the tumor serum (See Lane 4 in FIG. 3a) and the primary tumor cells (See Lane 6 in FIG. 3a) but not from the exosomes from normal human fibroblasts (See Lane 5 in FIG. 3a). The 216bp fragment could not be amplified from exosomes of all three origins. However, fragments of both 112bp and 216bp were amplified when the genomic DNA isolated from the glioblastoma cell was used as templates (See Lane 3 in FIG. 3a). Thus, spliced GAPDH DNA exists within exosomes isolated from tumor cells but not within exosomes isolated from normal fibroblast cells.

[0091] In contrast, in another experiment, isolated exosomes were not treated with DNase before being lysed for DNA extraction (FIG. 3b). Not only the 112bp fragments but also the 216bp fragments were amplified from exosomes isolated from primary melanoma cells (See Lane 3 in FIG. 3b), suggesting that non-spliced GAPDH DNA or partially spliced cDNA that has been reverse transcribed exists outside of the exosomes.

[0092] For the Human Endogenous Retrovirus K (HERV-K) gene, the following primers were used: HERVK_6Forw (SEQ ID NO: 3) and HERVK_6Rev (SEQ ID NO: 4). The primer pair amplifies a 172bp amplicon. DNA was extracted from exosomes that were isolated and treated with DNase, and used as the template for PCR amplification. As shown 34 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 in FIG. 3c, 172bp fragments were amplified in all tumor and normal human serum exosomes but not in exosomes from normal human fibroblasts. These data suggest that unlike exosomes from normal human fibroblasts, tumor and normal human serum exosomes contain endogenous retrovirus DNA sequences. To examine if tumor exosomes also contain transposable elements, the following LINE-1 specific primers were used for PCR amplifications: Linel_Forw (SEQ ID NO: 5) and Linel_Rev (SEQ ID NO: 6). These two primers are designed to detect LINE-1 in all species since each primer contains equal amounts of two different oligos. For the Linel_Forw primer, one oligo contains a C and the other oligo contains a G at the position designated with “s”. For the Linel_Rev primer, one oligo contains an A and the other oligo contains a G at the position designated with “r”. The primer pair amplifies a 290bp amplicon. The template was the DNA extracted from exosomes that were treated with DNase (as described above). As shown in FIG. 3e, 290bp LINE-1 fragments could be amplified from the exosomes from tumor cells and normal human serum but not from exosomes from the normal human fibroblasts.

[0093] To test if exosomes also contain Tenascin-C DNA, the following primer pair was used to perform PCR: Tenascin C Forw (SEQ ID NO: 7) and Tenascin C Rev (SEQ ID NO: 8). The primer pair amplifies a 197bp amplicon. The template was the DNA extracted from exosomes that were isolated and then treated with DNase before lysis. As shown in FIG. 3d, 197bp Tenascin C fragments were amplified in exosomes from tumor cells or normal human serum but not in exosomes from normal human fibroblasts. Thus, Tenascin-C DNA exists in tumor and normal human serum exosomes but not in exosomes from normal human fibroblasts.

[0094] To further confirm the presence of DNA in exosomes, exosomal DNA was extracted from D425 medulloblastoma cells using the method described above. Specifically, the exosomes were isolated and treated with DNase before lysis. Equal volumes of the final DNA extract were either treated with DNase or not treated with DNase before being visualized by Ethidium Bromide staining in 1% agarose gel. Ethidium Bromide is a dye that specifically stains nucleic acids and can be visualized under ultraviolet light. As shown in FIG. 3f, Ethidium Bromide staining disappeared after DNase treatment (See Lane 3 in FIG. 3f) while strong staining could be visualized in the un-treated aliquot (See Lane 2 in FIG. 3f). The DNase treated and non-treated extracts were also analyzed on a RNA pico chip (Agilent Technologies). As shown in FIG. 3g, single stranded DNA could be readily detected in the 35 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 DNase-non-treated extract (See upper panel in FIG. 3g) but could barely be detected in the DNase-treated extract (See lower panel in FIG. 3g).

[0095] To test whether the extracted DNA was single-stranded, nucleic acids were extracted from the treated exosomes as described in the previous paragraph and further treated with RNAse to eliminate any RNA contamination. The treated nucleic acids were then analyzed on a RNA pico Bioanalyzer chip and in a DNA 1000 chip. The RNA pico chip only detects single stranded nucleic acids. The DNA 1000 chip detected double stranded nucleic acids. As shown in FIG. 3h, single stranded nucleic acids were detected (See upper panel) but double stranded nucleic acids were not detected (See lower panel). Thus, the DNA contained within tumor exosomes are mostly single stranded.

[0096] To demonstrate that single stranded DNA exists in tumor cells but not in normal human fibroblasts, nucleic acids were extracted from exosomes from either glioblastoma patient serum or normal human fibroblasts. The exosomes were treated with DNase before lysis and the purified nucleic acids were treated with RNase before analysis. As shown in FIG. 3i, exosomal nucleic acids extracted from glioblastoma patient serum could be detected by a RNA pico chip. In contrast, only a very small amount of single stranded DNA was extracted from normal human fibroblasts.

[0097] Accordingly, exosomes from tumor cells and normal human serum were found to contain contain single-stranded DNA. The single-stranded DNA is a reverse transcription product since the amplification products do not contain introns (FIG. 3a and FIG. 3b). It is known that tumor cells as well as normal progenitor cells/stem cells have active reverse transcriptase (RT) activity although the activity in normal progenitor cells/stem cells is relatively much lower. This RT activity makes it plausible that RNA transcripts in the cell can be reverse transcribed and packaged into exosomes as cDNA. Interestingly, exosomes from tumor cells contain more cDNAs corresponding to tumor-specific gene transcripts since tumor cells usually have up-regulated reverse transcriptase activity. Therefore, tumor specific cDNA in exosomes may be used as biomarkers for the diagnosis or prognosis of different tumor types. The use of cDNAs as biomarkers would skip the step of reverse transcription compared to the used of mRNA as biomarkers for tumors. In addition, the use of exosomal cDNA is advantageous over the use of whole serum/plasma DNA because serum/plasma contains genomic DNA released from dying cells. When testing amplified whole serum/plasma DNA, there will be more background. 36 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

Example 4: Most extracellular RNA in human serum is contained within exosomes.

[0098] To determine the amount of RNA circulating in serum as “free RNA’YRNA-protein complex versus the amount of RNA contained within the exosomes, we isolated serum from a healthy human subject, and evenly split the serum into two samples with equal volume. For sample 1, the serum was ultracentrifuged to remove most micro vesicles. Then the serum supernatant was collected and RNA left in the supernatant was extracted using Trizol LS. For sample 2, the serum was not ultracentrifuged and total RNA was extracted from the serum using Trizol LS. The amount of RNA in the sample 1 supernatant and sample 2 serum was measured. As a result, it was found that the amount of free RNA in sample 1 supernatant was less than 10% of the amount of total RNA isolated from the serum sample 2. Therefore, a majority of the RNA in serum is associated with the exosomes.

Example 5: High efficiency of serum extracellular nucleic acid extraction is achieved by incorporating a serum exosome isolation step.

[0099] Whole serum and plasma contain large amounts of circulating DNA and possibly also RNA protected in protein complexes, while free RNA have a half-life of a few minutes in serum. Extracellular nucleic acid profiles in serum vary between normal and diseased mammals and thus may be biomarkers for certain diseases. To examine the profiles, nucleic acids need to be extracted. However, direct extraction of nucleic acids from serum and plasma is not practical, especially from large serum/plasma volumes. In this case, large volumes of Trizol LS (a RNA extraction reagent) are used to instantly inactivate all serum nucleases before extracting the exosomal nucleic acids. Subsequently, contaminants precipitate into the sample and affect subsequent analyses. As shown in Example 4, most extracellular RNAs in serum are contained in serum exosomes. Therefore, we tested whether it is more efficient to isolate extracellular nucleic acids by isolating the serum exosomes before nucleic acid extraction.

[00100] Four milliliter (ml) blood serum from a patient was split into 2 aliquots of 2 ml each. Serum exosomes from one aliquot were isolated prior to RNA extraction. The methods of exosome isolation and RNA extraction are the same as mentioned in Example 2. For the other aliquot, RNA was extracted directly using Trizol LS according to manufacturer’s recommendation. The nucleic acids from these two extractions were analyzed on a Bioanalyzer RNA chip (Agilent Technologies). As shown in Figure 4, the amount of RNA extracted with the former method is significantly more than that obtained from the latter 37 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 method. Further, the quality of RNA extracted with the latter method is relatively poor compared to that with the former method. Thus, the step of exosome isolation contributes to the efficiency of extracellular RNA extraction from serum.

Example 6: Microarray analysis of mRNA.

[00101] Microarray analysis of the mRNA population in glioblastoma cells and micro vesicles derived from them was performed by Miltenyi Biotech (Auburn, CA, USA) using the Agilent Whole Human Genome Microarray, 4x44K, two color array. The microarray analysis was performed on two different RNA preparations from primary glioblastoma cells and their corresponding microvesicles RNA preparations prepared as described in Examples 1 and 2. The data was analyzed using the GeneSifter software (Vizxlabs, Seattle, WA, USA). The Intersector software (Vizxlabs) was used to extract the genes readily detected on both arrays. The microarray data have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO series accession number GSE13470.

[00102] We found approximately 22,000 gene transcripts in the cells and 27,000 gene transcripts in the microvesicles that were detected well above background levels (99% confidence interval) on both arrays. Approximately 4,700 different mRNAs were detected exclusively in microvesicles on both arrays, indicating a selective enrichment process within the micro vesicles. Consistent with this, there was a poor overall correlation in levels of mRNAs in the microvesicles as compared to their cells of origin from two tumor cell preparations (FIGS. 2a and 2b). In contrast, there was a good correlation in levels of mRNA from one cell culture (A) versus the second cell culture (B) (FIG. 2c) and a similar correlation in levels of mRNA from the corresponding micro vesicles (A) and (B) (FIG. 2d).

Accordingly, there is a consistency of mRNA distribution within the tumor cells and micro vesicles. In comparing the ratio of transcripts in the micro vesicles versus their cells of origin, we found 3,426 transcripts differentially distributed more than 5-fold (p-value <0.01). Of these, 2,238 transcripts were enriched (up to 380 fold) and 1,188 transcripts were less abundant (up to 90 fold) than in the cells (FIG. 5). The intensities and ratios of all gene transcripts were documented. The ontologies of mRNA transcripts enriched or reduced more than 10-fold were recorded and reviewed.

[00103] The mRNA transcripts that were highly enriched in the microvesicles were not always the ones that were most abundant in the micro vesicles. The most abundant transcripts 38 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 would be more likely to generate an effect in the recipient cell upon delivery, and therefore the 500 most abundant mRNA transcripts present in microvesicles were divided into different biological processes based on their ontology descriptions (FIG. 6a). Of the various ontologies, angiogenesis, cell proliferation, immune response, cell migration and histone modification were selected for further study as they represent specific functions that could be involved in remodeling the tumor stroma and enhancing tumor growth. Glioblastoma microvesicle mRNAs belonging to these five ontologies were plotted to compare their levels and contribution to the mRNA spectrum (FIG. 6b). All five ontologies contained mRNAs with very high expression levels compared to the median signal intensity level of the array.

[00104] A thorough analysis of mRNAs that are enriched in the microvesicles versus donor cells, suggests that there may be a cellular mechanism for localizing these messages into microvesicles, possibly via a “zip code” in the 3’UTR as described for mRNAs translated in specific cellular locations, such as that for beta actin (Kislauskis et al., 1994). The conformation of the mRNAs in the microvesicles is not known, but they may be present as ribonuclear particles (RNPs) (Mallardo et al., 2003) which would then prevent degradation and premature translation in the donor cell.

[00105] Microarray analysis of the mRNA populations in glioblastoma cells and microvesicles derived from glioblastoma cells, melanoma cells, and microvesicles derived from melanoma cells was performed by Illumina Inc. (San Diego, CA, USA) using the Whole-Genome cDNA-mediated Annealing, Selection, Extension, and Ligation (DASL) Assay. The Whole-Genome DASL Assay combines the PCR and labeling steps of Illumina’s DASL Assay with the gene-based hybridization and whole-genome probe set of Illumina’s HumanRef-8 BeadChip. This BeadChip covers more than 24,000 annotated genes derived from RefSeq (Build 36.2, Release 22). The microarray analysis was performed on two different RNA preparations from primary glioblastoma cells, micro vesicles from glioblastomas cells (derived with the method as described in Examples 1 and 2), melanoma cells, and microvesicles from melanoma cells (derived with the method as described in Examples 1 and 2).

[00106] The expression data for each RNA preparation were pooled together and used to generate a cluster diagram. As shown in FIG. 7, mRNA expression profiles for glioblastoma cells, microvesicles from glioblastomas cells, melanoma cells, and microvesicles from melanoma cells are clustered together, respectively. Expression profiles of the two primary glioblastoma cell lines 20/3C and ll/5c are clustered with a distance of about 0.06. 39 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

Expression profiles of the two primary melanoma cell lines 0105C and 0664C are clustered with a distance of about 0.09. Expression profiles of exosomes from the two primary melanoma cell lines 0105C and 0664C are clustered together with a distance of around 0.15. Expression profiles of exosomes from the two primary glioblastomas cell lines 20/3C and ll/5c are clustered together with a distance of around 0.098. Thus, exosomes from glioblastoma and melanoma have distinctive mRNA expression signatures and the gene expression signature of exosomes differs from that of their original cells. These data demonstrate that mRNA expression profiles from microvesicles may be used in the methods described herein for the diagnosis and prognosis of cancers.

Example 7: Glioblastoma microvesicles contain miRNA

[00107] Mature miRNA from microvesicles and from donor cells was detected using a quantitative miRNA reverse transcription PCR. Specifically, total RNA was isolated from microvesicles and from donor cells using the mirVana RNA isolation kit (Applied Biosystems, Foster City, CA, USA). Using the TaqMan® MicroRNA Assay kits (Applied Biosystems, Foster City, CA, USA), 30 ng total RNA was converted into cDNA using specific miR-primers and further amplified according to the manufacturer’s protocol.

[00108] A subset of 11 miRNAs among those known to be up-regulated and abundant in gliomas was analyzed in microvesicles purified from two different primary glioblastomas (GBM 1 and GBM 2). These subset contained let-7a, miR-15b, miR-16, miR-19b, miR-21, miR-26a, miR-27a, miR-92, miR-93, miR-320 and miR-20. All of these miRNA were readily detected in donor cells and in microvesicles (FIG. 8). The levels were generally lower in microvesicles per pg total RNA than in parental cells (10%, corresponding to approximately 3 Ct-values), but the levels were well correlated, indicating that these 11 miRNA species are not enriched in microvesicles.

[00109] Microarray analysis of the microRNA populations in glioblastoma cells and microvesicles derived from glioblastoma cells, melanoma cells, and microvesicles derived from melanoma cells was performed by lllumina Inc. (San Diego, CA, USA) using the MicroRNA Expression Profiling Panel, powered by the DASL Assay. The human MicroRNA Panels include 1146 microRNA species. The microarray analysis was performed on two different RNA preparations from primary glioblastoma cells, microvesicles from glioblastomas cells (derived using the method described in Examples 1 and 2), melanoma 40 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 cells, and microvesicles from melanoma cells (derived using the method described in Examples 1 and 2).

[00110] The expression data for each RNA preparation were pooled together and used to generate a cluster diagram. As shown in FIG. 9, microRNA expression profiles for glioblastoma cells, microvesicles from glioblastomas cells, melanoma cells, and microvesicles from melanoma cells are clustered together, respectively. Expression profiles of the two primary melanoma cell lines 0105C and 0664C are clustered with a distance of about 0.13. Expression profiles of the two primary glioblastomas cell lines 20/3C and 1 l/5c are clustered with a distance of about 0.12. Expression profiles of exosomes from the two primary glioblastomas cell lines 20/3C and 1 l/5c are clustered together with a distance of around 0.12. Expression profiles of exosomes from the two primary melanoma cell lines 0105C and 0664C are clustered together with a distance of around 0.17. Thus, exosomes from glioblastoma and melanoma have distinctive microRNA expression signatures and that the gene expression signature of exosomes differs from that of their original cells. Furthermore, as demonstrated herein, microRNA expression profiles from microvesicles may be used in the methods described herein for the diagnosis and prognosis of cancers.

[00111] The finding of miRNAs in microvesicles suggests that tumor-derived microvesicles can modify the surrounding normal cells by changing their transcriptional/translational profiles. Furthermore, as demonstrated herein, miRNA expression profile from microvesicles may be used in the methods described herein for the diagnosis and prognosis of cancers, including but not limited to glioblastoma.

Examples 8-15. These examples show that nucleic acids within exosomes from bodily fluids can be used as biomarkers for diseases or other medical conditions.

Example 8: Expression profiles of miRNAs in microvesicles can be used as sensitive biomarkers for glioblastoma.

[00112] To determine if microRNAs within exosomes may be used as biomarkers for a disease and/or medical condition, we examined the existence of a correlation between the expression level of microRNA and disease status. Since microRNA-21 is expressed at high levels in glioblastoma cells and is readily detectable in exosomes isolated from serum of glioblastoma patients, we measured quantitatively microRNA-21 copy numbers within exosomes from the sera of glioblastoma patients by quantitative RT-PCR. Specifically, exosomes were isolated from 4 ml serum samples from 9 normal human subjects and 9 41 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 glioblastoma patients. The RNA extraction procedure was similar to the RNA extraction procedure as described in Example 2. The level of miR-21 was analyzed using singleplex qPCR (Applied Biosystems) and normalized to GAPDH expression level.

[00113] As shown in FIG. 10, the average Ct-value was 5.98 lower in the glioblastoma serum sample, suggesting that the exosomal miRNA-21 expression level in glioblastoma patients is approximately 63 fold higher than that in a normal human subject. The difference is statistically significant with a p value of 0.01. Therefore, there is a correlation between microRNA-21 expression level and glioblastoma disease status, which demonstrates that validity and applicability of the non-invasive diagnostic methods disclosed herein. For example, in one aspect, the method comprised the steps of isolating exosomes from the bodily fluid of a subject and analyzing microRNA-21 expression levels within the exosomes by measuring the copy number of microRNA-21 and comparing the number to that within exosomes from a normal subject or to a standard number generated by analyzing microRNA-21 contents within exosomes from a group of normal subjects. An increased copy number indicates the existence of glioblastoma in the subject; while the absence of an increased copy number indicates the absence of glioblastoma in the subject. This basic method may be extrapolated to diagnose/monitor other diseases and/or medical conditions associated with other species of microRNAs.

Example 9: mRNAs in micro vesicles can be used as sensitive biomarkers for diagnosis [00114] Nucleic acids are of high value as biomarkers because of their ability to be detected with high sensitivity by PCR methods. Accordingly, the following tests were designed and carried out to determine whether the mRNA in microvesicles could be used as biomarkers for a medical disease or condition, in this case glioblastoma tumors. The epidermal growth factor receptor (EGFR) mRNA was selected because the expression of the EGFRvIII mutation is specific to some tumors and defines a clinically distinct subtype of glioma (Pelloski et al., 2007). In addition, EGFRvIII mutations traditionally cannot be detected using tissues other than the lesion tissues since these mutations are somatic mutations but not germ line mutations. Therefore, a biopsy from lesion tissues such as glioma tumor is conventionally required for detecting EGFRvIII mutations. As detailed below, nested RT-PCR was used to identify EGFRvIII mRNA in glioma tumor biopsy samples and the results compared with the mRNA species found in microvesicles purified from a serum sample from the same patient. 42 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 [00115] Microvesicles were purified from primary human glioblastoma cells followed by RNA extraction from both the microvesicles and donor cells (biopsy). The samples were coded and the PCRs were performed in a blind fashion. Gli-36EGFRvIEI (human glioma cell stably expressing EGFRvIII) was included as a positive control. The micro vesicles from 0.5- 2 ml of frozen serum samples were pelleted as described in Example 2 and the RNA was extracted using the MirVana Microvesicles RNA isolation kit. Nested RT-PCR was then used to amplify both the wild type EGFR (1153 bp) and EGFRvIII (352 bp) transcripts from both the microvesicles and donor cells using the same set of primers. Specifically, the RNA was converted to cDNA using the Omniscript RT kit (Qiagen Inc, Valencia, CA, USA) according to the manufacturer’s recommended protocol. GAPDH primers were GAPDH Forward (SEQ ID NO: 9) and GAPDH Reverse (SEQ ID NO: 10). The EGER/EGFRvIII PCR1 primers were SEQ ID NO: 11 and SEQ ID NO: 12. The EGFR/EGFRvin PCR2 primers were SEQ ID NO: 13 and SEQ ID NO: 14. The PCR cycling protocol was 94 °C for 3 minutes; 94 °C for 45 seconds, 60 °C for 45 seconds, 72 °C for 2 minutes for 35 cycles; and a final step 72 °C for 7 minutes.

[00116] We analyzed the biopsy sample to determine whether the EGFRvIII mRNA was present and compared the result with RNA extracted from exosomes purified from a frozen serum sample from the same patient. Fourteen of the 30 tumor samples (47%) contained the EGFRvIII transcript, which is consistent with the percentage of glioblastomas found to contain this mutation in other studies (Nishikawa et al., 2004). EGFRvIII could be amplified from exosomes in seven of the 25 patients (28%) from whom serum was drawn around the time of surgery (FIG. 11 and Table 1). When a new pair of primers EGFR/EGFRvIII PCR3: SEQ ID NO: 15 and SEQ ID NO: 16, were used as the second primer pair for the above nested PCR amplification, more individuals were found to harbor EGFRvIII mutations (Table 1). EGFRvIII could be amplified from exosomes in the six patients who was identified as negatives with the old pair of primers EGFRvIII PCR2: SEQ ID NO: 13 AND SEQ ID NO: 14. Notably, exosomes from individual 13, whose biopsy did not show EGFRvIII mutation, was shown to contain EGFRvIII mutation, suggesting an increased sensivity of EGFRvIII mutation detection using exosomes technology. From the exosomes isolated from 52 normal control serum samples, EGFRvIII could not be amplified (FIG. 12). Interestingly, two patients with an EGFRvIII negative tumor sample turned out to be EGFRvIII positive in the serum exosomes, supporting heterogeneous foci of EGFRvIII expression in the glioma tumor. Furthermore, our data also showed that intact RNAs in microvesicles were, unexpectedly, 43 PCT/U S2009/032881 WO 2009/100029 2015203111 11 Jun2015 able to be isolated from frozen bodily serum of glioblastoma patients. These blind serum samples from confirmed glioblastoma patients were obtained from the Cancer Research Center (VU medical center, Amsterdam, the Netherlands) and were kept at -80°C until use. The identification of tumor specific RNAs in serum microvesicles allows the detection of somatic mutations which are present in the tumor cells. Such technology should result in improved diagnosis and therapeutic decisions.

[00117] The RNA found in the microvesicles contains a “snapshot” of a substantial array of the cellular gene expression profile at a given time. Among the mRNA found in glioblastoma-derived microvesicles, the EGFR mRNA is of special interest since the EGFRvIII splice variant is specifically associated with glioblastomas (Nishikawa et al., 2004) . Here it is demonstrated that brain tumors release microvesicles into the bloodstream across the blood-brain-barrier (BBB), which has not been shown before. It is further demonstrated that mRNA variants, such as EGFRvIII in brain tumors, are able to be detected by a method comprising the steps of isolating exosomes from a small amount of patient serum and analyzing the RNA in said micro vesicles.

[00118] Knowledge of the EGFRvIII mutation in tumors is important in choosing an optimal treatment regimen. EGFRvIII-positive gliomas are over 50 times more likely to respond to treatment with EGFR-inhibitors like erlotinib or gefitinib (Mellinghoff et ah, 2005) .

Example 10: Diagnosis of iron metabolism disorders [00119] The exosome diagnostics method can be adapted for other purposes as shown by the following example.

[00120] Hepcidin, an antimicrobial peptide, is the master hormonal regulator of iron metabolism. This peptide is produced mainly in mammalian liver and is controlled by the erythropoietic activity of the bone-marrow, the amount of circulating and stored body iron, and inflammation. Upon stimulation, hepcidin is secreted into the circulation or urine where it may act on target ferroportin-expressing cells. Ferroportin is the sole iron exporter identified to date and when bound to hepcidin, it is internalized and degraded. The resulting destruction of ferroportin leads to iron retention in ferroportin expressing cells such as macrophages and enterocytes. This pathophysiological mechanism underlies anemia of chronic diseases. More specifically, inappropriately high levels of hepcidin and elevated iron content within the reticuloendothelial system characterize anemia. Indeed, anemia may be 44 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 associated with many diseases and/or medical conditions such as infections (acute and chronic), cancer, autoimmune, chronic rejection after solid-organ transplantation, and chronic kidney disease and inflammation (Weiss and Goodnough, 2005). On the other hand, in a genetic iron overload disease such as hereditary hemochromatosis, inappropriately low expression levels of hepcidin encourage a potentially fatal excessive efflux of iron from within the reticuloendothelial system. So, hepcidin is up-regulated in anemia associated with chronic disease, but down-regulated in hemochromatosis.

[00121] Currently, there is no suitable assay to quantitatively measure hepcidin levels in circulation or urine (Kemna et al., 2008) except time-of-flight mass spectrometry (TOF MS), which needs highly specialized equipment, and therefore is not readily accessible. Recently, the method of Enzyme Linked ImmunoSorbent Assay (ELISA) has been proposed to quantitatively measure hepcidin hormone levels but this method is not consistent because of the lack of clear correlations with hepcidin (Kemna et al., 2005; Kemna et al., 2007) and other iron related parameters (Brookes et al., 2005; Roe et al., 2007).

[00122] Hepcidin mRNA was detected in exosomes from human serum, as follows. Exosomes were first isolated from human serum and their mRNA contents extracted before conversion to cDNA and PCR amplification. PCR primers were designed to amplify a 129 nucleotide fragment of human Hepcidin. The sequences of the primers are SEQ ID NO: 57 and SEQ ID NO: 58. A hepcidin transcript of 129 nucleotides (the middle peak in FIG. 13D) was readily detected by Bioanalyzer. As a positive control (FIG. 13B), RNA from a human hepatoma cell line Huh-7 was extracted and converted to cDNA. The negative control (FIG. 13C) is without mRNA. These Bioanalyzer data are also shown in the pseudogel in FIG. 13A.

[00123] Hepcidin mRNA in microvesicles in circulation correlates with hepcidin mRNA in liver cells. Hence, measuring hepcidin mRNA within micro vesicles in a bodily fluid sample would allow one to diagnose or monitor anemia or hemochromatosis in the subject.

[00124] Thus, it is possible to diagnose and/or monitor anemia and hemochromatosis in a subject by isolating microvesicles from a bodily fluid and comparing the hepcidin mRNA in said microvesicles with the mRNA from from a normal subject. With an anemic subject, the copy number of mRNA is increased over the normal, non-anemic level. In a subject suffering from hemochromatosis, the copy number is decreased relative to the mRNA in a normal subject. 45 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

Example 11: Non-invasive transcriptional profiling of exosomes for diabetic nephropathy diagnosis [00125] Diabetic nephropathy (DN) is a life threatening complication that currently lacks specific treatments. Thus, there is a need to develop sensitive diagnostics to identify patients developing or at risk of developing DN, enabling early intervention and monitoring.

[00126] Urine analysis provides a way to examine kidney function without having to take a biopsy. To date, this analysis has been limited to the study of protein in the urine.

This Example sets forth a method to obtain from urine transcriptional profiles derived from cells that normally could only be obtained by kidney biopsy. Specifically, the method comprises the steps of isolating urine exosomes and analyzing the RNAs within said exosomes to obtain transcriptional profiles, which can be used to examine molecular changes being made by kidney cells in diabetic individuals and provide a 'snap shot' of any new proteins being made by the kidney. State-of-the-art technologies to obtain exosomal transcription profiles include, but are not limited to, contemporary hybridization arrays, PCR based technologies, and next generation sequencing methods. Since direct sequencing does not require pre-designed primers or spotted DNA oligos, it will provide a non-biased description of exosomal RNA profiles. An example of next generation sequencing technology is provided by the Illumina Genome Analyzer, which utilizes massively parallel sequencing technology which allows it to sequence the equivalent of 1/3 a human genome per run. The data obtainable from this analysis would enable one to rapidly and comprehensively examine the urinary exosomal transcriptional profile and allow comparison to the whole kidney. Using such a method, one could obtain much needed information regarding the transcription profile of urinary exosomes. A comparison of transcripts in control versus diabetes-derived urinary exosomes could further provide one with a comprehensive list of both predicted and new biomarkers for diabetic nephropathy.

[00127] In order to prove the feasibility of the diagnostic method described above, an experiment was designed and carried out to isolate urinary exosomes and to confirm the presence of renal specific biomarkers within these exosomes. In this experiment, a fresh morning urine sample of 220 ml was collected from a 28-year old healthy male subject and processed via differential centrifugation to isolate urinary exosomes. Specifically, urine was first spun at 300 x g spin for 10 minutes to remove any cells from the sample. The supernatant was collected and then underwent a 20-minute 16,500 x g spin to bring down any cell debris or protein aggregates. The supernatant was then passed through a 0.22 uM 46 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 membrane filter to remove debris with diameters larger than 0.22uM. Finally, the sample underwent ultra-centrifugation at 100,000 x g for 1 hour to pellet the exosomes (Thery et al., 2006). The pellet was gently washed in phosphate buffered saline (PBS) and RNA was extracted using a Qiagen RNeasy kit pursuant to the manufacturer’s instructions. The isolated RNA was converted to cDNA using the Omniscript RT kit (Qiagen) followed by PCR amplification of renal specific genes.

[00128] The renal specific genes examined and their corresponding renal area where the gene is expressed are as follows: AQP1 - proximal tubules; AQP2 - distal tubule (principal cells); CUBN - proximal tubules; LRP2 - proximal tubules; AVPR2 - proximal and distal tubules; SLC9A3 (NHE-3) - Proximal tubule; ATP6V1B1 - distal tubule (intercalated cells); NPHS1 - glomerulus (podocyte cells); NPHS2 - glomerulus (podocyte cells); and CLCN3 -Type B intercalated cells of collecting ducts. The sequences of the primers designed to amplify each gene are AQP1-F (SEQ ID NO: 17) and AQP1-R (SEQ ID NO: 18); AQP2-F (SEQ ID NO: 19) and AQP2-R (SEQ ID NO: 20); CUBN-F (SEQ ID NO: 21) and CUBN-R (SEQ ID NO: 22); LRP2-F (SEQ ID NO: 23) and LRP2-R (SEQ ID NO: 24); AVPR2-F (SEQ ID NO: 25) and AVPR2-R (SEQ ID NO: 26); SLC9A3-F (SEQ ID NO: 27) and SLC9A3-R (SEQ ID NO: 28); ATP6V1B1-F (SEQ ID NO: 29) and ATP6V1B1-R (SEQ ID NO: 30); NPHS1-F (SEQ ID NO: 31) and NPHS1-R (SEQ ID NO: 32); NPHS2-F (SEQ ID NO: 33) and NPHS2-R (SEQ ID NO: 34); CLCN5-F (SEQ ID NO: 35) and CLCN5-R (SEQ ID NO: 36).

[00129] The expected sizes of the PCR products for each gene are AQPl-226bp, AQP2-208bp, CUBN-285bp, LRP2-220bp, AVPR2-290bp, SLC9A3-200bp, ATP6VlBl-226bp, NPHSl-201bp, NPHS2-266bp and CLCN5-204bp. The PCR cycling protocol was 95 °C for 8 minutes; 95 °C for 30 seconds, 60 °C for 30 seconds, 72 °C for 45 seconds for 30 cycles; and a final step 72 °C for 10 minutes.

[00130] As shown in FIG. 14a, kidney tubule cells contain multivesicular bodies, which is an intermediate step during exosome generation. Exosomes isolated from these cells can be identified by electron microscopy (FIG. 14b). Analysis of total RNA extracted from urinary exosomes indicates the presence of RNA species with a broad range of sizes (FIG. 14c). 18S and 28S ribosomal RNAs were not found. PCR analysis confirmed the presence of renal specific transcripts within urinary exosomes (FIG. 14d). These data show that kidney cells shed exosomes into urine and these urinary exosomes contain transcripts of renal 47 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 origin, and that the exosome method can detect renal biomarkers associated with certain renal diseases and/or other medical conditions.

[00131] To further confirm the presence of renal specific mRNA transcripts in urinary exosomes, an independent set of experiments were performed using urine samples from six individuals. Exosomal nucleic acids were extracted from 200ml morning urine samples from each indivisual following a procedure as mentioned above. Specifically, urine samples underwent differential centrifugation starting with a 1000 xg centrifugation to spin down whole cells and cell debris. The supernatant was carefully removed and centrifuged at 16,500 xg for 20 minutes. The follow-on supernatant was then removed and filtered through a 0.8pm filter to remove residual debris from the exosome containing supernatant. The final supernatant then underwent ultracentrifugation at 100,000 xg for lhr lOmin. The pellet was washed in nuclease free PBS and re-centrifuged at 100,000 xg for lhr lOmin to obtain the exosomes pellet which is ready for nucleic acid extraction. Nucleic acids were extracted from the pelleted exosomes using the Arcturus PicoPure RNA Isolation kit and the nucleic acid concentration and integrity was analyzed using a Bioanalyzer (Agilent) Pico chip. As shown in FIG. 14e, nucleic acids isolated from urinary exosomes vary from individual to individual. To test whether the presence of renal biomarkers also varies from individual to individual, PCR amplifications were carried out for Aquaporinl, Aquaporin2 and Cubilin gene using a new set of primer pairs: AQP1 new primer pair: SEQ ID NO: 37 and SEQ ID NO: 38; AQP2 new primer pair: SEQ ID NO: 39 and SEQ ID NO: 40; CUBN new primer pair: SEQ ID NO: 41 and SEQ ID NO: 42. These primer pairs were designed specifically to amplify the spliced and reverse transcribed cDNA fragments. Reverse transcription was performed using the Qiagen Sensiscript kit. As shown in FIG. 14f, no amplification was seen in individual 1, probably due to failed nucleic acid extraction. AQP1 was amplified only in individual 2. CUBN was amplified in indivisual 2 and 3. And AQP2 was amplified in individual 2, 3, 4 and 5. In comparison actin gene (indicated by “House” in FIG. 14f) was amplified in individual 2, 3, 4, 5 and 6. These data provide more evidence that urinary exosomes contain renal specific mRNA transcripts although the expression levels are different between different individuals.

[00132] To test the presence of cDNAs in urinary exosomes, a 200ml human urine sample was split into two 100ml urine samples. Urinary exosomes were isolated from each sample. Exosomes from one sample were treated with DNase and those from the other sample were mock treated. Exosomes from each sample were then lysed for nucleic acid 48 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 extraction using PicoPure RNA isolation kit (Acturus). The nucleic acids were used as templates for nested-PCR amplification (PCR protocols described in Example 9) without prior reverse transcription. The primer pairs to amplify the actin gene were Actin-FOR (SEQ ID NO: 43) and Actin-REV (SEQ ID NO: 44); Actin-nest-FOR (SEQ ID NO: 45) and Actin-nest-REV (SEQ ID NO: 46) with an expected final amplicon of lOObp based on the actin gene cDNA sequence. As shown in FIG. 14g, the lOObp fragments were present in the positive control (human kidney cDNA as templates), DNase treated and non-treated exosomes, but absent in the negative control lane (without templates). Accordingly, actin cDNA is present in both the DNase treated and non-treated urinary exosomes.

[00133] To test whether most nucleic acids extracted using the method were present within exosomes, the nucleic acids extracted from the DNase treated and non-treated exosomes were dissolved in equal volumes and analyzed using a RNA Pico chip (Agilent Technologies). As shown in FIG. 14h, the concentration of the isolated nucleic acids from the DNase treated sample was 1,131 pg/ul and that from the non-treated sample was 1,378 pg/ul. Thus, more than 80% nucleic acids extracted from urinary exosomes using the above method were from inside exosomes.

[00134] To identify the content of urinary exosomes systematically, nucleic acids were extracted from urinary exosomes and submitted to the Broad Institute for sequencing. Approximately 14 million sequence reads were generated, each 76 nucleotides in length. These sequence reads correspond to fragments of DNA/RNA transcripts present within urinary exosomes. Using an extremely strict alignment parameter (100% identity over full length sequence), approximately 15% of the reads were aligned to the human genome. This percentage would likely increase if less stringent alignment criteria was used. A majority of these 15% reads did not align with protein coding genes but rather with non-coding genomic elements such are transposons and various LINE &amp; SINE repeat elements. Notably, for those reads that are not aligned to the human genome, many are aligned to viral sequences. To the extent that the compositions and levels of nucleic acids contained in urinary exosomes change with respect to a disease status, profiles of the nucleic acids could be used according to the present methods as biomarkers for disease diagnosis.

[00135] This example demonstrates that the exosome method of analyzing urine exosomes can be used to determine cellular changes in the kidney in diabetes-related kidney disease without having to take a high-risk, invasive renal biopsy. The method provides a new and sensitive diagnostic tool using exosomes for early detection of kidney diseases such as 49 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 diabetic nephropathy. This will allow immediate intervention and treatment. In sum, the exosome diagnostic method and technology described herein provides a means of much-needed diagnostics for diabetic nephropathy and other diseases which are associated with certain profiles of nucleic acids contained in urinary exosomes.

Example 12: Prostate cancer diagnosis and urinary exosomes [00136] Prostate cancer is the most common cancer in men today. The risk of prostate cancer is approximately 16%. More than 218,000 men in the United States were diagnosed in 2008. The earlier prostate cancer is detected, the greater are the chances of successful treatment. According to the American Cancer Society, if prostate cancers are found while they are still in the prostate itself or nearby areas, the five-year relative survival rate is over 98%.

[00137] One established diagnostic method is carried out by measuring the level of prostate specific antigen (PSA) in the blood, combined with a digital rectal examination. However, both the sensitivity and specificity of the PSA test requires significant improvement. This low specificity results in a high number of false positives, which generate numerous unnecessary and expensive biopsies. Other diagnostic methods are carried out by detecting the genetic profiles of newly identified biomarkers including, but not limited to, prostate cancer gene 3 (PCA3) (Groskopf et al., 2006; Nakanishi et al., 2008), a fusion gene between transmembrane protease serine 2 and ETS-related gene (TMPRSS2-ERG) (Tomlins et al., 2005), glutathione S-transferase pi (Goessl et al., 2000; Gonzalgo et al., 2004), and alpha-methylacyl CoA racemase (AMACR) (Zehentner et al., 2006; Zielie et al., 2004) in prostate cancer cells found in bodily fluids such as serum and urine (Groskopf et al., 2006; Wright and Lange, 2007). Although these biomarkers may give increased specificity due to overexpression in prostate cancer cells (e.g., PCA3 expression is increased 60- to 100-fold in prostate cancer cells), a digital rectal examination is required to milk prostate cells into the urine just before specimen collection (Nakanishi et al., 2008). Such rectal examinations have inherent disadvantages such as the bias on collecting those cancer cells that are easily milked into urine and the involvement of medical doctors which is costly and time consuming.

[00138] Here, a new method of detecting the genetic profiles of these biomarkers is proposed to overcome the limitation mentioned above. The method comprises the steps of isolating exosomes from a bodily fluid and analyzing the nucleic acid from said exosomes. The procedures of the method are similar to those detailed in Example 9. In this example, the 50 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 urine samples were from four diagnosed prostate cancer patients. As shown in FIG. 15c, the cancer stages were characterized in terms of grade, Gleason stage and PSA levels. In addition, the nucleic acids analyzed by nested-RT-PCR as detailed in Example 7 were TMPRSS2-ERG and PCA3, two of the newly identified biomarkers of prostate cancer. For amplification of TMPRSS2-ERG, the primer pair for the first amplification step was TMPRSS2-ERG FI (SEQ ID NO: 47) and TMPRSS2-ERG R1 (SEQ ID NO: 48); and the primer pair for the second amplification step was TMPRSS2-ERG F2 (SEQ ID NO: 49) and TMPRSS2-ERG R2 (SEQ ID NO: 50). The expected amplicon is 122 base pairs (bp) and gives two fragments (one is 68 bp, the other is 54 bp) after digestion with the restriction enzyme Haell. For amplification of PCA3, the primer pair for the first amplification step was PCA3 FI (SEQ ID NO: 51) and PCA3 R1 (SEQ ID NO: 52); and the primer pair for the second amplification step was PCA3 F2 (SEQ ID NO: 53) and PCA3 R2 (SEQ ID NO: 54). The expected amplicon is 152 bp in length and gives two fragments (one is 90 bp, the other is 62 bp) after digestion with the restriction enzyme Seal.

[00139] As shown in FIG. 15a, in both patient 1 and 2, but not in patient 3 and 4, the expected amplicon of TMPRSS2-ERG could be detected and digested into two fragments of expected sizes. As shown in FIG. 15b, in all four patients, the expected amplicon of PCA3 could be detected and digested into two fragments of expected sizes. Therefore, PCA3 expression could be detected in urine samples from all four patients, while TMPRSS2-ERG expression could only be detected in urine samples from patient 1 and 2 (FIG. 15c). These data, although not conclusive due to the small sample size, demonstrate the applicability of the new method in detecting biomarkers of prostate cancer. Further, the exosome method is not limited to diagnosis but can be employed for prognosis and/or monitoring other medical conditions related to prostate cancer.

Example 13: Microvesicles in non-invasive prenatal diagnosis [00140] Prenatal diagnosis is now part of established obstetric practice all over the world. Conventional methods of obtaining fetal tissues for genetic analysis includes amniocentesis and chorionic villus sampling, both of which are invasive and confer risk to the unborn fetus. There is a long-felt need in clinical genetics to develop methods of non-invasive diagnosis. One approach that has been investigated extensively is based on the discovery of circulating fetal cells in maternal plasma. However, there are a number of barriers that hinder its application in clinical settings. Such barriers include the scarcity of fetal cells (only 1.2 cells/ml maternal blood), which requires relatively large volume blood 51 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 samples, and the long half life of residual fetal cells from previous pregnancy, which may cause false positives. Another approach is based on the discovery of fetal DNA in maternal plasma. Sufficient fetal DNA amounts and short clearance time overcome the barriers associated with the fetal cell method. Nevertheless, DNA only confers inheritable genetic and some epigenetic information, both of which may not represent the dynamic gene expression profiles that are linked to fetal medical conditions. The discovery of circulating fetal RNA in maternal plasma (Ng et al., 2003b; Wong et al., 2005) may be the method of choice for non-invasive prenatal diagnosis.

[00141] Several studies suggest that fetal RNAs are of high diagnostic value. For example, elevated expression of fetal corticotropin-releasing hormone (CRH) transcript is associated with pre-eclampsia (a clinical condition manifested by hypertension, edema and proteinuria) during pregnancy (Ng et ah, 2003a). In addition, the placenta-specific 4 (PLAC4) mRNA in maternal plasma was successfully used in a non-invasive test for aneuploid pregnancy (such as trisomy 21, Down syndrome) (Lo et ah, 2007). Furthermore, fetal human chorionic gonadotropin (hCG) transcript in maternal plasma may be a marker of gestational trophoblastic diseases (GTDs), which is a tumorous growth of fetal tissues in a maternal host. Circulating fetal RNAs are mainly of placenta origin (Ng et ah, 2003b). These fetal RNAs can be detected as early as the 4th week of gestation and such RNA is cleared rapidly postpartum.

[00142] Prenatal diagnosis using circulating fetal RNAs in maternal plasma, nevertheless, has several limitations. The first limitation is that circulating fetal RNA is mixed with circulating maternal RNA and is not effectively separable. Currently, fetal transcripts are identified, based on an assumption, as those that are detected in pregnant women antepartum as well as in their infant’s cord blood, yet are significantly reduced or absent in maternal blood within 24 or 36 hours postpartum (Maron et ah, 2007). The second limitation is that no method is established to enrich the circulating fetal RNA for enhanced diagnostic sensitivity since it is still unknown how fetal RNA is packaged and released. The way to overcome these limitations may lie in the isolation of microvesicles and the analysis of the fetal RNAs therein.

[00143] Several facts suggest that microvesicles, which are shed by eukaryotic cells, are the vehicles for circulating fetal RNAs in maternal plasma. First, circulating RNAs within microvesicles are protected from RNase degradation. Second, circulating fetal RNAs have been shown to remain in the non-cellular fraction of maternal plasma, which is consistent 52 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 with the notion that microvesicles encompassing these fetal RNAs are able to be filtered through 0.22 um membrane. Third, similar to tumorous tissues which are know to shed micro vesicles, placental cells, which are a pseudo-malignant fetal tissue, are most likely capable of shedding micro vesicles. Thus, a novel method of non-invasive prenatal diagnosis is comprised of isolating fetal microvesicles from maternal blood plasma and then analyzing the nucleic acids within the microvesicles for any genetic variants associated with certain diseases and/or other medical conditions.

