WO2015039006A1

WO2015039006A1 - Methods of treating cancer

Info

Publication number: WO2015039006A1
Application number: PCT/US2014/055589
Authority: WO
Inventors: Anthony John Iafrate; Long Phi LE; Zongli ZHENG
Original assignee: The General Hospital Corporation
Priority date: 2013-09-16
Filing date: 2014-09-15
Publication date: 2015-03-19

Abstract

Described herein are methods relating to the treatment of cancer. As described herein, subjects with genetic fusions of NTRK1 (e.g. with CHTOP or ARHGEF2) have NTRK1 activity that contributes to the pathophysiology of cancer. By inhibiting this aberrant NTRK1 activity, cancers with this fusion can be more effectively treated.

Description

METHODS OF TREATING CANCER

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims benefit under 35 U.S.C. § 119(e) of U.S. Provisional Application No. 61/878,088 filed September 16, 2013, the contents of which are incorporated herein by reference in their entirety.

GOVERNMENT SUPPORT

[0002] This invention was made with federal funding under Grant No. 1 R21 CA161590 awarded by the National Institutes of Health. The U.S. government has certain rights in the invention.

SEQUENCE LISTING

[0003] The instant application contains a Sequence Listing which has been submitted electronically in ASCII format and is hereby incorporated by reference in its entirety. Said ASCII copy, created on September 8, 2014, is named 030258-077821-PCT_SL.txt and is 63,797 bytes in size.

TECHNICAL FIELD

[0004] The technology described herein relates to the diagnosis and treatment of cancer.

BACKGROUND

[0005] The rearrangement of certain genes (e.g. ALK, RET, and ROS1) is known to play a role in the pathology and drug responsiveness of cancers (Druker, B. J. et al. N. Engl. J. Med. 344, 1031- 1037, 2001; Kwak, E. L. et al. N. Engl. J. Med. 363, 1693-1703, 2010; Bergethon, K. et al. J. Clin. Oncol. Off. J. Am. Soc. Clin. Oncol. 30, 863-870, 2012; Drilon, A. et al. Cancer Discov., 2013). Accordingly, subjects can be tested for the presence of such rearragnements (e.g. genetic fusions) in order to guide cancer treatments.

SUMMARY

[0006] Described herein are methods of treating cancer. Aspects of the technology described herein relate to the inventors' discovery that genetic fusions of NTRKl (e.g. with CHTOP or

ARHGEF2) lead to NTRKl activity that contributes to the pathophysiology of cancer. By inhibiting this aberrant NTRKl activity, cancers with this fusion can be more effectively treated.

[0007] In one aspect, described herein is a method of treating cancer in a subject in need thereof the method comprising administering an inhibitor of NTRKl kinase activity to a subject determined to have a genetic fusion of NTRKl and a second gene. In some embodiments, the second gene can be CHTOP or ARHGEF2. In some embodiments, the genetic fusion can comprise NTRKl as the 3' fusion partner. In some embodiments, the genetic fusion can comprise a chromosomal rearrangement.

[0008] In some embodiments, the subject can be determined to have a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl by detecting the presence of a CHTOP-NTRK1 or

ARHGEF2-NTRK1 fusion protein. In some embodiments, the fusion protein can have the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 3. In some embodiments, the presence of the fusion protein can be detected using an immunoassay.

[0009] In some embodiments, the subject can be determined to have a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRK1 by detecting the presence of a nucleic acid encoding a CHTOP-NTRKl or ARHGEF2 -NTRKl fusion protein. In some embodiments, the nucleic acid can have the sequence of SEQ ID NO: 2 or SEQ ID NO: 4. In some embodiments, the presence of the nucleic acid can be detected using a method selected from the group consisting of karyotyping; PCR; RT-PCR; sequencing; and FISH.

[0010] In some embodiments, the inhibitor of NTRKl kinase activity can be selected from the group consisting of AZD7451 ; Crizotinib; ARRY-470; CEP-701 ; AG 879; GW 441756; and Ro 08- 2750. In some embodiments, the cancer can be a brain cancer. In some embodiments, the brain cancer can be a glioblastoma.

[0011] In one aspect, described herein is a method of identifying an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl, the method comprising contacting a CHTOP-NTRKl or ARHGEF2 -NTRKl polypeptide with a candidate agent; detecting the level of kinase activity of the polypeptide; wherein a decreased level of kinase activity in the presence of the candidate agent, as compared to a reference level, indicates the candidate agent is an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl . In some embodiments, the cancer can be a brain cancer. In some embodiments, the brain cancer can be a glioblastoma.

BRIEF DESCRIPTION OF THE DRAWINGS

[0012] Fig. 1 depicts a schematic of anchored multiplex PCR (AMP) for targeted RNA and DNA sequencing. (1) Double-stranded cDNA synthesis starts with total nucleic acid or RNA from fresh or FFPE material without the need for ribosomal RNA or genomic DNA depletion. (2) SPRI-cleaned double stranded cDNA or fragmented/sheared gDNA is processed with end-repair and dA tailing, directly followed by ligation with a half-functional adapter. (3) SPRI-cleaned, ligated fragments are amplified with 10 to 14 cycles of multiplex PCR using gene specific primers (GSPl) and a primer complementary to a portion of the universal ligated adapter. (4) SPRI-cleaned PCR1 amplicons are amplified with a second round of 10-cycle multiplex PCR using a combination of GSP2 nested gene specific primers (3' downstream of GSPl) which are tagged with the second adapter sequence specific for Ion Torrent or MiSeq, and a second nested primer against the ligated universal adapter. (5) After a final SPRI cleanup, the target amplicon library is ready for quantitation, downstream clonal amplification, and sequencing.