[00144] A hypothetical case of non-invasive prenatal diagnosis is as follows: peripheral blood samples are collected from pregnant women and undergo magnetic activated cell sorting (MACS) or other affinity purification to isolate and enrich fetus-specific microvesicles. The microvesicular pellet is resuspended in PBS and used immediately or stored at -20°C for further processing. RNA is extracted from the isolated microvesicles using the Qiagen RNA extraction kit as per the manufacturer’s instructions. RNA content is analyzed for the expression level of fetal human chorionic gonadotropin (hCG) transcript.

An increased expression level of hCG compared to the standard range points to the development of gestational trophoblastic diseases (GTDs) and entail further the need for clinical treatment for this abnormal growth in the fetus. The sensitivity of micro vesicle technology makes it possible to detect the GTDs at a very early stage before any symptomatic manifestation or structural changes become detectable under ultrasonic examination. The standard range of hCG transcript levels may be determined by examining a statistically significant number of circulating fetal RNA samples from normal pregnancies.

[00145] This prenatal diagnostic method may be extrapolated to the prenatal diagnosis and/or monitoring of other diseases or medical conditions by examining those transcripts associated with these diseases or medical conditions. For example, extraction and analysis of anaplastic lymphoma kinase (ALK) nucleic acid from microvesicles of fetus origin from maternal blood is a non-invasive prenatal diagnosis of neuroblastoma, which is closely associated with mutations within the kinase domain or elevated expression of ALK (Mosse et al., 2008). Accordingly, the microvesicle methods and technology described herein may lead to a new era of much-needed, non-invasive prenatal genetic diagnosis.

Example 14: Melanoma diagnosis 53 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 [00146] Melanoma is a malignant tumor of melanocytes (pigment cells) and is found predominantly in skin. It is a serious form of skin cancer and accounts for 75 percent of all deaths associated with skin cancer. Somatic activating mutations (e.g. V600E) of BRAF are the earliest and most common genetic abnormality detected in the genesis of human melanoma. Activated BRAF promotes melanoma cell cycle progression and/or survival.

[00147] Currently, the diagnosis of melanoma is made on the basis of physical examination and excisional biopsy. However, a biopsy can sample only a limited number of foci within the lesion and may give false positives or false negatives. The exosome method provides a more accurate means for diagnosing melanoma. As discussed above, the method is comprised of the steps of isolating exosomes from a bodily fluid of a subject and analyzing the nucleic acid from said exosomes.

[00148] To determine whether exosomes shed by melanoma cells contain BRAF mRNA, we cultured primary melanoma cells in DMEM media supplemented with exosome-depleted FBS and harvested the exosomes in the media using a similar procedure as detailed in Example 2. The primary cell lines were Yumel and M34. The Yumel cells do not have the V600E mutation in BRAF, while M34 cells have the V600E mutation in BRAF. RNAs were extracted from the exosomes and then analyzed for the presence of BRAF mRNA by RT-PCR. The primers used for PCR amplification were: BRAF forward (SEQ ID NO: 55) and BRAF reverse (SEQ ID NO: 56). The amplicon is 118 base pairs (bp) long and covers the part of BRAF cDNA sequence where the V600E mutation is located. As shown in FIG. 16a, a band of 118 bp was detected in exosomes from primary melanoma cells (Yumel and M34 cells), but not in exosomes from human fibroblast cells or negative controls. The negative detection of a band of 118 bp PCR product is not due to a mistaken RNA extraction since GAPDH transcripts could be detected in exosomes from both melanoma cell and human fibroblast cells (FIG. 16b). The 118 bp PCR products were further sequenced to detect the V600E mutation. As shown in FIGS. 16c and 16d, PCR products from YUMEF cells, as expected, contain wild type BRAF mRNA. In contrast, PCR products from M34 cells, as expected, contain mutant BRAF mRNA with a T-A point mutation, which causes the amino acid Valine (V) to be replaced by Glutamic acid (E) at the amino acid position 600 of the BRAF protein. Furthermore, BRAF mRNA cannot be detected in exosomes from normal human fibroblast cells, suggesting the BRAF mRNA is not contained in exosomes of all tissue origins. 54 PCT/U S2009/032881 WO 2009/100029 2015203111 11 Jun2015 [00149] These data suggest that melanoma cells shed exosomes into the blood circulation and thus melanoma can be diagnosed by isolating these exosomes from blood serum and analyzing the nucleic acid therefrom for the presence or absence of mutations (e.g., V600E) in BRAF. The method described above can also be employed to diagnose melanomas that are associated with other BRAF mutations and mutations in other genes. The method can also be employed to diagnose melanomas that are associated with the expression profiles of BRAF and other nucleic acids.

Example 15: Detection of MMP levels from exosomes to monitor post transplantation conditions.

[00150] Organ transplants are usually effective treatments for organ failures. Kidney failure, heart disease, end-stage lung disease and cirrhosis of the liver are all conditions that can be effectively treated by a transplant. However, organ rejections caused by posttransplantation complications are major obstacles for long-term survival of the allograft recipients. For example, in lung transplantations, bronchiolitis obliterans syndrome is a severe complication affecting survival rates. In kidney transplants, chronic allograft nephropathy remains one of the major causes of renal allograft failure. Ischemia-reperfusion injury damages the donor heart after heart transplantation, as well as the donor liver after orthotopic liver transplantation. These post-transplantation complications may be ameliorated once detected at early stages. Therefore, it is essential to monitor posttransplantation conditions in order to alleviate adverse complications.

[00151] Alterations in the extracellular matrix contribute to the interstitial remodeling in post-transplantation complications. Matrix metalloproteinases (MMPs) are involved in both the turnover and degradation of extracellular matrix (ECM) proteins. MMPs are a family of proteolytic, zinc-dependent enzymes, with 27 members described to date, displaying multidomain structures and substrate specificities, and functioning in the processing, activation, or deactivation of a variety of soluble factors. Serum MMP levels may indicate the status of post-transplantation conditions. Indeed, circulating MMP-2 is associated with cystatin C, post-transplant duration, and diabetes mellitus in kidney transplant recipients (Chang et al., 2008). Disproportional expression of MMP-9 is linked to the development of bronchiolitis obliterans syndrome after lung transplantation (Hubner et al., 2005).

[00152] MMP mRNAs (MMP1, 8, 12, 15, 20, 21, 24, 26 and 27) can be detected in exosomes shed by glioblastoma cells as shown in Example 4 and Table 10. The present 55 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 exosome method, isolating exosomes from a bodily fluid and analyzing nucleic acids from said exosomes, can be used to monitor transplantation conditions. The exosome isolation procedure is similar to that detailed in Example 2. The present procedures to analyze nucleic acid contained within exosomes are detailed in Example 9. A significant increase in the expression level of MMP-2 after kidney transplantation will indicate the onset and/or deterioration of post-transplantation complications. Similarly, a significantly elevated level of MMP-9 after lung transplantation, suggests the onset and/or deterioration of bronchiolitis obliterans syndrome.

[00153] Therefore, the exosome method can be used to monitor post-transplantation conditions by determining the expression levels of MMP proteins associated with posttransplantation complications. It is also expected that the method can be extrapolated to monitor post-transplantation conditions by determining the expression of other marker genes as well as monitor other medical conditions by determining the genetic profile of nucleic acids associated with these medical conditions.

Examples 16-18. Micro vesicles can be therapeutic agents or delivery vehicles of therapeutic agents.

Example 16: Microvesicle proteins induce angiogenesis in vitro.

[00154] A study was designed and carried out to demonstrate glioblastoma microvesicles contribute to angiogenesis. HBMVECs (30,000 cells), a brain endothelial cell line, (Cell Systems, Catalogue #ACBRI-376, Kirkland, WA, USA) were cultured on Matrigel-coated wells in a 24-well plate in basal medium only (EBM) (Lonza Biologies Inc., Portsmouth, NH, USA), basal medium supplemented with glioblastoma microvesicles (EBM+ MV) (7 pg/well), or basal medium supplemented with a cocktail of angiogenic factors (EGM; hydrocortisone, EGF, FGF, VEGF, IGF, ascorbic acid, FBS, and heparin; Singlequots (EBM positive control). Tubule formation was measured after 16 hours and analyzed with the Image J software. HBMVECs cultured in the presence of glioblastoma microvesicles demonstrated a doubling of tubule length within 1 6 hours. The result was comparable to the result obtained with HBMCECs cultured in the presence of angiogenic factors (FIG. 18a). These results show that glioblastoma-derived microvesicles play a role in initiating angiogenesis in brain endothelial cells.

[00155] Levels of angiogenic proteins in microvesicles were also analyzed and compared with levels in glioblastoma donor cells. Using a human angiogenesis antibody 56 PCT/U S2009/032881 WO 2009/100029 2015203111 11 Jun2015 array, we were able to detect 19 proteins involved in angiogenesis. Specifically, total protein from either primary glioblastoma cells or purified microvesicles isolated from said cells were lysed in lysis buffer (Promega, Madison, WI, USA) and added to the human angiogenesis antibody array (Panomics, Fremont CA, USA) according to manufacturer’s recommendations. The arrays were scanned and analyzed with the Image J software. As shown in FIG. 18b, of the seven of the 19 angiogenic proteins were readily detected in the microvesicles, 6 (angiogenin, IL-6,1L-8, TIMP-I, VEGF and TIMP-2) were present at higher levels on a total protein basis as compared to the glioblastoma cells (FIG. 18c). The three angiogenic proteins most enriched in micro vesicles compared to tumor cells were angiogenin, IL-6 and 1L-8, all of which have been implicated in glioma angiogenesis with higher levels associated with increased malignancy (25-27).

[00156] Microvesicles isolated from primary glioblastoma cells were also found to promote proliferation of a human U87 glioma cell line. In these studies, 100 000 U87 cells were seeded in wells of a 24-well plate and allowed to grow for three days (DMEM-5%FBS) or DMEM-5%FBS supplemented with 125 pg microvesicles isolated from primary glioblastoma cells. After three days, untreated U87 cells (FIG. 19a) were found to be fewer in number as determined using a Burker chamber, than those supplemented with microvesicles (FIG. 19b). Both non-supplemented and supplemented U87 cells had increased 5-and 8-fold in number over this period, respectively (FIG. 19c). Thus, glioblastoma micro vesicles appear to stimulate proliferation of other glioma cells.

Example 17: Glioblastoma microvesicles are taken up by HBMVECs.

[00157] To demonstrate that glioblastoma microvesicles are able to be taken up by human brain microvesicular endothelial cells (HBMVECs), purified glioblastoma microvesicles were labeled with PKH67 Green Fluorescent labeling kit (Sigma-Aldrich, St Louis, MO, USA). The labeled microvesicles were incubated with HBMVEC in culture (5 pg/50,000 cells) for 20 min at 4°C. The cells were washed and incubated at 37°C for 1 hour. Within 30 min the PKH67-labeled microvesicles were internalized into endosome-like structures within the HBMVECs (FIG. 17a). These results show that glioblastoma microvesicles can be internalized by brain endothelial cells.

[00158] Similar results were obtained when adding the fluorescently labeled microvesicles to primary glioblastoma cells. 57 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

Example 18: mRNA delivered by glioblastoma microvesicles can be translated in recipient cells.

[00159] To determine whether glioblastoma-derived microvesicles mRNA could be delivered to and expressed in recipient cells, primary human glioblastoma cells were infected with a self-inactivating lentivirus vector expressing secreted Gaussia luciferase (Glue) using a CMV promoter at an infection efficiency of >95%. The cells were stably transduced and generated micro vesicles during the subsequent passages (2-10 passages were analyzed). Microvesicles were isolated from the cells and purified as described above. RT-PCR analysis showed that the mRNA for Glue (555 bp) as well as GAPDH (226 bp) were present in the microvesicles (FIG. 17b). The level of Glue mRNA was even higher than that for GAPDH as evaluated with quantitative RT-PCR.

[00160] Fifty micrograms of the purified microvesicles were added to 50,000 HBMVE cells and incubated for 24 hrs. The Glue activity in the supernatant was measured directly after microvesicle addition (0 hrs), and after 15 hrs and 24 hrs. The Glue activity in the supernatant was normalized to the Glue protein activity associated with the micro vesicles.

The results are presented as the mean + SEM (n=4). Specifically, the activity in the recipient HBMVE cells demonstrated a continual translation of the microvesicular Glue mRNA. Thus, mRNA incorporated into the tumor microvesicles can be delivered into recipient cells and generate a functional protein.

[00161] The statistical analyses in all examples were performed using the Student's t-test.

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Table 1. RNA in glioblastoma microvesicles can be used as sensitive biomarkers.

Nested RT-PCR was used to monitor EGFRvIII mRNA in glioma biopsy tissue as well as exosomes purified from a frozen serum sample from the same patient. Samples from 30 patients were analysed in a blinded fashion and PCR reactions were repeated at least three times for each sample. No EGFRvIII mRNA was found in serum microvesicles from 30 normal controls. PP1 refers to primer pair composed of SEQ ID NOs: 13 and 14. PP2 refers to primer pair composed of SEQ ID NOS: 15 and 16. refers to “not available”.

Patient# Time of serum collection* Serum volume Biopsy EGFRvIII Serum exosome EGFRvlll(PPl) Serum exosome EGFRvlll(PP2) 1 0 3 ml Yes Yes - 2 0 2 ml No No - 3 0 2.5 ml No No - 4 0 1ml Yes No Yes 5 0 1ml Yes No Yes 6 0 1ml No No - 7 0 0.6 ml Yes Yes - 8 0 1ml No No - 9 0 1ml Yes Yes - 10 0 1ml No Yes - 11 0 2 ml Yes No Yes 12 0 2 ml Yes Yes - 13 0 2 ml No Yes - 14 0 2 ml Yes Yes - 15 0 2 ml No No - 16 0 2 ml No No - 17 0 1ml Yes No - 18 0 0.8 ml Yes No - 19 0 1ml No No - 20 0 1ml No No - 21 0 1ml No No - 22 0 1ml No No - 23 0 1ml No No - 24 0 1ml No No - 25 0 1ml No No - 26 14 0.6 ml Yes No Yes 27 14 1.2 ml No No No 28 14 0.8 ml Yes No Yes 29 14 0.9 ml Yes No No 30 14 0.6 ml Yes No Yes *Days post-surgery of tumor removal 69 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Table 2 Abbreviations used in Table 3.

Abbreviation A AEL AL ALCL ALL AML AML* APL B-ALL B-CLL B-NHL CLL CML CMML CNS D DLSP DLBL DLCL Dom E L GIST JMML L M MALT MDS Mis MLCLS MM MPD N NHL NK/T NSCLC O PMBL pre-B All Rec S T T-ALL T-CLL TGCT T-PLL

Term amplification acute eosinophilic leukemia acute leukemia anaplastic large-cell lymphoma acute lymphocytic leukemia acute myelogenous leukemia acute myelogenous leukemia (primarily treatment associated) acute promyelocytic leukemia B-cell acute lymphocyte leukemia B-cell Lymphocytic leukemia B-cell Non-Hodgkin Lymphoma chronic lymphatic leukemia chronic myeloid leukemia chronic myelomonocytic leukemia central nervous system large deletion dermatfibrosarcoma protuberans diffuse large B-cell lymphoma diffuse large-cell lymphoma dominant epithelial frames gastrointestinal stromal tumour juvenile myelomonocytic leukemia leukaemia/lymphoma mesenchymal mucosa-associated lymphoid tissue lymphoma myelodysplastic syndrome Missense mediastinal large cell lymphoma with sclerosis multiple myeloma Myeloproliferative disorder nonsense non-Hodgkin lymphoma natural killer T cell non small cell lung cancer other primary mediastinal B-cell lymphoma pre-B-cell acute lymphablastic leukaemia reccesive splice site translocation T-cell acute lymphoblastic leukemia T-cell chronic lymphocytic leukaemia testicular germ cell tumour T cell prolymphocytic leukaemia 70 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Cancer Locuslink Protein Chromosome Tumour types Tumour types Cancer Tissue molecular : Mutation : Translocation Symbol ID ID* band (somatic) (germline) syndrome type genetics type partner ABLl 25 P00519 9q34.1 (’ML, ALL - i L • Dom : T ! BCR, ETV6 ABL2 27 P42684 Iq24-q25 AML - L • Dom T \ ETV6 AFI5QI4 57082 NP 06511 3 15ql4 AML - - L • Dom T MLL AF1Q 10962 Q13015 lq21 ALL - : L j Dom ! T \ MLL . \ / '(>21 51517_ Q9NZQ3 3p21_ ALL_ _ _! L i Dom : T \ MLL AF5q31 27125 NP_05523 8 5q31 ALL - - L j Dom ! T \ MLL AKT2 208 P31751 19ql3.1-ql3.2 Ovarian, pancreatic _ _ ; E : Dom ! A ALK 238 Q9UM73 2p23 ALCL L j Dom ; T ; NPM1, TPM3, : TFG, TPM4, : ATIC, CLTC, \ MSN, ALOl 7 AL017 57714 XP_29076 9 17q25.3 ALCL - i L : Dom : τ \ ALK APC 324 P25054 5q21 Colorectal, Colorectal, pancreatic, Adenomatous E, Μ, O ; Rec i D*, Mis, : _ pancreatic, desmoid, hepatoblastoma, polyposis coli; ! N, F, S desmoid, glioma, other CNS Turcot hepatoblastoma, glioma, other CNS syndrome ARHGEF1 23365 NP 05612 llq23.3 AML - i L i Dom i T : MLL "ARHH......... 399 Q15669 4pl3....................... NHL........................... - : i.................. i Dom j f................. bctjs.................... ARNT 405 P27540 Iq21 AML - i L j Dom i τ : ETV6 ASPSCR1 79058 NP 07698 17q25 Alveolar soft part - ; M ; Dom : τ : TFE3 8 sarcoma ATF1 466 P18846 12ql3 Malignant melanoma of soft - i E,M ; Dom : τ \ EWSR1 parts, angiomatoid fibrous histiocytoma ATIC 471 P31939 2q35 ALCL - : L I Dom ! T i ALK ATM 472 Q13315 1 lq22.3 T-PLL Leukaemia, lymphoma, Ataxia j L, O I Rec i D, Mis, N, \ - medulloblastoma, glioma telangiectasia j : F, S BCL10 8915 095999 lp22 MALT - ! L i Dom 1 τ \ IGHa BCL11A 53335 NP_06048 4 2pl3 B-CLL - - L i Dom ; τ \ IGHa siozvnt π meoKioz WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner BCL11B 64919 NP61280 8 14q32.1 T-ALL - - L Dom T TLX3 BCL2 596 P10415 18q21.3 NHL, CLL - - L Dom T IGHa BCL3 602 P20749 19q 13 CLL - - L Dom T IGHa BCL5 603 152586 17q22 CLL - - L Dom T MYC BCL6 604 P41182 3q27 NHL, CLL L Dom T, Mis IG loci, ZNFN1A1, LCP1, PIM1, TFRC, MHC2TA, NACA, HSPCB, HSPCA, HIST1H4I, IL21R, POU2AF1, ARHH, EIF4A2 BCL7A BCL9 BCR 605 607 613 NP 06627 3 000512 PI 1274 12q24.1 lq21 22qll.21 B-NHL U-ALL CML, ALL - - T, L L Dom Dom Dom T T T MYC IGHa, IGLa ABL1, FGFR1 BHD 201163 NP 65943 4 17p 11.2 Renal, fibrofolliculomas, trichodiscomas Birt-Hogg-Dube syndrome E, M Rec? Mis, N, F ' BIRC3 330 Q13489 Ilq22-q23 MALT - - L Dom T MALT1 BLM 641 P54132 15q26.1 Leukaemia, lymphoma, skin squamous cell, other cancers Bloom Syndrome L, E Rec Mis, N, F BMPR1A 657 P36894 10q22.3 - Gastrointestinal polyps Juvenile polyposis E Rec Mis, N, F ~ BRAF 673 P15056 7q34 Melanoma, colorectal, papillary thyroid, borderline ovarian, NSCLC, cholangiocarcinoma E Dom M BRCA1 672 P38398 17q21 Ovarian Breast, ovarian Hereditary breast/ovarian E Rec D, Mis, N, F, S ~ BRCA2 675 P51587 13ql2 Breast, ovarian, pancreatic Breast, ovarian, pancreatic, leukaemia (FANCB, Hereditary breast/ L, E ovarian Rec D, Mis, N, - F, S S10Zmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner BRD4 23476 060885 19pl3.1 Lethal midline carcinoma of young people FANCDl) - L Dom T NUT BTG1 694 P31607 12q22 BCLL - - L Dom T MYC CBFA2T1 862 Q06455 8q22 AML - - L Dom T MLL, RUNX1 CBFA2T3 863 NP 00517 8 16q24 AML - - L Dom T RUNX1 CBFB 865 Q13951 16q22 AML - - L Dom T MYH11 CBL 867 P22681 11q 23.3 AML - - L Dom T MLL CCND1 595 P24385 11 q 13 CLL, B-ALL, breast - - L,E Dom T IGHa, FSTL3 CDH1 999 P12830 16q22.1 Lobular breast, gastric Gastric Familial gastric carcinoma E Rec Mis, N, F, S - CDK4 1019 PI 1802 12ql4 Melanoma Familial malignant melanoma E Dom Mis — CDKN2A- p!4ARF 1029 NP 47810 2 9p21 Melanoma, multiple other Melanoma, pancreatic Familial malignant melanoma L, E, Μ, O Rec D, S - CDKN2A- p16,NK4A 1029 P42771 9p21 Melanoma, multiple other Melanoma, pancreatic Familial malignant melanoma L, E, Μ, O Rec D, Mis, N, F, S CDX2 1045 Q99626 13ql2.3 AML - - L Dom T ETV6 CEBPA 1050 NP 00435 5 1 lpl5.5 AML, MDS - - L Dom Mis, N, F - CEP1 11064 NP 00894 9 9q33 MPD/NHL - - L Dom T FGFR1 CHIC2 26511 NP 03624 2 4qll-ql2 AML - - L Dom T ETV6 CHN1 1123 P15882 2q31-q32.1 Extraskeletal myxoid chondrosarcoma — — M Dom T TAF15 CLTC 1213 Q00610 17q 11-qter ALCL - - L Dom T ATX COL1A1 1277 P02452 17q21.31-q22 Dermatofibrosarc oma protuberans - - M Dom T PDGFB COPEB 1316 Q99612 10pl5 Prostatic, glioma - - E, O Rec Mis, N - S10Zmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner COX6C 1345 P09669 8q22-q23 Uterine leiomyoma - - M Dom T HMGA2 CREBBP 1387 Q92793 16pl3.3 AL, AML - - L Dom T MEL, MORF, RUNXBP2 CTNNB1 1499 P35222 3p22-p21.3 Colorectal, ovarian, hepatoblastoma, others — — E, Μ, O Dom H, Mis — CYLD 1540 NP_05606 2 16ql2-ql3 Cylindroma Cylindroma Familial cylindromatosis E Rec Mis, N, F, S ~ DIOS 170 8030 NP 00542 7 10q21 Papillary thyroid, CML - - E Dom T RET, PDGFRB DDB2 1643 Q92466 1 lpl2 - Skin basal cell, skin squamous cell, melanoma Xeroderma pigmentosum E E Rec M,N - DDIT3 1649 P35638 12q13.1 -ql3.2 Liposarcoma — — M Dom T FUS DDX10 DEK.............. EGER EIF4A2 ELKS 1662 7913................. 1956 1974 23085 Q13206 P35659....... P00533 Q 142.40 NP 05587 9 1 Iq22-q23 '.MZZZZ 7pl2.3-pl2.1 MliZZZI J 2pi 3.3 AML§ "AML.......................... Glioma NHL Papillary thyroid L L O L E Dom Dom Dom Dom Dom T "t.................. A, Ol! T T NUP98 NUP214 Hi Ί ,-: RET ELL 8178 P55199 l9pl3.J AI. - - L Dom T MLL EP300 2033 Q09472 22ql3 Colorectal, breast, pancreatic, AJV1L L, E Rec T MEL, RUNXBP2 EPS! 5 2060 P42566 lp32 ALL L Dom T MLL ERBB2 2064 P04626 17q21.1 Breast, ovarian, other tumour types - - E Dom A - ERCC2 2068 PI8074 19ql3.2-ql3.3 - Skin basal cell, skin Xeroderma squamous cell, melanoma pig-m ntosum D £ Rec Μ, N, F, S - ERCC3 2071 PI 9447 2q21 - Skin basal cell, skin squamous cell, melanoma Xeroderma pigmentosum B E Rec M, S - ERCC4 2072 Q92889 16pl3.3- Skin basal cell, skin squamous cell, melanoma Xeroderma pigmentosum F E Rec Μ, N, F ERCC5 2073 P28715 13q33 Skin basal cell, skin squamous cell, melanoma Xeroderma pigmentosum G E Rec Μ, N, F ERG 2078 PI 1308 21q22.3 Ewing's sarcoma - - M Dom T EWSR1

SIOZ unf II IIie03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner KTV1! 2Π5 ETV4 i 2118 P50549 P43268 7p22 17q21 Ewing’s sarcoma j -- ; — i M i Dom Ewing’s sarcoma j — - · M · Dom T : EWSRI T i EWSRI ETV6 2120 P41212 12p 13 Congenital fibrosarcoma, multiple leukaemia and lymphoma, secretory breast - - L, E, M Dom T NTRK3, RUNX1, PDGFRB, ABU, MNJ, ABL2, FACL6, CmC2, ARNT, JAK2, EVIL CDX2, STL EVU 2122 Q03I12 3q26 AML, CML - ... L Dom T RUNX1, ETV6 EWSR1 2130 NP 00523 4 22ql2 Ewing’s sarcoma, desmoplastic small round cell, ALL - - L,M Dom T FLU, ERG, ZNF278, NR4A3, TEC, FEV, ATF1, EIYJ, ETV4, WT1, ZNF384 EXT1 2131 NP 00011 8 8q24.ll-q24.13 - Exostoses, osteosarcoma Multiple exostoses type 1 M Rec Mis, N, F, S - ΕΧΊ2 2132 Q93063 11 p 12-p J1 - Exostoses, osteosarcoma Multiple exostoses type 2 M Rec Mis, N, F, S - EACH, 23305 NP 05607 1 5q31 AML, ALL - - L Dom T ETV6 FANCA 2175 NP_00012 6 16q24.3 - AML, leukaemia Fanconi anaemia A L Rec D, Mis, N, F, S - FANCC 2176 Q00597 9q22.3 AMI., leukaemia Fanconi anaemia C L Rec D. Mis, N, F,S FANCD2 2177 NP.J4907 5 3p26 - AML, leukaemia Fanconi anaemia D2 L Rec D, Mis, N, F - FANCE 2178 NP 06874 1 6p21 -p22 - .., . , . : Fanconi anaemia AML, leukaemia ^, L Rec N, F, S - FANCF 2188 Q9NPI8 1 ip 15 - s., .Y , . . : Fanconi anaemia : T AML. leukaemia „ : L F Rec N, F - FANCC- 2189 015287 9pl3 - AML, leukaemia Fanconi anaemia G L Rec Mis, N, F, S - FEV 54738 NP 05999 1 2q36 Ewing’s sarcoma - - M Dom T EWSRI FGFR1 FGFRIOP 2260 11116 PI 1362 NP 0089 ' Spl 1,2,-pl 1.1 6q27 MPD/NHL MPD/NI1L .- .- L L Dom Dom T T BCR, FOP, 7.NF198, CEP! FGFRl S10Zmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner FGFR2 2263 6 P21802 10q26 Gastric E Dom Mis FGFR3 2261 P22607 4pl6.3 Bladder, MM L, E Dom Mis, T IGHa FH 2271 P07954 lq42.1 Leiomyomatosis, renal Hereditary leiomyomatosis and renal-cell cancer E, M Rec Mis, N, F FIP1L1 81608 NP_11217 9 4ql2 Idiopathic hypereosinophilic syndrome L Dom T PDGFRA FLI1 2313 Q01543 1 lq24 Ewing’s sarcoma - - M Dom T EWSR1 FLT3 2322 P36888 13q 12 AMT,, AT T. - - L Dom Mis, O - FLT4 2324 P35916 5q35.3 Angiosarcoma - - M Dom Mis - FNBP1 23048 XP_05266 6 9q23 AML - - L Dom T MEL FOXOIA 2308 Q12778 13ql4.1 Alveolar rhabdomyosarcoma s M Dom T PAX3 FOX03A 2309 043524 6q21 AL - - L Dom T MLL FSTL3 10272 095633 19pl3 : 15-( PL - - L Dom T CCND1 FUS 2521 P35637 16pll.2 ! Liposarcoma - - M Dom T DDIT3 GAS7 8522 060861 17p : AML§ - - L Dom T MLL GATA1 2623 P15976 Xp 11.23 Megakaryoblastic leukaemia of Down syndrome L Dom Mis, F GMPS 8833 P49915 3q24 AML - - L Dom T MLL GNAS 2778 P04895 20ql3.2 Pituitary adenoma - - E Dom Mis - GOLGA5 9950 NP 00510 4 14q Papillary thyroid - - E Dom T RET GPC3 2719 P51654 Xq26.1 Wilms’ tumour Simpson-Golabi-Behmel O syndrome O Rec T, D, Mis, N, F, S GPHN 10243 Q9NQX3 14q24 AL - - L Dom T MLL GRAF 23092 NP 05588 6 5q31 AML, MDS - - L Dom T, F, S MLL HEI10 57820 NP 06700 1 14ql 1.1 Uterine leiomyoma - - M Dom T HMGA2 HIP1 3092 000291 7qll.23 CMML - - L Dom T PDGFRB HIST1H4I 8294 NP 00348 6p21.3 NHL - - L Dom T BCL6 SIOZmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner //// 3131 6 (.)1653 : 17q22 ALL L Dom T /(/.<· HMGA2 8091 P52926 12ql5 Lipoma M Dom T LHFP, RAD51L1, LPP, HEI10, COX6C HOXA11 3207 P31270 7pl5-pl4.2 CML - - L Dom T NUP98 HOXA13 3209 P31271 7pl5-pl4.2 AML - - L Dom T NUP98 HOXA9 3205 P31269 7pl5-pl4.2 AML§ - - L Dom T NUP98 HOXC13 3229 P31276 12ql3.3 AML - - L Dom T NUP98 HOXD11 3237 P31277 2q31-q32 AML - - L Dom T NUP98 HOXD13 3239 P35453 2q31-q32 AML§ - - L Dom T NUP98 HRAS 3265 P01112 llpl5.5 Infrequent sarcomas, rare other types L, M Dom Mis HRPT2 3279 NP01352 2 Iq21-q31 Parathyroid adenoma Parathyroid adenoma, multiple ossifying jaw fibroma Hyperparathyroidism jaw tumour syndrome E, M Rec Mis, N, L HSPCA 3320 P07900 Iq21.2-q22 NHL - - L Dom T BCL6 HSPCB 3326 P08238 6pl2 NHL - - L Dom T BCL6 IGHa 3492 14q32.33 MM, Burkitt’ s lymphoma, NHL, CLL, B-ATT,, MALT L Dom T MYC, FGFR3, PAX5, IRTA1, IRF4, CCND1, BCL9, BCL6, BCL8, BCL2, BCL3, BCL10, BCL11A. LHX4 IGKa 50802 : 2pl2 Burkitt’s lymphoma - - L Dom T i MYC IGLa 3535 : 22qll.l-qll.2 Burkitt’s lymphoma - - L Dom T i BCL9, MYC IL21R 50615 Q9HBE5 : 16pll NHL - - L Dom T i BCL6 IRF4 3662 Q15306 6p25-p23 MM - - L Dom T IGHa IRTA1 83417 NP_11257 2 1α21 B-NHL - - L Dom T IGHa JAK2 3717 060674 : 9p24 1 ALL, AML L Dom : T ETV6 KIT 3815 P10721 4ql2 GIST, AML, TGCT GIST, epithelioma Familial gastrointestinal stromal 1 Μ, O Dom Mis, O KRAS2 3845 NP 00497 6 12pl2.1 Pancreatic, colorectal, lung, thyroid, AML, L, E, Μ, O Dom Mis SIOZmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner LAF4 3899 1*51826 2q 1 1.2 q 1 2 others ATI, L Dom T MEL LASPI 3927 Q14847 17qll-q21.3 AML L Dom T MLL LCK 3932 NP 00534 7 Ip35-p34.3 T-AT.T. — — L Dom T TRBa LCP1 3936 P13796 13ql4.1-ql4.3 NHL - L Dom T BCL6 LCX 80312 XP_16761 2 10q21 AML - - L Dom T MLL LHFP 10186 NP 00577 1 13ql2 Lipoma - - M Dom T HMGA2 LMOl 4004 P25800 llpl5 T-AT.T. - - L Dom T TRDa LM02 4005 P25791 llpl3 T-AT.T. - - L Dom T TRDa LPP 4026 NP_00556 9 3q28 Lipoma, leukaemia - - L,M Dom T HMGA2, MLL LYL1 4066 P12980 19pl3.2-pl3.1 T-AT.T. - - L Dom T TRBa MADH4 4089 Q13485 18q21.1 Colorectal, pancreatic, small intestine Gastrointestinal polyps Juvenile polyposis E Rec D, Mis, N, F MALT1 10892 Q9UDY8 18q21 MALT - - L Dom T BIRC3 MAML2 84441 XP 04571 6 Ilq22-q23 Salivary-gland mucoepidermoid - - E Dom T MECT1 MAP2K4 6416 P45985 17pl 1.2 Pancreatic, breast, colorectal - - E Rec D, Mis, N ~ MDS1 4197 Q13465 3q26 MDS, AML - - L Dom T RUNX1 MECT1 94159 AAK9383 2.1 19pl3 Salivary-gland mucoepidermoid — — E Dom T MAML2 MEN1 4221 000255 1 lql3 Parathyroid Parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid Multiple endocrine neoplasia type 1 E Rec D, Mis, N, F, S MET 4233 P08581 7q31 Papillary renal, head-neck squamous cell Papillary renal Familial papillary renal E Dom Mis MHC2TA 4261 P33076 : 16pl3 1 NHL - L Dom ! T i BCL6 MLF1 4291 P58340 : 3q25.1 1 AML - L Dom ! T i NPM1 MLH1 4292 P40692 3p21.3 colorectal, endometrial, ovarian, CNS Colorectal, endometrial, ovarian, CNS Hereditary nonpolyposis colorectal, Turcot syndrome E, O Rec D, Mis, N, F, S S10Zmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner MLL 4297 Q03164 1 lq23 AMT,, AT T, L Dom T, O MLL, MLLT1, MLLT2, MLLT3, MLLT4, MLLT7, MLLT10, MLLT6, ELL, EPS15, AF1Q, CREBBP, SH3GL1, FNBP1, PNUTL1, MSF, GPHN, GMPS, SSH3BP1, ARHGEF12, GAS7, FOX03A, LAF4, LCX, SEPT6, LPP, CBFA2T1, GRAF, EP300, PICALM MLLT1 4298 Q03 111 19pl3.3 AL - - L Dom T MLL MLLT10 8028 P55197 10pl2 AL - - L Dom T MLL, PICALM MLLT2 4299 P51825 4q21 AL - - L Dom T MLL MLLT3 4300 P42568 9p22 ATT, - - L Dom T MLL MLLT4 4301 P55196 6q27 AL - - L Dom T MLL MLLT6 4302 P55198 17q21 AL - - L Dom T MLL MLLT7 4303 NP 00592 9 Xql3.1 AL - - L Dom T MLL MN1 4330 Q10571 22ql3 AML, meningioma - - L, O Dom T ETV6 MSF 10801 NP 00663 1 17q25 AML§ - - L Dom T MLL MSH2 4436 P43246 2p22-p21 Colorectal, endometrial, ovarian Colorectal, endometrial, ovarian Hereditary nonpolyposis colorectal E Rec D, Mis, N, F, S MSH6 2956 P52701 2pl6 Colorectal Colorectal, endometrial, ovarian Hereditary nonpolyposis colorectal E Rec Mis, N, F, S MSN 4478 P26038 Xqll.2-ql2 ALCL - - L Dom T ATX MUTYH 4595 NP 03635 4 Ip34.3-lp32.1 Colorectal Adenomatous polyposis coli E Rec Mis, N, F, S ~ SIOZmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner MYC 4609 P01106 8q24.12-q24.13 Burkitt’s lymphoma, amplified in other cancers, B-CLL L, E Dom A, T IGKa, BCL5, BCL7A, BTG1, TRAa. IGHa MYCL1 4610 P12524 P04198 P35749 P35579 lp34.3 : Small cell lung - E Dom A - MYCN : 4613 MYH11 : 4629 MYH9 : 4627 2p24.1 : Neuroblastoma i -16p 13.13-p 13.12 : AML - O Dom A CBFB ATX - L Dom T 22ql3.1 AI.C'L - L Dom T MYST4 23522 NP 03646 2 10q22 AML — — L Dom T CREBBP NACA 4666 NP 00558 5 12q23-q24.1 NHL — — L Dom T BCL6 NBS1 4683 NP 00247 6 8q21 NHL, glioma, medulloblastoma, rhabdomyosarcoma Nijmegen breakage syndrome L, E, Μ, O Rec Mis, N, F NCOA2 10499 Q15596 8ql3.1 AML : L Dom T RUNXBP2 NCOA4 8031 Q13772 10qll.2 Papillary thyroid - E Dom T RET NF1 4763 P21359 17ql2 Neurofibroma, glioma Neurofibroma, glioma Neurofibromatos is type 1 O Rec D, Mis, N, F, S, O ~ NF2 4771 P35240 22ql2.2 Meningioma, acoustic neuroma Meningioma, acoustic neuroma Neurofibromatos is type 2 O Rec D, Mis, N, F, S.O ~ NOTCH1 4851 P46531 9q34.3 T-ATL - - L Dom T TRBa NPM1 4869 P06748 5q35 NHL, APL, AML - - L Dom T ATX, RARA, MLF1 NR4A3 8013 Q92570 9q22 Extraskeletal myxoid chondrosarcoma M Dom T EWSR1 NRAS 4893 P01111 lpl3.2 Melanoma, MM, AML, thyroid - - L, E Dom Mis ~ NSD1 64324 NP07190 0 5q35 AML - - L Dom T NUP98 NTRK1 4914 P04629 Iq21-q22 Papillary thyroid - - E Dom T TPM3, TPR, TFG NTRK3 4916 Q16288 15q25 Congenital fibrosarcoma, secretory breast E, M Dom T ETV6 NUMA1 4926 NP 00617 6 1 lql3 APL - - L Dom T RARA NUP214 8021 P35658 9q34.1 AML - - L Dom T DEX, SET NUP98 4928 P52948 llpl5 AML - - L Dom T HOXA9, NSD1, S10Zmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner WHSC1L1, DDX10, TOPI, HOXD13, PMX1, HOXA13, HOXD11, HOXA11, RAP1GDS1 NUT 256646 XP17172 4 15ql3 Lethal midline carcinoma of young people E Dom T BRD4 OLIG2 10215 Q13516 21q22.11 T-AT.T. - - L Dom T TRAa PAX3 5077 P23760 2q35 Alveolar rhabdomyosarcoma - - M Dom T FOXOIA PAX5 5079 Q02548 9pl3 NHL - - L Dom T IGHa PAX7 5081 P23759 Ip36.2-p36.12 Alveolar rhabdomyosarcoma - - M Dom T FOXOIA PAX8 7849 Q06710 2ql2-ql4 Follicular thyroid - - L Dom T PPARG PBX1 5087 NP 00257 6 lq23 Pre-R-ALL L Dom T TCF3 PCM1 5108 NP 00618 8 8p22-p21.3 Papillary thyroid - - E Dom T RET PDGFB 5155 P01127 22ql2.3-ql3.1 DFSP - - M Dom T COL1A1 PDGFRA 5156 P16234 4q11-q13 GIST - - Μ, O Dom Mis, O - PDGFRB 5159 NP 00260 0 5q31-q32 MPD, AML, CMML, CML L Dom T ETV6, TRIP11, HIP1, RAB5EP, H4 PICALM 8301 Q13492 1 lql4 T-AT.T., AML - - L Dom T MLLT10, MET PIM1 5292 PI 1309 6p21.2 NHL - - L Dom T BCL6 PML 5371 P29590 15q22 APL - - L Dom T RARA PMS1 5378 P54277 2q31-q33 Colorectal, endometrial, ovarian Hereditary nonpolyposis colorectal cancer E Rec Mis, N PMS2 5395 P54278 7p22 Colorectal, endometrial, ovarian, medulloblastoma, glioma Hereditary nonpolyposis colorectal cancer, Turcot syndrome E Rec Mis, N, F PMX1 5396 P54821 lq24 AML - L Dom T NUP98 PNUTL1 5413 NP 00267 22ql 1.2 AML - L Dom T MEL SIOZmf ii me03^I03 WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Cancer Locuslink Protein Chromosome Tumour types Tumour types Cancer Tissue molecular j Mutation i Translocation Symbol ID ID* band (somatic) (germline) syndrome type genetics type partner : 9 POU2AF1 ; 5450 i Q16633 1 lq23.1 NHL : - L ! Dom i T : BCL6 PPARG ; 5468 i P37231 3p25 1'ollicular thyroid - L : Dom : T l PAX8 PRCC ; 5546 i Q92733 1q21.1 Papillary renal - - E : Dom : T : TFE3 PRKAR1A ; 5573 ; P10644 17q23-q24 Papillary thyroid Myxoma, endocrine, Carney complex E, M j Dom, Rec : T, Mis, N, : RET papillary thyroid : F, S PRO1073 ! 29005 i Q9UHZ2 1lq31.1 Renal-cell - - E i Dom : T : TFEB carcinoma (childhood epithelioid) PSIP2 ; 11168 : NP 15009 : 1 9p22.2 AML - - L : Dom : T : NUP98 PTCH ; 5727 ; Q13635 9q22.3 Skin basal cell, Skin basal cell, Nevoid basal- E, M : Rec : Mis, N, F, i - medulloblastoma medulloblastoma cell carcinoma syndrome : S PTEN : 5728 ; 000633 10q23.3 Glioma, prostatic, Harmartoma, glioma, Cowden L, E, Μ, O ; Rec i D, Mis, N, ; - endometrial prostatic, endometrial syndrome, Bannayan- Riley- Ruvalcaba : F, S syndrome ΡΤΡΝΪ1 I 5781 ; Q06124 12q24.1 JMML, AML, MDS — — L • Dom : Mis : — RAB5EP i 9135 ! NP_00469 17pl3 CMML - - L i Dom i T !PDGFRB RAD.'II /..... "5890............... ΪΝΡ "00286 "I4q23-q24.2......... Lipoma, uterine _ _ M................. ; Dom "t................. \HMGA2 ! 8 leiomyoma RAP1GDS1 i 5910 ; P52306 4q21-q25 T-AT.T, - - L : Dom i T : NUP98 RARA i 5914 : PI0276 17ql2 APL L ; Dom ! T \ PML, ZNF145, \ TIF1, NUMA1, \ NPM1 RBI : 5925 ; P06400 13ql4 Retinoblastoma, Retinoblastoma, sarcoma, Familial L, E, Μ, O i Rec 1 D, Mis, N, \ - sarcoma, breast, small-cell lung breast, small-cell lung retinoblastoma j F, S RECQL4 : 9401 : 094761 8q24.3 - Osteosarcoma, skin basal Rothmund- M ; Rec N,F,S : - and squamous cell Thompson syndrome "rel : 5966 ; Q04864 2pl3-pl2 Hodgkin Lymphoma — — L j Dom ; A : “ RET j 5979 ; P07949 iOqil.2 Medullary thyroid, Medullary thyroid, Multiple Ε,Ο j Dom ; T, Mis, N, ΙΪ4, PR FARIA,

SIOZ unf II

UK0ZS10Z WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner papillary thyroid, pheochromocytoma papillary thyroid, pheochromocytomaneoplas ia endocrine 2A/2B F NCOA4, PCMl, GOLGA5, TRIM33 RPL22 6146 P35268 3q26 AML, CML - - L Dom T RUNX'l RUNX1 861 Q01196 21q22.3 AML, pre-B-ALL L Dom T RPL22, MDS1, EVI1, CBFA2T3, CBFA2T1, ETV6 RUNXBP2 799 NP_00675 7 8pll AML - L Dom T CREBBP, NCOA2, EP300 SBDS 51119 Q9Y3A5 7qll AML, MDS Schwachman- Diamond syndrome L Rec Gene conversion SDHB 6390 P21912 Ip36.1-p35 - Paraganglioma, pheochromocytoma Familial paraganglioma O Rec Mis, N, F — SDHC 6391 075609 lq21 - Paraganglioma, pheochromocytoma Familial paraganglioma O Rec Mis, N, F — SDHD 6392 014521 1 lq23 - Paraganglioma, pheochromocytoma Familial paraganglioma o Rec Mis, N, F, S — SEPT6 23157 NP_05594 4 Xq24 AML - - L Dom T MEL SET 6418 Q01105 9q34 AML - - L Dom T NUP214 SFPQ 6421 P23246 lp34.3 Papillary renal cell - - E Dom T TFE3 SH3GL1 6455 099961 19pl3.3 AL - - L Dom T MLL SMARCB1 6598 Q12824 22ql 1 Malignant rhabdoid Malignant rhabdoid Rhabdoid predisposition syndrome M Rec D, N, F, S SMO 6608 Q99835 7q31-q32 Skin basal cell - - E Dom Mis - SS18 6760 Q15532 18ql 1.2 Synovial sarcoma - - M Dom T SSXI, 88X2 SS18L1 26039 075177 20ql3.3 Synovial sarcoma - M Dom T SSXI SSH3BP1 10006 NP 00546 1 ''016384'''''' 10pll.2 AML - - L Dom T ssxi...... 6756'............. Xpll.23-pii.22 Synovial sarcoma _ _ m""" Dom T 88/8...................... SSX2 6757 Q16385 Xpll.23-pll.22 Synovial sarcoma - - M Dom T 8818 SSX4 6759 060224 Xp 11.23 Synovial sarcoma - - M Dom T SS18 STK11 6794 Q15831 19pl3.3 NSCLC Jejunal harmartoma, ovarian, testicular, pancreatic Peutz-Jeghers syndrome E, Μ, O Rec D, Mis, N, STL 7955 NOPROT 6q23 BALL - - L Dom T ETV6

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Table 3: Genes Commonly Mutated in Cancers Cancer Locuslink Protein Chromosome Tnmour types Tumour types Cancer Tissue j molecular Mutation : Translocation ; Symbol ID ID* band (somatic) (germline) syndrome type genetics type partner EIN SUFU 51684 NP 05725 10q24.32 Medulloblastoma Medulloblastoma Medulloblastom : o : Rec D, F, S : - 3 a predisposition TAF15 8148 Q92804 17q 11.1 -q 11.2 Extraskeletal - - : L, M i Dom T ; TEC, CHNl, myxoid chondrosarcomas, \ ZNF384 ATT, TALI 6886 P17542 lp32 Lymphoblastic leukaemia/ biphasic - - i L j Dom T \ TRDa TAL2 6887 016559 9q31 T-AT.T, - - : L i Dom T : TRBa fCFl 6927 P20823 12q24.2 Hepatic adenoma, Hepatic adenoma, Familial hepatic : E i Rec Mis, F \ ~ hepatocellular hepatocellular carcinoma adenoma carcinoma TCF12 6938 Q99081 15q21 Extraskeletal myxoid chondrosarcoma : M : Dom T \ TEC TCF3 6929 P15923 19pl3.3 pre-B-ALL - - : L j Dom T j PBX1, HLF, : tfpt TCL1A 8115 NP 06880 1 P42680 14q32.1 T-CLL - - i L i Dom T \ TRAa TEC............... 7006................. 4pl2...................... Extraskeletal _ _ : M................ i Dom T ! EWSRI, /.1/-75. j myxoid chondrosarcoma j 7(7-72 TFE3 7030 P19532 Xp 11.22 Papillary renal, - - : E i Dom T : SFPQ, alveolar soft part ; ASPSCRl, sarcoma : prcc TFEB 7942 PI9484 6p21 Renal (childhood epithelioid) - - : E,M j Dom T : ALPHA f) (, 10342 NP 00606 3qll-ql2 Papillary thyroid, - - : E,L i Dom T : NTRK1, MX 1 ALCL TFPT 29844 NP_03747 19ql3 Pre-B-ALL - - i L i Dom T \ TCF3 TFRC............. '7037................ P02786........ 3q29....................... MIL _ _ i l.................. I Dom T................. BCL6.................... 77/-7 8805 015164 7q32-q34 API, - - ; 1, I Dom T : RARA TLX I 3195 P31314 10q24 T-ALL - - : L i Dom T : TRBa, TRDa ΤΪ.Χ3 30012 043711 5q35.1 T-ALL - - : L i Dom T : BCL11B TNFRSF6 355 P25445 10q24.1 TGCT, nasal NK/T lymphoma, skin squamous-cell carcinoma (burn- : L, E, O j Rec Mis siozvnt π meoKioz WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Cancer Locuslink Protein Chromosome T umour types Tumour types Cancer Tissue molecular Mutation Translocation Symbol ID ID* band (somatic) (germline) syndrome type genetics type partner scar related) TOPI 7150 PI 1387 20ql2-ql3.1 AML§ - L Dom T NUP98 TP53 7157 P04637 17pl3 Breast, colorectal, Breast, sarcoma, Li-Fraumeni L, E, Μ, O Rec Mis, N, F - lung, sarcoma, adrenocortical carcinoma, syndrome adrenocortical, glioma, multiple other glioma, multiple types Iq22-q23 Papillary thyroid, ALCL - - E, L Dom TPM4 7171 P07226 19p 13.1 ALCL - - L Dom T ALK TPR 7175 P12270 lq25 Papillary thyroid - - E Dom T NTRK1 TRAa 6955 — 14ql 1.2 T-ALL - - L Dom T ATL, OLIG2, MYC, TCL1A TRBa 6957 7q35 T-AT.T. L Dom T HOX11, LCK, NOTCH1, TAL2, LYL1 TRDa 6964 14ql 1 T-cell leukaemia L Dom T TALI, HOX11, TLX1, IMOl, LM02 TRIM33 51592 Q9UPN9 lpl3 Papillary thyroid - - E Dom T RET TRIP 11 9321 NP_00423 0 14q31-q32 AML - - L Dom T PDGFRB TSC1 7248 Q92574 9q34 - Hamartoma, renal cell Tuberous E, O Rec D, Mis, N, - sclerosis 1 F, S TSC2 7249 P49815 16pl3.3 - Hamartoma, renal cell Tuberous E, O Rec D, Mis, N, - sclerosis 2 F, S TSHR 7253 P16473 14q31 Toxic thyroid adenoma Thyroid adenoma - E Dom Mis - VHL 7428 P40337 3p25 Renal, Renal, hemangioma, von Hippel- E, Μ, O Rec D, Mis, N, - hemangioma, pheochromocytoma Lindau F, S pheochromocytoma syndrome WAS 7454 P42768 Xpll.23-pll.22 - Lymphoma Wiskott-Aldrich L Rec Mis, N, F, - syndrome S WHSC1L1 54904 NP_06024 8pl2 AML - - L Dom T NUP98 WRN............. "7486................. Qi-19i....... 8ρΪ2-ρΙ 1.2........... _ Osteosarcoma, Werner L. 1.. M.O..... Rec Mis. \. 1...... — meningioma, others syndrome S WT1 7490 NP_00036 Ilpl3 Wilms’, Wilms’ Denys-Drash O Rec D, Mis, N, EWSR1 9 desmoplastic small syndrome, F, S round cell Frasier

SIOZunf ii lUiOZSIOZ WO 2009/100029 PCT/US2009/032881

Table 3: Genes Commonly Mutated in Cancers Symbol Locuslink ID Protein ID* Chromosome band Tumour types (somatic) Tumour types (germline) Cancer syndrome Tissue type Cancer molecular genetics Mutation type Translocation partner "XPA.............. "xpc"'"""""""""""" "7507................ "7508 P23025 (,)()1831 9q223.................... 3p25 -................................. Skin basal cell, skin squamous cell, melanoma Skin basal cell, skin squamous cell, melanoma syndrome, Familial Wilms’ tumour Xeroderma pigmentosum A Xeroderma pigmentosum C Έ.................... E.................... Rec Rec Mis, N, Fi S Mis, N, I·, S ............................ ZNF145 7704 Q05516 1 lq23.1 APL - - L Dom T RARA ZNF198 7750 Q9UBW7 13qll-ql2 MPD/NHL - - L Dom T FGFR1 ZNF278 23598 NP_05513 22ql2-ql4 Ewing’s sarcoma - - M Dom T EWSR1 ZNF384......... 1/1017............. "\i>" 59773" 3 Ϊ2ρ13.................... "all........................... ............................................. ............................. L................... Dom "t................... /·/ wsii / , y it /· / .V ZNFN1A1 10320 NP 00605 1 7pl2 ALL, DLBCL — — L Dom T BCL6 *From S wiss-Prot/Refseq. tD (large deletion) covers the abnormalities that result in allele loss/loss of heterozygosity at many recessive cancer genes. §Refers to cases of acute myeloid leukaemia that are associated with treatment. HO (other) in the ‘mutation type’ column refers primarily to small in-frame deletions/insertions as found in KIT/PDGFRA, and larger duplications/insertions as found in FLT3 and EGFR. Note that where an inversion/large deletion has been shown to result in a fusions protein, these have been listed under translocations. The Wellcome Trust Sanger Institute web version of the cancer-gene set can be found at http://www.sanger.ac.uk/genetics/CPG/Census/. A, amplification; AEL, acute eosinophilic leukaemia; AL, acute leukaemia; ALCL, anaplastic large-cell lymphoma; ALL, acute lymphocytic leukaemia; AML, acute myelogenous leukaemia; APL, acute promyelocytic leukaemia; B-ALL, B-cell acute lymphocytic leukaemia; B-CLL, B-cell lymphocytic leukaemia; B-NHL, B-cell non-Hodgkin's lymphoma; CLL, chronic lymphatic leukaemia; CML, chronic myeloid leukaemia; CMML, chronic myelomonocytic leukaemia; CNS, central nervous system; D, large deletion; DFSP, dermatofibrosarcoma protuberans; DLBCL, diffuse large B-cell lymphoma; Dom, dominant; E, epithelial; F, ffameshift; GIST, gastrointestinal stromal tumour; JMML, juvenile myelomonocytic leukaemia; L, leukaemia/lymphoma; M, mesenchymal; MALT, mucosa-associated lymphoid tissue; MDS, myelodysplastic syndrome; MM, multiple myeloma; Mis, missense; N, nonsense; NHL, non-Hodgkin's lymphoma; NK/T, natural killer T cell; NSCLC, non-small-cell lung cancer; O, other; pre-B-ALL, pre-B-cell acute lymphoblastic leukaemia; Rec, recessive; S, splice site; T, translocation; T-ALL, T-cell acute lymphoblastic leukaemia; T-CLL, T-cell chronic lymphocytic leukaemia; TGCT, testicular germ-cell tumour; T-PLL, T-cell prolymphocytic leukaemia. ve 90 S10Zunf ii ιιιεοκιοζ WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Table 4: Commonly Upregulated Genes in Cancers JnlGene Gene symbol N Up# Down # UniGene Gene symbol N Up# Down O is. 159430 ENDC3B 11 10 0 Hs. 239388 PAQR8 8 5 1 CN is. 518201 DTX3L 8 7 0 Hs. 592827 RBAK 8 5 1 -H is. 530899 LOCI 62073 8 7 0 Hs. 525157 TNFSF13B 8 5 1 5 is. 15159 CKLF 11 9 1 Hs. 126774 DTL 13 8 0 is. 474150 BID 16 13 0 Hs. 385913 ANP32E 13 8 1 is. 7753 CALU 15 12 0 Hs. 532968 DKFP762E1312 13 8 1 r—1 is. 418795 GLT2SDI 10 8 0 Hs. 372429 PDIA6 13 8 1 '~~i is 435556 BFAR 12 9 0 Hs. 233952 PSMA7 13 8 1 is. 459362 PACI 12 9 1 Hs. 533770 SLC38A1 13 8 1 is. 521800 Cborf76 8 6 0 Hs. 489284 ARPC18 18 11 0 H is. 209561 KIAA1715 8 6 0 Hs. 497788 EPRS 18 11 0 i—1 is. 585011 Clorf96 8 6 1 Hs. 79110 NCL 18 11 0 1 is. .403933 FBX032 8 6 1 Hs. 251531 PSMA4 18 11 0 CO is. 368853 AYTL2 15 11 1 Hs. 429180 Elf2S2 18 11 1 O is. 511093 NUSAP1 11 8 0 Hs. 46S885 ILF3 18 11 1 (N is. 370895 RPN2 14 10 0 Hs. 169840 TTK 18 11 1 is. 180062 PSMBB 17 12 0 Hs. 489365 APIST 15 9 1 t—1 is. 444600 BOLAZ 10 7 0 Hs. 256639 PPM 15 9 1 O is. 445890 CHM4 13 9 0 Hs. 14559 CEP55 10 6 1 CN is. 534392 KDELR3 13 9 0 Hs. 308613 MTERFD1 10 6 1 is. 632 191 XTP3TPA 13 9 0 Hs. 21331 ZW1LCH 10 6 1 is. 387567 ACLV 19 13 1 Hs. 524S99 NAPIL! 17 10 1 is. 533282 ΝΟΝΟ 18 12 0 Hs. 78171 PGKI 17 10 2 is. 83753 SNRPB 18 12 0 Hs. 512380 PLEKHB2 12 7 1 is. 471441 PSMBZ 18 12 1 Hs. 352018 TAPI 19 11 1 is. 482497 TNPOI 18 12 1 Hs. 194698 CCNB2 14 8 1 is. 370937 TAPBP 15 10 0 Hs. 153357 PLOD3 14 8 1 is .126941 FAM49B 12 8 0 Hs. 471200 NRP2 14 8 2 is. 408629 KDELCI 12 8 0 Hs. 250822 AURKA 16 9 1 is. 497384 IP09 12 8 1 Hs. 75528 GN12 16 9 1 is. 8752 TMEM4 12 8 1 Hs. 1197 HSPEI 16 9 1 is. 195642 C17orf27 9 6 0 Hs. 202672 DNMTI 18 10 1 is. 358997 TTL 9 6 0 Hs. 433670 FTL 18 10 1 is. 1600 CCT5 20 13 0 Hs. 519972 HLA-F 18 10 1 is. 269408 E2F3 17 11 0 HS. 520210 KDELR2 18 10 1 is. 234027 ZBTB12 17 11 1 Hs. 40515.1 CARDA 11 6 1 is. 520205 EIF2AK1 14 9 0 Hs. 477700 DBRI 11 6 1 is. 89545 PSMB4 14 9 0 Hs. 14468 FIJI1286 11 6 1 is. 449415 EIF2C2 14 9 1 Hs. 516077 FLJ14668 11 6 1 is. 409065 FEN1 14 9 1 HS. 494337 GOLPH2 11 6 1 is. 313 SPP1 14 9 2 Hs.. 371036 NOX4 11 6 1 is. .525135 FARP1 14 9 2 Hs. .438683 SLAMF8 11 6 1 Hs. 524390 K-ALPHA-1 11 7 0 Hs. 520714 SNXIO 11 6 1 Hs. .432360 SCNM1 11 7 0 Hs. 159428 BAX 13 7 1 Hs. 172028 ADAM 10 19 12 0 Hs. .311609 DDX39 13 7 1 Hs. 381189 CBX3 19 12 0 Hs. 463035 FKBP10 13 7 1 Hs. 522257 HNRPK 19 12 0 Hs. 438695 FKBP11 13 7 1 Hs. 470943 STATI 19 12 0 Hs. 515255 LSM4 13 7 1 Hs. 118638 NME1 19 12 1 Hs. 55285 MORC2 13 7 1 Hs. 519452 NPM1 19 12 1 Hs. 43666 PTP4A3 13 7 1 Hs. 506748 HDGF 16 10 0 Hs. 369440 SFXN1 13 7 1 Hs. 386283 ADAM 12 16 10 2 Hs. 517155 TMEPAI 13 7 1 Hs. 474740 APOL2 8 5 0 Hs. 631580 UBA2 13 7 1 Hs. 552608 Clorf58 8 5 0 Hs. 46346S UTP16 13 7 1 Hs. 470654 CDCA7 8 5 0 Hs. 492974 WISP1 13 7 1 Hs. 179Έ8 FMNL3 8 5 0 Hs. 113876 WHS Cl 13 7 1 Hs. 143618 GEMIN6 8 5 0 Hs. 494614 BAT2D1 15 8 2 Hs. 6459 GPRI72A 8 5 0 Hs. 166463 HNRPU 19 10 2 Hs. 133294 IQGAP3 8 5 0 No number of studies (types of cancer) which have available expression data on a test gene. Up # or down # number of cancer types whose expression of the tested gene is up or down -regulated. All these genes are significantly consistently up-regulated (P<10) in a large majority of cancer types, doi: 10.137/journalpone. 0001149.001 87 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015

Atty. Docket No. 030258-61532_ _Table 5: Commonly Downregulated Genes in Cancers

UnlGene Gene symbol N Up# Down # UniGene Gene symbol N Up# Down # Hs. 401835 TCEA12 10 0 8 Hs. 306083 LOC91689 8 0 5 Hs. 58351 ABCA8 13 0 10 Hs. 160953 PS3AIP1 8 0 5 Hs. 525205 NDRG2 12 0 9 Hs. 2112252 SLC24A3 8 0 5 Hs. 524085 USP2 12 0 9 Hs. 163079 TUBAL3 8 0 5 Hs. 172755 BRP44L 11 0 8 Hs. 389171 PINK1 13 0 8 Hs. 22242 ECHDC3 11 0 8 Hs. 470887 GULP1 13 1 8 Hs. 196952 HLF 19 1 13 Hs. 490981 MSRA 13 1 8 Hs. 496587 CHRDL1 12 0 8 Hs. 476092 CLEC3B 18 0 11 Hs. 476319 ECHDC2 12 0 8 Hs. 386502 FM04 18 0 11 Hs. 409352 FLJ20701 12 0 8 Hs. 137367 ANK2 18 1 11 Hs. 103253 PLIN 12 0 8 Hs. 212088 EPHX2 18 1 11 Hs. 293970 ALDH6A1 18 1 12 Hs. 157818 KCNAB1 18 1 11 Hs. 390729 ERBB4 17 0 11 Hs. 163924 NR3C2 18 1 11 Hs. 553502 RORA 17 0 11 Hs. 269128 PPP2R1B 18 1 11 Hs. 388918 RECK 14 0 9 Hs. 40582 CDC148 15 1 9 Hs. 216226 SYNGR1 14 0 9 Hs. 438867 FL20489 10 1 6 Hs. 506357 faml07a 14 1 9 Hs. 224008 FEZ1 17 1 10 Hs. 476454 ABHD6 11 0 7 Hs. 443789 C6orf60 12 1 7 Hs. 519694 Csorf4 11 0 7 Hs. 475319 LRRFIP2 12 1 7 Hs. 528385 DHR54 11 0 7 Hs. 514713 MPPE1 12 1 7 Hs. 477288 TRPM3 1 0 7 Hs. 183153 ARL4D 19 1 11 Hs. 420830 HIF3A 11 1 7 Hs. 642660 ClOorfll 16 19 1 11 Hs. 511265 SEMA6D 11 1 7 Hs. 495912 DMD 19 1 11 Hs. 436657 CLU 19 1 12 Hs. 503126 SHANK2 14 1 8 Hs. 78482 PALM 16 0 10 Hs. 481342 SORBS2 14 1 8 Hs. 82318 WASF3 16 0 10 Hs. 169441 MAGI1 16 1 9 Hs. 268869 ADHFE1 8 0 5 Hs. 75652 GSTM5 18 1 10 Hs. 34494 AGXT2 8 0 5 Hs. 405156 PPAP28 18 1 10 Hs. 249129 CIDEA 8 0 5 Hs. 271771 SNCA 18 1 10 Hs. 302754 EFCBP1 8 0 5 Hs. 181855 CASC5 9 1 5 Hs. 521953 EFHC2 8 0 5 Hs. 506458 ANKS1B 11 1 6 Hs. 200100 Ellsl 8 0 5 Hs. 445885 KIAA1217 11 1 6 Hs. 479703 FL21511 8 0 5 Hs. 643583 DKFZp667G2110 13 1 7 Hs.. 500750 HPSE2 8 0 5 Hs. 406787 FBX03 13 1 7 Hs. 380929 LDHD 8 0 5 Hs. 431498 FOXP1 13 1 7

All these genes are significantly consistently down-regulated (P < 105) in a large majority of cancer types, doi :10.1371/j ournal.pone.0001149. t002 88 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015

Table 6: Commonly Upregulated Genes in Pancreatic Cancer Accession Gene Svmbol Gene Name FC NM 006475 POSTN periostin, osteoblast specific factor 13.28 NM 005980 SI OOP S100 calcium binding protein P 12.36 NM 004385 CSPG2 chondroitin sulfate proteoglycan 2 (versican) 10.57 NM 003118 SPARC secreted protein, acidic cysteine-rich (osteonectin) 10.46 NM 003225 TFF1 trefoil factor 1 (breast cancer, estrogen-inducible sequence expressed in) 8.13 NM 002026 FN1 fibronectin 1 7.93 NM 006142 SFN stratifin 7.81 NM 000393 COL5A2 collagen, type V, alpha 2 7.22 NM 005940 MMP11 matrix metalloproteinase 11 (stromelysin 3) 7.17 NM 000088 COL1A1 collagen, type I, alpha 1 6.50 NM 000930 PLAT plasminogen activator, tissue 6.46 NM 003064 SLPI secretory leukocyte protease inhibitor (antileukoproteinase) 6.01 NM 006516 SLC2A1 solute carrier family 2 (facilitated glucose transporter), member 1 5.39 NM 003226 TFF3 trefoil factor 3 (intestinal) 5.28 NM 004460 FAP fibroblast activation protein alpha 5.20 NM 003467 CXCR4 chemokine (C-X-C motif) receptor 4 5.18 NM 003247 THBS2 thrombospondin 2 5.Of NM 012101 TRIM 29 tripartite motif-containing 4.91 NM 033664 CDH11 cadherin 11, type 2, OB-cadherin (osteoblast) 4.52 NM 006169 NNMT nicotinamide N-methyltransferase 4.51 NM 004425 ECM1 extracellular matrix protein 1 4.39 NM 003358 UGCG UDP-glucose ceramide glucosyltransferase 4.36 NM 000700 ANXA1 annexin A1 4.31 NM 004772 C5orfl3 chromosome 5 open reading frame 13 4.29 NM 182470 PKM2 pyruvate kinase, muscle 4.28 NM 004994 MMP9 matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase) 4.19 NM 006868 RAB31 RAB31, member RAS oncogene family 4.18 NM 001932 MPP3 membrane protein, palmitoylated 3 (MAGUKp55 subfamily member 3) 4.16 AF200348 D2S448 Melanoma associated gene 4.14 NM 000574 DAF decay accelerating factor for complement (CD55, Cromer blood group system) 4.11 NM 000213 ITGB4 integrin beta 4.11 NM 001645 APOC1 apolipoprotein C-I 3.86 NM 198129 LAMA3 laminin, alpha 3 3.86 NM 002997 SDC1 syndecan 1 3.80 NM 001769 CD9 CD9 antigen (p24) 3.78 BC004376 ANXA8 annexim A8 3.74 NM 005620 S100A11 S100 calcium binding protein All (calgizzarin) 3.72 NM 002659 PLAUR plasminogen activator urokinase receptor 3.70 NM 002966 S100A10 S100 calcium binding protein A10 (annexin II ligand, calpactin I, light polypeptide (pi 1)) 3.67 NM 004898 CLOCK clock homolog (mouse) 3.65 NM 002345 LUM lumican 3.59 NM 006097 MYL9 myosin light polypeptide 9, regulatory 3.44 NM 004120 GBP2 guanylate binding protein 2, interferon-inducible 3.44 AK056875 LOC91316 similar to bK246H3.1 (immunoglobulin lambda-like polypeptide 1, pre-B-cell specific) 3.40 NM 001827 CKS2 CDC28 protein kinase requlatorv subunit 2 3.36 NM 002203 ITGA2 integrin alpha 2 (CD49B, alpha 2 subunit of VLA-2 receptor) 3.35 NM 000599 IGFBP5 insulin-like growth factor binding protein 5 3.33 NM 004530 MMP2 matrix metalloproteinase 2 (gelatinase A, 72kDa gelatinase, 72kDa type IV collagenase) 3.33 NM 004335 BST2 bone marrow stromal cell antigen 3.30 NM 000593 TAPI transporter 1, ATP-binding cassette, sub-family B (MDR/TAP) 3.29 NM 004915 ABCG1 ATP-bindina cassette sub-familv G (WHITE), member 3.27 NM 001235 SERPINH 1 serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 1 (collagen binding protein 1) 3.25 NM 001165 BIRC3 baculoviral IAP repeat-containing 3 3.23 NM 002658 PLAU plasminogen activator, urokinase 3.20 NM 021103 TMSB10 thymosin, beta 10 3.18 NM 000304 PMP22 peripheral myelin protein 22 3.15 XM 371541 K1AA1641 KIAA1641 protein 3.11 NM 012329 MMD monocyte to macrophage differentiation-associated 3.07 NM 182744 NBL1 neuroblastoma suppression of tumorigenicity 1 3.06 NM 002245 KCNK1 potassium channel, subfamily K, member 1 3.03 NM 000627 LTBP1 latent transforming growth factor beta binding protein 1 3.02 NM 000063 C2 complement component 2 3.01 NM 000100 CSTB cystatin B (stefin B) 2.99 NM 000396 CTSK cathepsin K (pycnodysostosis) 2.98 89 WO 2009/100029 PCT/US2009/032881 Atty. Docket No. 030258-61532 2015203111 11 Jun2015 NM 016816 OAS1 2' 5'-oliaoadenylate synthetase 1,40/46kDa 2.98 NM 004240 TRIP 10 thyroid hormone receptor interactor 10 2.95 NM 000138 FBN1 fibrillin 1 (Marfan syndrome) 2.94 NM 002318 LOXL2 lysyl oxidase-like 2 2.92 NM 002053 GBP1 guanylate binding orotein 1 interferon-inducible, lysyl 67kDa 2.90 NM 005564 LCN2 lipocalin 2 (oncogene 24p3) 2.88 NM 153490 KRT13 keratin 13 2.85 NM 004723 ARHGEF2 rho/rac guanine nucleotide exchange factor (GEF) 2 2.80 NM 004146 NDUFB7 NADH dehydrozenase (ubiquinone) 1 beta subcomplex, 7, 18kDa 2.79 NM 003937 KYNU kynureninase (L-kynurenine hvdrolase) 2.77 NM 002574 PRDX1 Peroxiredoxin 1 2.77 NM 002444 MSN moesin 2.73 NM 002901 RCN1 reticulocalbin 1, EF-hand calcium binding domain 2.73 NM 005165 ALDOC aldolase C, ffuctose-bisphosphate 2.72 NM 002204 ITGA3 integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor) 2.72 NM 033138 CALD1 caldesmon 1 2.71 NM 003816 ADAM9 a disintegrin and metalloproteinase domain 9 (meltrin gamma) 2.69 NM 173843 IL1RN interleukin 1 receptor antagonist 2.66 NM 000602 SERPINE 1 serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminggen activator inhibitor type 1), member 1 2.65 NM 002213 ITGB5 integrin, beta 5 2.64 NM 004447 EPS 8 epidermal growth factor receptor pathway substrate 8 2.64 NM 002928 RGS16 regulator of G-protein singalling 16 2.62 NM 001288 CLIC1 chloride intracellular channel 1 2.61 NM 015996 TAGLN transgelin 2.57 NM 002087 GRN granulin 2.55 NM 001183 ATP6AP1 ATPase, H+ transporting, lysosomal accessory protein 1 2.54 NM 001730 KLF5 Kruppel-like factor 5 (intestinal) 2.51 NM 003516 HIST2H2 AA histone 2, H2aa 2.50 NM 014736 KIAA0101 KIAA0101 gene product 2.49 NM 002290 LAMA4 laminin, alpha 4 2.49 NM 001826 CKS1B CDC28 protein kinase reaulatory subunit IB 2.48 NM 001814 CTSC cathepsin C 2.45 NM 176825 SULT1C1 sulfotransferase family cytosolic, 1C, member 1 2.43 NM 002862 PYGB phosphorylase, glycogen; brain 2.41 NM 000917 P4HA1 procollagen-proline, 2-oxoglutarate 4-dioxygenase (probne 4- hydroxylase), alpha polypeptidel 2.41 NM 001428 EN01 enolase 1 (alpha) 2.40 NM 001425 EMP3 epithelial membrane protein 3 2.40 NM 019111 HLA-DRA maior histocompatibility complex, class II, DR alpha 2.38 NM 001387 DPYSL3 dihydropyrimidinase-like 3 2.36 NM 006471 MRCL3 myosin regulatory light chain MRCL3 2.34 NM 006332 IFI30 interferon gamma-inducible protein 30 2.34 NM 001312 CRIP2 cysteine-rich protein 2 2.33 NM 002224 ITPR3 inositol 1 4 5-triphosphate receptor tvpe 3 2.31 NM 053025 MYLK myosin light peptide kinase 2.29 NM 002785 PSG11 pregnancy specific beta-1-glycoprotein 11 2.27 NM 000900 MGP matrix Gla protein 2.26 NM 000962 PTGS1 prostaglandin-endoperoxide synthase 1 (prostaglandin G/H synthase and cyclooxyenase) 2.25 NM 005915 MCM6 minichromosome maintenance deficient 6 (MIS5 homolog, S. pombe) (S. cerevisiae) 2.24 NM 001067 TOP2A topoisomerase (DNA) II alpha 170kDa 2.23 NM 001878 CRABP2 cellular retinoic acid binding protein 2 2.23 NM 006745 SC4MOL sterol-C4-methyl oxidase-like 2.22 NM 003528 HIST2H2 histone 2, H2be 2.22 BF347579 Transcribed sequence with strong similarity to protein pir:I38500 (H.sapiens) 138500 interferon gamma receptor accessory factor-1 precursor - human 2.21 NM 005261 GEM GTP binding protein overexpressed in skeletal muscle 2.19 NM 021874 CDC25B cell division cycle 25B 2.18 NM 022550 XRCC4 X-ray repair complementing defective repair in Chinese hamster cells 4 2.17 NM 020250 GSN gelsolin (amyloidosis, Finnish type) 2.17 NM 002916 RFC4 replication factor C (activator 1) 4, 37kDa 2.16 NM 005606 LGMN legumain 2.14 NM 006762 LAPTM5 Lysosomal-associated multispanning membrane protein-5 2.14 NM 002727 PRG1 proteoglycan 1, secretory granule 2.14 NM 002609 PDGFRB platelet-derived growth factor receptor, beta polypeptide 2.14 NM 001424 EMP2 epithelial membrane protein 2 2.12 NM_005022 PFN1 profilin 1 2.12 NM_001657 AREG amphiregulin amphireaulin (schwannoma-derived growth factor) 2.11 NM_005100 AKAP12 A kinase (PRKA) anchor protein (gravin) 12 2.11 NM_000860 HPGD hydroxyprostaglandin dehydrogenase 15 (NAD) 2.10 90 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015 NM_007115 TNFAIP6 tumor necrosis factor alpha-induced protein 6 2.09 NM_021638 AFAP actin filament associated protein 2.08 NM_001946 DUSP6 dual specificity phosphatase 6 2.05 NM_181802 UBE2C ubiquitin-conjugating enzyme E2C 2.04 NM_002593 PCOLCE procollagen C-endopeptidase enhancer 2.02 NM_033292 CASP1 caspase 1, apoptosis-related cysteine protease (interleukin 1, heta, convertase) 2.02 NM_003870 IQGAP1 IQ motif containing GTPase activating protein 1 2.02 NM 005563 STMN1 stathmin 1/oncoprotein 18 2.01 NM_005558 LAD1 ladinin 1 2.01 NM_001776 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 2.00 NM_001299 CNN1 calponin 1, basic, smooth muscle 2.00 AK055128 PSMD14 proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 2.00 NM_006304 SIIl'MI split hand/foot malformation (ectrodactyly) type 1 1.98 NM_004024 ATF3 activating transcription factor 3 1.98 NM_000291 PGK1 phosphoglycerate kinase 1 1.98 NM_006520 TCTE1L t-complex-associated-testis-expressed 1 -like 1.97 NM_201380 PLEC1 plectin 1 intermediate filament binding protein 500kDa 1.97 NM_002838 PTPRC protein tyrosine phosphatase, receptor type, C 1.97 NM_000211 ITGB2 integrin, beta 2 (antigen CD18 (p95), lymphocyte function-associated antigen 1; macrophage antigen 1 (mac-1) beta subunit) 1.97 NM_002577 PAK2 p21 (CDKNlA)-activated kinase 2 1.96 NM_000295 SERPINA 1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 1.96 NM_183001 SHC1 SHC (Src homology 2 domain containing) transforming protein 1 1.96 NM_005019 PDE1A phosphodiesterase 1A, calmodulin-dependent 1.95 NM_002298 LCP1 lymphocyte cytosolic protein 1 (L-plastin) 1.95 NM_006769 LM04 LIM domain only 4 1.94 NM_001465 FYB FYN binding protein (FYB-120/130) 1.93 NM_183422 TSC22 transforming growth factor beta-stimulated protein TSC-22 1.92 NM_001777 CD47 CD47 antigen (Rh-related antigen, integrin-associated signal transducer) 1.92 NM_001755 CBFB core-binding factor, beta subunit 1.90 NM_005544 IRS1 insulin receptor substrate 1 1.88 NM_000698 ALOX5 arachidonate 5-lipoxygenase 1.88 NM_006096 NDRG1 N-myc downstream regulated gene 1 1.88 NM_001105 ACVR1 activin A receptor, type 1 1.87 NM_003105 SORL1 sortilin-related receptor, L(DLR class) A repeats-containing 1.85 NM_001998 FBLN2 fibulin 2 1.85 NM_014791 MELK maternal embryonic leucine zipper kinase 1.85 NM_003092 SNRPB2 small nuclear ribonucleoprotein polypeptide B 1.84 NM_001120 TETRAN tetracycline transporter-like protein 1.84 NM_182943 PLOD2 procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2 1.83 NM_181862 BACH brain acyl-CoA hydrolase 1.82 NM_021102 SPINT2 serine protease inhibitor, Kunitz type, 2 1.82 NM_004419 DUSP5 dual specificity phosphatase 5 1.81 NM_006482 DYRK2 dual specificity tyrosine-(Y)-phosphorylation regulated kinase 2 1.81 NM_145690 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide 1.81 NM_000714 BZRP benzodiazapine receptor (peripheral) 1.81 NM_013995 LAMP2 lysosomal-associated membrane protein 2 1.80 CA450153 ACYP1 acylphosphatase 1, erythrocyte (common) type 1.80 NM_000405 GM2A GM2 ganglioside activator protein 1.79 NM_139275 AKAP1 A kinase (PRKA) anchor protein 1 1.79 NM_001679 ATP1B3 ATPase, Na+/K+ transporting, beta 3 polypeptide 1.79 NM_016343 CENPF centromere protein F, 350/400ka (mitosin) 1.79 NM_002201 ISG20 interferon stimulated gene 20kDa 1.79 NM_002463 MX2 myxovirus (influenza virus) resistance 2 (mouse) 1.79 NM_006820 Clorf29 chromosome 1 open reading frame 29 1.79 NM_201397 GPX1 glutathione peroxidase 1 1.79 NM_005738 ARL4 ADP-ribosylation factor-like 4 1.78 NM_001038 SCNN1A sodium channel nonvoltage-gated 1 alpha 1.78 NM_002863 PYGL phosphorylase, glycogen; liver (Hers disease, glycogen storage disease type VI) 1.78 NM_001281 CKAP1 cytoskeleton associated protein 1 1.77 NM_003879 CFLAR CASP8 and FADD-like apoptosis regulator 1.76 NM_182948 PRKACB protein kinase, cAMP-dependent catalytic, beta 1.75 NM_006009 TUB A3 tubulin, alpha 3 1.75 NM_201444 DGKA diacylglycerol kinase, alpha 80kDa 1.74 NM_005471 GNPDA1 glucosamine-6-phosphate deaminase 1 1.74 NM_001451 FOXF1 forkhead box FI 1.74 NM_001988 EVPL envoplakin 1.73 NM_021724 NR1D1 nuclear receptor subfamily 1, group D member 1 1.73 NM_006364 SEC23A Sec23 homolog A (S. cerevisiae) 1.72 NM_002129 HMGB2 high-mobility group box 2 1.72 91 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 NM_004172 SLC1A3 solute carrier family 1 (glial high affinity glutamate transporter), member 3 1.71 NM_001421 ELF4 E74-like factor 4 (ets domain transcription factor) 1.71 NM_005566 LDHA lactate dehydrogenase A 1.70 NM_000270 NP nucleoside phosphorylase 1.69 NM_153425 TRADD TNFRSFlA-associated via death domain 1.67 NM_004762 PSCD1 pleckstrin homology, Sec7 and coiled-coil domains (cytohesin 1) 1.67 NM_001985 ETFB electron-transfer-flavoprotein, beta polypeptide 1.67 NM 016587 CBX3 chromobox homolog 3 (F1P1 gamma homolog, Drosophila) 1.66 NM_002085 GPX4 glutathione peroxidase 4 (phospholipid hydroperoxidase) 1.66 NM_002795 PSMB3 proteasome (prosome, macropain) subunit, beta type, 3 1.65 NM_000963 PTGS2 prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclopxyoenase) 1.65 NM_001642 APLP2 amyloid beta (A4) precursor-like protein 2 1.65 NM_000569 FCGR3A Fc fragment of lgG low affinity iiia receptor for (CD16) 1.64 NM_000362 TIMP3 tissue inhibitor of metalloproteinase 3 (Sorshy fundus dystrophy, pseudoinflammatory) 1.63 NM_002417 MKI67 antigen identified by monoclonal antibody Ki-67 1.63 NM_000175 GPI glucose phosophate isomcrasc 1.63 AF179995 SEPT8 septin 8 1.62 NM_004121 GGTLA1 gamma-glutamyltransferase-like activity 1 1.62 NM_002690 POLB polymerase (DNA directed), beta 1.62 NM_004334 BST1 bone marrow stromal cell antigen 1 1.61 NM_001892 CSNK1A1 casein kinase 1, alpha 1 1.61 NM_014670 BZW1 basic leucine zipper and W2 domains 1 1.60 NM 001110 ADAM 10 a disintegrin and metalloproteinase domain 10 1.60 NM_005792 MPHOSP H6 M-phase phosphoprotein 6 1.60 NM_001126 ADSS adenylosuccinate synthase 1.59 XM 376059 SERTAD2 SERTA domain containing 2 1.59 NM 001664 ARHA ras homolog gene family, member A 1.59 NM_002475 MLC1SA myosin light chain 1 slow a 1.59 NM_014498 GOLPH4 golgi phosphoprotein 4 1.59 NM_005964 MYH10 myosin heavy polypeptide 10 non-muscle 1.59 NM_003330 TXNRD1 thioredoxin reductase 1 1.59 NM_001757 CBR1 carbonyl reductase 1 1.58 NM_003130 SRI sorcin 1.57 NM_006765 TUSC3 tumor suppressor candidate 3 1.57 NM 183047 PRKCBP1 protein kinase C binding protein 1 1.57 NM_005333 HCCS holocytochrome c synthase (cytochrome c heme-lyase) 1.57 NM 001444 FABP5 fatty acid binding protein 5 (psoriasis-associated) 1.57 NM 001799 CDK7 cyclin-dependent kinase 7 (M015 homolog, Xenopus laevis, cdk-activating kinase) 1.57 NM_001539 DNAJA1 DnaJ (Hsp40) homolog subfamily A member 1 1.57 NM_004475 FLOT2 flotillin 2 1.57 NM_004308 ARHGAP1 Rho GTPase activating protein 1 1.56 NM 002388 MCM3 MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) 1.56 NM_006435 IFITM2 interferon induced transmembrane protein 2 (1-8D) 1.56 NM_000454 SOD1 superoxide dismutase 1, soluble (amyotrophic lateral sclerosis 1 (adult)) 1.56 NM_015161 ARL6IP ADP-ribosylation factor-like 6 interacting protein 1.56 NM_078480 SIAHBP1 fuse-binding protein-interacting repressor 1.56 NM_025207 PP591 FAD-synthetase 1.56 NM_002833 PTPN9 protein tyrosine phosphatase non-receptor type 9 1.55 NM_001753 CAV1 caveolin 1 caveolae protein 22kDa 1.55 NM_003286 TOPI topoisomerase (DNA) I 1.55 BU739663 Transcribed sequence with moderate similarity to protein sp:P13196 (H.sapiens) HEM1_HUMAN 5-aminolevulinic acid synthase, nonspecific mitochondrial precursor 1.55 NM_006788 RALBP1 ralA binding protein 1 1.54 NM_000944 PPP3CA protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha) 1.54 NM_003374 VDAC1 voltaqe-dependent anion channel 1 1.54 NM_000560 CD53 CD53 antigen 1.54 NM_002037 FYN FYN oncogene related to SRC FGR, YES 1.54 NM_002885 RAP1GA1 RAP1 GTPase activating protein 1 1.53 NM_018979 PRKWNK 1 lprotein kinase, lysine deficient 1 1.53 NM_002835 PTPN12 protein tyrosine phosphatase, non-receptor type 12 1.53 NM_007315 STAT1 signal transducer and activator of transcription 1, 91kDa 1.52 NM_014846 KIAA0196 KIAA0196 gene product 1.52 NM_001237 CCNA2 cyclin A2 1.52 NM_004596 SNRPA small nuclear ribonucleoprotein polypeptide A 1.52 NM_002790 PSMA5 proteasome (prosome, macropoain) subunit, alpha type, 5 1.52 NM_015361 R3HDM R3H domain (binds single-stranded nucleic acids) containing 1.52 NM_001665 ARHG ras homolog gene family, member G (rho G) 1.51 NM_002788 PSMA3 proteasome (prosome macropain) subunit, alpha type, 3 1.50 NM_006904 PRKDC protein kinase, DNA-activated, catalytic polypeptide 1.50 NM_003400 XPOl exportin 1 (CRM1 homolog, yeast) 1.50 92 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015 NM_178014 OK/SW-cl.56 beta 5-tubulin 1.50 NM_002634 PHB prohibitin 1.49 NM_004792 PPIG peptidyl-prolyl isomerase G (cyclophilin G) 1.49 NM_002508 NID nidogen (enactin) 1.49 NM_001765 CD1C CD1C antigen, c polypeptide 1.48 NM_000311 PRNP prion protein (p27-30) (Creutzfeld-Jakob disease, Gerstmann-Strausler-Scheinker syndrome, fatal familial insomnia) 1.48 NM_006437 ADPRTL1 ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1 1.48 NM_002759 PRKR protein kinase, interferon-inducible double stranded RNA dependent 1.48 NM_014669 KIAA0095 KIAA0095 gene product 1.47 NM_003391 WNT2 wingless-type MMTV integration site family member 2 1.47 NM_004309 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha 1.47 NM_000418 IL4R interleukin 4 receptor 1.46 NM_003352 UBL1 ubiquitin-like 1 (sentrin) 1.46 NM_006290 TNFAIP3 tumor necrosis factor alpha-induced protein 3 1.45 NM_004763 ITGB1BP1 integrin beta 1 binding protein 1 1.45 NM_005754 G3BP Ras-GTPase-activating protein SH3-domain-binding protein 1.45 NM_021990 GABRE gamma-aminobutyric acid (GABA) A receptor, epsilon 1.44 NM_001379 DNMT1 DNA (cytosine-5-)-methyltransferase 1 1.44 NM_001154 ANXA5 annexin A5 1.44 NM_004354 CCNG2 cyclin G2 1.44 NM_005002 NDUFA9 NADH dehydroaenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa 1.43 NM_001931 DLAT dihydroMpoamide S-acetyltransferase (E2 component of pyruvate dehydroaenase complex) 1.43 NM_005902 MADH3 MAD mothers against decapentaplegic homolog 3 (Drosophila) 1.43 NM_000110 DPYD dihydropyrimidine dehydrogenase 1.43 NM_001316 CSE1L CSE1 chromosome segregation 1-like (yeast) 1.43 NM_000167 GK glycerol kinase 1.43 NM_001924 GADD45 A growth arrest and DNA-damage-inducible, alpha 1.42 NM_014225 PPP2R1A protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform 1.42 NM_001233 CAV2 caveolin 2 1.42 NM_176863 PSME3 proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki) 1.42 NM_001905 CTPS CTP synthase 1.41 NM_005653 TFCP2 transcription factor CP2 1.41 NM_003405 YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, eta polypeptide 1.41 NM_003392 WNT5A wingless-type MMTV integration site family, member 5A 1.40 NM_002375 MAP4 microtubule-associated protein 4 1.40 NM_006353 HMGN4 high mobility qroup nucleosomal binding domain 4 1.39 NM_006527 SLBP stem-loop (histone) bindino protein 1.39 NM_000517 HBA2 hemoglobin alpha 2 1.38 NM_002661 PLCG2 phospholipase C, gamma 2 (phosphatidylinositol-specific) 1.38 NM_001493 GDI1 GDP dissociation inhibitor 1 1.38 NM 181430 FOXK2 forkhead box K2 1.38 NM_002086 GRB2 growth factor receptor-bound protein 2 1.38 NM_002868 RAB5B RAB5B, member RAS oncogene family 1.37 NM_002768 PCOLN3 procollagen (type ΙΠ) N-endopeptidase 1.37 NM_014742 TM9SF4 transmembrane 9 superfamily protein member 4 1.37 NM_004344 CETN2 centrin, EF-hand protein, 2 1.37 NM_002881 RALB v-ral simian leukemia viral oncogene homolog B (ras related; GTP binding protein) 1.36 NM_004099 STOM stomatin 1.36 NM_031844 HNRPU heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) 1.36 NM_000480 AMPD3 adenosine monophosphate deaminase (isoform E) 1.35 NM_006561 CUGBP2 CUG triplet repeat RNA binding protein 2 1.35 NM_152879 DGKD diacylglycerol kinase delta 130kDa 1.35 NM_138558 PPP1R8 protein phosphatase 1 reQulatory (inhibitor) subunit 8 1.35 NM_004941 DHX8 DEAH (Asp-Glu-Ala-FIis) box polypeptide 8 1.34 NM_021079 NMT1 N-myristoyltransferase 1 1.33 NM 004622 TSN translin 1.33 NM_002473 MYH9 myosin, heavy polypeptide 9, non-muscle 1.33 NM_006889 CD86 CD86 antigen (CD28 antigen ligand 2, B7-2 antigen) 1.33 NM_004383 CSK c-src tyrosine kinase 1.33 NM_004317 ASNA1 arsA arsenite transoorter ATP-binding homolog 1 (bacterial) 1.33 NM_024298 LENG4 leukocyte receptor cluster (LRC) member 4 1.32 NM_001912 CTSL cathepsin L 1.32 NM_001357 DHX9 DEAH (Asp-Glu-Ala-His) box polypeptide 9 1.32 NM_006849 PDIP protein disulfide isomerase, pancreatic 1.32 NM_018457 DKFZP56 4J157 DKFZ, 0564J157 protein 1.31 NM_024880 TCF7L2 transcription factor 7-like 2 (T-cell specific, HMG-box) 1.31 NM_002081 GPC1 glypican 1 1.31 NM_004235 KLF4 Kruppel-like factor 4 (gut) 1.31 93 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015 NM_005565 LCP2 lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa) 1.30 NM_002667 PLN phospholamban 1.30 NM_004946 DOCK2 dedicator of cytokinesis 2 1.30 NM_002035 FVT1 follicular lymphoma variant translocation 1 1.29 NM_002865 RAB2 RAB2 member RAS oncogene family 1.29 NM_002806 PSMC6 proteasome (prosome macropain) 26S subunit ATPase 6 1.29 NM_004240 TRIP 10 thyroid hormone receptor interactor 10 1.28 NM_003760 EIF4G3 eukaryotic translation initiation factor 4 gamma, 3 1.28 NM_005151 USP14 ubiquitin specific protease 14 (tRNA quanine transglycosylase) 1.28 NM_015922 H105E3 NAD(P) deoendent steroid dehydropenase-like 1.27 NM_033306 CASP4 caspase 4 apoptosis-related cysteine protease 1.27 NM.198189 COPS8 COP9 constitutive photomorphogenic homolog subunit 8 (Arabidopsis) 1.27 NM_001933 DLST dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-qlutarate complex) 1.27 NM_015004 K1AA0116 K1AA0116 protein 1.27 NM_033362 MRPS12 mitochondrial ribosomal protein S12 1.27 NM_004180 TANK TRAF family member-associated NFKB activator 1.26 NM_014734 K1AA0247 K1AA0247 1.26 NM_005271 GLUD1 glutamate dehydropenase 1 1.25 NM_003009 SEPW1 selenoprotein W, 1 1.25 NM_182641 FALZ fetal Alzheimer antigen 1.24 NM_007362 NCBP2 nuclear cap binding protein subunit 2 20kDa 1.24 NM_004292 RIN1 Ras and Rab interactor 1 1.24 NM 014608 CYFIP1 cytoplasmic FMR1 interacting protein 1 1.23 NM_022333 TIAL1 TIA1 cytotoxic oranule-associated RNA binding protein-like 1 1.23 NM_003126 SPTA1 spectrin alpha erythrocytic 1 (elliptocytosis 2) 1.22 NM_014602 PIK3R4 phosphoinositide-3-kinase regulatory subunit 4, pl50 1.18 NM_002194 INPP1 inositol polyphosphate-l-phosphatase 1.16 Note: Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore). 94 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Table 7: Commonly Downregulated Genes in Pancreatic Cancer Accession Gene Symbol Gene Name FC NM_006499 LGALS8 galoctosite-binding, soluble, 8 (galectin 8) 0.87 NM_000466 PEX1 peroxisome biogenesis factor 1 0.81 NM_002766 PRPSAP1 phosphoribosyl pyrophosphate synthetase-associated protein 1 0.81 NM_ 147131 GALT galactose-1 -phosphate uridylyltransferase 0.80 NM_002101 GYPC glycophorin C (Gerbich blood group) 0.80 NM_002880 RAF1 v-raf-1 murine leukemia viral oncogene homolog 1 0.80 NM_004649 C218rf33 chromosome 21 open reading frame 33 0.80 NM_003262 TLOC1 translocation protein 1 0.79 NM_147223 NCOA1 nuclear receptor coactivator 1 0.79 NM_007062 PWP1 nuclear phosphoprotein similar to S. cerevisiae PWP1 0.79 NM 005561 LAMP1 lysosomal-associated membrane protein 1 0.79 NM_006810 PDIR for protein disulfide isomerase-related 0.78 NM_033360 KRAS2 v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog 0.77 NM_001513 GSTZ1 glutathione transferase zeta 1 (maleylacetoacetate isomerase) 0.77 NM 006184 NUCB1 nucleobindin 1 0.77 NM_001634 AMD1 adenosylmethionine decarboxylase 1 0.76 NM_006749 SLC20A2 solute carrier family 20 (phosphate transporter), member 2 0.76 NM_003144 SSR1 signal sequence receptor alpha (translocon-associated protein alpha) 0.76 NM_004606 TAF1 TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor 250kDa 0.75 BX648788 MRNA; cDNA DKFZP686M12165 (from clone DKFZP686M12165) 0.75 NM_004035 ACOX1 acyl-Coenzyme A oxidase 1 palmitoyl 0.74 NM_000287 PEX6 peroxisomal biogenesis factor 6 0.73 NM_003884 PCAF p300/CBP-associated factor 0.73 NM_006870 DSTN destrin (actin depolymerizing factor) 0.73 NM_001604 PAX6 paired box gene 6 (aniridia keratitis) 0.72 NM 000722 CACNA2 D1 calcium channel voltage-dependent alpha 2/delta suhunit 1 0.72 NMJB3022 RPS24 ribosomal protein S24 0.72 NM_004563 PCK2 phosphoenolpyruvate carhoxykinase 2 (mitochondrial) 0.72 NM_002602 PDE6G phosphodiesterase 6G cGMP-specific, rod, gamma 0.72 NM 001889 CRYZ crystalline, zeta (quinone reductase) 0.72 NM_002339 LSP1 lymphocyte-specific protein 1 0.72 NM_016848 SHC3 src homology 2 domain containing transforming protein C3 0.71 NM_002906 RDX radixin 0.71 NM_007014 WWP2 Nedd-4-like ubiquitin-protein ligase 0.71 NM_000414 HSD17B4 hydroxysteroid (17-beta) dehydrogenase 4 0.71 NM_001127 AP1B1 adaptor-related protein complex 1, beta 1 subunit 0.71 NM_002402 MEST mesoderm specific transcript homolog (mouse) 0.70 NM_033251 RPL13 ribosomal protein LI3 0.70 NM_139069 MAPK9 mitogen-activated protein kinase 9 0.70 NM_002913 RFC1 replication factor C (activator 1) 1, 145kDa 0.70 NM_000487 ARSA arvlsulfatase A 0.70 NM_006973 ZNF32 zinc finger protein 32 (KOX 30) 0.70 NM_005310 GRB7 growth factor receptor-bound protein 7 0.70 NM_005962 MX11 MAX interacting protein 1 0.69 NM 005359 MADH4 MAD, mothers against decapentaplegic homolog 4 (Drosophila) 0.69 NM_002340 LSS lanosterol synthase (2 3-oxidosqualene-lanosterol cyclase) 0.69 NM_003684 MKNK1 MAP kinase-interacting serine/threonine kinase 1 0.68 NM_005671 D8S2298E reproduction 8 0.68 NM_000309 PPOX protoporphyrinogen oxidase 0.68 NM_000994 RPL32 ribosomal protein L32 0.68 NM_000972 RPL7A ribosomal protein L7a 0.68 NM_005101 G1P2 interferon, alpha-inducible protein (clone IFI-15K) 0.67 NM_001129 AEBP1 AE binding protein 1 0.67 NM_001011 RPS7 ribosomal protein S7 0.67 NM_001153 ANXA4 annexin A4 0.67 NM_012335 MY01F myosin IF 0.66 NM_005007 NFKBIL1 nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 1 0.66 NM_001870 CP A3 carboxypeptidase A3 (mast cell) 0.66 NM_181826 NF2 neurofibromin 2 (bilateral acoustic neuroma) 0.66 NM_000285 PEPD peptidase D 0.66 NM_006180 NTRK2 neurotrophic tyrosine kinase, receptor type 2 0.66 NM_000543 SMPD1 sphingomyelin phosphodiesterase 1, acid lysosomal (acid sphinagmyelinase) 0.66 NM_001459 FLT3LG fms-related tyrosine kinase 3 ligand 0.65 NM_003750 EIF3S10 eukaryotic translation initiation factor 3, subunit 10 theta, 150/170kDa 0.65 95 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015 NM_005570 LMAN1 lectin mannose-binding, 1 0.65 NM_004409 DMPK dystrophia myotonica-protein kinase 0.65 NM_172159 KCNAB1 potassium voltage-gated channel, shaker-related subfamily, beta member 1 0.65 XM 352750 COL14A1 collagen, type XIV, alpha 1 (undulin) 0.65 NM_001731 BTG1 B-cell translocation gene 1, anti-proliferative 0.65 NM_000884 IMPDH2 IMP (inosine monophosphate) dehydrogenase 2 0.64 NM_001885 CRYAB crystallin, alpha B 0.64 NM_000240 MAOA monoamine oxidase A 0.64 NM_003136 SRP54 siqnal recognition particle 54kDa 0.63 NM_000281 PCBD 6-pyruvoyl-tetrahydropterin synthase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 0.63 NM_005729 PPIF peptidylprolpyl isomerase F (cyclophilin F) 0.63 NM_006481 TCF2 transcription factor 2, hepatic; LF-B3' variant hepatic nuclear factor 0.63 NM_002089 CXCL2 chemokine (C-X-C motif) liqand 2 0.63 NM_001961 EEF2 eukaryotic translation elonqation factor 2 0.63 NM_001801 CDOl cysteine dioxygenase type I 0.63 NM_006389 HYOU1 hypoxia up-regulated 1 0.63 XM 167711 ITGA8 integrin, alpha 8 0.62 NM_014765 TOMM20 translocase of outer mitochondrial membrane 20 homolog (yeast) 0.62 NM_006714 SMPDL3 A sphingomyelin phosphodiesterase, acid-like 3A 0.62 NM_000016 ACAOM acyl-Coenzyme A dehydrogenase C-4 to C-12 straiqht chain 0.62 NM_003924 PHOX2B paired-like homeobox 2b 0.62 NM_002078 GOLGA4 golgi autoantigen, golgin subfamily a 4 0.62 NM_002736 PRKAR2B protein kinase cAMP-dependent, requlatory, type II beta 0.62 BQ217469 K1AA0114 K1AA0114 gene product 0.61 NM_006307 SRPX sushi-repeat-containing protein X-linked 0.61 NM_002184 IL6ST interleukin 6 siqnal transducer (gpl30 oncostatin M receptor) 0.61 NM_153186 ANKR015 ankyrin repeat domain 15 0.61 NM_003038 S1C1A4 solute carrier family 1 (glutamate/neutral amino acid transporter), member 4 0.60 NM_006195 PBX3 pre-B-cell leukemia transcription factor 3 0.60 NM_000327 ROM1 retinal outer segment membrane protein 1 0.60 NM_003463 PTP4A1 protein tyrosine phosphatase type IVA, member 1 0.60 NM_001520 GTF3C1 general transcription factor iiiC polypeptide 1 alpha 220kDa 0.60 NM_006277 ITSN2 intersectin 2 0.59 NM 000985 RPL17 ribosomal protein L17 0.59 NM_000909 NPY1R neuropeptide Y receptor Y1 0.59 NM 001014 RPS10 ribosomal protein S10 0.59 NM 022307 ICA1 islet cell autoantigen 1 69kDa 0.58 NM 002567 PBP prostatic binding protein 0.58 NM_012324 MAPK81P 2 mitogen-activated protein kinase 8 interacting protein 2 0.58 NM_004490 GRB14 growth factor receptor-bound protein 14 0.58 NM 004733 SLC33A1 solute carrier family 33 (acetyl-CoA transporter), member 1 0.57 NM 002197 AC01 aconitase 1, soluble 0.57 NM_000505 F12 coagulation factor Xii (Hageman factor) 0.57 NM_005010 NRCAM neuronal cell adhesion molecule 0.56 NM 006963 ZNF22 zinc finger protein 22 (KOX 15) 0.56 NM 006827 TMP21 transmembrane trafficking protein 0.55 NM 004394 DAP death-associated protein 0.54 NM 001089 ABCA3 ATP-binding cassette, sub-family A (ABC), member 3 0.54 NM 004470 FKBP2 FK506 binding protein 2, 13kDa 0.53 NM 005749 TOB1 transducer of ERBB2, 1 0.53 NM 001355 DDT D-dopachrome tautomerase 0.53 NM 002111 HD huntington (Huntington disease) 0.53 NM 002635 S1C25A3 solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 3 0.53 NM 005596 NFIB nuclear factor I/B 0.53 NM 006273 CCL7 chemokine (C-C motif) liqand 7 0.53 NM 001013 RPS9 ribosomal protein S9 0.52 NM 001551 IGBP1 immunoglobulin (CD79A) binding protein 1 0.52 NM 004498 ONECUT1 one cut domain, family member 1 0.52 NM 004484 GPC3 glypican 3 0.52 NM 130797 DPP6 dipeptidylpeptidase 6 0.52 NM 000746 CHRNA7 cholineragic receptor, nicotinic, alpha polypeptide 7 0.51 NM 001756 SERPINA 6 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase antitrypsin), member 6 0.51 NM 001327 CTAG1 cancer/testis antigen 1 0.51 NM 003651 CSDA cold shock domain protein A 0.50 NM 005848 IRLB c-myc promoter-binding protein 0.50 BC040073 H19 H19, imprinted maternally expressed untranslated mRNA 0.50 NM 002228 JUN v-jun sarcoma virus 17 oncogene homolog (avian) 0.49 NM 000795 DRD2 dopamine receptor D2 0.48 NM_002084 GPX3 glutathione peroxidase 3 (plasma) 0.48 96 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 NM_002716 PPP2R1B protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), beta isoform 0.48 NM_005166 APLP1 amyloid beta (A4) precursor-like protein 1 0.48 NM_005911 MAT2A methionine adenosyltransferase II, alpha 0.47 NM_000208 INSR insulin receptor 0.47 NM_170736 KCNJ15 potassium inwardly-rectifying channel, subfamily J, member 15 0.47 NM_001190 BCAT2 branched chain aminotransferase 2, mitochondrial 0.47 NM_005336 HDLBP hiqh density lipoprotein binding protein (viqilin) 0.46 NM 001076 UGT2B15 UDP glycosyltransferase 2 family, polypeptide B15 0.46 NM_001152 SLC25A5 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator, member 5 0.46 NM_002729 HHEX hematopoietically expressed homeobox 0.46 NM_002847 PTPRN2 protein tyrosine phosphatase, receptor type, N polypeptide 2 0.44 NM_000447 PSEN2 presenilin 2 (Alzheimer disease 4) 0.44 NM_152868 KCNJ4 potassium inwardly-rectifying channel, subfamily J, member 4 0.44 NM_001759 CCND2 cyclin D2 0.44 NM_000316 PTHR1 parathyroid hormone receptor 1 0.44 NM_001612 ACRV1 acrosomal vesicle protein 1 0.43 NM_002467 MYC v-mc myelocytomatosis viral oncogene homolog (avian) 0.43 NM_004454 ETV5 ets variant gene 5 (ets-related molecule) 0.43 NM_002846 PTPRN protein tyrosine phosphatase, receptor type N 0.43 NM_005622 SAH SA hypertension-associated homolog (rat) 0.42 NM_001989 EVX1 eve, even-skipped homeo box homolog 1 (Drosophila) 0.42 NM_000166 GJB1 gap junction protein, beta 1, 32kDa (connexin 32, Charcot-Marie-Tooth neuropathy, X-linked) 0.42 NM 014685 HERPUD 1 homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 0.42 NM 001735 C5 complement component 5 0.41 NM 005504 BCAT1 branched chain aminotransferase 1, ctyosolic 0.41 NM 006808 SEC61B Sec61 beta subunit 0.40 NM 006751 SSFA02 sperm specific antigen 2 0.39 NM 005947 MT1B metallothionein IB (functional) 0.38 NM 005576 LOXL1 lysyl oxidase-like 1 0.37 NM 005627 SGK serum/glucocorticoid regulated kinase 0.36 NM 004683 RGN regucalcin (senescence marker protein-30) 0.36 NM 00918 P4HB procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55) 0.36 BC044862 Macrophage stimulating 1 (hepatocyte growth factor-like), mRNA (cDNA clone IMAGE:4821945), with apparent retained intron 0.35 NM 005952 MT1X metallothionein IX 0.35 NM 000429 ΜΑΤΙΑ methionine adenosyltransferase 1, alpha 0.35 NM 004010 DMD dystrophin (muscular dystrophy, Duchenne and Becker types) 0.34 NM 000689 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 0.34 NM 002889 RARRES2 retinoic acid receptor responder (tazarotene induced) 2 0.33 NM 006280 SSRA signal sequence receptor, delta (translocon-associated protein delta) 0.33 NM 003819 PABPC4 poly(A) binding protein, cytoplasmic 4 (inducible form) 0.32 NM 000755 CRAT carnitine aceltyltransferase 0.32 NM 015684 ATP5S ATP synthase, H+ transporting, mitochondrial F0 complex, subunit s (factor B) .030 NM 033200 BC002942 hypothetical protein BC002942 0.30 BCG986717 Transcribed sequences 0.29 NM 148923 CYB5 cytochrome b-5 0.29 NM 000609 CXCL12 chemokine (C-X-C motif) ligand 12 (stromal cell-derived factor 1) 0.29 NM 001979 EPHX2 epoxide hydrolase 2, cytoplasmic 0.28 NM 001332 CTNND2 catenin (caherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein) 0.27 NM 001831 CLU clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) 0.27 NM 005080 XBP1 X-box binding protein 1 0.27 NM 000156 GAMT guanidinoacetate N-methyltransferase 0.27 NM 182848 CLDN10 claudin 10 0.26 NM 000065 C6 complement component 6 0.26 NM 000128 Fll coagulation factor XI (plasma thromboplasin antecedent) 0.24 NM 003822 MR5A2 nuclear receptor subfamily 5, group A, member 2 0.24 NM 006406 PRDX4 peroxiredoxin 4 0.21 BM799844 BNIP3 BCL2/adenovirus E1B 19kDa interacting protein 3 0.21 NM 018646 TRPV6 transient receptor potential cation channel, subfamily V, member 6 0.21 NM 005013 NUCB2 nucleobindin 2 0.21 NM 000624 SERPINA 3 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 0.19 NM 005065 SEL 1L sel-1 suppressor of lin-12-like (C. elegans) 0.18 NM 198235 RNASE 1 ribonuclease, RNase A family, 1 (pancreatic) 0.17 NM 006498 LGALS2 lectin, galactoside-binding, soluble, 2 (galectin 2) 0.16 NM 002899 RBP1 retinol binding protein 1, cellular 0.12 NM 004413 DPEP1 dipeptidase 1 (renal) 0.12 NM 021603 FXYD2 FXYD domain contaning ion transport regulator 2 0.09 NM 138938 PAP pancreatitis-associated protein 0.08 97 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 NM 201553 FGL fibrinogen-like 1 0.07 NM 001482 GATM glycerine amidinotransferase (L-arrginine: glycine amidinotransferase) 0.04 NM 033240 ELA2A elastase 2a 0.02 NM 000101 CYBA cytochrome b-245, alpha polypeptide 0.02 Note: Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore). 98 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 ible 8. microRNAs that are up-regulated in glioblastoma cells.