[0013] Figs. 2A-2D depict targeted sequencing applications using anchored multiplex PCR. Fig. 2A demonstrates targeted RNA sequencing for rearrangement detection of unknown 5' or 3' fusion partners involved in gene fusions. A list of gene fusions detected with AMP from a cohort of clinical FFPE samples is shown on the left (genes boxed in dashed lines were targeted on the anchored end with GSPl and GSP2 primers; genes boxed in solid lines are the unknown fusion partners discovered by sequencing). Most fusions were detected by targeting the 3' receptor tyrosine kinase end to look for the 5' partner. In contrast, FGFR3 was targeted on the 5' end to look for its TACC3 fusion partner on the 3' end. In addition to verifying other previously reported fusion partners, a novel gene fusion involving MSN Exon 9 and ROSl Exon 34 was discovered during routine screening with AMP. Deep sequencing revealed two in- frame splicing variants of a CD74 (exon 6) and ROSl (exons 34 and 35) gene fusion. Figs, on the right depict sequence read pileups for two example gene fusions from Ion Torrent sequencing. The y-axis represents read coverage; the x-axis represents reference bases and their respective codons below. Shown in dark grey are read portions corresponding to the randomly ligated universal adapter end. Note the staggered distribution of reads with differing start positions. Shown in light gray are read portions corresponding to the anchored end targeted with GSPl and GSP2. Note the blunted end mostly representing the beginning of GSP2. Black bars denote indels while lighter bars denote base insertions. Fig. 2B depicts AMP optimization for genomic DNA sequencing. Four conditions were tested for AMP optimization using a 626 amplicon assay targeting 18 tumor suppressor genes (370 exons total): Platinum Taq polymerase alone, Platinum Taq polymerase with Tetramethyl ammonium chloride (TMAC), OneTaq polymerase, and Phusion HF polymerase. Normalized coverage relative to the mean coverage of the Platinum Taq polymerase alone condition (log 10 scale) is plotted against the percentage of covered total target. For the Platinum Taq polymerase alone condition, note that more than 97% of targeted bases showed 100X minimal coverage while more than 94% of targeted bases showed 500X minimal coverage. Fig. 2C depicts AMP detection of a clinical deletion variant. Read pileup on EGFR exon 19 showed an 18-bp deletion targeted in the 96 amplicon cancer panel. Fig. 2D depicts example coverage of the PTEN gene showing even coverage of on-target exons (black) and off-target pseudogene regions (grey) across the entire coding sequence.

[0014] Fig. 3 depicts a table of anchored multiplex PCR enrichment metrics and variant detection.

[0015] Fig. 4 depicts a table of two targeted RNA-Seq AMP panels for gene fusion detection.

[0016] Fig. 5 depicts a table of the 626-amplicon tumor suppressor AMP panel. All coding exons were covered in a bi-template design with GSPl and GSP2 primers targeting both the sense and anti-sense strands of exons longer than 200 bp in a 2-tube format.

[0017] Fig. 6 depicts a schematic of the primer design strategy for gene fusion detection (targeted RNA-Seq).

[0018] Figs. 7A-7B depict schematics of NTRKl fusions. In Fig. 7A, a case was confirmed to be positive for a novel ARHGEF2-NTRK1 fusion gene by the AMP gene rearrangement assay (sequencing data not shown). Two other glioblastoma cases showed another novel CHTOP-NTRK1 fusion gene by the AMP gene rearrangement assay (sequencing data not shown) which was confirmed by RT-PCR (data not shown)(Fig. 7B).

[0019] Fig. 8 depicts charts demonstrating that duplication rate increases and library complexity decreases with low amount of input DNA. Input DNA in parentheses represent total double-stranded DNA split into two AMP reactions for the 96-amplicon cancer panel.

[0020] Fig. 9 depicts a schematic of read coverage. A clinical EGFR amplified glioblastoma case (A42) showed overabundant read coverage (Y axis) relative to the mean coverage of other tested normal samples and relative to the intra-sample coverage for BRAF which is also located on chromosome 7. The low number of PCR cycling used for the nested multiplex PCR steps maintains the fidelity of allelic dosage to enable copy number detection.

[0021] Fig. 10 depicts a schematic of Anchored Multiplex PCR Library Construction Workflow. cDNA synthesis not required if using fragmented genomic DNA from FFPE material. ER = End repair, AddA = Adenylation, SPRI = Solid Phase Reversible Immobilization.

DETAILED DESCRIPTION

[0022] As described herein, the inventors have discovered that certain fusions of NTRK1 (e.g. with CHTOP or ARHGEF2) lead to NTRK1 activity that contributes to the pathophysiology of cancer. Accordingly, provided herein are methods of treating cancer relating to inhibiting NTRK1 activy. In one aspect, described herein is a method of treating cancer in a subject in need thereof, the method comprising administering an inhibitor of NTRK1 kinase activity to a subject determined to have a genetic fusion of NTRK1 and a second gene. In one aspect, described herein is a method of treating cancer in a subject in need thereof, the method comprising administering an inhibitor of NTRK1 kinase activity to a subject determined to have a genetic fusion of CHTOP and NTRK1 or ARHGEF2 and NTRK1.

[0023] As used herein, "NTRK1," "neurotrophic tyrosine kinase, receptor, type 1," or "TRKA" refers to a tyrosine kinase receptor of the neurotrophic tyrosine kinase receptor family. Upon binding of neurotrophin, NTRK1 autophosphorylates and phosphorylates it's targets, known to include beta- amyloid precursor protein (APP), PLCGl, phospho lipase C gamma, PI3K, and She. The sequence of NTRK1 for a number of species is well known in the art, e.g., human NTRK1 (e.g. NCBl Gene ID: 4914; (mRNA: SEQ ID NO: 7, NCBl Ref Seq: NM_002529)(polypeptide: SEQ ID NO: 8, NCBl Ref Seq: NP_002520).

[0024] NTRK1 activity refers to the kinase activity of NTRK1, i.e. phosphorylation of target polypeptides. NTRKl activity in the context of a genetic fusion polypeptide can include kinase activity which is limited to the targets of wild-type NTRKl, or kinase activity which is "off-target." Assays for measuring the activity of NTRKl are known in the art. For example, see "Kinases" in Ausubel et al,, eds, (1994-1998) Current Protocols in Molecular Biology and references cited therein. Different kinase activity assays are also described, e.g. in Ma et al. Expert Opin Drug Discov 2008 3:607-621. Each of the foregoing references is incorporated by reference herein in its entirety. As a non-limiting example, an assay for tyrosine kinase activity can be performed using the Universal Tyrosine Kinase Assay Kit (GenWay Biotech, San Diego, Calif.). Briefly, the universal protein tyrosine kinase substrate peptide, Poly (Glu-Tyr) (4: 1, 20-50 kDa), is pre-coated onto 96-well microtiter plates. Serial dilutions of prepared 5-point standards (with known TK activities) and plasma (1 : 100 dilution) or serum samples are added to the plate in triplicate along with an ATP -containing kinase buffer. After incubation at 37° C. for 30 min to allow phosphorylation of tyrosine residues, the sample solution is removed and the wells are washed with Washing buffer (PBS with 0.05% Tween- 20) and blocked with Blocking reagent, Anti-phosphotyrosine (PY20)-horseradish peroxidase (HRP) conjugate is then added to the plate. After incubation at 37° C. for 30 min, the PY20-HRP solution is replaced by HRP substrate solution (TMBZ). For colorimetric determination of kinase activity, the sample's specific absorbance at 450 nm is calculated from a standard curve.