Fold change microRNA Up 10X miFMOb, miFMOa, miR-96 Up 2-1 OX miR-182, miR-199b, miR-21, miR124, miR-199a, miR-199-s, miR-199a, miR-106b, miR-15b, miR-188, miR-148a, miR-104, miR-224, miR-368, miR-23a, miR-21 ON, miR-183, miR-25, miR-200cN, miR-373, miR-17-5p, let-7a, miR-16, miR-19b, miR-26a, miR-27a, miR-92, miR-93, miR-320 and miR-20 Up 1-2 X miR-143, miR-186. miR-337, miR-30a-3p, miR-355, miR-324-3p etc. 99 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 ible 9. microRNAs that are down-regulated in glioblastoma cells.

Fold change microRNA Down 10X miR-218, miR-124a, miR-124b, miR-137, miR-184, miR-129, miR-33, miR-139, miR-128b, miR-128a, miR-330, miR-133a, miR-203, miR-153, miR-326, miR-105, miR-338, miR-133b, miR-132, miR-154, miR-29bN Down 2-1 OX miR-7N, miR-323, miR-219, miR-328, miR-149, miR-122a, miR-321, miR-107, miR-190, miR-29cN, miR-95, miR-154, miR-221, miR-299, miR-31, miR-370, miR-331, miR-342, miR-340 100 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015

Table 10. MMP genes contained within microvesicles isolated from glioblastoma cell line. Gene Symbol Accession ID Gene Description MMP1 AK097805 Homo sapiens cDNA FLJ40486 fis, clone TESTI2043866. [AK097805] Homo sapiens matrix metallopeptidase 8 (neutrophil collagenase) MMP8 NM_002424 (MMP8), mRNA [NM_002424] Homo sapiens matrix metallopeptidase 12 (macrophage elastase) MMP12 NM_002426 (MMP 12), mRNA [NM_002426] Homo sapiens matrix metallopeptidase 15 (membrane-inserted) MMP15 NM_002428 (MMP15), mRNA [NM_002428] Homo sapiens matrix metallopeptidase 20 (enamelysin) (MMP20), MMP20 NM_004771 mRNA [NM_004771] Homo sapiens matrix metallopeptidase 21 (MMP21), mRNA MMP21 NM_147191 [NM_147191] Homo sapiens matrix metallopeptidase 24 (membrane-inserted) MMP24 NM_006690 (MMP24), mRNA [NM_006690] Homo sapiens matrix metallopeptidase 26 (MMP26), mRNA MMP26 NM_021801 [NM_021801] Homo sapiens matrix metallopeptidase 27 (MMP27), mRNA MMP27 NM_022122 [NM_022122] Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene). Accession IDs are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/entrez?db=nuccore). 101 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 ’able 11. Genes containing omatic mutations in lioblastoma adapted from lie result of TCGA project McLendon et al., 2008).

Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld BCL11A 53335 CHEK2 11200 BCL11A 53335 CHEK2 11200 BCL11A 53335 CHEK2 11200 BCL11A 53335 CHEK2 11200 BCL11A 53335 CHEK2 11200 BCL2L13 23786 CHEK2 11200 BCR 613 CHEK2 11200 BMPR1A 657 CHEK2 11200 BRCA1 672 CHEK2 11200 BRCA2 675 CHEK2 11200 BRCA2 675 CHEK2 11200 BRCA2 675 CHI3L2 1117 BTK 695 CHIC2 26511 C18orf25 147339 CHL1 10752 C20orf160 140706 CHL1 10752 C20orf160 140706 CMTM3 123920 C22orf24 25775 CNTFR 1271 C6orf60 79632 COL11A1 1301 C6orf60 79632 COL1A1 1277 C9orf72 203228 COL1A1 1277 CAND1 55832 COL1A1 1277 CASP9 842 COL1A1 1277 CAST 831 COL1A2 1278 CAST 831 COL1A2 1278 CAST 831 COL3A1 1281 CBL 867 COL3A1 1281 CBL 867 COL3A1 1281 CCR5 1234 COL3A1 1281 CD46 4179 COL5A1 1289 CDC123 8872 COL6A2 1292 CDKL5 6792 COL6A2 1292 CDKN2A 1029 COL6A2 1292 CDKN2A 1029 CRLF1 9244 CDKN2A 1029 CSF3R 1441 CENPF 1063 CSF3R 1441 CENPF 1063 CSMD3 114788 CENTG1 116986 CSMD3 114788 CENTG1 116986 CSNK1E 1454 CES3 23491 CTNNB1 1499 CES3 23491 CTSH 1512 CHAT 1103 CTSH 1512 CHAT 1103 CYLD 1540 CHD5 26038 CYP27B1 1594 CHEK1 1111 CYP27B1 1594 CHEK1 1111 CYP3A4 1576 CHEK1 1111 DCX 1641 CHEK1 1111 DDIT3 1649 CHEK2 11200 DDR2 4921 CHEK2 11200 DDR2 4921 CHEK2 11200 DDR2 4921 CHEK2 11200 DES 1674 CHEK2 11200 DES 1674

Hugo Gene Symbol EntrezGeneJd A2M 2 A2M 2 A2M 2 ABCA3 21 ABCC4 10257 ABCC4 10257 ABCC4 10257 ADAM12 8038 ADAM15 8751 ADAMTSL3 57188 ADAMTSL3 57188 ADM 133 AIFM1 9131 AKAP2 11217 AKAP2 11217 ALK 238 ANK2 287 ANK2 287 ANK2 287 ANK2 287 ANK2 287 ANXA1 301 ANXA7 310 AOC3 8639 AOC3 8639 APBB1IP 54518 APC 324 ARNT 405 AS PM 259266 AS PM 259266 ASXL1 171023 ASXL1 171023 ATM 472 ATM 472 ATM 472 ATP6V1 E1 529 ATR 545 AVIL 10677 AXL 558 BAI3 577 BAI3 577 BAI3 577 BAMBI 25805 BCAR1 9564 BCAR1 9564 BCL11A 53335 102 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld DGKD 8527 EPHA4 2043 FN1 2335 DGKG 1608 EPHA4 2043 F0X03 2309 DHTKD1 55526 EPHA6 285220 F0X03 2309 DMBT1 1755 EPHA7 2045 FOX03 2309 DMRT3 58524 EPHA7 2045 FRAP1 2475 DOCK1 1793 EPHA8 2046 FURIN 5045 DOCK1 1793 EPHA8 2046 FURIN 5045 DOCK1 1793 EPHB1 2047 FURIN 5045 DOCK8 81704 ERBB2 2064 GARNL3 84253 DOCK8 81704 ERBB2 2064 GATA3 2625 DPYSL4 10570 ERBB2 2064 GATA3 2625 DPYSL4 10570 ERBB2 2064 GCLC 2729 DST 667 ERBB2 2064 GDF10 2662 DST 667 ERBB2 2064 GLI1 2735 DST 667 ERBB2 2064 GLI3 2737 DST 667 ERBB2 2064 GLTSCR2 29997 DST 667 ERBB2 2064 GNAI1 2770 DST 667 ERBB2 2064 GNAS 2778 DST 667 ERBB2 2064 GNAS 2778 DST 667 ERBB3 2065 GPR78 27201 DTX3 196403 ESR1 2099 GRIA2 2891 EGFR 1956 ETNK2 55224 GRLF1 2909 EGFR 1956 EYA1 2138 GRN 2896 EGFR 1956 EYA1 2138 GRN 2896 EGFR 1956 F13A1 2162 GSTM5 2949 EGFR 1956 FBXW7 55294 GSTM5 2949 EGFR 1956 FBXW7 55294 GSTM5 2949 EGFR 1956 FGFR1 2260 GSTM5 2949 EGFR 1956 FGFR1 2260 GSTM5 2949 EGFR 1956 FGFR2 2263 GSTM5 2949 EGFR 1956 FGFR3 2261 GSTM5 2949 EGFR 1956 FKBP9 11328 GSTM5 2949 EGFR 1956 FKBP9 11328 GSTM5 2949 EGFR 1956 FKBP9 11328 GYPC 2995 EGFR 1956 FKBP9 11328 HCK 3055 EGFR 1956 FKBP9 11328 HCK 3055 EGFR 1956 FKBP9 11328 HELB 92797 EGFR 1956 FKBP9 11328 HLA-E 3133 EGFR 1956 FKBP9 11328 HLA-E 3133 EGFR 1956 FKBP9 11328 HLA-E 3133 EGFR 1956 FKBP9 11328 HLA-E 3133 EGFR 1956 FKBP9 11328 HS3ST3A1 9955 EGFR 1956 FKBP9 11328 HSP90AA1 3320 EGFR 1956 FKBP9 11328 HSP90AA1 3320 ELAVL2 1993 FLI1 2313 HSPA8 3312 EP300 2033 FLI1 2313 HSPA8 3312 EP300 2033 FLT1 2321 HSPA8 3312 EP400 57634 FLT4 2324 HSPA8 3312 EP400 57634 FN1 2335 HSPA8 3312 EP400 56734 FN1 2335 HSPA8 3312 EPHA2 1969 FN1 2335 HSPA8 3312 EPHA3 2042 FN1 2335 ID3 3399 EPHA3 2042 FN1 2335 IFITM3 10410 103 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld IFITM3 10410 LRRN2 10446 NF1 4763 IFITM3 10410 LTF 4057 NF1 4763 IFITM3 10410 LTF 4057 NF1 4763 IFITM3 10410 LYN 4067 NF1 4763 IFITM3 10410 MAG 4099 NF1 4763 IFITM3 10410 MAP3K6 9064 NF1 4763 IL1RL1 9173 MAPK13 5603 NF1 4763 IL31 386653 MAPK7 5598 NF1 4763 ILK 3611 MAPK8IP2 23542 NF1 4763 ING4 51147 MAPK8IP3 23162 NF1 4763 ING4 51147 MAPK9 5601 NF1 4763 ING4 51147 MAPK9 5601 NF1 4763 INHBE 83729 MARK1 4139 NF1 4763 IQGAP1 8826 MARK1 4139 NF1 4763 IRAK3 11213 MDM2 4193 NMBR 4829 IRS1 3667 MDM4 4194 NMBR 4829 IRS1 3667 ME OX2 4223 NOS3 4846 ISL1 3670 MET 4233 NOS3 4846 ITGAL 3683 MET 4233 NOTCH1 4851 ITGB2 3689 MET 4233 NOTCH1 4851 ITGB2 3689 MLH1 4292 NRXN3 9369 ITGB2 3689 MLH1 4292 NTRK3 4916 ITGB3 3690 MLH1 4292 NUMA1 4926 ITGB3 3690 MLL4 9757 NUP214 8021 ITGB3 3690 MLL4 9757 ONECUT2 9480 ITGB3 3690 MLL4 9757 OR5P2 120065 ITGB3 3690 MLLT7 4303 PAX5 5079 JAG1 182 MMD2 221938 PDGFRA 5156 KIAA1632 57724 MN1 4330 PDGFRA 5156 KIF3B 9371 MSH2 4436 PDGFRA 5156 KIT 3815 MSH2 4436 PDGFRB 5159 KIT 3815 MSH6 2956 PDGFRB 5159 KIT 3815 MSH6 2956 PDK2 5164 KLF4 9314 MSH6 2956 PDPK1 5170 KLF4 9314 MSH6 2956 PDZD2 23037 KLF6 1316 MSI1 4440 PDZD2 23037 KLF6 1316 MSI1 4440 PHLPP 23239 KLK8 11202 MTAP 4507 PI15 51050 KPNA2 3838 MUSK 4593 PI15 51050 KPNA2 3838 MYCN 4613 PIK3C2A 5286 KRAS 3845 MYCN 4613 PIK3C2B 5287 KSR2 283455 MYLK2 85366 PIK3C2G 5288 KSR2 283455 MY03A 53904 PIK3C2G 5288 KTN1 3895 MYST4 23522 PIK3C2G 5288 LAMP1 3916 MYST4 23522 PIK3C2G 5288 LAMP1 3916 MYST4 23522 PIK3C2G 5288 LAX1 54900 MYST4 23522 PIK3CA 5290 LCK 3932 NBN 4683 PIK3CA 5290 LDHA 3939 NDUFA10 4705 PIK3CA 5290 LDHA 3939 NEK10 152110 PIK3CA 5290 LGALS3BP 3959 NELL2 4753 PIK3CA 5290 LGALS3BP 3959 NF1 4763 PIK3R1 5295 LGALS3BP 3959 NF1 4763 PIK3R1 5295 104 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld Hugo Gene Symbol Entrez_Gene_ld PIK3R1 5295 PTEN 5728 SLIT2 9353 PIK3R1 5295 PTEN 5728 SMAD2 4087 PIK3R1 5295 PTEN 5728 SMAD4 4089 PIK3R1 5295 PTEN 5728 SNF1LK2 23235 PIM1 5292 PTEN 5728 SNF1LK2 23235 PLAG1 5324 PTEN 5728 SNX13 23161 PML 5371 PTEN 5728 SOCS1 8651 PMS2 5395 PTEN 5728 SOX11 6664 POU2F1 5451 PTEN 5728 SOX11 6664 PPP2R5D 5528 PTEN 5728 SPARC 6678 PRKCA 5578 PTEN 5728 SPDEF 25803 PRKCA 5578 PTEN 5728 SPN 6693 PRKCB1 5579 PTEN 5728 SPRED3 399473 PRKCB1 5579 PTK2B 2185 SRPK2 6733 PRKCD 5580 PTPN11 5781 ST7 7982 PRKCD 5580 PTPN11 5781 STAT1 6772 PRKCD 5580 RADIL 55698 STAT3 6774 PRKCD 5580 RADIL 55698 STK32B 55351 PRKCD 5580 RB1 5925 STK36 27148 PRKCD 5580 RB1 5925 SYP 6855 PRKCZ 5590 RB1 5925 TAF1 6872 PRKCZ 5590 RB1 5925 TAF1 6872 PRKD2 25865 RB1 5925 TAOK3 51347 PRKD2 25865 RB1 5925 TAS1R1 80835 PRKDC 5591 RB1 5925 TBK1 29110 PRKDC 5591 RB1 5925 TBK1 29110 PRKDC 5591 RB1 5925 TCF12 6938 PROX1 5629 RINT1 60561 TCF12 6938 PSMD13 5719 RIPK4 54101 TCF12 6938 PSMD13 5719 RNF38 152006 TERT 7015 PSMD13 5719 ROR2 4920 TERT 7015 PTCH1 5727 ROR2 4920 TGFBR2 7048 PTCH1 5727 ROS1 6098 TIMP2 7077 PTEN 5728 ROS1 6098 TNC 3371 PTEN 5728 RPN1 6184 TNC 3371 PTEN 5728 RPS6KA3 6197 TNC 3371 PTEN 5728 RTN1 6252 TNFRSF11B 4982 PTEN 5728 RUNX1T1 862 TNK2 10188 PTEN 5728 RYR3 6263 TNK2 10188 PTEN 5728 RYR3 6263 TNK2 10188 PTEN 5728 SAC 55811 TNK2 10188 PTEN 5728 SAC 55811 TOP1 7150 PTEN 5728 SEMA3B 7869 TP53 7157 PTEN 5728 SERPINA3 12 TP53 7157 PTEN 5728 SERPINE1 5054 TP53 7157 PTEN 5728 SHH 6469 TP53 7157 PTEN 5728 SLC12A6 9990 TP53 7157 PTEN 5728 SLC12A6 9990 TP53 7157 PTEN 5728 SLC25A13 10165 TP53 7157 PTEN 5728 SLC25A13 10165 TP53 7157 PTEN 5728 SLC2A2 6514 TP53 7157 PTEN 5728 SLIT2 9353 TP53 7157 PTEN 5728 SLIT2 9353 TP53 7157 105 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Hugo Gene Symbol Entrez_Gene_ld TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TP53 7157 TPBG 7162 TRIM24 8805 TRIM3 10612 TRIM33 51592 TRIP6 7205 TRRAP 8295 TRRAP 8295 TSC1 7248

Hugo Gene Symbol Entrez_Gene_ld TSC2 7249 TSC2 7249 TSC2 7249 UNG 7374 UPF2 26019 UPF2 26019 VAV2 7410 VLDLR 7436 WNT2 7472 ZEB1 6935 ZEB1 6935 ZNF384 171017 ZNF384 171017 Note: Hugo Gene Symbols are assigned to individual genes by HUGO Gene Nomenclature Committee (http ://ww w. genenames. org/). Entrez_Gene_Ids are assigned to individual genes by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/ent rez?db=gene). 106 PCT/US2009/032881 WO 2009/100029 2015203111 11 Jun2015 'able 12. Genes containing omatic mutations in lioblastoma adapted from be paper by Parsons et. al. Parsons et al., 2008)

Gene symbol Accession ID A2M NM 000014 A4GALT CCDS 14041.1 A4GNT CCDS3097.1 AACS CCDS9263.1 ABCA10 CCDS 11684.1 ABCA12 NM 015657 ABCA13 NM 152701 ABCA4 CCDS747.1 ABCA5 CCDS11685.1 ABCA7 CCDS 12055.1 ABCA9 CCDS11681.1 ABCB1 CCDS5608.1 ABCB6 CCDS2436.1 ABCC10 CCDS4896.1 ABCC11 CCDS 10732.1 ABCC3 NM_003786 ABCC5 NM_005688 ABCD2 CCDS 8734.1 ABCF2 CCDS5922.1 ABCG2 CCDS3628.1 ABHD3 NM 138340 ABHD4 CCDS9572.1 ABHD7 CCDS736.1 ABL2 NM 007314 ABTB2 CCDS7890.1 ACAD9 CCDS3053.1 ACADS CCDS9207.1 ACADSB CCDS7634.1 ACAT2 CCDS5268.1 ACCN1 CCDS11276.1 ACCN3 CCDS5914.1 ACF CCDS7241.1 ACLY CCDS11412.1 ACOX3 CCDS3401.1 ACP5 CCDS12265.1 ACRBP CCDS 8554.1 ACTG1 CCDS11782.1 ACTN1 CCDS9792.1 ACTR10 NM_018477 ACTR1A CCDS7536.1 ACTR8 CCDS2875.1 ACTRT1 CCDS14611.1 ADAM 12 CCDS7653.1 ADAM 15 CCDS 1084.1 ADAM 18 CCDS6113.1 ADAM28 ΝΜ 014265

Gene symbol Accession ID ADAM29 CCDS3823.1 ADAMTS1 NM_006988 ADAMTS13 CCDS6970.1 AD AMTS 17 CCDS10383.1 ADAMTS20 NM_175851 ADAMTS4 CCDS 1223.1 ADAMTS8 NM_007037 ADAR CCDS1071.1 ADARB2 CCDS7058.1 ADCY1 NM_021116 ADCY8 CCDS6363.1 ADRBK2 CCDS13832.1 AGC1 NM_001135 AGL CCDS759.1 AGPAT1 CCDS4744.1 AGPS CCDS2275.1 AGRN NM_198576 AHDC1 NM_001029882 AHI1 NM_017651 AIM1L NM_017977 AKAP11 CCDS9383.1 AKAP13 NM_007200 AKAP4 CCDS 14329.1 AKAP9 CCDS5622.1 AKNA CCDS6805.1 AKR7A2 CCDS 194.1 ALDH18A1 CCDS7443.1 ALDH1A2 CCDS10163.1 ALDH1L1 CCDS3034.1 ALDH2 CCDS9155.1 Al 1C NM_018436 ALOX12 CCDS 11084.1 ALOXE3 CCDS11130.1 ALPI CCDS2492.1 ALPK2 CCDS 11966.1 ALPK3 CCDS10333.1 ALPL CCDS217.1 ALS2CL CCDS2743.1 ALS2CR12 CCDS2346.1 AMACO CCDS7589.1 AMID CCDS7297.1 ANK2 CCDS3702.1 ANK3 CCDS7258.1 ANKMY1 CCDS2536.1 ANKRD10 CCDS9520.1 ANKRD11 NM_013275 ANKRD12 CCDS 11843.1 ANKRD15 CCDS6441.1 ANKRD28 NM_015199 ANP32D ΝΜ 012404 AP3B1 CCDS4041.1 APG7L CCDS2605.1 API5 NM 006595

Gene symbol Accession ID APOB CCDS 1703.1 APOBEC3G CCDS 13984.1 APRG1 NM_178339 AQP10 CCDS 1065.1 AR CCDS 14387.1 ARD1B ENST00000286794 ARHGAP4 CCDS 14736.1 ARHGAP5 NM_001173 ARHGAP8 CCDS 14058.1 ARHGDIG CCDS 10404.1 ARHGEF9 NM_015185 ARID1A CCDS285.1 ARL1 NM_001177 ARNT2 NM_014862 ARP10 CCDS 13985.1 ARSE CCDS14122.1 ASB4 CCDS5641.1 ASCL4 NM_203436 ASCL5 ENST00000344317 ASGR1 CCDS11089.1 ASH1L CCDS 1113.1 AS IP CCDS13232.1 ASTN CCDS1319.1 ATAD2B ENST00000295142 ATP 10B ENST00000327245 ATP12A NM 001676 ATP13A1 NM 020410 ATP13A2 CCDS175.1 ATP1A2 CCDS 1196.1 ATP2A1 CCDS10643.1 ATP2A3 CCDS11041.1 ATP2B1 CCDS9035.1 ATP2B2 CCDS2601.1 ATP6V1G3 CCDS 1396.1 ATP7B NM_000053 ATP8A1 CCDS3466.1 ATP8B1 CCDS 11965.1 ATRNL1 CCDS7592.1 ATXN1 NM_000332 AUTS2 CCDS5539.1 AXIN2 CCDS11662.1 AZI1 NM_001009811 B3Gn-T6 NM_138706 BAD CCDS8065.1 BAI2 CCDS346.1 BAMBI CCDS7162.1 BAT2D1 CCDS 1296.1 BAZ1A CCDS9651.1 BCAR3 CCDS745.1 BCL2L1 CCDS13188.1 BCL2L12 CCDS 12776.1 BCL2L2 CCDS9591.1 BCL6 CCDS3289.1 107 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID BCOR CCDS 14250.1 Clorfl47 NM_001025592 CACNG4 CCDS11667.1 BFSP1 CCDS13126.1 Clorfl51 ΝΜ 001032363 CADPS CCDS 2898.1 BIN1 CCDS2137.1 Clorfl6 CCDS 1355.1 CADPS2 NM_017954 BIRC1 CCDS4009.1 Clorfl73 NM_001002912 CALM1 CCDS9892.1 BIRC6 NM_016252 Clorf84 NM_015284 CAMS API NM_015447 BMP3 CCDS3588.1 C1QDC1 CCDS 8720.1 CAPN12 CCDS 12519.1 BMPER CCDS5442.1 C20orfl0 CCDS13352.1 CAPN3 CCDS 10084.1 BNC2 CCDS6482.1 C20orfl02 CCDS 13299.1 CAPN3 CCDS 10084.1 BOC CCDS2971.1 C20orfl 14 CCDS13218.1 CAPZA3 CCDS 8681.1 BPY2IP1 NM_018174 C20orf23 CCDS13122.1 CARD 11 CCDS5336.1 BRAF CCDS5863.1 C20orf78 ENST00000278779 CART1 CCDS9028.1 BRF1 CCDS 10001.1 C21orf29 CCDS13712.1 CASC5 NM_170589 BRP44L CCDS5293.1 C21orf5 CCDS13643.1 CASQ1 CCDS 1198.1 BRPF1 CCDS2575.1 C21orf69 NM 058189 CCDC15 NM_025004 BSN CCDS2800.1 C2orfl7 CCDS2434.1 CCNF CCDS10467.1 BST1 CCDS 3416.1 C2orf29 CCDS2050.1 CCNL2 ENST00000321423 BTAF1 CCDS7419.1 C2orf3 CCDS 1961.1 CCNYL1 ENST00000339882 BTBD1 CCDS 10322.1 C3orfl4 CCDS2896.1 CD19 CCDS10644.1 BTBD3 CCDS13113.1 C4orf7 CCDS3537.1 CD84 CCDS 1206.1 BTC CCDS3566.1 C5AR1 NM_001736 CD96 CCDS2958.1 BTK CCDS 14482.1 C6 CCDS3936.1 CDA08 CCDS 10728.1 BTNL2 CCDS4749.1 C6orfl03 ENST00000326929 CDC2L6 CCDS5085.1 BTNL9 CCDS4460.1 C6orfl50 CCDS4978.1 CDC7 CCDS734.1 BUCS1 CCDS10587.1 C6orfl63 NM_001010868 CDCA8 CCDS424.1 C10orfl8 ENST00000263123 C6orfl65 CCDS5009.1 CDH23 NM_022124 C10orf26 CCDS7540.1 C6orfl68 NM 032511 CDH24 CCDS9585.1 C10orf33 CCDS7474.1 C6orfl70 NM 152730 CDH26 CCDS 13485.1 C10orf47 CCDS7085.1 C6or£21 NM_001003693 CDH5 CCDS 10804.1 C10orf64 ENST00000265453 C6orf213 NM 001010852 CDK5 NM_004935 C10orf71 ENST00000323 868 C6orf29 CCDS4724.1 CDK6 CCDS5628.1 C10orf80 NM_001008723 C6orf4 CCDS5092.1 CDT1 NM_030928 C10orf81 CCDS7583.1 C6orf68 CCDS5118.1 CDX1 CCDS4304.1 Cllorfll NM 006133 C7orfl6 CCDS5436.1 CDYL2 NM_152342 C110RF4 CCDS 8066.1 C8A CCDS606.1 CEACAM1 CCDS12609.1 C12orfll CCDS 8708.1 C8B NM 000066 CELSR3 CCDS2775.1 C12orf42 NM 198521 C8orf77 NMOO1039382 CENPF NM_016343 C14orfll5 CCDS9830.1 C80RFK23 NM_001039112 CENTG3 NM_031946 C14orfl31 NM_018335 C9orfl26 NM 173690 CEP135 NM_025009 C14orfl33 CCDS9862.1 C9orfl9 CCDS6598.1 Cep 164 NM_014956 C14orfl45 NM_152446 C9orf5 NM_032012 CEP2 CCDS13255.1 C14orfl55 CCDS9679.1 C9orf50 NM 199350 CETP CCDS 10772.1 C14orfl59 NM_024952 CA2 CCDS6239.1 CFTR CCDS5773.1 C14orf31 CCDS9704.1 CAB39 CCDS2478.1 CGI-38 CCDS10835.1 C14orf43 CCDS9819.1 CAB INI CCDS13823.1 CGI-96 CCDS 14036.1 C14orf49 CCDS9935.1 CABP1 CCDS9204.1 CGNL1 CCDS10161.1 C15orf2 CCDS10015.1 CACNA1A NM_000068 CHAD CCDS11568.1 C15orf42 ENST00000268138 CACNA1C NM 000719 CHD4 CCDS8552.1 C16orf9 CCDS10402.1 CACNA1E NM 000721 CHD5 CCDS57.1 C17or£27 NM_020914 CACNA1H NM_021098 CHD6 CCDS13317.1 C17or£31 CCDS11016.1 CACNA1I NMOO1003406 CHD9 NM_025134 C18or£25 ΝΜ 001008239 CACNA1S CCDS 1407.1 CHDH CCDS2873.1 C18orf4 CCDS11995.1 CACNA2D3 NM_018398 CHEK1 CCDS8459.1 C19or£29 ENST00000221899 CACNB2 CCDS7125.1 ChGn CCDS6010.1 108 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID CHKA CCDS8178.1 CPBl NM_001871 DDXl CCDS 1686.1 CHL1 CCDS2556.1 CPN1 CCDS7486.1 DDX31 CCDS6951.1 CHRM2 CCDS5843.1 CPNE2 CCDS 10774.1 DDX54 NM 024072 CHRM5 CCDS 1003 El CPNE4 CCDS3072.1 DEFB112 NM_001037498 CHRNA3 CCDS 10305.1 CPS1 CCDS2393.1 DEFB125 CCDS 12989.1 CHRNA4 CCDS13517.1 CPSF4 CCDS5664.1 DELGEF CCDS7828.1 CHRNA9 CCDS3459.1 CPT1B CCDS 14098.1 DEPDC5 NM_014662 CHST13 CCDS3039.1 CPT1C CCDS12779.1 DFNB31 CCDS6806.1 CIDEA CCDS 11856.1 CRA CCDS942.1 DGCR6 CCDS13753.1 CIDEC CCDS2587.1 CRAT CCDS6919.1 DGKD CCDS2504.1 cm CCDS6894.1 CREB1 CCDS2374.1 DHPS CCDS 12276.1 CKLFSF5 CCDS9599.1 CRIM2 ENST00000257704 DHX29 NM_019030 CLASP1 NM 015282 CRISPLD1 CCDS6219.1 DI03 NM_001362 CLASP2 NM 015097 CRR9 CCDS3862.1 DKFZp434I099 CCDS10787.1 CLCN1 CCDS5881.1 CRX CCDS 12706.1 DKFZp547A023 CCDS845.1 CLCN5 CCDS14328.1 CRY2 CCDS7915.1 DKFZp547B1713 CCDS1591.1 CLDN11 CCDS3213.1 CRYAA CCDS 13695.1 DKFZP564B1023 CCDS 1403.1 CLEC1A CCDS 8612.1 CSK CCDS 10269.1 DKFZp56411922 CCDS14124.1 CLEC4E CCDS8594.1 CSMD1 NM_033225 DKFZp761L1417 CCDS5658.1 CLEC7A CCDS 8613.1 CSN3 CCDS3538.1 DKFZp761N1114 CCDS 1455.1 CLIC6 CCDS13638.1 CSNK2A2 CCDS 10794.1 Dll) CCDS5749.1 CLN8 CCDS5956.1 CSPG2 CCDS4060.1 DLEC1 ENST00000337335 CLSPN CCDS396.1 CSPG5 CCDS2757.1 DLGAP2 NM 004745 CLSTN2 CCDS3112.1 CSPG6 NM 005445 DMN NM 015286 CLTA CCDS6600.1 CSTF1 CCDS 13452.1 DMTF1 CCDS5601.1 CMIP NM_198390 CTEN CCDS 11368.1 DNAH1 NM_015512 CMYA1 CCDS2683.1 CTNNA2 NM_004389 DNAH10 CCDS9255.1 CMYA4 CCDS11292.1 CTNNA3 CCDS7269.1 DNAH11 NM_003777 CNNM2 CCDS7543.1 CTSW CCDS8117.1 DNAH3 CCDS 10594.1 CNOT1 CCDS10799.1 CUBN CCDS7113.1 DNAH5 CCDS3882.1 CNOTIO CCDS2655.1 CUGBP1 CCDS7938.1 DNAH8 CCDS4838.1 CNOT7 CCDS6000.1 CUGBP1 CCDS7939.1 DNAH9 CCDS11160.1 CNR2 CCDS245.1 CUL4B NM_003588 DNAI2 CCDS 11697.1 CNTN4 CCDS2558.1 CUTL1 CCDS5721.1 DNCH1 CCDS9966.1 CNTNAP2 CCDS5889.1 CX40.1 CCDS7191.1 DNCLI2 CCDS10818.1 COCH CCDS9640.1 CXCR3 CCDS14416.1 DNHD3 NM 020877 COG5 CCDS5742.1 CXorf 17 CCDS 14356.1 DNTTIP1 CCDS 13369.1 COG5 CCDS5742.1 CXorf20 CCDS 14184.1 DOCK4 NM 014705 COH1 CCDS6280.1 CXorf27 ENST00000341016 DOCK8 CCDS6440.1 COL14A1 NM021110 CXorf37 CCDS 14322.1 DOCK9 NM_015296 COL18A1 NM 030582 CXXC5 NM_016463 DOK6 NM 152721 COL23A1 CCDS4436.1 CYBB CCDS 14242.1 DONSON CCDS 13632.1 COL24A1 NM_152890 CYP26C1 CCDS7425.1 DRCTNNB1A CCDS5377.1 COL3A1 CCDS2297.1 CYP2C19 CCDS7436.1 DRD3 CCDS2978.1 COL4A2 NM 001846 CYP2R1 CCDS7818.1 DRG1 CCDS13897.1 COL4A4 NM_000092 CYP4F12 NM_023944 DSG1 CCDS 11896.1 COL4A5 CCDS 14543.1 DAB2IP CCDS6832.1 DSG2 NM 001943 COL5A3 CCDS 12222.1 DCBLD2 NM_080927 DSG3 CCDS 11898.1 COL6A3 NM_004369 DCC CCDS11952.1 DSG4 CCDS 11897.1 COL6A3 NM 057167 DCT CCDS9470.1 DSPP NM 014208 COL8A2 CCDS403.1 DCTN4 CCDS4310.1 DST CCDS4959.1 COPB CCDS7815.1 DDB1 NM_001923 DTX1 CCDS9164.1 COQ2 NM 015697 DDR1 CCDS4690.1 DTX4 ENST00000227451 109 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID DULLARD CCDS11093.1 EPHA6 ENST00000334709 FU12700 CCDS5898.1 DUSP22 CCDS4468.1 EPHA8 CCDS225.1 FU13273 CCDS3672.1 DUSP3 CCDS 11469.1 EPO CCDS5705.1 FU13576 CCDS5757.1 DYRK3 NM_001004023 ERCC5 NM 000123 FU13725 CCDS 10840.1 DZIP3 CCDS2952.1 ERF CCDS 12600.1 FU13841 CCDS11819.1 E2F4 NM_001950 ERN1 NM_001433 FU13941 CCDS40.1 EAF1 CCDS2626.1 ESC02 NM_001017420 FLJ14397 CCDS 1945.1 EBF CCDS4343.1 ESPNP ENST00000270691 FLJ16165 NM 001004318 EBF3 NM_001005463 ESR1 CCDS5234.1 FLJ16331 NM 001004326 ECEL1 CCDS2493.1 ESR2 CCDS9762.1 FLJ16478 NM_001004341 ECHDC2 CCDS571.1 ETV1 NM_004956 FLJ20035 NM_017631 ECOP NM 030796 EVI1 CCDS3205.1 FLJ20097 ENST00000317751 EDD1 NM_015902 EVPL CCDS11737.1 FLJ20186 CCDS 10989.1 EDG3 CCDS6680.1 EXOC6B ENST00000272427 FLJ20232 CCDS 13995.1 EDG8 CCDS 12240.1 EXTL1 CCDS271.1 FLJ20272 NM_017735 EEF1A1 ENST00000331523 F13B CCDS 1388.1 FLJ20294 NM_017749 EFCBP1 NM_022351 F2RL1 CCDS4033.1 FLJ20298 CCDS 14522.1 EFHC2 NM_025184 F3 CCDS750.1 FLJ21159 CCDS3792.1 EGF CCDS3689.1 F5 CCDS 1281.1 FLJ21963 CCDS9022.1 EGFR CCDS5514.1 FAD158 CCDS725.1 FLJ22709 CCDS 12351.1 EHBP1L1 ENST00000309295 FADS1 CCDS 8011.1 FLJ23049 CCDS3199.1 EIF2A NM_032025 FAM43A NM_153690 FLJ23447 CCDS 12300.1 EIF3S12 CCDS 12517.1 FAM46B CCDS294.1 FLJ23577 ENST00000303168 EIF4G1 CCDS3259.1 FAM47A NM_203408 FLJ23577 CCDS3910.1 EIF4G2 NM_001418 FAM48A ENST00000360252 FU23790 CCDS6346.1 EME2 NM_001010865 FAM63B NM_019092 FU25715 NM_182570 EML4 CCDS 1807.1 FAM78B NM_001017961 FU25801 CCDS3850.1 EMR4 ENST00000359590 FAM92B NM_198491 FU27465 NM_001039843 EN2 CCDS5940.1 FANCA NM_000135 FU30525 CCDS787.1 ENOl CCDS 97.1 FANCD2 CCDS2595.1 FU30655 CCDS3740.1 ENPP2 CCDS6329.1 FASN CCDS 11801.1 FU30707 CCDS9427.1 ENPP6 CCDS3834.1 FAT NM_005245 FU31438 NMJ52385 ENPP7 CCDS 11763.1 FBN3 CCDS 12196.1 FU32796 CCDS 1507.1 ENSA CCDS958.1 FBXO40 NM_016298 FU32934 CCDS 1082.1 ENST00000294635 ENST00000294635 FBXW7 CCDS3777.1 FU33167 CCDS3837.1 ENST00000310882 ENST00000310882 FCGBP CCDS 12546.1 FU33387 CCDS9783.1 ENST00000326382 ENST00000326382 FCHSD1 NM_033449 FU34512 CCDS 10424.1 ENST00000328067 ENST00000328067 FECH CCDS 11964.1 FU34658 CCDS3913.1 ENST00000331583 ENST00000331583 FEZ1 NM_005103 FU35709 CCDS7767.1 ENST00000334627 ENST00000334627 FGD1 CCDS 14359.1 EU35728 CCDS 1537.1 ENST00000336168 ENST00000336168 FGD4 CCDS8727.1 FU36004 CCDS8704.1 ENST00000355177 ENST00000355177 FGF2 NM_002006 FU36208 NM 145270 ENST00000355324 ENST00000355324 FGFR3 CCDS3353.1 FU36601 CCDS 14238.1 ENST00000355607 ENST00000355607 FGIF CCDS8300.1 FU37440 CCDS2095.1 ENST00000357689 ENST00000357689 FIGF CCDS 14166.1 FU38964 NM 173527 ENST00000358347 ENST00000358347 FLU CCDS11192.1 FU38973 NM_153689 ENST00000359736 ENST00000359736 FU 10276 CCDS363.1 FU39058 CCDS8489.1 EPB41L2 CCDS5141.1 FU10514 CCDS1311.1 FU39198 ΝΜ 001039769 EPB41L4B NM_019114 FU 11088 CCDS8716.1 FU39873 CCDS2980.1 EPB49 CCDS6020.1 FU 11535 CCDS 12043.1 FU40243 NM 173489 EPC1 CCDS7172.1 FU 12529 CCDS8006.1 FU40342 CCDS11512.1 EPHA2 CCDS169.1 FU 12644 CCDS 12843.1 FU40869 CCDS 1691.1 EPHA5 CCDS3513.1 FU 12671 CCDS 1153.1 FU41170 NM 001004332 110 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID FLJ41766 ENST00000338573 GBFl CCDS7533.1 GPSl CCDS 11800.1 FLJ43706 ΝΜ 00103 9774 GCGR NM 000160 GPS 2 NM_032442 FLJ44186 CCDS5854.1 GCM1 CCDS4950.1 GPSM2 CCDS792.1 FLJ44861 CCDS11778.1 GCM2 CCDS4517.1 GPT CCDS6430.1 FLJ45300 NM 001001681 GCNT3 CCDS10172.1 GRAP2 CCDS 13999.1 FLJ45744 CCDS 12424.1 GDF3 CCDS 8581.1 GRASP CCDS8817.1 FLJ45964 CCDS2530.1 GEFT CCDS 8947.1 GRCA CCDS8563.1 FLJ45974 NM 001001707 GFI1B CCDS6957.1 GREB1 ΝΜ 014668 FLJ46072 CCDS6410.1 GFM1 NM_024996 GRIA4 CCDS8333.1 FLJ90650 CCDS4124.1 GGA2 CCDS10611.1 GRIK4 CCDS8433.1 FLT1 CCDS9330.1 GGPS1 CCDS 1604.1 GRIN2B CCDS 8662.1 FMN2 NM 020066 GHSR CCDS3218.1 GRIN3A CCDS6758.1 FMNL2 NMOO1004417 GIMAP1 CCDS5906.1 GRINA NM_001009184 FN1 CCDS2399.1 GIMAP5 CCDS5907.1 GRM1 CCDS5209.1 FNBP1 NM_015033 GIMAP8 NM_175571 GRM3 CCDS5600.1 FNDC1 NM_032532 GIT2 CCDS9138.1 GSR NM_000637 FOXA2 CCDS 13147.1 GJA4 NM 002060 GST02 CCDS7556.1 FOXB1 NM012182 GJB4 CCDS383.1 GTF2A2 CCDS10173.1 FOXI1 CCDS4372.1 GK CCDS 14225.1 GTF2H4 NM_020442 FOXM1 CCDS8515.1 GLRA1 CCDS4320.1 GTF3C4 CCDS6953.1 FOXR2 NM 198451 GMCL1L CCDS4433.1 GUCY1A3 NM 000856 FRAS1 NM_025074 GMDS CCDS4474.1 GUCY1B2 CCDS9426.1 FREM2 NM_207361 GML CCDS6391.1 GZMH CCDS9632.1 FRMD3 NM_174938 GNAI2 CCDS2813.1 HAMP CCDS 12454.1 FRMD4B ENST00000264546 GNAT1 CCDS2812.1 HBB NM_000519 FRMPD1 CCDS6612.1 GNL2 CCDS421.1 HBXAP CCDS8253.1 FRMPD4 NM_014728 GNPTG CCDS 10436.1 HCFC2 CCDS9097.1 FSD2 NM_001007122 GNS CCDS 8970.1 HDAC2 NM_001527 FSTL1 CCDS2998.1 GOLGA3 CCDS9281.1 HDAC9 NM_178425 FSTL4 NM_015082 GOLGA4 CCDS2666.1 HDC CCDS10134.1 FSTL5 CCDS3802.1 GORASP2 NMJH5530 HECW2 NM_020760 FUBP1 CCDS683.1 GOT2 CCDS 10801.1 HERC1 NM_003922 FUT2 NM 000511 GP6 NM 016363 HERC2 CCDS 10021.1 FXYD6 CCDS8387.1 GPBP1 NM_022913 HGSNAT ENST00000332689 FYCOl CCDS2734.1 GPI7 CCDS3336.1 HHIP CCDS3762.1 FZD10 CCDS9267.1 GPR114 CCDS 10785.1 HIF3A CCDS12681.1 FZD3 CCDS6069.1 GPR116 CCDS4919.1 HIP1 NM_005338 FZD6 CCDS6298.1 GPR132 CCDS9997.1 HIVEP1 NM_002114 FZD9 CCDS5548.1 GPR142 CCDS11698.1 HIVEP2 NM_006734 G3BP2 CCDS3571.1 GPR144 NM_182611 HIVEP3 CCDS463.1 GAB PA CCDS13575.1 GPR145 CCDS5044.1 HMG20A CCDS 10295.1 GABRA6 CCDS4356.1 GPR174 CCDS 14443.1 HMGCL CCDS243.1 GABRD CCDS36.1 GPR37 CCDS5792.1 HMP19 CCDS4391.1 GAD2 CCDS7149.1 GPR37L1 CCDS 1420.1 HNT CCDS 8491.1 GALNT13 CCDS2199.1 GPR40 CCDS 12458.1 HORMAD1 CCDS967.1 GALNT3 CCDS2226.1 GPR43 CCDS 12461.1 HOXA6 CCDS5407.1 GALNT7 CCDS3815.1 GPR61 CCDS801.1 HP NM_005143 GALNTL1 NM 020692 GPR73L1 CCDS 13089.1 HP1BP3 NM_016287 GANAB CCDS 8026.1 GPR74 CCDS3551.1 HPCAL4 CCDS441.1 GAPVD1 NM_015635 GPR78 CCDS3403.1 HRB CCDS2467.1 GAS 6 CCDS9540.1 GPR83 CCDS 8297.1 HRBL CCDS5697.1 GATA4 CCDS5983.1 GPR85 CCDS5758.1 HRG CCDS3280.1 GATA6 CCDS 11872.1 GPRC5C CCDS11699.1 HS2ST1 CCDS712.1 111 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID HS2ST1 CCDS711.1 ITPR3 CCDS4783.1 KIAA0863 NM_014913 HSA9761 CCDS3981.1 IVNS1ABP CCDS 1368.1 KIAA0980 NM 025176 HSD17B2 CCDS 10936.1 JMJD1A CCDS 1990.1 KIAA1024 NM 015206 HSD17B8 CCDS4769.1 JMJD1B NM_016604 KIAA1033 NM_015275 HSPA4L CCDS3734.1 JUNB CCDS 12280.1 KIAA1086 ENST00000262961 HSPC111 NM_016391 K0574_HUMAN ENST00000261275 KIAA1109 ENST00000264501 HSPG2 NM_005529 KATNAL2 NM 031303 KIAA1223 NM_020337 HTR3C CCDS3250.1 KBTBD3 CCDS 8334.1 KIAA1274 NM_014431 HTR3E CCDS3251.1 KBTBD4 CCDS7940.1 KIAA1328 NM_020776 HXMA CCDS 10586.1 KCNA4 NM_002233 KIAA1377 NM_020802 HYPB CCDS2749.1 KCNA7 CCDS 12755.1 KIAA1411 NM 020819 IBTK NM_015525 KCNB2 CCDS6209.1 KIAA1441 CCDS992.1 ICAM3 CCDS 12235.1 KCNC4 CCDS821.1 KIAA1467 NM_020853 ICEBERG NM_021571 KCND2 CCDS5776.1 KIAA1505 NM_020879 IDE CCDS7421.1 KCNG3 CCDS 1809.1 KIAA1524 NM 020890 IDH1 CCDS 2381.1 KCNH1 CCDS 1496.1 KIAA1576 NM_020927 IFI44 CCDS688.1 KCNH5 CCDS9756.1 KIAA1618 CCDS 11772.1 ΙΕΓΓ3 CCDS7402.1 KCNJ15 CCDS 13656.1 KIAA1754L NM_178495 IFNAR1 CCDS 13624.1 KCNK1 CCDS 1599.1 KIAA1804 CCDS 1598.1 IFRD1 NM_001007245 KCNK5 CCDS4841.1 KIAA1862 NM_032534 IGF1 CCDS9091.1 KCNN1 NM_002248 KIAA1909 NM 052909 IGF2 CCDS7728.1 KCNQ3 NM_004519 KIAA1946 NM_177454 IGFBP7 CCDS3512.1 KCNQ4 CCDS456.1 KIAA1967 NM_021174 IGSF1 CCDS 14629.1 KCTD7 CCDS5534.1 KIAA2022 ΝΜ 001008537 IGSF10 CCDS3160.1 KCTD8 CCDS3467.1 KIAA2026 NM_001017969 IGSF9 CCDS 1190.1 KDELR2 CCDS5351.1 KID1NS220 NM_020738 IKBKE NM_014002 KDR CCDS3497.1 KIFC2 CCDS6427.1 IL12RB2 CCDS638.1 KEL NM_000420 KIFC3 CCDS 10789.1 IL17B CCDS4297.1 KIAA0082 CCDS4835.1 KIRRF.L2 CCDS12479.1 IL17RE CCDS2589.1 KIAA0101 CCDS10193.1 KIRRF.L3 NM_032531 IL1F9 CCDS2108.1 KIAA0103 CCDS6309.1 KLHDC5 NM_020782 IL1RL1 CCDS2057.1 KIAA0133 NM_014777 KLHL10 NM_152467 IL3 CCDS4149.1 KIAA0143 NM_015137 TCT.HT4 CCDS 14456.1 ILT7 CCDS12890.1 KIAA0153 CCDS 14047.1 KT.K9 CCDS12816.1 MP4 CCDS2160.1 KIAA0317 NM 001039479 KT.P1 CCDS 12926.1 MPDH1 NM_183243 KIAA0329 ΝΜ 014844 KLRG1 CCDS8599.1 INDO NM_002164 KIAA0350 NM_015226 KNTC1 NM_014708 INSIG2 CCDS2122.1 KIAA0367 NM_015225 KREMEN2 CCDS10484.1 IP013 CCDS503.1 KIAA0404 NM_015104 KREMEN2 CCDS10483.1 IP08 CCDS 8719.1 KIAA0406 CCDS13300.1 KRT9 NM_000226 IQGAP2 NM 006633 KIAA0528 NM 014802 KRTAP12-3 NM_198697 IQWD1 CCDS 1267.1 KIAA0649 CCDS6988.1 KRTAP20-2 CCDS 13604.1 IRS1 CCDS2463.1 KIAA0652 CCDS7921.1 KRTHA4 CCDS 11390.1 IRTA2 CCDS 1165.1 KIAA0664 NM_015229 KSR1 NM_014238 IRX6 NM_024335 KIAA0672 NM_014859 LI CAM CCDS14733.1 ISL1 NM_002202 KIAA0690 CCDS7457.1 L3MBTL2 CCDS14011.1 ITGA4 NM 000885 KIAA0701 NM_001006947 LACE1 CCDS5067.1 ITGA7 CCDS8888.1 KIAA0703 NM 014861 LACRT CCDS8883.1 ITGAL NM_002209 KIAA0748 ENST00000316577 LAMA1 NM_005559 ITGAX CCDS 10711.1 KIAA0759 CCDS9852.1 LAM A3 CCDS 11880.1 ΓΓΙΗ5 NM_032817 KIAA0774 NM_001033602 LAMA4 NM_002290 FTLNl CCDS 1211.1 KIAA0802 CCDS 11841.1 LAMB 3 CCDS 1487.1 ITPKB CCDS 1555.1 KIAA0831 NM_014924 LAMP3 CCDS3242.1 112 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID LAP IB CCDS 1335.1 LOC648272 ENST00000343945 MAN1B1 CCDS7029.1 LARGE CCDS13912.1 LOC651746 ENST00000296657 MAN2A1 NM_002372 LARP5 NM_015155 LOC651863 ENST00000333744 MAN2B1 NM_000528 LATS1 NM_004690 LOC90379 NM_138353 MAP IB CCDS4012.1 LATS2 CCDS9294.1 LOC90826 CCDS3771.1 MAP3K11 CCDS8107.1 LAX CCDS 1441.1 LOC92154 NM_138383 MAP3K14 NM_003954 LBP CCDS13304.1 LOC93349 NM_138402 MAP3K8 CCDS7166.1 LCA10 NM_001039768 LPAL2 ENST00000342479 MAP3K9 NM_033141 LCT CCDS2178.1 LPHN1 CCDS 12307.1 MAP4K4 NM_004834 LDLRAD3 NM_174902 LPHN2 CCDS689.1 MAP7D3 ENST00000218318 LEMD2 CCDS4785.1 LPHN3 NM_015236 MARCO CCDS2124.1 LENG8 CCDS 12894.1 LPIN3 NM_022896 MARIO NM_002376 LETM1 CCDS3355.1 LPL CCDS 6012.1 MARS CCDS 8942.1 LETMD1 CCDS 8806.1 LRAT CCDS3789.1 MARS 2 NM 138395 LIP8 CCDS 11126.1 LRCH1 NM_015116 MASS1 NM 032119 LIPM ENST00000282673 LRFN5 CCDS9678.1 MAST4 ENST00000261569 LMNB1 CCDS4140.1 LRP1 CCDS 8932.1 MATN1 CCDS336.1 LMX1A CCDS 1247.1 LRP10 CCDS9578.1 MBD1 CCDS11941.1 LNX CCDS3492.1 LRP1B CCDS2182.1 MBNL1 CCDS3163.1 LNX2 CCDS9323.1 LRP2 CCDS2232.1 MCCC1 CCDS3241.1 LOCI 13655 CCDS6431.1 LRRC16 NM_017640 MCF2L ENST00000261963 LOCI 24842 CCDS 11283.1 LRRC4 CCDS5799.1 MCFD2 NM_139279 LOCI 26248 CCDS 12429.1 LRRC4B ENST00000253728 MCM10 CCDS7095.1 LOC131368 CCDS2947.1 LRRC7 CCDS645.1 MCPH1 NM 024596 LOC131873 ENST00000358511 LRRIQ1 NM_032165 MDGA1 NM_153487 LOCI 34145 NM 199133 LRRK1 NM_024652 MDH2 CCDS5581.1 LOCI46562 CCDS 10521.1 LRRN1 NM_020873 MEA CCDS4879.1 LOC158830 NM 001025265 LRRN3 CCDS5754.1 MED 12 NM_005120 LOC200312 ΝΜ 001017981 LRRN5 CCDS 1448.1 MEFV CCDS 10498.1 LOC221955 CCDS5350.1 LTB4R2 CCDS9624.1 MEN1 CCDS8083.1 LOC257106 CCDS 1215.1 LTBP1 NM_000627 METTL5 NM_014168 LOC283537 CCDS9332.1 LTBP3 CCDS8103.1 MGAM NM_004668 LOC284912 CCDS13918.1 LTBP4 NM_003573 MGC16635 CCDS 14097.1 LOC284948 CCDS 1976.1 LTK CCDS 10077.1 MGC19764 NM_144975 LOC339977 NM_001024611 LUC7L CCDS 10401.1 MGC20419 CCDS562.1 LOC374768 NM 199339 LY6K CCDS6385.1 MGC20741 CCDS4861.1 LOC387755 NM_001031853 LYNX1 ENST00000317543 MGC21830 CCDS10463.1 LOC387856 ΝΜ 001013635 LYPLA1 CCDS6157.1 MGC24039 NM 144973 LOC388595 NMOO1013641 LYRIC CCDS6274.1 MGC2655 CCDS10491.1 LOC388969 NM_001013649 LYST NM_000081 MGC26598 CCDS9036.1 LOC391123 NM 001013661 LYZL4 CCDS2697.1 MGC26818 CCDS44.1 LOC392617 ENST00000333066 LZTR2 NM_033127 MGC27016 CCDS3790.1 LOC400707 NM_001013673 M160 CCDS8577.1 MGC29814 CCDS11742.1 LOC441136 NMOO 1013719 MACFl CCDS435.1 MGC29875 CCDS 1493.1 LOC441233 NMOO1013724 MAEA NM_001017405 MGC33367 CCDS 10738.1 LOC442213 NM_001013732 MAGEA4 CCDS 14702.1 MGC33414 CCDS279.1 LOC494115 NMOO1008662 MAGEB10 NM_182506 MGC33486 CCDS8133.1 LOC51058 CCDS476.1 MAGEC1 NM_005462 MGC33889 CCDS14216.1 LOC54103 NM_017439 MAGEH1 CCDS14369.1 MGC34647 CCDS 10895.1 LOC54499 CCDS 1251.1 MAGI-3 CCDS859.1 MGC35118 CCDS 10046.1 LOC550631 NMOO1017437 MAK10 CCDS6673.1 MGC35194 CCDS147.1 LOC63928 CCDS10617.1 MALT1 CCDS 11967.1 MGC35366 CCDS9057.1 LOC643866 NM 001039771 MAMDC2 CCDS6631.1 MGC39581 CCDS 12149.1 113 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID MGC42174 NM_152383 MYBPC3 NM_000256 NLGN2 CCDS11103.1 MGC4251 CCDS 11474.1 MYBPHL NM_001010985 NLN CCDS3989.1 MGC4268 CCDS2152.1 MYF6 CCDS9019.1 NM_001080470.1 ENST00000271263 MGC45562 CCDS11371.1 MYH14 NM_024729 NMBR CCDS5196.1 MGC45780 CCDS6064.1 MYH15 ENST00000273353 NMUR1 CCDS2486.1 MGC47869 CCDS 8667.1 MYH3 CCDS11157.1 NNT CCDS3949.1 MHC2TA CCDS 10544.1 MYH4 CCDS 11154.1 NOD3 NM_178844 MIA3 ENST00000320831 MY015A NM_016239 NOR1 CCDS409.1 MICAL-L2 CCDS5324.1 MY018B NM_032608 NOS 3 CCDS5912.1 MINK1 NM_170663 MYOIB CCDS2311.1 NOTCH 1 NM_017617 MIPEP CCDS9303.1 MYOID NM_015194 NOTCH2 CCDS908.1 MIR16 CCDS 10578.1 MYOIE NM_004998 NOTCH3 CCDS12326.1 MKI67 CCDS7659.1 MY03A CCDS7148.1 NOTCH4 NMJXH557 MLL NM_005933 MY03B NMJ38995 NOX4 CCDS8285.1 MLL3 CCDS5931.1 MY05A NM 000259 NP_001073909.1 ENST00000327928 MLL4 NM_014727 MY05C NM_018728 NP_001073931.1 ENST00000341689 MLLT4 CCDS5303.1 MY09B NM 004145 NP_001073940.1 ENST00000292357 MLLT7 NM_005938 MYOCD CCDS11163.1 NP_001073948.1 ENST00000296794 MME CCDS3172.1 MYOM1 NM_003803 NP_001073961.1 ENST00000219301 MMP10 CCDS 8321.1 MYOM2 CCDS5957.1 NP_001073971.1 ENST00000266524 MMP16 CCDS6246.1 MYR8 NM015011 NP_001074294.1 ENST00000342607 MOCS1 CCDS4845.1 MYRIP CCDS2689.1 NPC1L1 CCDS5491.1 MON2 NM_015026 MYST3 CCDS6124.1 NPL CCDS 1350.1 MPDU1 CCDS 11115.1 MYT1L ΝΜ 015025 NPLOC4 NM_017921 MPDZ NM_003829 NAGA CCDS 14030.1 NPPA CCDS139.1 MPP1 CCDS 14762.1 NALP1 NM_014922 NPR3 NM 000908 MPZ CCDS 1229.1 NALP11 CCDS 12935.1 NPTXR ΝΜ 014293 MRC2 CCDS11634.1 NALP7 CCDS12912.1 NR_002781.1 ENST00000246203 MRGX1 CCDS7846.1 NAPSB ENST00000253720 NR2E1 CCDS5063.1 MRPL13 CCDS6332.1 NARG1L CCDS9379.1 NRAP CCDS7578.1 MRPL16 CCDS7976.1 NAVI CCDS 1414.1 NRBP2 NM_178564 MRPL37 ENST00000329505 NCBP1 CCDS6728.1 NRK NM 198465 MRPL44 CCDS2459.1 NCKAP1L NM_005337 NRP1 CCDS7177.1 MRPL46 CCDS 10341.1 NCOA5 CCDS13392.1 NRP2 CCDS2364.1 MRPL55 CCDS 1567.1 NCOA6 CCDS 13241.1 NRXN2 CCDS8077.1 MRPS5 CCDS2010.1 NDUFA11 CCDS12155.1 NS3TP2 CCDS4136.1 MRPS7 CCDS11718.1 NDUFB2 CCDS5862.1 NT5E CCDS5002.1 MR VII NM 006069 NDUFS6 CCDS3866.1 NTN2L CCDS 10469.1 MS4A7 CCDS7985.1 NEB NM 004543 NTRK3 CCDS 10340.1 MSI2 CCDS11596.1 NEIL3 CCDS3828.1 NUAK1 NM_014840 MSL2LI NM018133 NEUROG2 CCDS3698.1 NUP160 ΝΜ 015231 MSRB3 CCDS8973.1 NF1 CCDS 11264.1 NUP188 NM 015354 MTA1 NM_004689 NFATC3 CCDS 10862.1 NUP205 NM_015135 MTHFD2L NMOO1004346 NFATC4 CCDS9629.1 NUP210L NM 207308 MTNR1B CCDS8290.1 NGEF CCDS2500.1 NUP98 CCDS7746.1 MTP CCDS3651.1 NHS CCDS14181.1 NURIT CCDS9399.1 MTR CCDS 1614.1 NIF3L1BP1 CCDS2900.1 NXF3 CCDS14503.1 MTX2 CCDS2272.1 NIN NM_182944 NXF5 CCDS 14491.1 MUC15 CCDS7859.1 NISCH NM_007184 NXPH1 NM_152745 MUC16 NM 024690 NKG7 CCDS 12830.1 OAS3 NM 006187 MUC5AC ENST00000349637 NKRF ΝΜ 017544 OBSCN CCDS 1570.1 MUC7 CCDS3541.1 NKX2-5 CCDS4387.1 ODZ2 ENST00000314238 MVP CCDS 10656.1 NLGN1 CCDS3222.1 OLIG2 CCDS 13620.1 114 WO 2009/100029 PCT/US2009/032881 in o <N Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID OPRDl CCDS329.1 OR9Q2 NM_001005283 PDZD7 NM_024895 3 OPRL1 CCDS 13556.1 OSAP NM 032623 PEG10 ENST00000362013 i OR10G3 NM 001005465 OSBPL2 CCDS 13494.1 PET.P1 NM_014389 ’—1 OR10G4 NM_001004462 OSBPL5 NM_145638 PENK CCDS6168.1 1 OR10H2 CCDS 12333.1 OSBPL9 CCDS558.1 PERQ1 NM_022574 OR10P1 NM 206899 OSR2 NM 053001 PEX1 CCDS5627.1 OR10T2 NM 001004475 OSTM1 CCDS5062.1 FEX10 CCDS41.1 H OR13J1 ΝΜ 001004487 OTOF CCDS 1725.1 PFAS CCDS11136.1 v—1 OR1L8 NM_001004454 OTOG ENST00000342528 PFKFB3 CCDS7078.1 m OR2A12 NM_001004135 OTOR CCDS 13124.1 PGAP1 CCDS2318.1 o OR2AG1 NM 001004489 OTUD1 ENST00000298035 PGBD5 CCDS 1583.1 (N OR2AG2 NM 001004490 OVCH1 NM 183378 PHC3 NM 024947 in OR2D2 NM_003700 OVOL1 CCDS8112.1 PHEMX CCDS7733.1 o OR2G3 NM 001001914 OXA1L CCDS9573.1 PHF2 ENST00000298216 CN OR2L13 CCDS 1637.1 p44S10 CCDS2901.1 PHF21A NM_016621 OR2L2 NM_001004686 PAD 12 CCDS177.1 PI II1’ CCDS4987.1 OR2S2 CCDS6596.1 PAPLN NM_173462 PHKA2 CCDS 14190.1 OR2T4 NM_001004696 PAPOLG CCDS 1863.1 PHLPP NM_194449 OR2V2 CCDS4461.1 PAPPA2 NM_020318 PHLPPL NM_015020 OR2Y1 NM 001001657 PARC CCDS4890.1 PHOX2B CCDS3463.1 OR2Z1 NM_001004699 PARP11 CCDS8523.1 PIGN NM_176787 OR3A1 CCDS 11023.1 PAX9 CCDS9662.1 PIGQ CCDS10411.1 OR4A5 NM_001005272 PCAF CCDS2634.1 PIGR CCDS 1474.1 OR4L1 NM_001004717 PCDH11X CCDS14463.1 PIK3C2G NM 004570 OR4N2 NM_001004723 PCDHA10 NM_031859 PIK3CA NM_006218 OR4P4 ΝΜ 001004124 PCDHA13 CCDS4240.1 PIK3CG CCDS5739.1 OR52A5 NM 001005160 PCDHB7 CCDS4249.1 PIK3R1 CCDS3993.1 OR52B2 NM_001004052 PCDHGA4 NM_032053 PIK3R4 CCDS3067.1 OR52D1 NM 001005163 PCDHGA9 NM 032089 PIK3R5 CCDS11147.1 OR52E6 NM 001005167 PCDHGB7 NM 032101 PIP5K1A CCDS990.1 OR52I1 NM_001005169 PCDHGC4 CCDS4260.1 PIP5K3 CCDS2382.1 OR52N4 NM 001005175 PCDHGC4 CCDS4261.1 PISD CCDS13899.1 OR56A4 NM 001005179 PCDHGC4 CCDS4263.1 ΡΓΓΡΝΜ1 NM_004910 OR56B1 NM_001005180 PCGF2 NM_007144 ΡΓΓΡΝΜ2 CCDS9242.1 OR56B4 NM 001005181 PCNXL2 ENST00000344698 ΡΓΓΡΝΜ3 CCDS 11076.1 OR5A1 ΝΜ 001004728 PCSK2 CCDS 13125.1 PIWIL3 ΝΜ 001008496 OR5AP2 NM_001002925 PCYOX1 CCDS 1902.1 PKD1 NM_000296 OR5AU1 NM_001004731 PDCD10 CCDS3202.1 PKD1L2 NM_182740 OR5B17 ENST00000357377 PDCD11 NM 014976 PKHD1 CCDS4935.1 OR5BF1 NM_001001918 PDE1C CCDS5437.1 PKHD1L1 NM_177531 OR5D14 ΝΜ 001004735 PDE4A CCDS12238.1 PKIA CCDS6222.1 OR5K4 NM_001005517 PDE4B CCDS632.1 PLA1A CCDS2991.1 OR5M1 ENST00000303005 PDE4C CCDS12373.1 PLCH2 NM_014638 OR5M8 ΝΜ 001005282 PDE4D NM 006203 PLCXD3 ΝΜ 001005473 OR5M9 ΝΜ 001004743 PDGFB CCDS13987.1 PLD2 CCDS11057.1 OR6C74 NM_001005490 PDGFRA CCDS3495.1 PLEC1 NM_201378 OR6K3 ΝΜ 001005327 PDGFRB CCDS4303.1 PLEKHA4 CCDS 12737.1 OR6W1P ENST00000340373 PDHA2 CCDS3644.1 PLEKHH2 CCDS1812.1 OR7A5 CCDS12318.1 PDHB CCDS2890.1 PLIN CCDS10353.1 OR7D4 NM 001005191 PDIA2 NM 006849 PLSCR3 NM 020360 OR8D2 NM_001002918 PDK1 CCDS2250.1 PLXDC2 CCDS7132.1 OR8K3 NM_001005202 PDLIM4 CCDS4152.1 PLXNA3 CCDS 14752.1 OR9K2 NM 001005243 PDZD2 NM 178140 PLXNB2 ENST00000359337 115 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID PLXNCl CCDS9049.1 PSRC2 NM_144982 Q96CK5_HUMAN ENST00000273582 PMS1 CCDS2302.1 PTAR1 ENST00000340434 Q96DR3HUMAN ENST00000324748 PMS2L4 ENST00000275546 PTCH2 CCDS516.1 Q96FF7 HUMAN ENST00000269720 PNLIP CCDS7594.1 PTEN NM_000314 Q96NE0_HUMAN ENST00000329922 PNOC CCDS6066.1 PTGDR CCDS9707.1 Q96NL2 HUMAN ENST00000272907 PODXL2 CCDS3044.1 PTGFR CCDS686.1 Q96PS2HUMAN ENST00000326978 POLD1 CCDS 12795.1 PTGS2 CCDS 1371.1 Q9H030_HUMAN ENST00000237449 POLE CCDS9278.1 PTPLA CCDS7121.1 Q9H6A9_HUMAN ENST00000309024 POLG2 NM 007215 PTPN23 CCDS2754.1 Q9H800 HUMAN ENST00000357106 POLM NM_013284 PTPRF CCDS489.1 Q9H8D1_HUMAN ENST00000360549 POLR3B CCDS9105.1 PTPRK CCDS5137.1 Q9HAC4 HUMAN ENST00000206466 POLR3E CCDS 10605.1 PTPRM CCDS 11840.1 Q9P1M5HUMAN ENST00000303007 POPDC2 CCDS2992.1 PTPRS CCDS12139.1 Q9ULE4_HUMAN ENST00000265018 POR CCDS5579.1 PTPRU CCDS334.1 Q9Y6V0-3 ENST00000333891 PORCN CCDS 14296.1 PTX3 CCDS3180.1 QPCT CCDS 1790.1 POT1 CCDS5793.1 PUM1 CCDS338.1 QRICH2 NM_032134 POU1F1 CCDS2919.1 PYGB CCDS13171.1 QSCN6 CCDS 1337.1 POU2F1 CCDS 1259.1 Q13034_HUM AN ENST00000225928 QSER1 NM 024774 POU6F2 NM 007252 Q4VXG5_HUMAN ENST00000327794 QTRTD1 NM_024638 PPAP2C CCDS12023.1 Q4VXG5_HUMAN ENST00000331811 RAB36 CCDS13805.1 PPARA NM 001001930 Q5JX50_HUMAN ENST00000325076 RAB3C CCDS3976.1 PPBP CCDS3563.1 Q5JYU7_HUMAN ENST00000333418 RAB3GAP2 NM_012414 PPEF2 NM 006239 Q5T740_HUMAN ENST00000343319 RAB3IL1 CCDS 8014.1 PPIG CCDS2235.1 Q5W0A0_HUMAN ENST00000298738 RAC2 CCDS 13945.1 PPL CCDS 10526.1 Q68CJ6_HUMAN ENST00000341513 RAD23A CCDS 12289.1 PPM2C CCDS6259.1 Q6IEE8_HUMAN ENST00000354872 RAD51L3 CCDS 11287.1 PPP1CC CCDS9150.1 Q6PK04HUMAN ENST00000329214 RAD52 CCDS8507.1 PPP1R12A NM_002480 Q6RGF6_HUMAN ENST00000359144 RAFTLIN NM_015150 PPP1R12C CCDS 12916.1 Q6ZRB0_HUMAN ENST00000297487 RAI1 CCDS 11188.1 PPP2CZ CCDS855.1 Q6ZSY1_HUMAN ENST00000320930 RALBP1 CCDS 11845.1 PPP2R2C CCDS3387.1 Q6ZT40_HUMAN ENST00000296564 RANBP17 NM_022897 PPRC1 CCDS7529.1 Q6ZUG5_HUMAN ENST00000344062 RANP1 ENST00000333828 PRCC CCDS 1157.1 Q6ZV46_HUMAN ENST00000341696 RAP 140 CCDS2877.1 PRDM16 NM_199454 Q76B61_HUMAN ENST00000360022 RAPGEF4 NM_007023 PRDM5 CCDS3716.1 Q86U37_HUMAN ENST00000335192 RAPGEF6 NM_016340 PRELP CCDS 1438.1 Q86XQ1_HUMAN ENST00000261673 RAPGEFL1 CCDS11363.1 PRIC285 CCDS 13527.1 Q86YU6_HUMAN ENST00000330768 RAPH1 CCDS2359.1 PRKCBP1 CCDS 13404.1 Q8IUR1_HUMAN ENST00000327506 RARSL CCDS5011.1 PRKCZ CCDS37.1 Q8N1R6_HUMAN ENST00000331014 RASGRF1 CCDS 10309.1 PRKDC NM_006904 Q8N646_HUMAN ENST00000359720 RASGRF2 CCDS4052.1 PRKG2 CCDS3589.1 Q8N800_HUMAN ENST00000322516 RASL11B CCDS3490.1 PRKRA CCDS2279.1 Q8N822_HUMAN ENST00000317280 RAX CCDS11972.1 PRO 1853 CCDS 1788.1 Q8N8C3_HUMAN ENST00000319889 RBI NM_000321 PRO 1855 CCDS 11566.1 Q8N8K0_HUMAN ENST00000301807 RBM14 CCDS8147.1 PROM1 NM_006017 Q8N9H1_HUMAN ENST00000359503 RBM19 CCDS9172.1 PROSC CCDS6096.1 Q8NBE0_HUMAN ENST00000297801 RBM21 CCDS8021.1 PRPF18 CCDS7100.1 Q8NDH2_HUMAN ENST00000322527 RBM25 NM_021239 PRR12 ENST00000246798 Q8NGK8_HUMAN ENST00000334020 RBM27 ENST00000265271 PRSS16 CCDS4623.1 Q8NGL5_HUMAN ENST00000328673 RBM34 ENST00000362051 PRSS22 CCDS10481.1 Q8NH06 HUMAN ENST00000324144 RBMS3 NM_001003792 PSF1 NM 021067 Q8NHB0 HUMAN ENST00000315712 RBP3 CCDS7218.1 PSIP1 CCDS6479.1 Q8TBR1_HUMAN ENST00000354206 RBPSUH CCDS3436.1 PSMD8 CCDS 12515.1 Q96CH6HUMAN ENST00000329920 RC74 NM_018250 116 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID RCD-8 CCDS 10849.1 SARG CCDS 1475.1 SIPA1L2 NM_020808 RDHE2 CCDS6167.1 SARS CCDS795.1 SIPA1L3 NM_015073 RDS CCDS4871.1 SASH1 CCDS5212.1 SKIV2L CCDS4731.1 REGIB CCDS 1963.1 scmpi CCDS3186.1 SKP2 CCDS3915.1 REN NM 000537 SCN1B CCDS12441.1 SLC10A4 CCDS3482.1 REPS2 CCDS 14180.1 SCN3A NM_006922 SLC11A1 CCDS2415.1 RET CCDS7200.1 SCN3B CCDS8442.1 SLC12A1 CCDS10129.1 RFC2 CCDS5567.1 SCN5A NM_000335 SLC12A5 CCDS13391.1 RFNG NM 002917 SCN9A NM_002977 SLC14A1 CCDS 11925.1 RFX3 CCDS6450.1 SCRIB CCDS6411.1 SLC14A2 CCDS 11924.1 RGS22 NM 015668 SCUBE1 CCDS14048.1 SLC16A5 CCDS11713.1 RGSL1 CCDS 1346.1 SDC3 NM 014654 SLC1A2 NM_004171 RHOT1 NM_001033568 SDR-O CCDS8926.1 SLC22A11 CCDS8074.1 RICTOR NM_152756 SEC24C CCDS7332.1 SLC22A18 CCDS7740.1 RIMBP2 NM_015347 SELO NM 031454 SLC22A3 CCDS5277.1 RIMS2 NM_014677 SEMA5A CCDS3875.1 SLC24A6 NM_024959 RIMS4 CCDS13338.1 SEMA5B CCDS3019.1 SLC25A13 CCDS5645.1 RIPK4 CCDS 13675.1 SEMA7A CCDS 10262.1 SLC26A4 CCDS5746.1 RLBP1 NM_000326 SEN2L CCDS2611.1 SLC2A1 CCDS477.1 RLTPR NM_001013838 SENP3 ΝΜ 015670 SLC30A1 CCDS 1499.1 RNASEH2A CCDS 12282.1 SEPT2 CCDS2548.1 SLC30A5 CCDS3996.1 RNF103 NM_005667 SERPINA12 CCDS9926.1 SLC30A9 CCDS3465.1 RNF127 CCDS 14575.1 SERPINA9 NM 175739 SLC35B2 NM_178148 RNF128 CCDS 14521.1 SERPINB3 CCDS11987.1 SLC35D3 NM_001008783 RNF19 CCDS6286.1 SERPINB7 CCDS11988.1 SLC35F2 NM_017515 RNF25 CCDS2420.1 SERPINE2 CCDS2460.1 SLC38A1 NM 030674 RNF40 CCDS10691.1 SERPING1 CCDS7962.1 SLC38A4 CCDS8750.1 RNPC2 CCDS 13265.1 SET7 CCDS3748.1 SLC38A6 CCDS9751.1 R0B03 NM_022370 SETDB2 CCDS9417.1 SLC39A2 CCDS9563.1 ROCK1 CCDS 11870.1 SEZ6 NM_178860 SLC43A3 CCDS7956.1 ROM1 CCDS 8024.1 SEZ6L CCDS13833.1 SLC4A1 CCDS11481.1 ROS1 CCDS5116.1 SFI1 NM_001007467 SLC4A5 CCDS 1936.1 RoXaN CCDS14013.1 SFMBT2 NM_001029880 SLC4A7 NM_003615 RP1L1 NM_178857 SFRP2 NM_003013 SLC5A5 CCDS12368.1 RPL11 CCDS238.1 SFTPB CCDS 1983.1 SLC5A7 CCDS2074.1 RPS14 CCDS4307.1 SG223 HUMAN ENST00000330777 SLC7A10 CCDS 12431.1 RPS6KA2 CCDS5294.1 SGCZ CCDS5992.1 SLC7A13 NM_138817 RPS6KB2 NM 003952 SGK2 CCDS13320.1 SLC7A14 NM_020949 RPUSD3 CCDS2586.1 SGPP1 CCDS9760.1 SLC7A6 NM_003983 RRAGD CCDS5022.1 SGPP2 CCDS2453.1 SLC8A1 CCDS 1806.1 RSHL1 CCDS 12675.1 SGSH CCDS 11770.1 SLC9A1 CCDS295.1 RSU1 CCDS7112.1 SH3BP1 CCDS13952.1 SLC9A2 CCDS2062.1 RTN1 CCDS9740.1 SH3BP2 NM_003023 SLC9A3R2 NM_004785 RTTN NM 173630 SH3GL3 CCDS 10325.1 SLC9A4 NM_001011552 RUNX1 CCDS 13639.1 SHANK2 CCDS8198.1 SLCOIBI CCDS8685.1 RUNX1T1 CCDS6256.1 SIIANK3 ENST00000262795 SLC02A1 CCDS3084.1 RWDD1 ΝΜ 001007464 SHB NM_003028 SLC04C1 NM_180991 RYR2 NM 001035 SHE NM_001010846 SLC06A1 NM_173488 RYR3 NM 001036 SHMT2 CCDS8934.1 SLIT2 CCDS3426.1 SALL3 CCDS12013.1 SIGLEC11 CCDS 12790.1 SLITRK1 CCDS9464.1 SAMD11 ENST00000294573 SIGLEC5 NM_003830 SLITRK5 CCDS9465.1 SAMD9 NM_017654 SIGLEC8 NM_014442 SLITRK6 ENST00000313206 SAPS2 NM 014678 SIM2 CCDS 13646.1 SMARCA2 NM 003070 117 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID SMARCA4 CCDS12253.1 STAP2 CCDS12128.1 TGFBRAPl CCDS2067.1 SMARCC2 CCDS8907.1 STIM2 CCDS3440.1 TGM1 CCDS9622.1 SMC5L1 CCDS6632.1 STK33 CCDS7789.1 TGM5 NM_004245 SMCR8 CCDS11195.1 STK39 NM_013233 THAP9 CCDS3598.1 SMF_HUMAN ENST00000261804 STRA6 CCDS 10261.1 THBS1 NM 003246 SN CCDS 13060.1 STS CCDS14127.1 THEA CCDS592.1 SNED1 ENST00000310397 STS-1 NM_032873 THOP1 CCDS 12095.1 SNRPA CCDS 12565.1 STX11 CCDS5205.1 THRAP3 ENST00000354618 SNX13 NM015132 STX12 CCDS310.1 THSD7B ENST00000272643 SNX27 CCDS 1001.1 STXBP2 CCDS12181.1 TIMP2 CCDS11758.1 SNX4 CCDS3032.1 STXBP3 CCDS790.1 TINAG CCDS4955.1 SOCS5 CCDS 1830.1 STYK1 CCDS 8629.1 TJP3 NM_014428 SOHLH1 NM_001012415 SUCLA2 CCDS9406.1 TLL1 CCDS3811.1 SORCS2 NM_020777 SUCLG2 NM_003848 TLN1 NM 006289 SORCS3 CCDS7558.1 SULT6B1 NM_00103 2377 TLX3 NM_021025 SORL1 CCDS 8436.1 SUNC1 NM_152782 TM4SF14 CCDS7369.1 SOS1 CCDS 1802.1 SUSD5 ENST00000309558 TM4SF3 CCDS 8999.1 SOSTDC1 CCDS5360.1 SV2B CCDS 10370.1 TM9SF4 CCDS13196.1 SOX 13 NM_005686 SWAP70 NM_015055 TMED1 CCDS 12249.1 SOX30 CCDS4339.1 SYDE2 ENST00000234668 TMEM131 ENST00000186436 SOX8 CCDS 10428.1 SYN2 NM_133625 TMEM132C ENST00000315208 SPIOO CCDS2477.1 SYNE1 CCDS5236.1 TMEM16B NM_020373 SPACA4 CCDS 12725.1 SYNE1 CCDS5237.1 TMEM16C NM_031418 SPAG1 NM_003114 SYNE2 CCDS9761.1 TMEM16E NM_213599 SPAG5 NM_006461 SYT15 NM_181519 TMEM16G NM_001001891 SPAG7 NM 004890 SYT16 NM_031914 TMEM16J ΝΜ 001012302 SPATA1 CCDS697.1 SYT6 CCDS871.1 TMEM38A CCDS 12349.1 SPATA2 CCDS 13422.1 TAAR9 ENST00000340640 TMEM46 NM_001007538 SPATC1 CCDS6413.1 TACC2 CCDS7626.1 TMEM63B ΝΜ 018426 Spc25 CCDS2229.1 TACC3 CCDS3352.1 TMEM8 CCDS 10407.1 SPEG ENST00000265327 TAF1L NM_153809 TMPRSS2 NM_005656 SPEN CCDS 164.1 TAF4B ENST00000269142 TMPRSS4 NM 019894 SPG3A CCDS9700.1 TAF6 CCDS5686.1 TNC CCDS6811.1 SPI1 CCDS7933.1 TANC1 NM_033394 TNFAIP2 CCDS9979.1 SPIN3 NM 001010862 TAOK1 NM 020791 TNFSF18 CCDS 1305.1 SPIRE2 NM 032451 TARBP2 CCDS8861.1 TNFSF4 CCDS 1306.1 SPN CCDS 10650.1 TAS1R2 CCDS 187.1 TNFSF9 CCDS12169.1 SPOCK3 NM_016950 TAS2R3 CCDS5867.1 TNIP1 NM_006058 SPON2 CCDS3347.1 TBC1D20 CCDS13002.1 TNIP2 CCDS3362.1 SPRED2 NM_181784 TBC1D4 NMJ114832 TNK1 NM_003985 SPTB NM_001024858 TBCD NM 001033052 TNMD CCDS 14469.1 SPTBN1 NM_178313 TBX20 CCDS5445.1 TNN NM_022093 SPTBN2 CCDS8150.1 TBX22 CCDS 14445.1 TNPOl CCDS4016.1 SPTBN4 CCDS12559.1 TCF7L1 CCDS 1971.1 TNR CCDS 1318.1 SPTBN5 NM_016642 TCF8 CCDS7169.1 TNRC15 NM 015575 SREBF2 CCDS 14023.1 ran i ENST00000290632 TNRC4 CCDS 1002.1 SRGAP1 CCDS 8967.1 TCN2 CCDS13881.1 TNRC6C NM 018996 SRPK2 CCDS5735.1 TDRD5 CCDS 1332.1 TOE1 CCDS521.1 SRRM2 NM_016333 TDRD9 CCDS9987.1 TOP2A NM_001067 SSFA2 CCDS2284.1 TEAD2 CCDS 12761.1 TORI A CCDS6930.1 ST14 CCDS 8487.1 TEPP CCDS 10790.1 TOSO CCDS 1473.1 ST8SIA4 CCDS4091.1 IERF2IP NM_018975 TP53 CCDS11118.1 STAB1 NM 015136 TFE3 CCDS 14315.1 TPH2 NM_173353 118 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene symbol Accession ID Gene symbol Accession ID Gene symbol Accession ID TPK NM_003292 UNQ689 CCDS3542.1 ZAN NM_173059 TPST2 CCDS13839.1 UPK3B CCDS5588.1 ZBTB16 CCDS8367.1 TRAM1L1 CCDS3707.1 URB1 ENST00000270201 ZBTB24 NM 014797 TRAPPC3 CCDS404.I USH2A CCDS 1516.1 ZBTB4 CCDS11107.1 TREML2 CCDS4853.1 USP11 CCDS 14277.1 ZBTB9 NM 006772 TREML3 ENST00000332842 USP26 CCDS 14635.1 ZC3H6 NM_198581 TRIM14 CCDS6734.1 USP8 CCDS10137.1 ZFPM1 NM_153813 TREM42 CCDS3113.1 VANGL1 CCDS883.1 ZFYVE9 CCDS563.1 TREM45 CCDS893.1 VCAM1 CCDS773.1 ZIC1 CCDS3136.1 TREM46 CCDS 1097.1 VCIP135 CCDS6192.1 ZKl NM_001010879 TREM55 CCDS6186.1 VCL CCDS7340.1 ZMAT4 NM_024645 TREM56 NM_030961 VDP NM 003715 ZNF10 CCDS9283.1 TREM58 CCDS 1636.1 VDR CCDS8757.1 ZNF160 CCDS 12859.1 TRIO CCDS3883.1 VGCNL1 CCDS9498.1 ZNF17 NM 006959 TRIOBP NM_007032 VGTJ.2 CCDS5115.1 ZNF18 NM 144680 TRIP 12 NMJ104238 VIPR2 CCDS5950.1 ZNF183L1 CCDS9486.1 TRIP6 CCDS5708.1 VMD2 NM_004183 ZNF189 CCDS6754.1 TRMT5 NM_020810 VN2R1P ENST00000312652 ZNF25 CCDS7195.1 TRPC4AP CCDS 13246.1 VPS 11 NM_021729 ZNF286 CCDS11172.1 TRPC6 CCDS 8311.1 VPS13A CCDS6655.1 ZNF294 NM_015565 TRPM2 CCDS13710.1 VPS 24 NM_001005753 ZNF295 CCDS 13678.1 TRPM3 CCDS6634.1 VPS41 CCDS5457.1 ZNF30 NM 194325 TRPM4 NM_017636 VPS45A CCDS944.1 ZNF31 NM 145238 TRPM5 NM_014555 VSIG2 CCDS8452.1 ZNF313 ΝΜ 018683 TRPM6 CCDS6647.1 VWF CCDS8539.1 ZNF318 CCDS4895.1 TRPM7 NM 017672 WBSCR17 CCDS5540.1 ZNF333 CCDS 12316.1 TRPV5 CCDS5875.1 WBSCR27 CCDS5561.1 ZNF339 CCDS13132.1 TRRAP CCDS5659.1 WDFY3 CCDS3609.1 ZNF343 CCDS 13028.1 TSAP6 CCDS2125.1 WDR21 CCDS9809.1 ZNF358 NM 018083 TSC2 CCDS 10458.1 WDR22 NM_003861 ZNF366 CCDS4015.1 TSCOT CCDS6786.1 WDR24 CCDS 10420.1 ZNF406 NM_001029939 TSGA10 CCDS2037.1 WDR27 NM_182552 ZNF440L NM_001012753 TTC12 CCDS8360.1 WDR32 CCDS6613.1 ZNF473 NM_015428 TTC18 CCDS7324.1 WDR34 CCDS6906.1 ZNF487 ENST00000315429 TTC6 ΝΜ 001007795 WDR42B ENST00000329763 ZNF496 CCDS1631.1 TTLL2 CCDS5301.1 WDR52 CCDS2972.1 ZNF497 CCDS 12977.1 TTLL5 NM 015072 WDR6 CCDS2782.1 ZNF507 NM_014910 TTN NM 133378 WDR70 ΝΜ 018034 ZNF545 CCDS 12493.1 TTN NM 133432 WDTC1 CCDS296.1 ZNF547 NM_173631 TUBGCP3 CCDS9525.1 WEE1 CCDS7800.1 ZNF558 CCDS12208.1 TUBGCP6 CCDS 14087.1 WFS1 CCDS3386.1 ZNF585A CCDS 12499.1 TULP1 CCDS4807.1 WNK1 CCDS8506.1 ZNF628 NM_033113 TXNDC3 CCDS5452.1 WNK2 CCDS6704.1 ZNF67 ENST00000323012 TYR CCDS8284.1 WNT9A NM 003395 ZNF79 CCDS6871.1 UBAP2L CCDS 1063.1 XAB2 NM 020196 ZP2 CCDS 10596.1 UBE2G2 CCDS 13714.1 XDH CCDS 1775.1 ZSCAN2 CCDS10329.1 UCHL1 CCDS3462.1 XPOl NM 003400 ZSWIM4 NM__023072 UGCGL2 CCDS9480.1 XP07 NM_015024 ZW10 CCDS 8363.1 UGDH CCDS3455.1 XRJH6172.1 ENST00000355015 UGT1A6 CCDS2510.1 XR_017335.1 ENST00000314295 Note: Gene symbols are standard ULK1 CCDS9274.1 YN004_HUMAN ENST00000281581 symbols assigned by Entrz Gene UNQ2446 CCDS 10850.1 YTHDC2 CCDS4113.1 (http://www.ncbi.nlm.nih.gov/sites/ent UNQ3030 CCDS3319.1 YWHAH CCDS13901.1 rez?db=gene). Accession IDs 119 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/ent rez?db=nuccore). Accession IDs “CCDSXXXX” are uniquely assigned to individual genes by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/CCDS/) . Accession IDs “ENSTXXXXXXXXXXX” are uniquely assigned to individual genes by Ensembl (http://www.ensembl.org/index.html). 120 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 able 13. Genes containing omatic mutations in ancreatic cancer adapted rom the paper by Jones et. al. Jones et al., 2008).