[0025] As used herein, the term "inhibitor" refers to an agent which can decrease the expression and/or activity of the targeted expression product (e.g. rriRNA encoding the target or a target polypeptide), e.g. by at least 10%> or more, e.g. by 10%> or more, 50% or more, 70% or more, 80% or more, 90%> or more, 95% or more, or 98 %> or more. The efficacy of an inhibitor of, for example, NTRKl activity, e.g. its ability to decrease NTRKl kinas activity can be determined, e.g. by measuring the level of activity of NTRKl . In some embodiments, the inhibitor can reduce the level of polypeptide expression products which have NTRKl kinase activity and/or the level of nucleic acids encoding such polypeptides. Methods for measuring the level of a given mRNA and/or polypeptide are known to one of skill in the art, e.g. RTPCR with primers can be used to determine the level of RNA and Western blotting with an antibody (e.g. an anti-NTRKl kinase domain antibody, e.g. Cat No. ab76291 ; Abeam; Cambridge, MA) can be used to determine the level of a polypeptide. The activity of, e.g. NTRKl can be determined using methods known in the art and described above herein. In some embodiments, the inhibitor of NTRKl can be an inhibitory nucleic acid; an antibody reagent; an antibody; or a small molecule. Non-limting examples of inhibitors of NTRKl kinase activity can include AZD7451 ; Crizotinib; ARRY-470; CEP-701 ; AG 879; GW 441756; and Ro 08- 2750.

[0026] As used herein, "CHTOP" or "chromatin target of PMT1" refers to a small nuclear protein that interact with protein arginine methyltransferases and influences estradiol-dependent transcription The sequence of CHTOP for a number of species is well known in the art, e.g., human CHTOP (e.g. NCBI Gene ID: 26097; (mRNA: SEQ ID NO: 9, NCBI Ref Seq:

NM_001206612)(polypeptide: SEQ ID NO: 10, NCBI Ref Seq: NP 001193541). [0027] As used herein, "ARHGEF2" or "Rho/Rac guanine nucleotide exchange factor (GEF) 2" refers to a protein that interacts with G protein coupled receptors to stimulate rho-dependent signals. The sequence of ARHGEF2 for a number of species is well known in the art, e.g., human ARHGEF2 (e.g. NCBI Gene ID: 9181 ; (mRNA: SEQ ID NO: 11, NCBI Ref Seq: NM 001162383)(polypeptide: SEQ ID NO: 12, NCBI Ref Seq: NP 001155855).

[0028] A polypeptide as described herein, e.g. a ARHGEF2 polypeptide, a CHTOP polypeptide, or a NTRKl polypeptide can be homolog, variant, and/or functional fragment of the polypeptides described herein, e.g. SEQ ID NOs: 12, 10, and 8, respectively. A nucleic acid encoding a polypeptide can comprise a sequence described herein, (e.g. SEQ ID NOs: 11, 9, or 7) or a homolog or variant thereof, including a nucleic acid encoding a functional fragment of the polypeptide.

[0029] As described herein, embodiments of the invention relate to the treatment of subjects determined to have a genetic fusion of NTRKl . As used herein, a "genetic fusion" refers to a nucleic acid molecule comprising a sequence having two parts, the first part comprising at least part of the sequence of a first gene and the second part comprising at least part of the sequence of a second gene or the polypeptide encoded by such a nucleic acid. The 3 '-most part is referred to herein as the 3' fusion partner, while the 5 '-most part is referred to herein as the 5' fusion partner. In some embodiments, NTRKl is the 3' fusion partner.

[0030] In some embodiments, the sequence comprised by either part of the genetic fusion is at least 10 base pairs in length, e.g. at least 10 bp in length, at least 20 bp in length, at least 50bp in length, at least 75 bp in length, at least 100 bp in length, at least 150 bp in length, at least 200 bp in length or longer. In some embodiments, the genetic fusion can comprise a chromosomal rearrangement. All or any part of a gene's full-length sequence can be part of a genetic fusion.

[0031] In some embodiments, the part of the genetic fusion comprising a NTRKl sequence comprises at least the intracellular domain of NTRKl, e.g. positions 440-796 of SEQ ID NO: 8. In some embodiments, the part of the genetic fusion comprising a NTRKl sequence comprises a portion of theintracellular domain of NTRKl, e.g. a subset of positions 440-796 of SEQ ID NO: 8.

[0032] In some embodiments, the part of the genetic fusion comprising a NTRKl sequence comprises at least the kinase domain of NTRKl, e.g. at least positions 504-783 of SEQ ID NO: 8 or positions 510-781 of SEQ ID NO: 8.

[0033] In some embodiments, the genetic fusion can be a fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl, i.e. the second gene of the genetic fusion can be CHTOP or ARHGEF2. In some embodiments, the genetic fusion can have the nucleic acid sequence of SEQ ID NO: 2, 4, 5 or the amino acid sequence of SEQ ID NO: 1 or 3. In the sequence of SEQ ID NO: 5, positions 1-312 and 2050-2257 encode UTRs, positions 313-853 encode a CHTOP polypeptide sequence, and positions 854-2049 encode a NTRKl polypeptide sequence. In the sequence of SEQ ID NO: 6, positions 1-100 and 4184-4391 encode UTRs, positions 101-2987 encode a ARHGEF2 polypeptide sequence, and positions 2988-4183 encode a NTRKl polypeptide sequence.

[0034] The presence of a genetic fusion as described herein can be determined by detecting the presence of a CHTOP-NTRKl or ARHGEF2-NTRK1 fusion protein and/or by detecting the presence of a nucleic acid encoding a CHTOP-NTRKl or ARHGEF2-NTRK1 fusion protein.