Gene Symbol 7h3

AARS ABCA1 ABCA12 ABCA7 ABCB5 ABCD2 ABLIM2

ACACB

ACD

ACE ACOT9

ACTL7B

ADA AD AMI 1 ADAM12 ADAM19 ADAM21 AD AMTS 10 ADAMTS15 ADAMTS16 ADAMTS18 ADAMTS2 ADAMTS20 ADAMTS20 ADAMTS5 ADAMTSL3 ADCY2 ADCY4 ADD2 ADPRHL2 AFF3

AHNAK

AHNAK

AHR

AICDA AIM2 AK3 AKAP12 ALDH18A1 ALDH1A3 ALDH3A1 ALDH3B1 ALDH8A1 ALG8 ALMS1 ALOX5 AMIG03

Accession

ID CCDS12324.1 NM_001605 CCDS6762.1 NM 015657 CCDS12055.1 CCDS5371.1 CCDS8734.1 NM 032432 NM_001093 CCDS 10842.1 CCDS11637.1 NM_001033583 CCDS6771.1 CCDS13335.1 CCDS11486.1 CCDS7653.1 CCDS4338.1 CCDS9804.1 CCDS 12206.1 CCDS8488.1 NM_139056 CCDS 10926.1 CCDS4444.1 NM_175851 NM_025003 CCDS13579.1 CCDS10326.1 CCDS3 872.1 CCDS9627.1 CCDS1906.1 CCDS402.1 NM 001025108 NM_024060 NM 001620 CCDS5366.1 NM 020661 CCDS1181.1 CCDS629.1 CCDS5229.1 CCDS7443.1 CCDS 10389.1 CCDS11212.1 NM_000694 CCDS5171.1 CCDS8258.1 NM_015120 CCDS7212.1 NM_198722

Gene Symbol Accession ID ANAPC4 CCDS3434.1 ANK3 CCDS7258.1 ANKAR ENS T00000313 581 ANKRD27 NM_032139 ANKRD6 NM_014942 ANKRD9 CCDS9973.1 ANXA13 NM_001003954 AOX1 NM_001159 AP3B2 NM_004644 APC2 CCDS12068.1 APG4A CCDS14538.1 APOB CCDS 1703.1 APRIN NM_015032 APXL2 CCDS4161.1 AQP8 CCDS 10626.1 ARFGAP1 CCDS13515.1 ARHGAP10 NM_024605 ARHGAP21 CCDS7144.1 ARHGAP28 NM 001010000 ARHGEF11 CCDS 1162.1 ARHGEF7 CCDS9521.1 ARHGEF9 NM015185 ARID 1A CCDS285.1 ARMC7 CCDS11714.1 ARMCX1 CCDS 14487.1 ARNT2 NM_014862 ARRDC2 CCDS 12370.1 ARSA CCDS 14100.1 ARSI NM_001012301 ARTS-1 CCDS4085.1 ASB2 CCDS9915.1 ASXL2 NM_018263 ATF2 CCDS2262.1 ATN1 NM_001940 ATP10A NM_024490 ATP10B ENST00000327245 ATP10D CCDS3476.1 ATP11B NM_014616 ATP1A3 CCDS 12594.1 ATP1B2 NM_001678 ATP2A1 CCDS10643.1 ATP2B3 CCDS 14722.1 ATP6V0A4 CCDS5849.1 AZU1 CCDS 12044.1 B3GALT1 CCDS2227.1 B3GNTL1 NM_001009905 B4GALT7 CCDS4429.1 BACH2 CCDS5026.1 BAI1 NM_001702 BAD CCDS4968.1 BAIAP2L2 NM_025045 BAIAP3 CCDS 10434.1 BC37295_3 NM_001005850

Gene Symbol Accession ID BCAN CCDS 1149.1 BCHE CCDS3198.1 BCL2A1 CCDS 10312.1 Beta4GalNAc-T4 CCDS7694.1 BMPR2 NM_001204 BOC CCDS2971.1 BPIL3 CCDS13211.1 BRCA2 CCDS9344.1 BSN CCDS2800.1 BTBD7 NM_001002860 ClOorfl 13 NM_001010896 C10orf31 NM_001012713 C10orf93 CCDS7672.1 C10orf99 CCDS7371.1 Cllorfl6 CCDS7794.1 C13orf22 CCDS9336.1 C13orf25 CCDS9467.1 C14orfl21 NM_138360 C14orfl24 NM_020195 C15orfl6 CCDS 10026.1 C15orf41 NM_032499 C17orf27 NM_020914 C17orf38 NM_001010855 C19orf20 NM_033513 C19orf22 CCDS12048.1 C19orf28 NM_174983 C19orf35 CCDS 12087.1 C19orf6 CCDS 12052.1 Clorfll3 NM_024676 Clorfl29 NM 025063 Clorfl4 NM 030933 Clorf25 CCDS 1366.1 Clorf45 NM_001025231 C1QL2 NM_182528 C1RL CCDS8573.1 C20orfl34 NM_001024675 C20orfl61 CCDS13377.1 C20orf26 NM_015585 C20orf42 CCDS13098.1 C20orf77 CCDS 13301.1 C21orf29 CCDS13712.1 C21orf63 CCDS13614.1 C2orfl0 CCDS2291.1 C2orf29 CCDS2050.1 C3 NM_000064 C3orfl5 CCDS2994.1 C3orfl8 CCDS2829.1 C4orf9 NM_003703 C6orfl03 ENST00000326916 C6orf213 NM_001010852 C6orf54 CCDS5304.1 C6orf60 NM_024581 C7orf27 CCDS5334.1 121 WO 2009/100029 PCT/U S2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol C9orfl38 CCDS6487.1 CFHR4 C9orf39 NM_017738 CGI-09 C9orf45 CCDS6850.1 CGN C9orf91 CCDS6808.1 CHD1 C9orf98 CCDS6954.1 CHD5 CABLES2 NM031215 CHD7 CACNA1A NM 000068 CHBL1 CACNA1E NM_000721 CHMP1B CACNA2D1 CCDS5598.1 CHPPR CACNG5 CCDS11666.1 CHST1 "AD CCDS 1742.1 CHURC1 CALB1 CCDS6251.1 CIAS1 CALCR CCDS5631.1 CILP CAMSAP1 NM_015447 CKLFSF4 CAMTA1 NM015215 CLEC4M CAND2 ENST00000295989 CLIPR-59 CAPN12 CCDS12519.1 CLK1 CARD9 CCDS6997.1 CLSTN2 CASKIN2 CCDS11723.1 CLUAP1 "ASP10 CCDS2338.1 CMAS "AT CCDS7891.1 CMYA1 CBFA2T2 CCDS 13221.1 CMYA3 CBLN4 CCDS13448.1 CMYA5 CCDC11 CCDS11940.1 CNGB1 CCDC18 NM_206886 CNGB3 CCKAR CCDS3438.1 CNTN4 CCL2 CCDS11277.1 CNTN5 CCNB3 CCDS14331.1 CNTN6 CCNYL3 ENST00000332505 CNTNAP2 CCR1 CCDS2737.1 CNTNAP4 CCT6A CCDS5523.1 COBLL1 CCT6B NM_006584 COCH CD 163 CCDS8578.1 COH1 CD1A CCDS1174.1 COL11A1 CD200R1 CCDS2969.1 COL14A1 CD44 CCDS7897.1 COL17A1 CD6 CCDS7999.1 COL22A1 CD79A CCDS12589.1 COL4A1 CD86 CCDS3009.1 COL4A4 CDC42BPA CCDS1558.1 COL5A1 CDH1 CCDS10869.1 COL6A3 CDH10 CCDS3 892.1 COEEC12 CDH20 CCDS11977.1 COR02A CDH7 CCDS11993.1 CPAMD8 CDKN2A CCDS6510.1 CPLX2 CDSN NM 001264 CPN1 CEBPZ CCDS1787.1 CPT1C CEECAM1 CCDS6901.1 CPZ CEL NM 001807 CREBBP CELSR1 CCDS14076.1 CSF2RB CENTD1 CCDS3441.1 CSMD1 Cepl92 NM 032142 CSMD2 CEP290 NM_025114 CSS3

Accession ID Gene Symbol Accession ID NM_006684 CTAG2 CCDS 14759.1 CCDS 13093.1 CTNNA2 NM_004389 CCDS999.1 CTNNA3 CCDS7269.1 NM_001270 CTNND2 CCDS3881.1 CCDS57.1 CUBN CCDS7113.1 NM 017780 CUL4B NM_003588 CCDS1435.1 CUTL1 CCDS5720.1 NM_020412 CX40.1 CCDS7191.1 CCDS6182.1 CXorf9 CCDS14614.1 CCDS7913.1 CYFIP1 CCDS 10009.1 NM_145165 CYFIP2 NM_014376 CCDS1632.1 CYP1A1 CCDS 10268.1 CCDS 10203.1 DACH2 CCDS 14455.1 CCDS10817.1 DAXX CCDS4776.1 CCDS12187.1 DBT CCDS767.1 CCDS12486.1 DCC1 CCDS6330.1 CCDS2331.1 DCHS1 CCDS7771.1 CCDS3112.1 DCHS2 CCDS3785.1 NM 015041 DCT CCDS9470.1 CCDS8696.1 DDX51 NM_175066 CCDS2683.1 DDX58 CCDS6526.1 NM_152381 DEPDC2 CCDS6201.1 NM_153610 DEPDC5 NM_014662 NM_001297 DET1 NM_017996 CCDS6244.1 DFNB31 CCDS6806.1 CCDS2558.1 DGKA CCDS8896.1 NM_014361 DGKD CCDS2504.1 CCDS2557.1 DGKK NM_001013742 CCDS5889.1 DGKZ CCDS7918.1 CCDS 10924.1 DHCR24 CCDS600.1 CCDS2223.1 DHX33 CCDS11072.1 CCDS9640.1 DHX8 CCDS 11464.1 CCDS6280.1 DICER 1 CCDS9931.1 CCDS778.1 DIP2B NM 173602 NM_021110 DKFZp313G1735 CCDS4073.1 CCDS7554.1 DKFZP434B0335 NM 015395 CCDS6376.1 DKFZP434G1415 CCDS8743.1 CCDS9511.1 DKFZP434L1717 CCDS3805.1 NM 000092 DKFZp434O0527 CCDS2430.1 CCDS6982.1 DKFZP564J0863 NM_015459 NM_004369 DKFZp566O084 CCDS11215.1 NM 130386 DKFZP586P0123 NM_015531 CCDS6735.1 DKFZp761A052 CCDS14313.1 NM_015692 DLC1 CCDS5989.1 ENST00000274615 DLEC1 ENST00000337335 CCDS7486.1 DLG2 NM_001364 CCDS 12779.1 DLG3 CCDS14403.1 CCDS3404.1 DLGAP1 CCDS11836.1 CCDS 10509.1 DMD CCDS14228.1 CCDS 13936.1 DMP1 CCDS3623.1 NM_033225 DNA2L ENST00000358410 CCDS380.1 DNAH11 NM 003777 NM_175856 DNAH5 CCDS3882.1 122 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol DNAH8 CCDS4838.1 EPPKl DNAH9 CCDS11160.1 EPS8L2 DNAPTP6 NM_015535 ERCC2 DNHD2 NM_178504 ERCC4 DNM1L CCDS8728.1 ERCC6 DOCK2 CCDS4371.1 EST1B DOT1L NM_032482 ETS2 DP58 NM_001004441 ETV6 DPP6 NM_130797 EVI1 DRD2 CCDS8361.1 EVPL DRD3 CCDS2978.1 EXOC2 DUOX2 CCDS10117.1 EXOSC8 DUSP15 CCDS13193.1 F10 DUSP19 CCDS2289.1 F13A1 DYSF CCDS1918.1 F8 EBF CCDS4343.1 FAD158 EBF3 NM_001005463 FADD EDG8 CCDS 12240.1 FADS1 EFEMP1 CCDS1857.1 FADS2 EHMT1 CCDS7050.1 FAM132B EIF2AK2 CCDS1786.1 FAM47B EIF5 CCDS9980.1 FAM50B EIF5B NM_015904 FAM53B ELA2 CCDS12045.1 FAM54B ELAVL4 CCDS553.1 FAM55C ELN CCDS5562.1 FAT EME2 NMOO1010865 FAT3 EMTT.TN1 CCDS1733.1 FAT4 EML1 NM_004434 FBN2 ENC1 CCDS4021.1 FBN3 ENS T00000294635 ENST00000294635 FBX015 ENST00000298876 ENST00000298876 FBX03 ENST00000309390 ENST00000309390 FBX041 ENST00000322493 ENST00000322493 FBX09 ENST00000324303 ENST00000324303 FBXW7 ENST00000326382 ENST00000326382 FBXW8 ENST00000326952 ENST00000326952 FGD2 ENST00000332477 ENST00000332477 FGD5 ENST00000333971 ENST00000333971 FKRP ENST00000334548 ENST00000334548 FKSG44 ENST00000336168 ENST00000336168 FU10324 ENST00000340260 ENST00000340260 FU 10407 ENST00000356555 ENST00000356555 FU 10521 ENTH NM_014666 FU 10647 EP300 CCDS14O10.1 FU12886 EPB41L1 CCDS13271.1 FU14011 EPC2 NM 015630 FU14299 EPHA3 CCDS2922.1 FU14490 EPHA7 CCDS5031.1 FU14640 EPHB1 NM_004441 FU20032 EPHB2 CCDS229.1 FU20035 EPHB6 CCDS5873.1 FU20244 EPM2A CCDS5206.1 FU20245

Accession ID Gene Symbol Accession ID NM 031308 FLJ20457 CCDS6774.1 NM_022772 FLJ20580 CCDS576.1 NM 000400 FLJ21628 CCDS4440.1 NM 005236 FLJ21816 NM 024675 CCDS7230.1 FLJ21986 NM_024913 CCDS1137.1 FLJ23420 CCDS12189.1 CCDS13659.1 FLJ23577 ENST00000303168 CCDS8643.1 FLJ23588 CCDS 14049.1 CCDS3205.1 FLJ25006 CCDS11237.1 CCDS11737.1 FLJ25530 CCDS8456.1 NM_018303 FLJ26175 NM_001001668 NM181503 FLJ31295 CCDS8763.1 CCDS9530.1 FLJ32110 CCDS5613.1 CCDS4496.1 FLJ32112 CCDS587.1 NM 000132 FLJ32416 CCDS 12086.1 CCDS725.1 FLJ32685 CCDS2645.1 CCDS8196.1 FLJ34969 NM_152678 CCDS8013.1 FLJ35220 NM_173627 CCDS8012.1 FLJ35843 CCDS9151.1 ENST00000344233 FLJ36180 CCDS3851.1 ENST00000329357 FLJ36748 NM_152406 CCDS4487.1 FLJ37396 CCDS5072.1 CCDS7641.1 FLJ38020 NM_001039775 NM 019557 FLJ38377 CCDS2164.1 CCDS2945.1 EU39155 CCDS3924.1 NM_005245 EU39501 CCDS12331.1 ENST00000298047 EU39502 CCDS2281.1 CCDS3732.1 FU40235 CCDS12827.1 NM_001999 FU41046 NM_207479 CCDS12196.1 FU41993 NM 001001694 CCDS 12002.1 FU45231 NM 001039778 CCDS7887.1 EU45909 CCDS12522.1 ENST00000295133 FU46072 CCDS6410.1 NM_033481 FU46365 CCDS6144.1 CCDS3777.1 FU46481 CCDS3384.1 CCDS9182.1 FU46536 NM_198483 CCDS4829.1 FU90805 CCDS 12603.1 NM_152536 FMN2 NM_020066 CCDS12691.1 FMNL1 CCDS11497.1 CCDS8102.1 FMNL3 NM_175736 NM. 018059 EMR1 CCDS14682.1 CCDS583.1 EMR2 CCDS14684.1 CCDS182.1 FN1 CCDS2399.1 CCDS406.1 FOXJ1 NM_001454 NM 019108 FOXP2 CCDS5760.1 CCDS 12944.1 FREM1 NM_144966 CCDS6094.1 FREM2 NM_207361 CCDS446.1 FRMPD4 NM_014728 NM 032816 FSTL5 CCDS3802.1 CCDS3666.1 FTCD CCDS 13731.1 NM 017631 FTHL17 CCDS14227.1 CCDS12293.1 GABRA1 CCDS4357.1 CCDS7041.1 GABRR1 CCDS5019.1 123 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol 3ALNT13 CCDS2199.1 HELB 3ALNT4 NM_003774 HELZ 3ALNT8 CCDS8533.1 HIP1 3AS 7 CCDS11152.1 HIST1H3A 3BP3 CCDS717.1 HIST1H4I 3DF6 NM_001001557 HKR2 3FAP CCDS 11491.1 HMGCLL1 3FRA1 CCDS7593.1 HOXCIO 3H2 CCDS11648.1 HOXC9 3IMAP7 CCDS5903.1 HOXD4 3JA3 CCDS9289.1 HPCAL1 3LB1L3 ENST00000299136 HPS5 3LI1 CCDS8940.1 HRB2 3LD CCDS5465.1 HRPT2 3LP1R CCDS4839.1 HS3ST2 3LTSCR1 NM015711 HS3ST5 3NAT1 CCDS2812.1 HSGT1 30LGA3 CCDS9281.1 HTR1A 3PC2 CCDS5689.1 HYPC 3PR CCDS 10051.1 IER5 3PR110 ENST00000326374 IL12RB1 3PR133 CCDS9272.1 IL17RB 3PR151 NM_194251 IL17RC 3PR154 CCDS5443.1 IL18R1 3PR158 NM_020752 IL2RG 3PR35 CCDS2541.1 ILK 3PR54 CCDS12049.1 IMP5 3PR73L1 CCDS13089.1 INHBB 3PR82 CCDS14259.1 INO80 3PRC5C CCDS11699.1 INPP5D 3PS2 CCDS11100.1 ENTS 2 3PX6 NM_182701 IQGAP1 3RCA CCDS8563.1 IRGQ 3RHL1 NM_198182 IRS4 GRIA3 CCDS14604.1 IRX1 GRIK2 CCDS5048.1 ISYNA1 GRIN3A CCDS6758.1 ITGA11 GRIP2 ENST00000273083 ITGA3 GRM6 CCDS4442.1 ITGA4 GRM8 CCDS5794.1 ITGA9 GSDML CCDS 11354.1 ITGAE GSR NM_000637 ITGB4BP GTF3C1 NM_001520 ITIH2 GTF3C3 CCDS2316.1 ITLN1 GUCA2A CCDS465.1 ITPR1 GUCY1A2 CCDS8335.1 EXL H1T2 CCDS8762.1 JAG1 HAPLN4 CCDS12398.1 JM11 HAS1 CCDS12838.1 JMJD3 HBXIP CCDS824.1 JPH3 HCK NM 002110 JPH4 HECW1 CCDS5469.1 K6IRS2 HECW2 NM_020760 KALI

Accession ID Gene Symbol Accession ID CCDS8976.1 KBTBDll NM_014867 NM_014877 KCNA3 CCDS828.1 NM 005338 KCNA4 NM_002233 CCDS4570.1 KCNB1 CCDS13418.1 CCDS4620.1 KCNB2 CCDS6209.1 CCDS12975.1 KCNC2 CCDS9005.1 NM 019036 KCNC3 CCDS 12793.1 CCDS8868.1 KCNJ3 CCDS2200.1 CCDS8869.1 KCNK10 CCDS9880.1 CCDS2269.1 KCNMA1 CCDS7352.1 CCDS1671.1 KCNT1 NM_020822 CCDS7836.1 KCTD15 CCDS 12434.1 CCDS9012.1 KEAP1 CCDS 12239.1 CCDS1382.1 KIAA0082 CCDS4835.1 CCDS 10606.1 KIAA0317 ENST00000338772 NM 153612 KIAA0367 NM 015225 CCDS7321.1 KIAA0372 CCDS4072.1 NM 000524 KIAA0590 CCDS10439.1 CCDS8789.1 KIAA0774 NM 001033602 CCDS1343.1 KIAA1024 NM_015206 NM 153701 KIAA1086 ENST00000262961 CCDS2874.1 KIAA1102 NM_014988 CCDS2590.1 KIAA1109 ENST00000264501 CCDS2060.1 KIAA1219 CCDS 13305.1 CCDS 14406.1 KIAA1543 ENST00000160298 CCDS7768.1 KIAA1704 CCDS9394.1 NM175882 KIAA1751 ENST00000270720 CCDS2132.1 KIAA1755 NM 001029864 CCDS 10071.1 KIAA1944 CCDS9266.1 NM 001017915 KIAA1957 ENST00000332235 NM 020748 KIAA1961 NM 133372 CCDS 10362.1 KIAA2013 ENST00000329923 NM 001007561 KIF21A NM 017641 CCDS 14544.1 KIF25 CCDS5305.1 NM_024337 KIF3A NM_007054 CCDS 12379.1 KIN CCDS7080.1 NM 001004439 KIRREL CCDS1172.1 CCDS11557.1 ΚΓΓ CCDS3496.1 NM 000885 KLF5 CCDS9448.1 CCDS2669.1 KLHDC1 CCDS9692.1 NM_002208 KLHDC4 CCDS10963.1 CCDS 13249.1 KLP1 CCDS12926.1 NM 002216 KPNB1 CCDS11513.1 CCDS1211.1 KRAS CCDS8702.1 NM 002222 KRT13 CCDS11396.1 NM 017592 KRT9 NM_000226 CCDS 13112.1 KRTAP11-1 CCDS13608.1 CCDS 14316.1 L3MBTL4 CCDS11839.1 ENST00000254846 LAMA1 NM_005559 CCDS 10962.1 LAMA4 NM_002290 CCDS9603.1 LAMA5 NM_005560 CCDS8833.1 LAMC3 CCDS6938.1 CCDS14130.1 LARP CCDS4328.1 124 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol LASS3 CCDS 103 84.1 LRRN3 LCT CCDS2178.1 LRRTM4 LENG8 CCDS 12894.1 MAGEE 1 LGI4 CCDS 12444.1 MAMDC1 LGR6 CCDS1424.1 MAN2A1 LIG3 CCDS11284.1 ΜΑΡΙΑ LIMR CCDS8780.1 MAP1B LIPH CCDS3272.1 MAP2 LMOD1 NM_012134 MAP2K6 LMTK2 CCDS5654.1 MAP4K2 LMX1A CCDS1247.1 MAP4K3 LOCI 13179 CCDS 12076.1 MAP4K4 LOCI 13386 NM_138781 MAPKBP1 LOCI 23 872 CCDS 10943.1 MAPT LOC126147 NM_145807 MARLIN 1 LOC128153 CCDS1519.1 MARS LOCI 3 0951 NM_138804 MASP2 LOC131873 ENST00000358511 MASS1 LOC163131 NM_001005851 MAST2 LOCI 67127 CCDS3914.1 MAT2B LOC222967 ENST00000297186 MBD3 LOC283219 NM 001029859 MCM7 LOC283398 ENST00000342823 MCTP2 LOC284434 NM 001007525 MEGF11 LOC339768 CCDS2525.1 ΜΕΡΙΑ LOC340578 NM_001013628 METTL3 LOC342979 ENST00000340790 MGC10731 LOC343521 NM_001013632 MGC13125 LOC387720 NM_001013633 MGC 15523 LOC388135 NM_001039614 MGC 15875 LOC392617 ENST00000333066 MGC20806 LOC399706 NM_001010910 MGC2494 LOC441136 NM 001013719 MGC26598 LOC441476 NM 001004353 MGC26988 LOC441722 ENST00000311061 MGC29649 LOC51334 CCDS4127.1 MGC33407 LOC63920 NM 022090 MGC34713 LOC89944 NM_138342 MGC35138 LPAL2 ENST00000342479 MGC35555 LPHN3 NM 015236 MGC39581 LPL CCDS6012.1 MGC4266 LRFN5 CCDS9678.1 MGC50721 LRP1 CCDS8932.1 MGC5297 LRP1B CCDS2182.1 MIDI LRP2 CCDS2232.1 MIZF LRP3 CCDS12430.1 MKL2 LRP5 CCDS8181.1 MLC1 LRRC16 NM_017640 MT.T. LRRC18 NM_001006939 MT.T.2 LRRC3B CCDS2644.1 MT.T.3 LRRC4 CCDS5799.1 MLL5 LRRC48 NM_031294 MMP9 LRRK2 NM_198578 MOBKL2C

Accession ID Gene Symbol Accession ID CCDS5754.1 MORC CCDS2955.1 NM_024993 MORC2 NM_014941 CCDS14433.1 MOXD1 CCDS5152.1 NM 182830 MPHOSPH1 CCDS7407.1 NM_002372 MPL CCDS483.1 NM 002373 MPN2 CCDS 1563.1 CCDS4012.1 MPO CCDS11604.1 CCDS2384.1 MPZ CCDS 1229.1 CCDS11686.1 MRGPRD ENST00000309106 CCDS8082.1 MRGX1 CCDS7846.1 CCDS 1803.1 MRPL38 CCDS11733.1 ENST00000302217 MRPS7 CCDS11718.1 NM 014994 MSLN NM_013404 CCDS11499.1 MTF1 NM_005955 CCDS3385.1 MTMR12 NM_019061 CCDS8942.1 MTMR2 CCDS8305.1 CCDS 123.1 MTOl CCDS4979.1 NM 032119 MTR CCDS1614.1 NM015112 MUC1 CCDS1098.1 CCDS4365.1 MUC15 CCDS7859.1 CCDS 12072.1 MUC16 NM_024690 CCDS5683.1 MUC2 NM_002457 NM_018349 MUF1 CCDS533.1 CCDS10213.1 MUM1L1 NM_152423 CCDS4918.1 MYBL1 ENST00000331406 NM_019852 MYBPHL NM_001010985 CCDS171.1 MYCBPAP NM 032133 CCDS8374.1 MYH2 CCDS11156.1 CCDS11780.1 MYH3 CCDS11157.1 CCDS4434.1 MYH6 CCDS9600.1 CCDS11797.1 MYH9 CCDS13927.1 CCDS10423.1 MYLIP CCDS4536.1 CCDS9036.1 MYO10 NM 012334 CCDS4335.1 MY015A NM 016239 CCDS 8033.1 MYOIG NM_033054 CCDS 12207.1 MY03A CCDS7148.1 CCDS4070.1 MY06 NM 004999 CCDS7701.1 MY07B ENST00000272666 CCDS6307.1 MY09A CCDS10239.1 CCDS12149.1 MYOM1 NM 003803 CCDS8522.1 MYST3 CCDS6124.1 CCDS 10602.1 NAALAD2 CCDS8288.1 CCDS3873.1 NAALADL2 NM_207015 CCDS14138.1 NALP10 CCDS7784.1 CCDS 8414.1 NALP13 NM_176810 NM 014048 NALP14 CCDS7776.1 CCDS 14083.1 NALP4 CCDS12936.1 NM 005933 NAV2 CCDS7 850.1 NM 003482 NAV3 NM_014903 CCDS5931.1 NCDN CCDS392.1 NM 182931 NCK1 CCDS3092.1 CCDS 13390.1 NCL NM_005381 CCDS539.1 NCOA2 NM_006540 125 WO 2009/100029 PCT/US2009/032881 ΙΟ O Gene Symbol (N Accession ID Gene Symbol Accession ID Gene Symbol Accession ID NEB NM_004543 OR2W3 NM_001001957 PCDHB2 CCDS4244.1 £3 NEK8 NM_178170 OR4A16 NM_001005274 PCDHB3 CCDS4245.1 ^ ΝΕΟΙ CCDS10247.1 OR4B1 NM_001005470 PCDHGA1 NM_031993 _, NFATC3 CCDS 10860.1 OR4E2 NM_001001912 PCDHGA11 NM_032091 NFIA CCDS615.1 OR4L1 NM_001004717 PCDHGA8 NM_014004 ΝΠ5 CCDS1608.1 OR4X1 NM_001004726 PCDHGC4 CCDS4260.1 ΝΠ52 CCDS9706.1 OR51B4 CCDS7757.1 PCNT NM_006031 1 NIF3L1BP1 CCDS2900.1 OR51E1 NM_152430 PCNXL2 ENST00000344698 r—1 NIPSNAP3B CCDS6761.1 OR51F2 NM_001004753 PCSK2 CCDS13125.1 1 NKX2-2 rf) ^ NLGNl CCDS13145.1 OR52I2 NM_001005170 PCSK6 NM 138321 CCDS3222.1 OR52L1 ENST00000332249 PDE6A CCDS4299.1 NMUR1 CCDS2486.1 OR5C1 NM_001001923 PDZRN3 NM_015009 l/~) NOD3 NM 178844 OR5D13 NM_001001967 PDZRN4 CCDS8739.1 I—1 NOL5A CCDS13030.1 OR5D3P ENST00000333984 PEG3 CCDS 12948.1 O NOPE CCDS 10206.1 OR5F1 NM_003697 PER3 CCDS89.1 CN v M NORl CCDS409.1 OR5J2 NM_001005492 PFAS CCDS11136.1 NOS1 NM_000620 OR5T1 NM_001004745 PGM5 CCDS6622.1 NOX5 NM 024505 OR6A2 CCDS7772.1 PGR CCDS8310.1 NP_001035826.1 ENST00000331090 OR6K2 NM_001005279 PHACTR3 CCDS13480.1 NP_001074311.1 ENST00000326096 OR8D2 NM_001002918 PHB2 NM_007273 NPD014 CCDS260.1 OR8H1 NM_001005199 PIAS4 CCDS12118.1 NPHP4 NM015102 OR8K1 NM_001002907 PIGK CCDS674.1 NPY1R NM_000909 OR8K5 NM_001004058 PIGT CCDS13353.1 NRG2 CCDS4217.1 OR9I1 NM_001005211 PIK3CG CCDS5739.1 NRXN2 CCDS8077.1 OR9K2 NM_001005243 PIK3R2 CCDS12371.1 NRXN3 CCDS9870.1 ORC5L CCDS5734.1 PIP5K3 CCDS2382.1 NSE1 CCDS 1684.1 OSBPL6 CCDS2277.1 PITRM1 NM_014889 NTF3 CCDS8538.1 OSCAR CCDS12873.1 PKD1L2 NM_182740 NIRK3 CCDS 10340.1 OSMR CCDS3928.1 PKHD1L1 NM_177531 NUDT5 CCDS7089.1 OSTN CCDS3299.1 PKIA CCDS6222.1 ENST00000318605 ENST00000318605 OTOF CCDS 1724.1 PKP2 CCDS8731.1 NUP210 NM_024923 OTP CCDS4039.1 PLCB2 NM 004573 NURIT CCDS9399.1 OTX1 CCDS1873.1 PLCB3 CCDS8064.1 NXN CCDS10998.1 OVCA2 NM 001383 PLCB4 CCDS13104.1 NXPH3 CCDS11550.1 OVCH1 NM_183378 PEEC1 NM_201380 OBSCN CCDS 1570.1 Pll CCDS8754.1 PEEC1 NM 201378 OBSL1 ENS T00000265318 PABPC5 CCDS 14460.1 PEEK2 CCDS9782.1 OCA2 CCDS 10020.1 PACS2 NM_015197 PEEKHA6 CCDS1444.1 ODZ4 ENST00000278550 PADI2 CCDS177.1 PEEKHG2 NM 022835 OGDHL CCDS7234.1 PALMD CCDS758.1 PLK5HUMAN ENST00000334770 OGFOD2 NM_024623 PAPPA CCDS6813.1 PLXNA1 NM_032242 OGT CCDS14414.1 PARP10 NM 032789 PLXNB1 CCDS2765.1 OR 10 A3 ENST00000360759 PARP14 NM_017554 PMP22CD NM 001013743 OR10K2 NM_001004476 PARP2 NM_005484 PNPLA1 NM_001039725 OR10P1 NM_206899 PARP9 CCDS3014.1 PODN CCDS573.1 OR10R2 NM_001004472 PAX6 NM_000280 PODXL NM001018111 OR10Z1 NM_001004478 PB1 CCDS2859.1 POLR2A NM_000937 OR11L1 NM_001001959 PCDH15 CCDS7248.1 POLRMT CCDS12036.1 OR13C3 NM_001001961 PCDH17 NM_014459 PON1 CCDS5638.1 OR13C5 NM_001004482 PCDH18 NM_019035 PPA2 CCDS3667.1 OR1J2 NM 054107 PCDH9 CCDS9443.1 PPFIA2 NM 003625 OR2AJ1 ENST00000318244 PCDHA13 NM_031864 PPP1CA CCDS8160.1 OR2T1 NM_030904 PCDHB16 CCDS4251.1 PPP1R15B CCDS1445.1 126 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol PPP1R3A CCDS5759.1 Q96M18_HUM AN PPP2R1A CCDS12849.1 Q96MJ2_HUMAN PPP2R3A CCDS3087.1 Q96QE0_HUMAN PPP2R4 CCDS6920.1 Q96RX8_HUMAN PPP5C CCDS 12684.1 Q96S27_HUMAN PRDM10 CCDS8484.1 Q9H557_HUMAN PRDM5 CCDS3716.1 Q9H5F0_HUMAN PRDM9 NM_020227 Q9H8A7_HUMAN PRELP CCDS1438.1 Q9HA39_HUMAN PREX1 CCDS 13410.1 Q9HCM3_HUMAN PRG-3 CCDS6751.1 Q9NSI0_HUMAN PRKACG CCDS6625.1 Q9NT86_HUMAN PRKCG CCDS12867.1 Q9P169_HUMAN PRKD1 CCDS9637.1 Q9P193_HUMAN ProSAPiPl CCDS13049.1 Q9P1M5_HUMAN PRR12 ENST00000246798 Q9Y6V0-3 PRSS23 CCDS8278.1 QRICH2 PSMD3 CCDS11356.1 RAB6B PSME4 NM_014614 RAD9B PTCHD2 ENS T00000294484 RAG1 PTCHD3 NM_001034842 RAG2 PTF1A CCDS7143.1 RaLP PTGER3 CCDS652.1 RANBP2 PEN CCDS5844.1 RARB PTPN12 CCDS5592.1 RARRES2 PTPRK CCDS5137.1 RASEF PTPRZ1 NM 002851 RASGRP3 PUM1 CCDS338.1 RASGRP4 PWP2H NM_005049 RASIP1 PXDN ENST00000252804 RASSF6 PXDNL NM 144651 RBAF600 PYHIN1 CCDS1178.1 RBBP6 Q08AG5_HUMAN ENST00000334213 RBM27 Q5JX50_HUMAN ENST00000325076 RC74 Q5SYT8_HUMAN ENST00000279434 RCHY1 Q6ZMX6_HUMAN ENST00000269197 RDH8 Q6ZT40_HUMAN ENST00000296564 RELN Q7Z2Q7_HUMAN ENST00000334994 RENBP Q7Z7L8_HUMAN ENST00000339446 REPIN 1 Q8N2V9_HUMAN ENST00000324414 RFX1 Q8N5S4_HUMAN ENST00000326474 RFX3 Q8N6V7_HUMAN ENST00000324928 RFXDC1 Q8N800_HUMAN ENST00000322516 RGS11 Q8N9F6_HUMAN ENST00000317122 RGS17 Q8N9G5_HUMAN ENST00000313957 RHBDF1 Q8N9S5HUMAN ENST00000329388 RHOT2 Q8N9V7_HUMAN ENST00000309765 RIC3 Q8N9Z1_HUMAN ENST00000326413 RIMBP2 Q8NCK2_HUMAN ENST00000325720 RIMS1 Q8NGP7_HUMAN ENST00000341231 RIMS2 Q8NH06HUMAN ENST00000324144 REF Q8NH08HUMAN ENST00000327198 RNF175 Q96GK3_HUMAN ENST00000315264 RNUT1

Accession ID Gene Symbol Accession ID ENST00000335239 RODH CCDS8925.1 ENST00000327832 RP1 CCDS6160.1 ENST00000301647 RPGRIP1 NM 020366 ENST00000301719 RREB1 NM 001003699 ENST00000301682 RIEl ENST00000331067 ENS T00000237253 RTTN NM 173630 ENST00000360484 RUNX1T1 CCDS6256.1 ENS T00000053084 RYR1 NM_000540 ENST00000329980 RYR2 NM_001035 ENST00000242365 SACS CCDS9300.1 ENST00000328881 SARS2 NM_017827 ENS T00000314272 SART3 CCDS9117.1 ENST00000342338 SBLF CCDS 1840.1 ENST00000359406 SCAP2 CCDS5400.1 ENST00000303007 SCFD2 NM_152540 ENST00000333891 SCGN CCDS4561.1 NM_032134 SCN11A NM_014139 CCDS3 082.1 SCN2A2 NM_021007 CCDS9148.1 SCN4A NM_000334 CCDS7902.1 SCN5A NM_000335 CCDS7903.1 SCN5A NM_198056 CCDS10130.1 SCN7A NM_002976 CCDS2079.1 SCNM1 CCDS987.1 CCDS2642.1 SCNN1B CCDS 10609.1 CCDS5902.1 SCNN1G CCDS10608.1 ENST00000330861 SCRIB CCDS6411.1 NM 170672 SDPR CCDS2313.1 NM 170603 SDS CCDS9169.1 CCDS12731.1 SEC14L3 CCDS13877.1 CCDS3558.1 SEMA4D CCDS6685.1 CCDS189.1 SEMA5B CCDS3019.1 CCDS10621.1 SENP1 NM 014554 ENST00000265271 SESN2 CCDS321.1 NM 018250 SEZ6L CCDS13833.1 CCDS3567.1 SF3A1 CCDS13875.1 CCDS12223.1 SF3B1 NM 012433 NM 005045 SFRS12 CCDS3991.1 CCDS 14738.1 SFRS16 CCDS12652.1 NM 013400 SGEF NM 015595 CCDS12301.1 SH2D1B NM 053282 CCDS6449.1 SH3GL3 CCDS10325.1 CCDS5113.1 SH3TC1 CCDS3399.1 CCDS10403.1 SHANK2 CCDS8198.1 CCDS5244.1 SHKBP1 CCDS12560.1 NM 022450 SI CCDS3196.1 CCDS10417.1 SIDT1 CCDS2974.1 CCDS7788.1 SIGLEC11 CCDS12790.1 NM 015347 SIPA1L2 NM 020808 NM 014989 SIX2 CCDS1822.1 NM_014677 SKD3 CCDS8215.1 CCDS448.1 SLC14A1 CCDS11925.1 NM 173662 SLC17A1 CCDS4565.1 CCDS10281.1 SLC17A7 CCDS12764.1 127 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol 3LC1A6 CCDS12321.1 STAC 3LC22A15 NM 018420 STAC2 3LC22A7 CCDS4893.1 STAMBP 3LC25A26 CCDS2905.1 STARD13 3LC28A3 CCDS6670.1 STARD8 3LC2A1 CCDS477.1 STAT4 3LC2A3 CCDS8586.1 STIM1 3LC2A5 CCDS99.1 STK10 3LC33A1 CCDS3173.1 STK23 3LC39A10 NM 020342 STK33 3LC39A6 NM_012319 STMN4 3LC45A1 ENST00000289877 STN2 SLC4A10 NM 022058 SULF1 5LC4A8 CCDS8814.1 SULF2 3LC4A9 NM 031467 SV2A 3LC6A15 CCDS9026.1 SYNE1 3LC6A17 NM_001010898 SYNE1 3LC6A2 CCDS10754.1 SYNE2 3LC6A3 CCDS3863.1 SYP SLC9A5 NM_004594 SYT1 3LC01A2 CCDS8686.1 SYT6 SLCOIBI CCDS8685.1 SYT7 3LC01C1 CCDS8683.1 T 3LC04C1 NM.180991 TAF1B 31JTRK2 CCDS14680.1 TAF1L SLriRK3 CCDS3197.1 TAF4 3LETRK5 CCDS9465.1 TAS2R41 3MAD3 CCDS10222.1 TATDN2 SMAD4 CCDS11950.1 TBC1D14 3MARCA4 CCDS12253.1 TBX15 3MOC1 CCDS9798.1 TBX18 SMTN CCDS13886.1 TBX5 3N CCDS13060.1 TBX6 3NCAIP CCDS4131.1 TCEB3B SNRPC NM.003093 TCFL1 SNX16 CCDS6234.1 TDRD7 SNX26 CCDS12477.1 TENC1 SORL1 CCDS8436.1 TESSP2 SOX3 CCDS14669.1 TEX14 SP8 CCDS5372.1 TFCP2L1 SPAP1 CCDS1168.1 TFF2 SPATA13 ENST00000360220 TFPI2 SPINLW1 CCDS13359.1 TFR2 SPTAN1 CCDS6905.1 TFSM1 .HUMAN SPTBN2 CCDS8150.1 TG SR140_HUMAN ENST00000319822 TGFBR2 SRCRB4D CCDS5585.1 TGIF2 SRRM2 NM 016333 THNSL1 SST CCDS3288.1 THSD7B ST6GAL2 CCDS2073.1 TIMELESS ST6GALNAC5 CCDS673.1 TJP1 ST8SIA5 CCDS11930.1 TLL2 STAB1 NM_015136 TM7SF4

Accession ID Gene Symbol Accession ID CCDS2662.1 TM9SF4 CCDS13196.1 CCDS11335.1 TMCC2 NM 014858 CCDS1929.1 TMEFF2 CCDS2314.1 CCDS9348.1 TMEM132B NM 052907 CCDS14390.1 TMEM16A NM 018043 CCDS2310.1 TMEM16C NM.031418 CCDS7749.1 TMEM16G NM.001001891 NM_005990 TMEM63B NM_018426 NM 014370 TMEM8 CCDS 10407.1 CCDS7789.1 TMEPAI CCDS13462.1 CCDS6055.1 TMPO CCDS9064.1 CCDS9875.1 TMPRSS13 NM.032046 CCDS6204.1 TNF CCDS4702.1 CCDS 13408.1 TNFRSF8 CCDS144.1 CCDS940.1 TNK1 NM.003985 CCDS5236.1 TNNI3 NM 000363 CCDS5 237.1 TNR CCDS1318.1 CCDS9761.1 TOR3A CCDS1329.1 CCDS14321.1 TP53 CCDS11118.1 CCDS9017.1 TP53BP1 CCDS10096.1 CCDS871.1 TPO CCDS1642.1 NM 004200 TREH NM 007180 CCDS5290.1 TRERF1 CCDS4867.1 NM 005680 TRIM37 NM.001005207 NM 153809 TRIM58 CCDS 1636.1 NM.003185 TRPM1 CCDS10024.1 NM_ 176883 TRPM2 CCDS 13710.1 NM.014760 TRPM3 CCDS6634.1 CCDS3394.1 TSC2 CCDS10458.1 NM.152380 TSP-NY CCDS9237.1 ENST00000330469 TSTA3 CCDS6408.1 CCDS9173.1 TTBK2 NM.173500 CCDS 10670.1 TTC12 CCDS8360.1 CCDS 11932.1 TTC21B NM.024753 CCDS989.1 TTC24 ENST00000340086 CCDS6725.1 TTF1 CCDS6948.1 CCDS8842.1 TTK CCDS4993.1 NM.182702 TTN NM.133378 NM 198393 TTN NM.133437 CCDS2134.1 TUBB3 CCDS10988.1 CCDS 13684.1 TXNDC6 CCDS3099.1 CCDS5632.1 UBE1L CCDS2805.1 NM.003227 UBE2M CCDS12987.1 ENST00000314720 UBQLN4 CCDS1127.1 NM_003235 UBR2 CCDS4870.1 CCDS2648.1 UBXD7 ENST00000296328 CCDS13278.1 UCP3 CCDS8229.1 CCDS7147.1 ULBP1 CCDS5 223.1 ENST00000272643 UNC13C ENST00000260323 CCDS8918.1 USP20 NM_001008563 NM.175610 USP31 CCDS10607.1 CCDS7449.1 USP38 CCDS3758.1 CCDS6301.1 USP42 NM.032172 128 WO 2009/100029 PCT/US2009/032881

Gene Symbol Accession ID LTTRN NM 007124 VDAC2 CCDS7348.1 VGCNL1 CCDS9498.1 VIM CCDS7120.1 VIT NM_053276 VLDLR CCDS6446.1 VMD2L1 NM 017682 VPS13A CCDS6655.1 VPS13D NM018156 VPS 16 CCDS13036.1 VPS 3 9 CCDS 10083.1 VSIG1 CCDS14535.1 VWF CCDS8539.1 WASF3 CCDS9318.1 WBSCR14 CCDS5553.1 WBSCR17 CCDS5540.1 WDR1 NM_005112 WDR17 CCDS3825.1 WDR27 NM 182552 WDR42B ENST00000329763 WDR44 CCDS14572.1 WHSC1 CCDS3357.1 WIRE CCDS11364.1 WNT9A NM 003395 WRNIP1 CCDS4475.1 XKR4 NM_052898 XPNPEP1 CCDS7560.1 XP07 NM 015024 XR_017918.1 ENST00000258651 XYLT2 CCDS11563.1 YLPM1 ENST00000238571 TO002_HUMAN ENST00000334389 ZAN NM 173059 ZBTB24 NM 014797 ZBTB33 CCDS14596.1 ZBTB7 CCDS12119.1 ZC3H12B NM 001010888 ZC3HDC7 CCDS10550.1 ZDHHC4 CCDS5352.1 ZFHX1B CCDS2186.1 ZFP36 CCDS12534.1 ZHX3 CCDS13315.1 ZIM3 NM 052882 ZMAT4 NM_024645 ZNF133 CCDS13134.1 ZNF136 NM 003437 ZNF148 CCDS3031.1 ZNF238 CCDS 1623.1 ZNF253 ENST00000327867 ZNF31 NM_145238 ZNF333 CCDS 12316.1 ZNF334 NM 199441 ZNF365 CCDS7264.1

Gene Symbol Accession ID ZNF423 NM 015069 ZNF443 NM_005815 ZNF451 CCDS4960.1 ZNF507 NM014910 ZNF537 CCDS 12421.1 ZNF560 CCDS12214.1 ZNF614 CCDS12847.1 ZNF638 CCDS1917.1 ZNF645 CCDS14205.1 ZNF648 ENST00000339948 ZNF682 NM_033196 ZYG11B NM 024646 2015203111 11 Jun2015