[0035] In some embodiments, the assays and methods can relate to detecting the presence of a genetic fusion described herein in a sample obtained from a subject. In some embodiments, the presence of the genetic fusion can be determined using an assay selected from the group consisting of: hybridization; sequencing; exome capture; PCR; high-throughput sequencing; allele-specific probe hybridization; allele-specific primer extension, allele-specific amplification; 5' nuclease digestion; molecular beacon assay; oligonucleotide ligation assay; size analysis; single-stranded conformation polymorphism; real-time quantitative PCR, FISH, karyotyping, and any combinations thereof.

[0036] In some embodiments, the presence and/or absence of a genetic fusion can be detected by determining the sequence of a genomic locus and/or an mRNA transcript. Such molecules can be isolated, derived, or amplified from a biological sample, such as a tumor sample. Nucleic acid (e.g. DNA) and ribonucleic acid (RNA) molecules can be isolated from a particular biological sample using any of a number of procedures, which are well-known in the art, the particular isolation procedure chosen being appropriate for the particular biological sample. For example, freeze-thaw and alkaline lysis procedures can be useful for obtaining nucleic acid molecules from solid materials; and proteinase K extraction can be used to obtain nucleic acid from blood (Roiff, A et al. PCR:

Clinical Diagnostics and Research, Springer (1994)).

[0037] In some embodiments, the nucleic acid sequence of a target gene (e.g. NTRKl) in a sample obtained from a subject can be determined and compared to a reference sequence to determine if a genetic fusion is present in the subject. In some embodiments, the reference sequence can be, e.g. the wildtype sequence of NTRKl or the genetic fusion sequences provided herein.

[0038] In some embodiments, the sequence of the target gene can be determined by sequencing the target gene (e.g. the genomic sequence and/or the mRNA transcript thereof). Methods of sequencing a nucleic acid sequence are well known in the art. Briefly, a sample obtained from a subject can be contacted with one or more primers which specifically hybridize to a single-strand nucleic acid sequence flanking the target gene sequence and a complementary strand is synthesized. In some next-generation technologies, an adaptor (double or single-stranded) is ligated to nucleic acid molecules in the sample and synthesis proceeds from the adaptor or adaptor compatible primers. In some third-generation technologies, the sequence can be determined, e.g. by determining the location and pattern of the hybridization of probes, or measuring one or more characteristics of a single molecule as it passes through a sensor (e.g. the modulation of an electrical field as a nucleic acid molecule passes through a nanopore). Exemplary methods of sequencing include, but are not limited to, Sanger sequencing, dideoxy chain termination, high-throughput sequencing, next generation sequencing, 454 sequencing, SOLiD sequencing, polony sequencing, Illumina sequencing, Ion Torrent sequencing, sequencing by hybridization, nanopore sequencing, Helioscope sequencing, single molecule real time sequencing, RNAP sequencing, and the like. Methods and protocols for performing these sequencing methods are known in the art, see, e.g. "Next Generation Genome Sequencing" Ed. Michal Janitz, Wiley- VCH; "High-Throughput Next Generation Sequencing" Eds. Kwon and Ricke, Humanna Press, 2011; and Sambrook et al., Molecular Cloning: A Laboratory Manual (3 ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2001); which are incorporated by reference herein in their entireties.

[0039] In some embodiments, the sequence of the target gene can be determined by anchored multiplex PCR (AMP) as described in the Examples herein and in U.S. Patent Application 13/793,564 filed March 11, 2013; which is incorporated by reference herein in its entirety.

[0040] In some embodiments, sequencing can comprise exome sequencing (i.e. targeted exome capture). Exome sequencing comprises enriching for an exome(s) of interest and then sequencing the nucleic acids comprised by the enriched sample. Sequencing can be according to any method known in the art, e.g. those described above herein. Methods of enrichment can include, e.g. PCR, molecular inversion probes, hybrid capture, and in solution capture. Exome capture methodologies are well known in the art, see, e.g. Sulonen et la. Genome Biology 2011 12:R94; and Teer and Mullikin. Hum Mol Genet 2010 19:R2; which are incorporated by reference herein in their entireties. Kits for performing exome capture are available commercially, e.g. the TRUSEQ™ Exome Enrichment Kit (Cat. No. FC-121-1008; Illumnia, San Diego, CA). Exome capture methods can also readily be adapted by one of skill in the art to enrich specific exomes of interest.

[0041] In some embodiments, the presence of a genetic fusion can be determined using a probe that is specific for the genetic fusion. In some embodiments, the probe can be detectably labeled. In some embodiments, a detectable signal can be generated by the probe when a genetic fusion is present.

[0042] In some embodiments, the probe specific for the genetic fusion can be a probe in a hybridization assay, i.e. the probe can specifically hybridize to a nucleic acid comprising a genetic fusion (as opposed to a wild-type nucleic acid sequence) and the hybridization can be detected, e.g. by having the probe and or the target nucleic acid be detectably labeled. Hybridization assays are well known in the art and include, e.g. northern blots and Southern blots.

[0043] In some embodiments, the probe specific for the genetic fusion can be a probe in a PCR assay, i.e. a primer. In general, the PCR procedure describes a method of gene amplification which is comprised of (i) sequence-specific hybridization of primers to specific genes within a nucleic acid sample or library, (ii) subsequent amplification involving multiple rounds of annealing, elongation, and denaturation using a thermostable DNA polymerase, and optionally, (iii) screening the PCR products for a band or product of the correct size. The primers used are oligonucleotides of sufficient length and appropriate sequence to provide initiation of polymerization, i.e. each primer is specifically designed to be complementary to a strand of the genomic locus to be amplified. In an alternative embodiment, the presence of a genetic fusion in an mRNA tramscript can be determined by reverse- transcription (RT) PCR and by quantitative RT-PCR (QRT-PCR) or real-time PCR methods. Methods of RT-PCR and QRT-PCR are well known in the art. In some embodiments, the PCR product can be labeled, e.g. the primers can comprise a detectable label, or a label can be incorporated and/or bound to the PCR product, e.g. EtBr detection methods. Other non-limiting detection methods can include the detection of a product by mass spectroscopy or MALDI-TOF. In some embodiments, a pair of primer is used such that a product will only be produced when a genetic fusion is present or, e.g. a uniquely-sized product is produced only when a genetic fusion is present. By way of non-limiting example, a primer pair comprising a primer that specifically recognizes the portion of SEQ ID NO: 1 derived from CHTOP and a compatible primer specifically recognizing the portion of SEQ ID NO: 1 derived from NTRK1 will only produce a product when the genetic fusion is present. Such aspects of primer design are familiar to one of ordinary skill in the art.