Note: Gene symbols are standard symbols assigned by Entrz Gene (http://www.ncbi.nlm.nih.gov/sites/ent rez?db=gene). Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/sites/ent rez?db=nuccore). Accession IDs “CCDSXXXX” are uniquely assigned to individual genes by National Center for Biotechnology Information (NCBI) (http://www.ncbi.nlm.nih.gov/CCDS/) . Accession IDs “ENSTXXXXXXXXXXX” are uniquely assigned to individual genes by Ensembl (http://www.ensembl.org/index.html). 129 WO 2009/100029 PCT/US2009/032881 ο _ .. .. _ Gene Symbol Accession ID Gene Symbol Accession ID (vq able 14. Genes containing rH omatic mutations in breast AP1M1 NM_032493.2 BLRl NM_001716.2 3 ancer adapted from the AP3B2 NM_004644 BMP1 NM_006129.2 1—5 aDer bv Wood et. al. (Wood APBB1 NM_145689 BOC NM_033254.2 APC2 NM_005883.1 BRCA1 NM_007296.1 1 t al., 2007). APCS NM_001639.2 BRCA2 NM_000059.1 Gene Symbol Accession ID APOC4 NM_001646.1 BSPRY NM_017688 APOL1 NM_145343.1 C10orf30 NM_152751.1 ABCA12 NM_173076 APPL NM_012096.1 C10orf38 NM_001010924 ABCA3 NM_001089.1 APXL NM_001649.2 C10orf39 NM_194303.1 ABCA4 NM_000350.1 AQP8 NM_001169.2 C10orf45 NM_031453.2 ro ABCB10 NM_012089.1 ARC NM_015193 C10orf54 NM_022153 O ABCB6 NM_005689.1 ARFGAP3 NM_014570.3 C10orf56 NM_153367.1 ABCB8 NM_007188.2 ΙΛ1 ARFGEF2 NM_006420.1 C10orf64 NM_173524 ' ABL2 NM_007314 ARFRP1 NM_003224.2 Cllorf37 NM_001007543 ¢-5 ABLIM1 NM_002313.4 ARHGAP11A NM_014783.2 Cllorf9 NM_013279 (N) ABP1 NM_001091 ARHGAP25 NM_001007231 C13orf24 NM_006346 ACADM NM_000016.2 ARHGEF4 NM_015320.2 C14orfl00 NM_016475 AC02 NM_001098.2 ARID IB NM_017519.1 C14orfl01 NM_017799.2 ACY1 NM_000666.1 ARRB1 NM_020251 C14orfl21 NM_138360 ADAM 12 NM_003474.2 ARRDC3 NM_020801 C14orfl55 NM_032135.2 AD AMTS 16 NM_139056 ARV1 NM_022786.1 C14orfl61 NM_024764 AD AMTS 19 NM_133638.1 ASB11 NM_080873.1 C14orf21 NM_174913.1 ADAR NM_001111.2 ASGR1 NM_001671.2 C14orf29 NM_181814.1 ADH1B NM_000668 ASL NM_000048.2 C14orf46 NM_001024674 ADHFE1 NM_144650.1 ASTN2 NM_014010.3 C17orf47 NM_001038704 ADRA1A NM_033302.1 ATCAY NM_033064 C17orf64 NM_181707 AEGP NM_206920.1 ATF2 NM_001880.2 C18orfl9 NM_152352.1 AGBL4 NM_032785 ATN1 NM_001940 C19orf28 NM_174983 AGC1 NM_001135 ATP10A NM_024490 C19orf6 NM_033420.2 AGRN NM_198576 ATP12A NM_001676 Clorfl90 NM_001013615 AHRR NM_020731 ATP2A3 NM_174955.1 Clorf2 NM_006589.2 AHSA2 NM_152392.1 ATP6AP1 NM_001183 C1QB NM_000491.2 AIM1 NM_001624 ATP6V0B NM_004047.2 C20orfl03 NM_012261.2 AKAP6 NM_004274.3 ATP8B1 NM_005603.1 C20orfl21 NM_024331.2 AKAP8 NM_005858.2 ATP8B4 NM_024837 C20orfl61 NM_033421.2 AKAP9 NM_005751.3 ATRN NM_139321.1 C20orfl77 NM_022106.1 ALCAM NM_001627 ATXN2 NM_002973 C20orf23 NM_024704.3 ALMS1 NM_015120 AVPI1 NM_021732.1 C20orf44 NM_018244.3 ALS2 NM_020919 AVPR2 NM_000054.2 C22orfl9 NM_003678.3 ALS2CL NM_147129.2 B3GALNT2 NM_152490.1 C4orfl4 NM_032313.2 ALS2CR12 NM_139163.1 B3GALT4 NM_003782 C5orfl4 NM_024715.2 ALS2CR19 NM_152526 BAI1 NM_001702 C6orfl02 NM_145027.3 AMFR NM_001144.3 BAP1 NM_004656.2 C6orfl45 NM_183373.2 AMIGO 1 NM_020703 BAT2 NM_080686.1 C6orfl74 NM_001012279 AMOTL1 NM_130847 BAT3 NM_080703.1 C6orf204 NM_206921.1 AMPD2 NM_139156.1 BAZ1A NM_013448.2 C6orf21 NM_001003693 AMPD2 NM_004037.5 BAZ1B NM_032408.1 C6orf213 NM_001010852 ANAPC5 NM_016237.3 BC002942 NM_033200.1 C6orf31 NM_030651.2 ANK1 NM_020476.1 BCAR1 NM_014567.2 C7orfl 1 NM_138701.1 ANK2 NM_001148.2 BCCIP NM_016567.2 C9orfl26 NM_173690 ANKRD28 NM_015199 BCL11A NM_018014.2 C9orf37 NM_032937 ANKRD29 NM_173505.1 BCORL1 NM_021946.2 C9orf67 NM_032728.2 ANKRD30A NM_052997.1 BGN NM_001711.3 CACNA1B NM_000718 ANKRD5 NM_198798.1 130 WO 2009/100029 PCT/US2009/032881 ΙΟ O Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID CACNA1F NM_005183 COL11A1 NM_001854.2 DIP2B NM_173602 £ CACNA1G NM_198385 COL12A1 NM_004370 DKFZP564B1023 NM_031306.1 H-5 CACNA1H NM_021098 COL19A1 NM_001858.3 DKFZP564J102 NM_001006655 CACNA1I NM_001003406 COL4A4 NM_000092 DKFZp761I2123 NMJM449 H CACNA2D3 NM_018398 COL7A1 NM_000094.2 DKFZp779B1540 NM_001010903 CAMTA1 NM_015215 COMMD7 NM_053041 DKK3 NM_015881.4 CAPN11 NM_007058 COPG NM_016128 DLEC1 NM_007335.1 i—H CBFB NM_001755.2 COQ9 NM_020312 DMD NM_004006.1 CCDC16 NM_052857 CP A3 NM_001870.1 DNAH17 NM_003727 1 CCDC18 NM_206886 CPAMD8 NM_015692 DNAH5 NM_001369.1 m o CCDC66 NM_001012506 CPEB1 NM_030594 DNAH9 NM_001372.2 (N CD2 NM_001767.2 CPS1 NM_001875.2 DNAJA3 NM_005147.3 tn CD74 NM_001025159 CPSF3 NM_016207.2 DNAJA5 NM_194283.1 i CD97 NM_001784 CROCC NM_014675 DNAJC10 NM_018981 o CDC27 NM_001256.2 CRR9 NM_030782.2 DNAJC13 NM_015268 <N CDH10 NM_006727.2 CRSP2 NM_004229.2 DNASE1L3 NM_004944.1 CDH20 NM_031891.2 CRTC1 NM_025021 DNM2 NM_004945 CDH8 NM_001796.2 CRX NM_000554.2 DNM3 NM_015569 CDKL2 NM_003948.2 CRYAA NM_000394.2 DOCK1 NM_001380 CDON NM_016952.2 CSEN NM_013434.3 DPAGT1 NM_001382.2 CDS1 NM_001263.2 CSMD1 NM_033225 DPAGT1 NM_203316.1 CENPE NM_001813 CSMD3 NM_198123.1 DPP10 NM_020868 CENTB1 NM_014716.2 CSNK1D NM_001893.3 DPP6 NM_130797 CENTD3 NM_022481.4 CSPP1 NM_024790 DPYD NM_000110 CENTG1 NM_014770.2 CST4 NM_001899.2 DRIM NM_014503.1 CEP290 NM_025114 CTF8 NM_001039690 DSCR6 NM_018962.1 CFHL5 NM_030787.1 CTNNA1 NM_001903 DSG2 NM_001943 Z¥L2 NM_138638.1 CTNNA2 NM_004389 DTNA NM_032978.4 2GI-14 NM_015944.2 CTNND1 NM_001331 DTX3L NM_138287.2 3GI-37 NM_016101.2 CUBN NM_001081.2 DUOX1 NM_017434 3HD1 NM_001270 CUTC NM_015960.1 DVL3 NM_004423.3 2HD5 NM_015557.1 CUTL1 NM_001913.2 DYSF NM_003494.2 3HD7 NM_017780 CUTL2 NM_015267 ECT2 NM_018098.4 3HD8 NM_020920 CYP1A1 NM_000499.2 EDEM1 NM_014674 CHD9 NM_025134 CYP1A2 NM_000761 EDNRA NM_001957.1 CHRND NM_000751.1 CYP26A1 NM_000783.2 EEF1G NM_001404 CIC NM_015125.2 CYP2D6 NM_000106 EGFL6 NM_015507.2 CLCA2 NM_006536.3 CYP4A22 NM_001010969 EHBP1 NM_015252.2 CLCN1 NM_000083.1 DACH1 NM_080759 EHMT1 NM_024757.3 CLCN3 NM_001829 DAZAP1 NM_018959.2 EIF4A2 NM_001967.2 CLEC6A NM_001007033 DBN1 NM_004395.2 EIF4B NM_001417 CLSPN NM_022111.2 DC2 NM_021227.2 EIF5 NM_183004.3 CLUAP1 NM_015041 DDO NM_003649.2 ELA1 NM_001971.3 CMYA1 NM_194293.2 DDX10 NM_004398.2 ELAVL3 NM_001420 CMYA4 NM_173167.1 DDX18 NM_006773.3 ENPEP NM_001977.2 CNGA2 NM_005140.1 DDX3X NM_024005.1 EOMES NM_005442.2 CNGB1 NM_001297 DEFB128 NM_001037732 EP400 NM_015409 CNNM4 NM_020184.2 DENND2A NM_015689 EPC2 NM_015630 CNTN3 NM_020872 DGKB NM_004080 ERCC3 NM_000122.1 CNTN5 NM_014361 DGKE NM_003647.1 ERCC6 NM_000124.1 CNTN6 NM_014461.2 DGKG NM_001346.1 EREG NM_001432.1 COG3 NM_031431.2 DHX32 NM_018180.2 ETV5 NM_004454 COH1 NM_017890.3 DIP NM_015124 EVI2A NM_001003927 131 PCT/US2009/032881 lΓ) O Gene Symbol <N EVI5 Accession ID Gene Symbol Accession ID Gene Symbol Accession ID NM_005665 FLJ34521 NM_001039787 GOLGA7 NM_016099 S EXOC2 NM_018303 FLJ36180 NM_178556.3 GOLGB1 NM_004487.1 EXOC5 NM_006544 FLJ36748 NM_152406 GOLPH4 NM_014498.2 _, EXOSC3 NM_016042 FLJ40342 NM_152347.3 GORASP2 NM_015530 FAAH NM_001441.1 FLJ40869 NM_182625.2 GP5 NM_004488.1 FABP4 NM_001442.1 FLJ41821 NM_001001697 GPC1 NM_002081.1 FAM44A NM_148894.1 FLJ45455 NM_207386 GPC2 NM_152742.1 1 FAM47B NM_152631.1 FLJ46321 NM_001001670 GPHB5 NM_145171 1 FAM80B NM_020734 FLJ46354 NM_198547.1 GPNMB NM_002510.1 1 FANCA NM_000135 FLJ46481 NM_207405.1 GPR115 NM_153838.1 CO W FANCM NM_020937 FU90579 NM_173591.1 GPR45 NM_007227.3 FARP1 NM_005766.1 FLNA NM_001456 GPR7 NM_005285.1 l/~) FBXO40 NM_016298 FLNB NM_001457.1 GPR81 NM_032554.2 1 FBX08 NM_012180.1 FLNC NM_001458 GRIK2 NM_021956.2 ® FBXW11 CN NM_012300 FMNL3 NM_175736 GRIK3 NM_000831.2 M FCHOl NM_015122 FMOD NM_002023 GRIN2C NM_000835 FCMD NM_006731.1 FN1 NM_002026.2 GRIN2D NM_000836.1 FCRH3 NM_052939.2 FNDC3B NM_022763.2 GRIP API NM_207672 FEM1C NM_020177.2 FOLR2 NM_000803.2 GRM6 NM_000843.2 FER1L3 NM_133337 FOXP2 NM_014491.1 GSDML NM_018530.1 FGD3 NM_033086 FOXP4 NM_138457.1 GSN NM_000177.3 FGD6 NM_018351 FREM1 NM_144966 GTF2A1 NM_015859.2 FGFR2 NM_022970.1 FRMPD1 NM_014907.1 GTF3C1 NM_001520 FHOD1 NM_013241.1 FUCA1 NM_000147.2 GUCY2F NM_001522.1 FHOD3 NM_025135 FUS NM_004960.1 HADHB NM_000183.1 FLG2 NM_001014342 FXR1 NM_005087.1 HCN3 NM_020897.1 FU10241 NM_018035 G3BP2 NM_203505.1 HDAC4 NM_006037.2 FU 10292 NM_018048.2 G6PC NM_000151.1 HDAC7A NM_015401.1 FU10324 NM_018059 GA17 NM_006360.2 HDLBP NM_203346.1 FU 10458 NM_018096.2 GAB1 NM_002039.2 HEBP1 NM_015987 FU 10726 NM_018195.2 GABRA4 NM_000809.2 HEL308 NM_133636.1 FLJ10874 NM_018252.1 GABRP NM_014211.1 HIST1H4L NM_003546.2 FLJ13089 NM_024953.2 GALK2 NM_001001556 HIST2H2AB NM_175065.2 FLJ13231 NM_023073 GALNT17 NM_001034845 HK3 NM_002115.1 FLJ13479 NM_024706.3 GALNT5 NM_014568.1 HLCS NM_000411.4 FLJ13868 NM_022744.1 GALNTL2 NM_054110 HM13 NM_030789.2 FLJ14503 NM_152780.2 GARNL1 NM_194301 HMG2L1 NM_001003681 FLJ14624 NM_032813.1 GDF6 NM_001001557 HOMER2 NM_199331 FLJ16331 NM_001004326 GGA1 NM_013365.2 HOOK1 NM_015888.3 FLJ20152 NM_019000 GGA3 NM_014001.2 HOOK2 NM_013312 FLJ20184 NM_017700.1 GIMAP1 NM_130759.2 HOOK3 NM_032410.2 FLJ20422 NM_017814.1 GIMAP8 NM_175571 HOXA3 NM_153631.1 FLJ20584 NM_017891.2 GIOT-1 NM_153257 HOXA4 NM_002141.2 FLJ20604 NM_017897.1 GIPC3 NM_133261 HS3ST4 NM_006040 FLJ21839 NM_021831.3 GJA8 NM_005267 HSD11B1 NM_181755.1 FLJ21945 NM_025203.1 GJB1 NM_000166.2 HSD17B8 NM_014234.3 FLJ23584 NM_024588 GKN1 NM_019617.2 HSHIN1 NM_199324.1 FLJ25955 NM_178821.1 GLG1 NM_012201 HSPA14 NM_016299.1 FLJ31413 NM_152557.3 GLI1 NM_005269.1 HSPA1B NM_005346 FLJ32115 NM_152321.1 GLT25D2 NM_015101.1 HSPC049 NM_014149 FLJ32363 NM_198566.1 GMCL1L NM_022471.2 HTF9C NM_182984.2 FLJ32440 NM_173685.1 GNB1L NM_053004.1 HUMCYT2A NM_015848.1 FLJ32830 NM_152781.1 GNPAT NM_014236.1 HUWE1 NM_031407 WO 2009/100029 132 PCT/US2009/032881 O Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID [CAM5 NM_003259.2 KIAA1324 NM_020775.2 LOC652968 NM_001037666 a [FNA2 NM_000605.2 KIAA1377 NM_020802 LOC88523 NM_033111 [FNB1 NM_002176.1 KIAA1414 NM_019024 LOC90529 NM_178122.2 [KBKAP NM_003640.2 KIAA1632 NM_020964.1 LOC91461 NM_138370 [KB KB NM_001556.1 KIAA1797 NM_017794 LOXL2 NM_002318 IL1RAPL2 NMJ117416.1 KIAA1826 NMJ132424 LPO NM_006151 IL7R NM_002185.2 KIAA1914 NM_001001936 LRBA NM_006726.1 i—H [NA NM_032727.2 KIAA1946 NM_177454 LRRC16 NM_017640 [NHBE NM_031479.3 KIBRA NM_015238.1 LRRC4 NM_022143.3 m o [PLA2(GAMMA) NM_015723 KIF14 NM_014875 LRRC43 NM_152759 [P07 NM_006391 KIR2DS4 NM_012314.2 LRRC7 NM_020794.1 (N [QSEC2 NM_015075 KLHL10 NM_152467 LRRFIP1 NM_004735.1 [RF8 NM_002163.1 KLHL15 NM_030624 LUZP5 NM_017760 1—1 [RS4 NM_003604.1 KLK15 NM_017509.2 LYST NM_000081 o [RTA2 NM_031281.1 KPNA5 NM_002269.2 LYST NM_001005736 CN [TGA9 NM_002207.1 KRTAP10-8 NM_198695.1 LZTS2 NM_032429.1 [TGAE NM_002208 KRTAP20-1 NM_181615.1 MACF1 NM_012090.3 [TGAL NM_002209 KTN1 NM_182926.1 MAGEA1 NM_004988.3 [TGB2 NM_000211.1 LAMA1 NM_005559 MAGEA4 NM_002362.3 [TPR1 NM_002222 LAMA2 NM_000426.2 MAGEB10 NM_182506 [TR NM_180989.3 LAMA4 NM_002290 MAGEC2 NM_016249.2 IARID1B NM_006618 LAMB4 NM_007356 MAGED2 NM_201222.1 IMJD1A NM_018433.3 LAP IB NM_015602.2 MAGEE 1 NM_020932.1 IMJD1C NM_004241 LDHB NM_002300.3 MAGI1 NM_173515.1 rup NM_021991.1 LEPREL1 NM_018192.2 MANEA NM_024641.2 KCNA5 NM_002234.2 LGALS2 NM_006498.1 MAOA NM_000240.2 KCNC2 NM_139136.2 LHCGR NM_000233.1 ΜΑΡΙΑ NM_002373 KCNJ1 NM_000220.2 LIP 8 NM_053051.1 MAP3K6 NM_004672.3 KCNJ15 NM_170737.1 LIPE NM_005357.2 MAPK13 NM_002754.3 KCNQ3 NM_004519 LLGL1 NM_004140 MAPKBP1 NM_014994 KEAP1 NM_203500.1 LM06 NM_006150.3 MASP1 NM_001879 ECIAA0100 NM_014680 LOCI 12703 NM_138411 MAZ NM_002383 KIAA0143 NM_015137 LOCI 13179 NM_138422.1 MCAM NM_006500 KIAA0256 NM_014701 LOCI 13828 NM_138435.1 MCART1 NM_033412.1 KIAA0284 NM_015005 LOCI 23876 NM_001010845 MCF2L2 NM_015078.2 KIAA0367 NM_015225 LOCI 26248 NM_173479.2 MCOLN1 NM_020533.1 KIAA0427 NM_014772.1 LOC200420 NM_145300 MDC1 NM_014641 KIAA0467 NM_015284 LOC220929 NM_182755.1 MED12 NM_005120 KIAA0513 NM_014732 LOC253012 NM_198151.1 MEF2C NM_002397 KIAA0528 NM_014802 LOC255374 NM_203397 MFAP5 NM_003480.2 KIAA0664 NM_015229 LOC283849 NM_178516.2 MGC11332 NM_032718.2 KIAA0672 NM_014859 LOC339123 NM_001005920 MGC17299 NM_144626.1 KIAA0676 NM_015043.3 LOC339745 NM_001001664 MGC21688 NM_144635.3 KIAA0703 NM_014861 LOC340156 NM_001012418 MGC24047 NM_178840.2 KIAA0774 NM_001033602 LOC374955 NM_198546.1 MGC27019 NM_144705.2 KIAA0789 NM_014653 LOC388595 NM_001013641 MGC33212 NM_152773 KIAA0863 NM_014913 LOC388915 NM_001010902 MGC33370 NM_173807.2 KIAA0913 NM_015037 LOC389151 NMJXJ1013650 MGC33657 NM_001029996 KIAA0934 NM_014974.1 LOC389549 NM_001024613 MGC34837 NM_152377.1 KIAA0999 NM_025164.3 LOC440925 NM_001013712 MGC42174 NM_152383 KIAA1012 NM_014939.2 LOC440944 NM_001013713 MGC5297 NM_024091.2 KIAA1117 NM_015018.2 LOC441070 NM_001013715 MIA2 NM_054024.3 KIAA1161 NM_020702 LOC646870 NM_001039790 MICAL1 NM_022765.2 WO 2009/100029 133 WO 2009/100029 PCT/US2009/032881 in O Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID CN MICAL-Ll NM_033386.1 NFl NM_000267.1 OSBP2 NMJB0758 a MKLN1 NM_013255 NF2 NM_000268.2 OSBPL11 NM_022776.3 ) MLL4 NM_014727 NFASC NM_015090 OTC NM_000531.3 Ύ—H MLLT2 NM_005935.1 NFIX NM_002501 OTOF NM_194323.1 ί—H MMP10 NM_002425.1 NFKB1 NM_003998.2 P15RS NM_018170.2 MMP15 NM_002428.2 NFKBIA NM 020529.1 PADI3 NM_016233.1 MOGAT1 NM_058165 NFKBIE NM_004556 PADI6 NM_207421 Ύ—H MOSPD1 NM_019556.1 NFYC NM_014223.2 PANX2 NM_052839.2 r-H MPFL NM_001025190 NGLY1 NM_018297 PAPPA2 NM_020318 ’“H MRE11A NM_005590.2 NHS NM_198270.2 PARP1 NM_001618.2 m o MSI1 NM_002442.2 NID2 NM_007361.2 PCDH19 NM_020766 (N MTA1 NM_004689 NIPBL NM_133433.2 PCDH20 NM_022843.2 in MTAC2D1 NM_152332.2 NOD27 NM_032206.2 PCDH8 NM_002590.2 i—1 MTL5 NM_004923.2 NOS2A NM_000625.3 PCDHA10 NM_031859 o <N MTMR3 NM_021090.2 NOTCH 1 NM_017617 PCDHA11 NM_031861 MTMR8 NM_017677.2 NOTCH4 NM_004557 PCDHA5 NM_031501 MUC16 NM_024690 NOX5 NM_024505 PCDHB15 NM_018935.2 MUC2 NM_002457 NRCAM NM_005010.2 PCDHGA1 NM_031993 MUF1 NM_006369.3 NRK NM_198465 PCDHGA3 NM_032011 MULK NM_018238.2 NRXN3 NM_004796.3 PCDHGA6 NM_032086 MYBPC2 NM_004533 NUFIP2 NM_020772 PCDHGB1 NM_032095 MYCBP2 NM_015057 NUP133 NM_018230.2 PCDHGB5 NM_032099 MYH1 NM_005963.2 NUP188 NM_015354 PCM1 NM_006197 MYH7B NM_020884 NUP205 NM_015135 PCNT NM_006031 MYH9 NM_002473.2 NUP214 NM_005085.2 PDCD11 NM_014976 MYLC2PL NM_138403 NUP98 NM_016320.2 PDCD4 NM_014456.3 MY015A NM_016239 NXN NM_022463.3 PDCD6 NM_013232.2 MY018B NM_032608 NYD-SP21 NM_032597 PDE2A NM_002599.1 MYOIG NM_033054 OATL1 NM_002536 PDLIM7 NM_005451.3 MY07A NM_000260 OBSCN NM_052843.1 PDPR NM_017990 MY09B NM_004145 OCA2 NM_000275.1 PDZD7 NM_024895 MYOD1 NM_002478.3 ODZ1 NM_014253.1 PDZK2 NM_024791.2 V1YR8 NM_015011 OR10A2 NM_001004460 PDZK4 NM_032512.2 VIYST4 NM_012330.1 OR10H4 NM_001004465 PEBP4 NM_144962 N4BP2 NM_018177.2 OR12D3 NM_030959.2 PERI NM_002616.1 NAG6 NM_022742 OR1J2 NM_054107 PER2 NM_022817.1 NALP1 NM_014922 OR1N1 NM_012363.1 PEX14 NM_004565 NALP14 NM_176822.2 OR1S1 NM_001004458 PFC NM_002621.1 NALP8 NM_176811.2 OR2AK2 NM_001004491 PFKFB4 NM_004567.2 NALP9 NM_176820.2 OR2M4 NM_017504 PGBD3 NM_170753.1 NAV3 NM_014903 OR2W3 NM_001001957 PHACS NM_032592.1 NCAM1 NM_000615 OR2W5 NM_001004698 PHC1 NM_004426.1 NCB50R NM_016230.2 OR4D2 NM_001004707 PHF19 NM_015651 NCOA6 NM_014071.2 OR52A1 NM_012375 PHF7 NM_016483.4 NDRG2 NM_201541.1 OR52H1 NM_001005289 PHKB NM_000293.1 NDST1 NM_001543 OR56A1 NM_001001917 PIGN NM_176787 NDUFA2 NM_002488.2 OR5H1 NM_001005338 PIGS NM_033198.2 NDUFA3 NM_004542.1 OR5J2 NM_001005492 PIK3C2G NM_004570 NDUFA8 NM_014222.2 OR5M11 NM_001005245 PIK3CA NM_006218 NEB NM_004543 OR8B12 NM_001005195 PIK3R1 NM_181523.1 NEDD4 NM_198400.1 OR8D2 NM_001002918 PIK3R4 NM_014602.1 NEF3 NM_005382.1 OR8I2 NM_001003750 PKD1L1 NM_138295 NET1 NM_005863.2 OR9Q2 NM_001005283 PKD1L2 NM_052892 134 PCT/U S2009/032881 lΓ) O Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID IN PKDREJ NM_006071.1 PTRF NM_012232.2 SAPSl NM_014931 a 2 PKHD1L1 NM_177531 PURG NM_013357.2 SATL1 NM_001012980 H-5 PKN1 NM_213560 PUS1 NM_025215.3 SBNOl NM_018183.2 PLA2G4A NM_024420.1 PUS7 NM_019042 SCARF2 NM_153334.3 H PLB1 NM_153021 RAB41 NM_001032726 SCGB3A2 NM_054023.2 PLCB1 NM_015192.2 RABEP2 NM_024816 SCML1 NM_006746.2 PLCB2 NM_004573 RAC2 NM_002872.3 SCN2A2 NM_021007 1 PLCD3 NM_133373 RAI17 NM_020338.1 SCN3A NM_006922 v—1 PLCG1 NM_002660.2 RANBP1 NM_002882.2 SCNN1B NM_000336.1 I PLD2 NM_002663.2 RANBP3 NM_007321 SCP2 NM_002979.2 m o PLEKHA8 NM_032639.2 RANBP3 NM_007322 SEC31L1 NM_014933.2 <N PLEKHG2 NM_022835 RAP1GA1 NM_002885.1 SEMA3A NM_006080.1 PLOD1 NM_000302.2 RAPH1 NM_213589.1 SEMA4B NM_198925 PLS3 NM_005032.3 RARG NM_000966.3 SEMA4G NM_017893.2 o PLXNB1 NM_002673.3 RASAL2 NM_170692.1 SEMA5B NM_018987.1 <N PNCK NM_198452.1 RASGRF2 NM_006909.1 SEMA6D NM_153616 PNLIPRP1 NM_006229.1 RASL10B NM_033315.2 SEMA7A NM_003612.1 PNPLA1 NM_001039725 RBAF600 NM_020765.1 SEPHS2 NM_012248 PODXL NM_001018111 RBM25 NM_021239 SERPINB1 NM_030666.2 POLH NM_006502.1 RCE1 NM_005133.1 SERPINB11 NM_080475 POLR2F NM_021974.2 RFC4 NM_181573.1 SERPINE2 NM_006216.2 POP1 NM_015029.1 RFX2 NM_000635.2 SF3B1 NM_012433 POU2F1 NM_002697.2 RG9MTD2 NM_152292.2 SF3B2 NM_006842 POU4F2 NM_004575 RGL1 NM_015149.2 SFRS1 NM_006924.3 PP NM_021129.2 RGS22 NM_015668 SFRS16 NM_007056.1 PPAPDC1A NM_001030059 RHAG NM_000324.1 SGKL NM_013257.3 PPFIBP2 NM_003621 RHD NM_016124.2 SH2D3A NM_005490.1 PPHLN1 NM_201439.1 RIF1 NM_018151.1 SH3RF1 NM_020870 PPM IE NM_014906.3 RIMS1 NM_014989 SHCBP1 NM_024745.2 PPM IF NM_014634.2 RIMS2 NM_014677 SIGLEC5 NM_003830 PPP1R12A NM_002480 RLTPR NM_001013838 SIPA1L1 NM_015556.1 PPP1R3A NM_002711.2 RNF123 NM_022064 SIX4 NM_017420.1 PRDM13 NM_021620 RNF127 NM_024778.3 SKIP NM_016532.2 PRDM4 NM_012406.3 RNF149 NM_173647.2 SKIV2L NM_006929.3 PRDX5 NM_012094.3 RNU3IP2 NM_004704.2 SLAMF1 NM_003037.1 PRKAA1 NM_006251.4 ROB03 NM_022370 SLC12A3 NM_000339.1 PRKAA2 NM_006252.2 ROR1 NM_005012.1 SLC16A2 NM_006517.1 PRODH NM_016335.2 RP1L1 NM_178857 SLC17A6 NM_020346.1 PRPF39 NM_017922.2 RPGRIP1 NM_020366 SLC22A2 NM_003058.2 PRPF4B NM_176800.1 RPL3 NM_000967.2 SLC22A9 NM_080866.2 PRPS1 NM_002764.2 RPRC1 NM_018067 SLC25A30 NM_001010875 PRPS1L1 NM_175886 RPS26 NM_001029 SLC35A2 NM_005660.1 PRRG1 NM_000950.1 RPS6KA3 NM_004586.1 SLC35F1 NM_001029858 PRSS7 NM_002772.1 RPS9 NM_001013.2 SLC38A3 NM_006841 PSD NM_002779 RPUSD4 NM_032795.1 SLC39A12 NM_152725.1 PSME4 NM_014614 RREB1 NM_001003699 SLC4A3 NM_005070.1 PSPC1 NM_018282 RSN NM_002956.2 SLC6A3 NM_001044.2 PSRC2 NM_144982 RTP1 NM_153708.1 SLC6A5 NM_004211.1 PTD004 NM_013341.2 RTTN NM_173630 SLC7A7 NM_003982.2 PTHLH NM_198964.1 RUFY1 NM_025158.2 SLC8A3 NM_033262.3 PTPN14 NM_005401.3 RYR1 NM_000540 SLC8A3 NM_182932.1 PTPN6 NM_080548 RYR2 NM_001035 SLC9A10 NM_183061 PTPRC NM_002838.2 SAMD9 NM_017654 SLC9A2 NM_003048.3 WO 2009/100029 135 WO 2009/100029 PCT/US2009/032881 in O Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID I N SLC02B1 NM_007256.2 TACC2 NM_206862.1 TREMLl NM_178174.2 G SLFN13 NM_144682 TAF1 NM_004606.2 TREML4 NM_198153 i SLICK NM_198503.2 TAF1B NM_005680 TRIAD3 NM_207116 SMARCAL1 NM_014140.2 TA KRP NM_032505.1 TRIF NM_182919.1 T—H 1—H SMC4L1 NM_005496.2 TAS2R13 NM_023920.1 TRIM25 NM_005082.3 SMC6L1 NM 024624.2 TAX1BP1 NM_006024.4 TRIM29 NM_012101.2 SMOX NM_175839.1 TBC1D19 NM_018317.1 TRIM36 NM_018700.2 1—H SN NM_023068.2 TBC1D2B NM_015079 TRIOBP NM_001039141 1—H SNTG2 NM_018968 TBX1 NM_005992.1 TRIP12 NM_004238 1—H SNX25 NM_031953 TBXAS1 NM_001061.2 TRPC4 NM_016179.1 m o SOHLH1 NM_001012415 TCEAL5 NM_001012979 TRPM5 NM_014555 (N SORBS 1 NM_015385.1 TCF1 NM_000545.3 TSN NM_004622 in SORCS1 NM_052918.2 TCF7L1 NM_031283.1 TTC15 NM_016030.5 f—H SORL1 NM_003105.3 TCFL1 NM_005997.1 TTC21B NM_024753 o SOX13 NM_005686 TCP1 NMJB0752.1 TTC3 NM_003316.2 CN SOX15 NM_006942 TCP10 NM_004610 TTC7A NM_020458 SP110 NM_004509.2 TDRD6 NM_001010870 TTN NM_133378 SPAG6 NM_012443.2 TECTA NM_005422.1 TXNDC3 NM_016616.2 SPATS2 NM_023071 TEK NM_000459.1 UBE2I NM_194261.1 SPCS2 NM_014752 TESK1 NM_006285.1 UBE20 NM_022066 SPEN NM_015001.2 TESK2 NM_007170 UGT1A9 NM_021027.2 SPG4 NM_014946.3 TEX11 NM_031276 UNQ9356 NM_207410.1 SPINK5 NM_006846 TFAP2D NM_172238.1 UQCR NM_006830.2 SPOll NM_012444.2 TG NM_003235 USP29 NM_020903 SPOCD1 NM_144569.3 TGM3 NM_003245 USP34 NM_014709 SPTA1 NM_003126 THBS3 NM_007112.3 USP54 NM_152586.2 SPTAN1 NM_003127.1 THG-1 NM_030935.3 UTP14C NM_021645 SPTBN1 NM_178313 TIAM2 NM_001010927 UTS2R NM_018949.1 SPTLC1 NM_006415.2 TIFA NM_052864 VAV3 NM_006113.3 SPTY2D1 NM_194285 TIMELESS NM_003920.1 VEPH1 NM_024621.1 SREBF2 NM_004599.2 TLL1 NM_012464.3 VGCNL1 NM_052867.1 SRGAP3 NM_014850.1 TLN1 NM_006289 VWF NM_000552.2 3SFA2 NM_006751.3 TLN2 NM_015059 WARS NM_173701.1 SSNA1 NM_003731.1 TM4SF7 NM_003271.3 WBP4 NM_007187.3 ST8SIA3 NM_015879 TMED1 NM_006858.2 WBSCR28 NM_182504 STAB1 NM_015136 TMEM123 NM_052932 WDR48 NM_020839 STARD8 NM_014725.2 TMEM132B NM_052907 WDR53 NM_182627.1 STAT1 NM_007315.2 TMEM28 NM_015686 WDR60 NM_018051 STAT4 NM_003151.2 TMEM37 NM_183240 WDSOF1 NM_015420 STATIP1 NM_018255.1 TMEM39A NM_018266.1 WFDC1 NM_021197.2 STRBP NM_018387.2 TMEM62 NM_024956 WNK1 NM_018979.1 STX12 NM_177424.1 TMEM63A NM_014698 WNT2 NM_003391.1 STX5A NM_003164.2 TMPRSS3 NM_024022.1 XAB2 NM_020196 SULF2 NM_018837.2 TMPRSS6 NM_153609.1 XBP1 NM_005080.2 SULT6B1 NM_001032377 TNFRSF25 NM_003790.2 XDH NM_000379.2 SUPT3H NM_181356 TNS NM_022648.2 XKR7 NM_001011718 SURF1 NM_003172.2 TOPI NM_003286.2 XP05 NM_020750 SUSD3 NM_145006.2 TOP2B NM_001068 XP07 NM_015024 SUV39H2 NM_024670.3 TP53 NM_000546.2 YY2 NM_206923.1 SYNE2 NM_182914.1 TPM4 NM_003290.1 ZBTB3 NM_024784.2 SYT3 NM_032298.1 TPTE NM_199261.1 ZBTB39 NM_014830 SYTL2 NM_032943 TRAD NM_007064.1 ZCCHC14 NM_015144.1 TAC4 NM_170685 TREM1 NM_018643.2 ZCSL3 NM_181706.3 136 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID ZDHHC4 NM_018106.2 ZNF142 NM_005081 ZNF281 NM_012482.3 ZFHX4 NM_024721 ZNF161 NM_007146 ZNF318 NM_014345.1 ZFP64 NM_199427.1 ZNF183 NM_006978.1 ZNF37A NM_001007094 ZFYVE26 NM_015346.2 ZNF22 NM_006963.2 ZNF425 NM_001001661 ZIC3 NM_003413.2 ZNF25 NM_145011.2 ZNF432 NM_014650.2 ZNF10 NM_015394.4 ZNF267 NM_003414 ZNF436 NM_030634.1 ZNF124 NM_003431 ZNF277 NM_021994.1 ZNF529 NM_020951 ZNF532 NM_018181.3 ZNF541 NM_032255.1 ZNF674 NM_001039891 ZNF546 NM_178544.2 ZNF694 NM_001012981 ZNF548 NM_152909 ZNF707 NM_173831 ZNF569 NM_152484.2 ZNF75A NM_153028.1 ZNF644 NM_201269.1 ZNHIT2 NM_014205.2 ZNF646 NM_014699.2 'ote: Gene symbols are standard /mbols assigned by Entrz Gene ittp://www.ncbi.nlm.nih.gov/sites/ent ;z?db=gene). Accession IDs \ M_XXXX” are uniquely assigned ) each gene by National Center for iotechnology Information (NCBI) ittp://www.ncbi. nlm.nih.gov/sites/ent ;z?db=nuccore) 137 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015 ^ "able 15. Genes containing (vq omatic mutations in £ olorectal cancer adapted ^ rom the paper bv Wood et. Gene Symbol Accession ID Gene Symbol Accession ID ANKRD26 NM_014915 C18orf4 NM_032160.1 APBB2 NM_173075 C1QR1 NM_012072.2 1—5 /.(Wood et al. , 2007). APC NM_000038.2 C20orf23 NM_024704.3 v Gene Symbol Accession ID APG5L API5 NM_004849.1 NM_006595 C21orfl8 C21orf29 NM_017438.1 NM_144991.2 ABCA1 NM_005502.2 APIN NM_017855.2 C21orf88 NM_153754 ABCA6 NM_080284.2 APOB NM_000384.1 C2orfl0 NM_194250.1 ^ ABCB1 NM_000927.3 APOB48R NM_182804 C2orfl6 NM_032266 ^ ABCB11 NM_003742 AQR NM_014691 C2orf33 NM_020194.4 CT) ABCB5 O ABCC5 NM_178559.3 ARAF NM_001654 C4BPA NM_000715.2 NM_005688 ARFGEF1 NM_006421.2 C4orfl5 NM_024511 CN ABCD4 NM_005050.1 ARHGEF1 NM_199002.1 C6orfl91 NM_001010876 ^ ABI3BP NM_015429 ARHGEF10 NM_014629 C6orf29 NM_025257.1 ACACA NM_198839.1 ARHGEF9 NM_015185 C8B NM_000066 CNJ ACINI NM_014977.1 ARR3 NM_004312.1 C9orf21 NM_153698 ACSL4 NM_022977.1 ASCC3L1 NM_014014.2 Cab45 NM_016547.1 ACSL5 NM_016234.3 ASE-1 NM_012099.1 CACNA1A NM_000068 AD026 NM_020683.5 AT ADI NM_032810.2 CACNA1B NM_000718 ADAM 19 NM_033274.1 ATP11A NM_032189 CACNA2D3 NM_018398 ADAM29 NM_014269.2 ATP11C NM_173694.2 CACNB1 NM_199247.1 ADAM33 NM_025220.2 ATP12A NM_001676 CACNB2 NM_201596.1 ADAM8 NM_001109 ATP13A1 NM_020410 CAD NM_004341.3 AD AMTS 1 NM_006988 ATP13A5 NM_198505 CAPN10 NM_023086.1 ADAMTS15 NM_139055.1 ATP13A5 NM_198505 CAPN13 NM_144575 ADAMTS18 NM_199355.1 ATP6V1E1 NM_001696.2 CAPN6 NM_014289.2 ADAMTS20 NM_025003 ATP8A2 NM_016529 CARD 12 NM_021209 ADAMTS20 NM_175851 ATP8B4 NM_024837 CBFA2T3 NM_005187.4 ADAMTSL3 NM_207517.1 AVPR1B NM_000707 CCAR1 NM_018237.2 ADARB2 NM_018702.1 AZI1 NM_001009811 CCNB3 NM_033031.1 ADCY8 NM_001115.1 BCAP29 NM_001008405 CD 109 NM_133493.1 ADCY9 NM_001116 BCAS2 NM_005872.1 CD248 NM_020404.2 ADD3 NM_016824.2 BCL11B NM_022898.1 CD99L2 NM_134445.1 ADORA1 NM_000674.1 BCL9 NM_004326 CDC14A NM_003672.2 AFMID NM_001010982 BICD1 NM_001714.1 CDH13 NM_001257 AGTPBP1 NM_015239.1 BMP6 NM_001718.2 CDH18 NM_004934.2 AIM1 NM_001624 BMPR2 NM_001204 CDH23 NM_022124 AKAP12 NM_005100.2 BPIL1 NM_025227.1 CDH6 NM_004932.2 AKAP3 NM_006422.2 BRAF NM_004333.2 CDKL5 NM_003159.1 AKAP6 NM_004274.3 BRF1 NM_001519.2 CDOl NM_001801.1 AKAP9 NM_005751.3 BRUNOL6 NM_052840.2 CDS1 NM_001263.2 ALDH1L1 NM_012190.2 BTBD4 NM_025224.1 CEACAM20 NM_198444 ALG9 NM_024740 BTF3L4 NM_152265 CENPF NM_016343 ALK NM_004304 C10orfl37 NM_015608.2 CENPH NM_022909.3 ALS2CR11 NM_152525.3 C10orf28 NM_014472 CENTB1 NM_014716.2 ALS2CR8 NM_024744 C10orf64 NM_173524 CENTB2 NM_012287 AMACO NM_198496.1 C10orf72 NM_144984.1 CENTD3 NM_022481.4 AMOTL2 NM_016201 C12orfll NM_018164.1 CGI-14 NM_015944.2 AMPD1 NM_000036.1 C13orf7 NM_024546 CHD7 NM_017780 AMPD3 NM_000480.1 C14orfll5 NM_018228.1 CHD8 NM_020920 ANAPC4 NM_013367.2 C15orf2 NM_018958.1 CHL1 NM_006614.2 ANK2 NM_001148.2 C17orf27 NM_020914 CHR415SYT NM_001014372 ANKFN1 NM_153228 C17orf46 NM_152343 CHST8 NM_022467.3 ANKRD11 NM_013275 C17orf49 NM_174893 CINP NM_032630.2 138 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID CIR NM_004882.3 DMD NM_004021.1 FBXL2 NM_012157.2 CLIC2 NM_001289.3 DMD NM_004006.1 FBXO30 NM_032145.3 CLSTN2 NM_022131.1 DMRTA1 NM_022160.1 FBXW7 NM_033632.1 CLSTN3 NM_014718.2 DNAH1 NM_015512 FCN1 NM_002003.2 CMKOR1 NM_020311.1 DNAH11 NM_003777 FCN2 NM_004108.1 CNKSR2 NM_014927.2 DNAH3 NM_017539.1 FERD3L NM_152898.2 CNOT6L NM_144571 DNAH8 NM_001371.1 FGF13 NM_033642.1 CNTN1 NM_001843.2 DNAJC10 NM_018981 FGF14 NM_175929.1 CNTN4 NM_175613.1 DNAJC6 NM_014787 FHOD3 NM_025135 COL12A1 NM_004370 DNALI1 NM_003462.3 FIGN NM_018086.1 COL3A1 NM_000090.2 DNAPTP6 NM_015535 FLJ10241 NM_018035 COL4A6 NM_001847.1 DNASE 1L3 NM_004944.1 FLJ10404 NM_019057 CORO IB NM_020441.1 DPEP1 NM_004413.1 FLJ10490 NM_018111 COR02B NM_006091.1 DPP10 NM_020868 FLJ10521 NM_018125.2 CP AMD 8 NM_015692 DPYSL2 NM_001386.3 FLJ10560 NM_018138.1 CPE NM_001873.1 DSCAML1 NM_020693.2 FLJ10665 NM_018173.1 CPO NM_173077.1 DSTN NM_006870.2 FLJ10996 NM_019044.2 CRB1 NM_201253.1 DTNB NM_183361 FLJ11000 NM_018295.1 CRNKL1 NM_016652 DUSP21 NM_022076.2 FLJ12770 NM_032174.3 CSDA NM_003651.3 DUX4C NM_001023569 FLJ13305 NM_032180 CSE1L NM_001316.2 EDA NM_001399.3 FLJ14803 NM_032842 CSMD1 NM_033225 EDD1 NM_015902 FLJ16171 NM_001004348 CSMD3 NM_198123.1 EFS NM_005864.2 FLJ16542 NM_001004301 CSNK1A1L NM_145203.2 EIF2S2 NM_003908.2 FLJ20294 NM_017749 CTCFL NM_080618.2 EIF4G1 NM_198241.1 FLJ20729 NM_017953.2 CTEN NM_032865.3 EML1 NMJJ04434 FU21019 NM_024927.3 CTNNA1 NM_001903 EML2 NM_012155.1 FU21986 NM_024913 CTNND2 NM_001332.2 EN1 NM_001426.2 FLJ22679 NM_032227.1 CTSH NM_004390.2 ENPP2 NM_006209.2 FLJ25477 NM_199138.1 CUBN NM_001081.2 EPHA3 NM_005233.3 FLJ32252 NM_182510 CUTL1 NM_001913.2 EPHA4 NM_004438.3 FLJ32312 NM_144709.1 CX40.1 NM_153368.1 EPHA7 NM_004440.2 FLJ33534 NM_182586.1 CXorf53 NM_024332 EPHB1 NM_004441 FLJ34633 NM_152365.1 CYP4F8 NM_007253 EPHB6 NM_004445.1 FLJ34922 NM_152270.2 DACT1 NM_016651.4 ERCC6 NM_000124.1 FLJ35834 NM_178827.3 DBC1 NM_014618.1 ESSPL NM_183375 FLJ36119 NM_153254.1 DCC NM_005215.1 ETAA16 NM_019002.2 FLJ38964 NM_173527 DCHS1 NM_003737.1 ETFDH NM_004453.1 FLJ40142 NM_207435.1 DDEFL1 NM_017707.2 EVC2 NM_147127.2 FLJ42418 NM_001001695 DDHD2 NM_015214 EVL NM_016337.1 FLJ43339 NM_207380.1 DDI1 NM_001001711 EYA4 NM_004100.2 FLJ43980 NM_001004299 DDIT3 NM_004083.3 EZH2 NM_004456.3 FLJ44653 NM_001001678 DDN NM_015086 F5 NM_000130.2 FLJ45273 NM_198461.1 DDX53 NM_182699 F8 NM_000132 FLJ46082 NM_207417.1 DEFA4 NM_001925.1 FAM102B NM_001010883 FLJ46154 NM_198462.1 DEFB111 NM_001037497 FAM19A5 NM_015381 FLNC NM_001458 DENND1C NM_024898 FAM26A NM_182494 FMN2 NM_020066 DEPDC2 NM_024870.2 FAM3A NM_021806 FN1 NM_002026.2 DGCR2 NM_005137 FAM40A NM_033088 FNDC1 NM_032532 DHRS2 NM_005794.2 FANCG NM_004629.1 FOLH1 NM_004476.1 DJ167A19.1 NM_018982.3 FAT NM_005245 FRAS1 NM_025074 DKFZp761I2123 NM_031449 FBN1 NM_000138 FRAS1 NM_032863 DLG3 NM_021120.1 FBN2 NM_001999 FRMPD2 NM_152428.2 139 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID FRMPD4 NM_014728 HS3ST4 NM_006040 KRTAP10-8 NM_198695.1 FRY NM_023037 HSPG2 NM_005529 KSR2 NM_173598 FSTL5 NM_020116.2 HTR3C NM_130770.2 LAMA1 NM_005559 FZD4 NM_012193.2 HTR5A NM_024012.1 LAMA4 NM_002290 GAB4 NM_001037814 HUWE1 NM_031407 LAMB3 NM_000228.1 □ABPB2 NM_016654.2 IDH1 NM_005896.2 LAMB4 NM_007356 GABRA6 NM_000811.1 IGFBP3 NM_000598.2 LAMC1 NM_002293.2 GALGT2 NM_153446.1 IGSF22 NM_173588 LAS1L NM_031206.2 GALNS NM_000512.2 IGSF9 NM_020789.2 LCN10 NM_001001712 GDAP1L1 NM_024034.3 IK NM_006083 LCN9 NM_001001676 GFI1 NM_005263 IL6ST NM_002184.2 LDB1 NM_003893.3 GFI1B NM_004188.2 IQSEC3 NM_015232 LDLRAD1 NM_001010978 GHRHR NM_000823.1 IREM2 NM_181449.1 LEF1 NM_016269.2 GJA8 NM_005267 IRS2 NM_003749.2 LGR6 NM_021636.1 GLB1 NM_000404 IRS4 NM_003604.1 LIFR NM_002310.2 GLI3 NM_000168.2 ISLR NM_201526.1 LIG1 NM_000234.1 GLIPR1 NM_006851.1 ITGAE NM_002208 LIG3 NM_013975.1 3MCL1L NM_022471.2 ITGB3 NM_000212.2 LILRB1 NM_006669 GNAS NM_000516.3 ITPR1 NM_002222 LMNB2 NM_032737.2 GNRH1 NM_000825 K6IRS3 NM_175068.2 LM07 NM_005358.3 3PBP1 NM_022913 KCNA10 NM_005549.2 LOCI 22258 NM_145248.2 GPR112 NM_153834 KCNB2 NM_004770.2 LOC126147 NM_145807 GPR124 NM_032777.6 KCNC4 NM_004978.2 LOC129531 NM_138798.1 GPR158 NM_020752 KCND3 NM_004980.3 LOCI 57697 NM_207332.1 GPR50 NM_004224 KCNH4 NM_012285.1 LOC167127 NM_174914.2 3PR8 NM_005286.2 KCNQ5 NM_019842.2 LOC223075 NM_194300.1 3PR87 NM_023915.2 KCNT1 NM_020822 LOC388199 NM_001013638 3PX1 NM_000581 KCTD16 NM_020768 LOC91807 NM_182493.1 3RID1 NM_017551 KDR NM_002253.1 LPIN1 NM_145693.1 3RID2 NM_001510.1 KIAA0182 NM_014615.1 LPPR2 NM_022737.1 3RIK1 NM_175611 KIAA0367 NM_015225 LRCH4 NM_002319 3RIK3 NM_000831.2 KIAA0415 NM_014855 LRP1 NM_002332.1 3RM1 NM_000838.2 KIAA0528 NM_014802 LRP2 NM_004525.1 GTF2B NM_001514.2 KIAA0555 NM_014790.3 LRRC4 NM_022143.3 GUCY1A2 NM_000855.1 KIAA0556 NM_015202 LRRN6D NM_001004432 HAPIP NM_003947.1 KIAA0789 NM_014653 LRTM2 NM_001039029 HAPLN1 NM_001884.2 KIAA0934 NM_014974.1 LSP1 NM_001013253 HAT1 NM_003642.1 KIAA1078 NM_203459.1 LZTS2 NM_032429.1 HBXIP NM_006402.2 KIAA1185 NM_020710.1 MAMDC1 NM_182830 HCAP-G NM_022346.2 KIAA1285 NM_015694 MAN2A2 NM_006122 HDC NM_002112.1 KIAA1409 NM_020818.1 MAP1B NM_005909.2 HECTD1 NM_015382 KIAA1468 NM_020854.2 MAP2 NM_002374.2 HIC1 NM_006497 KIAA1529 NM_020893 MAP2K7 NM_145185 HIST1H1B NM_005322.2 KIAA1727 NM_033393 MAPK8IP2 NM_012324 HIST1H1E NM_005321.2 KIAA1875 NM_032529 MARLIN 1 NM_144720.2 HIST1H2BM NM_003521.2 KIAA2022 NM_001008537 MAST1 NM_014975 HIVEP1 NM_002114 KIF13A NM_022113 MCF2L2 NM_015078.2 HIVEP3 NM_024503.1 KL NM_004795.2 MCM3AP NM_003906.3 HK3 NM_002115.1 KLF5 NM_001730.2 MCP NM_172350.1 HOXC9 NM_006897.1 KLRF1 NM_016523 MCRS1 NM_006337.3 HPS3 NM_032383.3 KRAS NM_004985.3 MED12L NM_053002 HR NM_005144.2 KRT20 NM_019010.1 MEF2C NM_002397 HRH1 NM_000861.2 KRTAP10-2 NM_198693 MEGF6 NM_001409 140 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID MET NM_000245 NID NM_002508.1 PDZD2 NM_178140 MFN1 NM_033540.2 NLGN4X NM_181332.1 PDZRN3 NM_015009 MGC13125 NM_032725.2 NODAL NM_018055.3 PDZRN4 NM_013377.2 MGC15730 NM_032880.2 NOS3 NM_000603.2 PEBP4 NM_144962 MGC16943 NM_080663.1 NR3C2 NM_000901.1 PEG3 NM_006210.1 MGC20470 NM_145053 NTNG1 NM_014917 PERI NM_002616.1 MGC26733 NM_144992 NUP210 NM_024923 PERQ1 NM_022574 MGC29671 NM_182538.3 NUP210L NM_207308 PEX5L NM_016559.1 MGC32124 NM_144611.2 OBSCN NM_052843.1 PF6 NM_206996.1 MGC33407 NM_178525.2 ODZ1 NM_014253.1 PHIP NM_017934.4 MGC33846 NM_175885 OLFM2 NM_058164.1 PHKB NM_000293.1 MGC39325 NM_147189.1 OMA1 NM_145243.2 PIGO NM_032634.2 MGC39545 NM_203452.1 OR10G3 NM_001005465 PIK3CA NM_006218 MGC48628 NM_207491 OR13F1 NM_001004485 PIK3R5 NM_014308.1 MGC52022 NM_198563.1 OR1E2 NM_003554.1 PKHD1 NM_138694.2 MGC52282 NM_178453.2 OR2T33 NM_001004695 PKHD1L1 NM_177531 MGC5242 NM_024033.1 OR2T34 NM_001001821 PKNOX1 NM_004571.3 MGC8685 NM_178012.3 OR4A16 NM_001005274 PLA2G4B NM_005090 MKRN3 NM_005664.1 OR4K14 NM_001004712 PLA2G4D NM_178034 MLF2 NM_005439.1 OR51E1 NM_152430 PLB1 NM_153021 MLL3 NM_170606.1 OR51T1 NM_001004759 PLCG2 NM_002661 MMP11 NM_005940.2 OR5H6 NM_001005479 PLEC1 NM_201378 MMP2 NM_004530.1 OR5J2 NM_001005492 PLXND1 NM_015103 MMRN2 NM_024756.1 OR5K1 NM_001004736 PNLIPRP2 NM_005396 MN1 NM_002430 OR6C1 NM_001005182 PNMA3 NM_013364 MPO NM_000250.1 OR6C6 NM_001005493 PNPLA1 NM_001039725 MPP3 NM_001932 OR6C75 NM_001005497 PPM1F NM_014634.2 MRGPRE NM_001039165 OR8K3 NM_001005202 PPP1R12A NM_002480 MRPL23 NM_021134 OSBP NM_002556.2 PQBP1 NM_005710.1 MS4A5 NM_023945.2 OSBPL5 NM 020896 PQLC1 NM_025078.3 MTHFD1L NM_015440.3 OSBPL5 NM_145638 PRDM9 NM_020227 MUC1 NM_002456.3 OTOP2 NM_178160.1 PRF1 NM_005041.3 MUC16 NM_024690 OVCH1 NM_183378 PRG2 NM_002728.4 MYADML NM_207329.1 OVGP1 NM_002557.2 PRIM A1 NM_178013.1 MY018B NM_032608 OXCT1 NM_000436.2 PRKCE NM_005400.2 MYOIB NM_012223.2 P2RX7 NM_002562.4 PRKCZ NM_002744.2 MYOID NM_015194 P2RY14 NM_014879.2 PRKD1 NM_002742.1 MY05C NM_018728 PAK6 NM_020168.3 PRKDC NM_006904 MYOHD1 NM_001033579 PANK4 NM_018216.1 PRNPIP NM_024066 MYR8 NM_015011 PAOX NM_207128.1 PRO0149 NM_014117.2 NALP7 NM_139176.2 PARP8 NM_024615.2 PROL1 NM_021225 NALP8 NM_176811.2 PBEF1 NM_005746.1 PROS1 NM_000313.1 NAV3 NM_014903 PBX4 NM_025245.1 PRPS1 NM_002764.2 NBEA NM_015678 PBXIP1 NM_020524.2 PRSS1 NM_002769.2 NCDN NM_014284.1 PCDH11X NM_032968.2 PRTG NM_173814 NCR1 NM_004829.3 PCDHA9 NM_014005 PSMA2 NM_002787.3 NDST3 NM_004784.1 PCDHGA7 NM_032087 PSMC5 NM_002805.4 NDUFA1 NM_004541.2 PCDHGB4 NM_032098 PTEN NM_000314 NEB NM_004543 PCP4 NM_006198 PTPRD NM_130391.1 NELLI NM_006157.2 PCSK2 NM_002594.2 PTPRH NM_002842 NEUGRIN NM_016645.1 PDE11A NM_016953 PTPRN2 NM_002847.2 NF1 NM_000267.1 PDGFD NM_033135.2 PTPRS NM_130853.1 NFATC1 NM_006162.3 PDILT NM_174924.1 PTPRU NM_005704.2 141 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol Accession ID Gene Symbol Accession ID PTPRZl NM_002851 SDCBP2 NM_080489.2 SUHW4 NM_001002843 PZP NM_002864.1 SDK1 NM_152744 SYNE1 NM_182961.1 QKI NM_006775.1 SEC24B NM_006323 SYNPO NM_007286.3 RAB38 NM_022337.1 SEC8L1 NM_021807.2 SYT9 NM_175733.2 RAB5C NM_201434.1 SEMA3D NM_152754 SYTL2 NM_206927 RABEP1 NM_004703 SERPINA3 NM_001085 T3JAM NM_025228.1 RALGDS NM_006266.2 SETBP1 NM_015559.1 TAF1L NM_153809 RAPGEF4 NM_007023 SEZ6 NM_178860 TAF2 NM_003184 RARB NM_000965.2 SF3A1 NM_005877.3 TAIP-2 NM_024969.2 RASAL2 NM_170692.1 SFMBT2 NM_001029880 TA-KRP NM_032505.1 RASGRF2 NM_006909.1 SFRS6 NM_006275.4 TBC1D2B NM_015079 RASGRP1 NM_005739 SGEF NM_015595 TBX1 NM_005992.1 RASSF2 NM_170774.1 SH3TC1 NM_018986.2 TBX15 NM_152380 RASSF4 NM_032023.3 SHANK1 NM_016148.1 TBX22 NM_016954.2 RAVER2 NM_018211 SHQ1 NMJH8130 TCEB3B NM_016427.2 RB1CC1 NM_014781 SIGLEC7 NM_014385.1 TCERG1L NM_174937.1 RBM10 NM_005676.3 SKIP NM_030623 TCF3 NM_003200.1 RBP3 NM_002900.1 SKIV2L NM_006929.3 TCF7L2 NM_030756.1 RCN1 NM_002901.1 SLB NM_015662.1 TCFL5 NM_006602.2 RDH13 NM_138412 SLC11A2 NM_000617.1 TCOF1 NM_000356.1 RET ,N NM_005045 SLC12A5 NM_020708.3 TFEC NM_012252.1 RET NM_020975.2 SLC12A7 NM_006598 TFG NM_006070.3 REV3L NM_002912.1 SLC1A7 NM_006671.3 TGFBR2 NM_003242.3 RFC4 NM_181573.1 SLC22A15 NM_018420 TGM2 NM_004613.2 RHEB NM_005614.2 SLC22A9 NM_080866.2 TGM3 NM_003245 RHPN1 NM_052924 SLC26A10 NM_133489.1 THAP9 NM_024672.2 RIC3 NM_024557.2 SLC29A1 NM_004955.1 THRAP1 NM_005121 RIMBP2 NM_015347 SLC33A1 NM_004733.2 TIAM1 NM_003253.1 RIMS2 NM_014677 SLC37A4 NM_001467 TLR8 NM_138636.2 RNF182 NM_152737.1 SLC39A7 NM_006979 TLR9 NM_017442.2 RNF31 NM_017999 SLC4A9 NM_031467 TM7SF4 NM_030788.2 RNPEPL1 NM_018226.2 SLC01A2 NM_134431.1 TMEM132B NM_052907 ROBOl NM_002941 SLC01B3 NM_019844.1 TMEM16B NM_020373 R0B02 NM_002942 SLITRK4 NM_173078.2 TMPRSS4 NM_019894 RORA NM_002943.2 SLITRK6 NM_032229 TNFRSF9 NM_001561.4 RPA3 NM_002947.2 SMAD2 NM_00590E2 TNN NM_022093 RPAP1 NM_015540.2 SMAD3 NM_005902.2 TNNI3K NM_015978.1 RPL6 NM_000970.2 SMAD4 NM_005359.3 TOP2A NM_001067 RPS6KB1 NM_003161.1 SMTN NM_006932.3 TP53 NM_000546.2 RREB1 NM_001003699 SNRPB2 NM_198220.1 TP53BP1 NM_005657.1 RTN4 NM_207521.1 SNTG2 NM_018968 TPX2 NM_012112.4 RUNX1T1 NM_175634.1 SNX5 NM_152227.1 TREX2 NM_080701 RYR2 NM_001035 SNX8 NM_01332E1 TRIM3 NM_033278.2 SACS NM_014363.3 SOCS6 NM_004232.2 TRIM71 NM_001039111 SALL2 NM_005407 SORL1 NM_003105.3 TRMT5 NM_020810 SALL3 NM_171999.1 SPOCK3 NM_016950 TSKS NM_021733.1 SCN10A NM_006514 SPTBN2 NM_006946.1 TSN NM_004622 SCN1A NM_006920 ST8SIA4 NM_005668.3 TSP-NY NM_032573.3 SCN3B NM_018400.2 STAB1 NM_015136 TSPYL5 NM_033512 SCN7A NM_002976 STAM NM_003473.2 TTID NM_006790.1 SCNN1B NM_000336.1 STK32C NM_173575.2 TTLL3 NM_015644.1 SCNN1G NM_001039.2 STMN4 NM_030795.2 TTN NM_133378 SDBCAG84 NM_015966.2 STX17 NM_017919.1 TTYH2 NM_032646 142 WO 2009/100029 PCT/US2009/032881 2015203111 11 Jun2015

Gene Symbol Accession ID Gene Symbol Accession ID TXLNB NM_153235 ZNF624 NM_020787.1 TYSND1 NM_173555 ZNF659 NM_024697.1 LJBE3C NM_014671 ZNF714 NM_182515 LJGDH NM_003359.1 ZNHIT1 NM_006349.2 LJHRF2 NM_152896.1 ZNRF4 NM_181710 LJNC13B NM_006377.2 ZSCAN5 NM_024303.1 LJNC84B NM_015374.1 ZZZ3 NM_015534.3 LJNQ689 NM_212557.1 LJQCRC2 NM_003366.1 Note: Gene symbols are standard LJSP28 NM_020886 symbols assigned by Entrz Gene LJSP32 NM_032582 (http://www. ncbi. nlm. nih. gov/sites/ent LJSP52 LJTP14C ETX VEST1 VIM VPS13A NM_014871.2 NM_021645 NM_021140.1 NM_052958.1 NM_003380.1 NM_033305.1 rez?db=gene). Accession IDs “NM_XXXX” are uniquely assigned to each gene by National Center for Biotechnology Information (NCBI) (http://www. ncbi. nlm. nih. gov/sites/ent rez ?db=nuccore). WAC NM_016628.2 WDR19 NM_025132 WDR49 NM_178824.3 WNK1 NM_018979.1 WNT16 NM_016087.2 WNT8B NM_003393.2 WRN NM_000553.2 XKR3 NM_175878 XP04 NM_022459 XRCC1 NM_006297.1 VEATS2 NM_018023 ZAN NM_173059 ZBTB8 NM_144621.2 ZD52F10 NM_033317.2 ZDHHC7 NM_017740.1 ZFHX1B NM_014795.2 ZFHX4 NM_024721 ZFPM2 NM_012082 ZNF155 NM_198089.1 ZNF217 NM_006526.2 ZNF232 NM_014519.2 ZNF235 NM_004234 ZNF262 NM_005095.2 ZNF291 NM_020843 ZNF43 NM_003423.1 ZNF435 NM_025231.1 ZNF442 NM_030824.1 ZNF471 NM_020813.1 ZNF480 NM_144684.1 ZNF521 NM_015461 ZNF536 NM_014717 ZNF540 NM_152606.2 ZNF560 NM_152476.1 ZNF568 NM_198539 ZNF572 NM_152412.1 ZNF582 NM_144690 143

Claims (13)

1. The claims defining the invention are as follows.

   1. A method for aiding in the diagnosis of cancer in a subject, comprising the steps of: (a) isolating a microvesicle fraction from a bodily fluid sample from a human subject; and (b) analyzing nucleic acids in the microvesicle fraction for the presence of a gene specific to a cancer, wherein the gene is Epidermal Growth Factor Receptor vIII (EGFRvIII), to thereby indicate the presence of cancer in the subject.
2. 2. The method of claim 1, wherein the bodily fluid sample is blood, plasma, cerebrospinal fluid, urine or serum.
3. 3. The method of claim 1, wherein the nucleic acids in the microvesicle fraction are DNA, RNA, or DNA and RNA.
4. 4. The method of claim 3, wherein the RNA is mRNA.
5. 5. The method of claim 1, wherein the cancer is a brain tumor, optionally wherein the brain tumor is glioma or glioblastoma.
6. 6. The method of any one of claims 1 to 5, wherein step (a) is performed by centrifugation, size exclusion chromatography, density gradient centrifugation, differential centrifugation, nanomembrane ultrafiltration, immunoabsorbent capture, affinity purification, microfluidic separation, or combinations thereof.
7. 7. The method of claim 6, wherein step (b) is performed by microarray analysis, PCR, hybridization with allele-specific probes, enzymatic mutation detection, ligation chain reaction (LCR), oligonucleotide ligation assay (OLA), flow-cytometric heteroduplex analysis, chemical cleavage of mismatches, mass spectrometry, nucleic acid sequencing, single strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE), temperature gradient gel electrophoresis (TGGE), restriction fragment polymorphisms, serial analysis of gene expression (SAGE), or combinations thereof.
8. 8. The method of any one of claims 1 to 7, wherein the isolating step includes filtering.
9. 9. The method of claim 8, wherein filtering is through a 0.8 micron filter.
10. 10. The method of claim 8 or claim 9, wherein filtering is followed by differential centrifugation, size exclusion chromatography, or affinity purification.
11. 11. The method of any one of claims 1 to 10, wherein the method further comprises step (c) choosing a treatment option for the subject when EGFRvIII is present in the bodily fluid sample.
12. 12. The method of claim 11, wherein the treatment option is treatment with an EGFR inhibitor, optionally wherein the EGFR inhibitor is erlotinib or gefitinib.
13. 13. The method of claim 1, wherein step (b) further comprises extracting one or more nucleic acids in the microvesicle fraction prior to analyzing.