[0044] The nucleic acid sequences of, e.g. NTRK1, CHTOP, and ARHGEF2 have been assigned NCBl accession numbers for different species such as human, mouse and rat. In particular, the NCBl accession numbers for the nucleic acid sequences of the human expression products are included herein, as are the sequences of exemplary genetic fusions. Accordingly, a skilled artisan can design appropriate primers based on the known sequence for detecting the presence of a genetic fusion.

[0045] A genetic fusion will typically be present in the genomic DNA of a tumor (e.g.

cancerous) cell. Accordingly, the genetic fusion can be detected in either or both of the genomic DNA or the mRNA transcripts of a cell. In some embodiments, the genetic fusion can occur within a DNA and/or RNA sequence that is translated. Accordingly, in some embodiments, the genetic fusion can be detected in the polypeptide of a cell.

[0046] Detection of polypeptides comprising a genetic fusion can be according to any method known in the art (e.g. mass spectroscopy, flow cytometry, and/or immunological-based methods). Immunological methods to detect polypeptides comprising a genetic fusion in accordance with the present technology include, but are not limited to antibody techniques such as immunohistochemistry, immunocytochemistry, flow cytometry, fluorescent-activated cell sorting (FACS), immunoblotting, radioimmunoassays, western blotting, immunoprecipitation, enzyme-linked immunosorbant assays (ELISA), and derivative techniques that make use of antibody reagents as described herein.

[0047] Immunochemical methods require the use of an antibody reagent specific for the target molecule (e.g. the antigen or in the embodiments described herein, a polypeptide or fragment thereof comprising a genetic fusion). In some embodiments, an antibody reagent for determining the presence of a genetic fusion in a sample can be an antibody reagent specific for a polypeptide comprising a genetic fusion, e.g. a polypeptide comprising SEQ ID NO: 2 or 4. In some embodiments, an antibody reagent specific for a genetic fusion can be, e.g. specific for an antigen comprising portions of both parts of the genetic fusion, e.g. the antigen comprises sequence from both of the genetic fusion partners. For example, the antigen can span the fusion point of the amino acid sequence, or comprise two or more parts of the sequence of the polypeptide that are brought into proximity to each other by the folding of the protein (i.e. they form an antigen that is not present in an unfolded polypeptide). In some embodiments, the antibody reagent specific for a genetic fusion can also be, e.g. a diabody or antibody reagent complex with two or more specific antigens (e.g. where each antigen is from one of the genetic fusion partners), and binding of the diabody or complex to only one of its antigens (e.g. if no genetic fusion is present) can be distinguished from binding to two or more of its antigens (e.g. if a genetic fusion is present, providing the two or more antigens in close proximity. Methods of making such reagents are known to one of skill in the art.

[0048] In some embodiments, the assays, methods, and/or systems described herein can comprise: an antibody reagent, e.g.. an antibody reagent specific for a genetic fusion as described herein. In some embodiments, the antibody reagent can be detectably labeled. In some embodiments, the antibody reagent can be attached to a solid support (e.g. bound to a solid support). In some embodiments, the solid support can comprise a particle (including, but not limited to an agarose or latex bead or particle or a magnetic particle), a bead, a nanoparticle, a polymer, a substrate, a slide, a coverslip, a plate, a dish, a well, a membrane, and/or a grating. The solid support can include many different materials including, but not limited to, polymers, plastics, resins, polysaccharides, silicon or silica based materials, carbon, metals, inorganic glasses, and membranes.

[0049] In one embodiment, an assay, method, and/or system as described herein can comprise an ELISA. In an exemplary embodiment, a first antibody reagent can be immobilized on a solid support (usually a polystyrene micro titer plate). The solid support can be contacted with a sample obtained from a subject, and the antibody reagent will bind ("capture") antigens for which it is specific (e.g. a polypeptide comprising a genetic fusion). The solid support can then be contacted with a second labeled antibody reagent (e.g. a detection antibody reagent). The detection antibody reagent can, e.g. comprise a detectable signal, be covalently linked to an enzyme, or can itself be detected by a secondary antibody, which is linked to an enzyme through bio-conjugation. The presence of a signal indicates that both the first antibody reagent immobilized on the support and the second "detection" antibody reagent have bound to an antigen, i.e. the presence of a signal indicated the presence of polypeptide comprising a genetic fusion. Between each step the plate is typically washed with a mild detergent solution to remove any proteins or antibodies that are not specifically bound. After the final wash step the plate is developed by adding an enzymatic substrate to produce a visible signal, which indicates the presence of a genetic fusion in the sample. Older ELISAs utilize chromogenic substrates, though newer assays employ fluorogenic substrates with much higher sensitivity. There are other different forms of ELISA, which are well known to those skilled in the art. The standard techniques known in the art for ELISA are described in "Methods in Immunodiagnosis", 2nd Edition, Rose and Bigazzi, eds. John Wiley & Sons, 1980; Campbell et al., "Methods and Immunology", W. A.

Benjamin, Inc., 1964; and Oellerich, M. 1984, J. Clin. Chem. Clin. Biochem. 22:895-904. These references are hereby incorporated by reference in their entirety.

[0050] In one embodiment, the assays, systems, and methods described herein can comprise a lateral flow immunoassay test (LFIA), also known as the immunochromatographic assay, or strip test to measure or determine the presence of a polypeptide comprising a genetic fusion. LFIAs are a simple device intended to detect the presence (or absence) of a target in a sample. There are currently many LFIA tests are used for medical diagnostics either for home testing, point of care testing, or laboratory use. LFIA tests are a form of immunoassay in which the test sample flows along a solid substrate via capillary action. After the sample is applied to the test it encounters a colored antibody reagent, which mixes with the sample, and if bound to a portion of the sample, transits the substrate encountering lines or zones which have been pretreated with a second antibody reagent. Depending upon the presence or absence of the target in the sample the colored antibody reagent can become bound at the test line or zone. LFIAs are essentially immunoassays adapted to operate along a single axis to suit the test strip format or a dipstick format. Strip tests are extremely versatile and can be easily modified by one skilled in the art for detecting an enormous range of antigens from fluid samples such as blood, tumor cell lysates etc. Strip tests are also known as dip stick test, the name bearing from the literal action of "dipping" the test strip into a fluid sample to be tested. LFIA strip test are easy to use, require minimum training and can easily be included as components of point-of- care test (POCT) diagnostics to be use on site in the field. LFIA tests can be operated as either competitive or sandwich assays. Sandwich LFIAs are similar to sandwich ELISA. The sample first encounters colored particles, which are labeled with antibody reagents specific for a target. The test line will also contain antibody reagents. The test line will show as a colored band in positive samples. In some embodiments, the lateral flow immunoassay can be a double antibody sandwich assay, a competitive assay, a quantitative assay or variations thereof. There are a number of variations on lateral flow technology. It is also possible to apply multiple capture zones to create a multiplex test.

[0051] A typical test strip consists of the following components: (1) sample application area comprising an absorbent pad (i. e. the matrix or material) onto which the test sample is applied; (2) conjugate or reagent pad- this contains antibody reagent(s) specific to the target which can be conjugated to colored particles (usually colloidal gold particles, or latex microspheres); (3) test results area comprising a reaction membrane - typically a hydrophobic nitrocellulose or cellulose acetate membrane onto which antibody reagents are immobilized in a line across the membrane as a capture zone or test line (a control zone may also be present, containing antibodies specific for the antibody reagents conjugated to the particles or microspheres); and (4) optional wick or waste reservoir - a further absorbent pad designed to draw the sample across the reaction membrane by capillary action and collect it. The components of the strip are usually fixed to an inert backing material and may be presented in a simple dipstick format or within a plastic casing with a sample port and reaction window showing the capture and control zones. While not strictly necessary, most tests will incorporate a second line, which contains an antibody that picks up free latex/gold in order to confirm the test has operated correctly.

[0052] The use of "dip sticks" or LFIA test strips and other solid supports have been described in the art in the context of an immunoassay for a number of antigen biomarkers. U.S. Pat. Nos.

4,943,522; 6,485,982; 6,187,598; 5,770,460; 5,622,871 ; 6,565,808, U. S. patent applications Ser. No. 10/278,676; U.S. Ser. No. 09/579,673 and U.S. Ser. No. 10/717,082, which are incorporated herein by reference in their entirety, are non- limiting examples of such lateral flow test devices. Three U.S. patents (U.S. Pat. No. 4,444,880, issued to H. Tom; U.S. Pat. No. 4,305,924, issued to R. N. Piasio; and U.S. Pat. No. 4,135,884, issued to J. T. Shen) describe the use of "dip stick" technology to detect soluble antigens via immunochemical assays. The apparatuses and methods of these three patents broadly describe a first component fixed to a solid surface on a "dip stick" which is exposed to a solution containing a soluble antigen that binds to the component fixed upon the "dip stick," prior to detection of the component-antigen complex upon the stick. It is within the skill of one in the art to modify the teaching of these "dip stick" technology for the detection of a genetic fusion.

[0053] Immunochemistry is a family of techniques based on the use of a specific antibody, wherein antibodies are used to specifically target molecules inside or on the surface of cells. In some embodiments, immunohistochemistry ("IHC") and immunocytochemistry ("ICC") techniques can be used to detect the presence of a genetic fusion. IHC is the application of immunochemistry to tissue sections, whereas ICC is the application of immunochemistry to cells or tissue imprints after they have undergone specific cytological preparations such as, for example, liquid-based preparations. In some instances, signal amplification may be integrated into the particular protocol, wherein a secondary antibody, that includes a label, follows the application of an antibody reagent specific for a polypeptide comprising a genetic fusion as described herein. Typically, for immunohistochemistry, tissue obtained from a subject and fixed by a suitable fixing agent such as alcohol, acetone, and paraformaldehyde, is sectioned and reacted with an antibody. Conventional methods for

immunohistochemistry are described in Buchwalow and Bocker (Eds) "Immunohistochemistry: Basics and Methods" Springer (2010): Lin and Prichard "Handbook of Practical

Immunohistochemistry" Springer (2011); which are incorporated by reference herein in their entireties. In some embodiments, immunocytochemistry may be utilized where, in general, tissue or cells are obtained from a subject are fixed by a suitable fixing agent such as alcohol, acetone, and paraformaldehyde, to which is reacted an antibody. Methods of immunocytological staining of human samples is known to those of skill in the art and described, for example, in Burry. "Immunocytochemistry: A Practical Guide for Biomedical Research" Springer (2009); which is incorporated by reference herein in its entirety.

[0054] In some embodiments, one or more of the detection reagents described herein can comprise a detectable label and/or comprise the ability to generate a detectable signal (e.g. by catalyzing reaction converting a compound to a detectable product). Detectable labels can comprise, for example, a light-absorbing dye, a fluorescent dye, or a radioactive label. Detectable labels, methods of detecting them, and methods of incorporating them into a reagent are well known in the art. The term "label" refers to a composition capable of producing a detectable signal indicative of the presence of a reagent (e.g. a bound antibody reagent).

[0055] In some embodiments, detectable labels can include labels that can be detected by spectroscopic, photochemical, biochemical, immunochemical, electromagnetic, radiochemical, or chemical means, such as fluorescence, chemifluoresence, or chemiluminescence, or any other appropriate means. The detectable labels used in the methods described herein can be primary labels (where the label comprises a moiety that is directly detectable or that produces a directly detectable moiety) or secondary labels (where the detectable label binds to another moiety to produce a detectable signal, e.g., as is common in immunological labeling using secondary and tertiary antibodies). The detectable label can be linked by covalent or non-covalent means to the antibody reagent. Alternatively, a detectable label can be linked such as by directly labeling a molecule that achieves binding to the antibody reagent via a ligand-receptor binding pair arrangement or other such specific recognition molecules. Detectable labels can include, but are not limited to radioisotopes, bioluminescent compounds, chromophores, antibodies, chemiluminescent compounds, fluorescent compounds, metal chelates, and enzymes.

[0056] In other embodiments, the detection reagent is label with a fluorescent compound. When the fluorescently labeled antibody is exposed to light of the proper wavelength, its presence can then be detected due to fluorescence. In some embodiments, a detectable label can be a fluorescent dye molecule, or fluorophore including, but not limited to fluorescein, phycoerythrin, phycocyanin, o- phthaldehyde, fluorescamine, Cy3™, Cy5™, allophycocyanine, Texas Red, peridenin chlorophyll, cyanine, tandem conjugates such as phycoerythrin-Cy5™, green fluorescent protein, rhodamine, fluorescein isothiocyanate (FITC) and Oregon Green™, rhodamine and derivatives (e.g., Texas red and tetrarhodimine isothiocynate (TRITC)), biotin, phycoerythrin, AMCA, CyDyes™, 6- carboxyfhiorescein (commonly known by the abbreviations FAM and F), 6-carboxy-2',4',7',4,7- hexachlorofiuorescein (HEX), 6-carboxy-4',5'-dichloro-2',7'-dimethoxyfiuorescein (JOE or J), N,N,N',N'-tetramethyl-6carboxyrhodamine (TAMRA or T), 6-carboxy-X-rhodamine (ROX or R), 5- carboxyrhodamine-6G (R6G5 or G5), 6-carboxyrhodamine-6G (R6G6 or G6), and rhodamine 110; cyanine dyes, e.g. Cy3, Cy5 and Cy7 dyes; coumarins, e.g umbelliferone; benzimide dyes, e.g.

Hoechst 33258; phenanthridine dyes, e.g. Texas Red; ethidium dyes; acridine dyes; carbazole dyes; phenoxazine dyes; porphyrin dyes; polymethine dyes, e.g. cyanine dyes such as Cy3, Cy5, etc;

BODIPY dyes and quinoline dyes. In some embodiments, a detectable label can be a radiolabel

3 125 35 14 32 33

including, but not limited to H, ^JJS, "C, "P, and "P. In some embodiments, a detectable label can be an enzyme including, but not limited to horseradish peroxidase and alkaline phosphatase. An enzymatic label can produce, for example, a chemiluminescent signal, a color signal, or a fluorescent signal. Enzymes contemplated for use to detectably label a detection reagent include, but are not limited to, malate dehydrogenase, staphylococcal nuclease, delta- V-steroid isomerase, yeast alcohol dehydrogenase, alpha-glycerophosphate dehydrogenase, triose phosphate isomerase, horseradish peroxidase, alkaline phosphatase, asparaginase, glucose oxidase, beta-galactosidase, ribonuclease, urease, catalase, glucose-VI-phosphate dehydrogenase, glucoamylase and acetylcholinesterase. In some embodiments, a detectable label is a chemiluminescent label, including, but not limited to lucigenin, luminol, luciferin, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester. In some embodiments, a detectable label can be a spectral colorimetric label including, but not limited to colloidal gold or colored glass or plastic (e.g., polystyrene, polypropylene, and latex) beads.

[0057] In some embodiments, detection reagents can also be labeled with a detectable tag, such as c-Myc, HA, VSV-G, HSV, FLAG, V5, HIS, or biotin. Other detection systems can also be used, for example, a biotin-streptavidin system. In this system, the antibodies immunoreactive (i. e. specific for) with the biomarker of interest is biotinylated. Quantity of biotinylated antibody bound to the biomarker is determined using a streptavidin-peroxidase conjugate and a chromagenic substrate. Such streptavidin peroxidase detection kits are commercially available, e. g. from DAKO; Carpinteria, CA. A detection reagent can also be detectably labeled using fluorescence emitting metals such as ¹⁵²Eu, or others of the lanthanide series. These metals can be attached to the antibody reagent using such metal chelating groups as diethylenetriaminepentaacetic acid (DTPA) or ethylenediaminetetraacetic acid (EDTA).

[0058] The term "sample" or "test sample" as used herein denotes a sample taken or isolated from a biological organism, e.g., a tumor sample from a subject. Exemplary biological samples include, but are not limited to, a biofluid sample; serum; plasma; urine; saliva; a tumor sample; a tumor biopsy and/or tissue sample etc. The term also includes a mixture of the above-mentioned samples. The term "test sample" also includes untreated or pretreated (or pre-processed) biological samples. In some embodiments, a test sample can comprise cells from subject. In some

embodiments, a test sample can be a tumor cell test sample, e.g. the sample can comprise cancerous cells, cells from a tumor, and/or a tumor biopsy.

[0059] The test sample can be obtained by removing a sample of cells from a subject, but can also be accomplished by using previously isolated cells (e.g. isolated at a prior timepoint and isolated by the same or another person). In addition, the test sample can be freshly collected or a previously collected sample.

[0060] In some embodiments, the test sample can be an untreated test sample. As used herein, the phrase "untreated test sample" refers to a test sample that has not had any prior sample pre- treatment except for dilution and/or suspension in a solution. Exemplary methods for treating a test sample include, but are not limited to, centrifugation, filtration, sonication, homogenization, heating, freezing and thawing, and combinations thereof. In some embodiments, the test sample can be a frozen test sample, e.g., a frozen tissue. The frozen sample can be thawed before employing methods, assays and systems described herein. After thawing, a frozen sample can be centrifuged before being subjected to methods, assays and systems described herein. In some embodiments, the test sample is a clarified test sample, for example, by centrifugation and collection of a supernatant comprising the clarified test sample. In some embodiments, a test sample can be a pre-processed test sample, for example, supernatant or filtrate resulting from a treatment selected from the group consisting of centrifugation, filtration, thawing, purification, and any combinations thereof. In some embodiments, the test sample can be treated with a chemical and/or biological reagent. Chemical and/or biological reagents can be employed to protect and/or maintain the stability of the sample, including

biomolecules (e.g., nucleic acid and protein) therein, during processing. One exemplary reagent is a protease inhibitor, which is generally used to protect or maintain the stability of protein during processing. The skilled artisan is well aware of methods and processes appropriate for pre-processing of biological samples required for determination of the presence of a genetic fusion as described herein.

[0061] In some embodiments, the methods, assays, and systems described herein can further comprise a step of obtaining a test sample from a subject. In some embodiments, the subject can be a human subject.

[0062] In some embodiments, the the methods and assays described herein can further comprise the step of generating a report based upon the detection of the presence or absence of the genetic fusions described herein.

[0063] In some embodiments, the methods described herein relate to treating a subject having or diagnosed as having cancer. In some embodiments, the cancer can be brain cancer, e.g. a

glioblastoma. Subjects having cancer can be identified by a physician using current methods of diagnosing cancer. Symptoms and/or complications of cancer which characterize these conditions and aid in diagnosis are well known in the art and include but are not limited to, growth of a tumor, impaired function of the organ or tissue harboring cancer cells, etc. Tests that may aid in a diagnosis of, e.g. cancer include, but are not limited to, tissue biopsies and histological examination. A family history of cancer, or exposure to risk factors for cancer (e.g. tobacco products, radiation, etc.) can also aid in determining if a subject is likely to have cancer or in making a diagnosis of cancer. [0064] The compositions and methods described herein can be administered to a subject having or diagnosed as having cancer. In some embodiments, the methods described herein comprise administering an effective amount of compositions described herein to a subject in order to alleviate a symptom of a cancer. As used herein, "alleviating a symptom of a cancer" is ameliorating any condition or symptom associated with the cancer. As compared with an equivalent untreated control, such reduction is by at least 5%, 10%, 20%, 40%, 50%, 60%, 80%, 90%, 95%, 99% or more as measured by any standard technique. A variety of means for administering the compositions described herein to subjects are known to those of skill in the art. Such methods can include, but are not limited to oral, parenteral, intravenous, intramuscular, subcutaneous, transdermal, airway (aerosol), pulmonary, cutaneous, topical, injection, or intratumoral administration. Administration can be local or systemic.

[0065] The term "effective amount" as used herein refers to the amount of a NTRK1 inhibitor needed to alleviate at least one or more symptom of the disease or disorder, and relates to a sufficient amount of pharmacological composition to provide the desired effect. The term "therapeutically effective amount" therefore refers to an amount of an inhibitor of NTRK1 kinase activity that is sufficient to provide a particular anti-tumor effect when administered to a typical subject. An effective amount as used herein, in various contexts, would also include an amount sufficient to delay the development of a symptom of the disease, alter the course of a symptom disease (for example but not limited to, slowing the progression of a symptom of the disease), or reverse a symptom of the disease. Thus, it is not generally practicable to specify an exact "effective amount". However, for any given case, an appropriate "effective amount" can be determined by one of ordinary skill in the art using only routine experimentation.

[0066] Effective amounts, toxicity, and therapeutic efficacy can be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., for determining the LD50 (the dose lethal to 50%> of the population) and the ED50 (the dose therapeutically effective in 50%> of the population). The dosage can vary depending upon the dosage form employed and the route of administration utilized. The dose ratio between toxic and therapeutic effects is the therapeutic index and can be expressed as the ratio LD50/ED50. Compositions and methods that exhibit large therapeutic indices are preferred. A therapeutically effective dose can be estimated initially from cell culture assays. Also, a dose can be formulated in animal models to achieve a circulating plasma concentration range that includes the IC50 (i.e., the concentration of a NTRK1 inhibitor, which achieves a half-maximal inhibition of symptoms) as determined in cell culture, or in an appropriate animal model. Levels in plasma can be measured, for example, by high performance liquid chromatography. The effects of any particular dosage can be monitored by a suitable bioassay, e.g., assay for tumor and/or cancer cell growth, among others. The dosage can be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment. [0067] In some embodiments, the technology described herein relates to a pharmaceutical composition comprising a NTRK1 inhibitor as described herein, and optionally a pharmaceutically acceptable carrier. Pharmaceutically acceptable carriers and diluents include saline, aqueous buffer solutions, solvents and/or dispersion media. The use of such carriers and diluents is well known in the art. Some non-limiting examples of materials which can serve as pharmaceutically-acceptable carriers include: (1) sugars, such as lactose, glucose and sucrose; (2) starches, such as corn starch and potato starch; (3) cellulose, and its derivatives, such as sodium carboxymethyl cellulose, methylcellulose, ethyl cellulose, microcrystalline cellulose and cellulose acetate; (4) powdered tragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such as magnesium stearate, sodium lauryl sulfate and talc; (8) excipients, such as cocoa butter and suppository waxes; (9) oils, such as peanut oil, cottonseed oil, safflower oil, sesame oil, olive oil, corn oil and soybean oil; (10) glycols, such as propylene glycol; (11) polyols, such as glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12) esters, such as ethyl oleate and ethyl laurate; (13) agar; (14) buffering agents, such as magnesium hydroxide and aluminum hydroxide; (15) alginic acid; (16) pyrogen- free water; (17) isotonic saline; (18) Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21) polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents, such as polypeptides and amino acids (23) serum component, such as serum albumin, HDL and LDL; (22) C₂-Ci₂ alcohols, such as ethanol; and (23) other nontoxic compatible substances employed in pharmaceutical formulations. Wetting agents, coloring agents, release agents, coating agents, sweetening agents, flavoring agents, perfuming agents, preservative and antioxidants can also be present in the formulation. The terms such as "excipient", "carrier", "pharmaceutically acceptable carrier" or the like are used interchangeably herein. In some embodiments, the carrier inhibits the degradation of the active agent, e.g. a NTRK1 inhibitor as described herein.

[0068] In some embodiments, the pharmaceutical composition comprising a NTRK1 inhibitor as described herein can be a parenteral dose form. Since administration of parenteral dosage forms typically bypasses the patient's natural defenses against contaminants, parenteral dosage forms are preferably sterile or capable of being sterilized prior to administration to a patient. Examples of parenteral dosage forms include, but are not limited to, solutions ready for injection, dry products ready to be dissolved or suspended in a pharmaceutically acceptable vehicle for injection, suspensions ready for injection, and emulsions. In addition, controlled-release parenteral dosage forms can be prepared for administration of a patient, including, but not limited to, DUROS^®-type dosage forms and dose-dumping.

[0069] Suitable vehicles that can be used to provide parenteral dosage forms of a NTRK1 inhibitor as disclosed within are well known to those skilled in the art. Examples include, without limitation: sterile water; water for injection USP; saline solution; glucose solution; aqueous vehicles such as but not limited to, sodium chloride injection, Ringer's injection, dextrose Injection, dextrose and sodium chloride injection, and lactated Ringer's injection; water-miscible vehicles such as, but not limited to, ethyl alcohol, polyethylene glycol, and propylene glycol; and non-aqueous vehicles such as, but not limited to, corn oil, cottonseed oil, peanut oil, sesame oil, ethyl oleate, isopropyl myristate, and benzyl benzoate. Compounds that alter or modify the solubility of a pharmaceutically acceptable salt can also be incorporated into the parenteral dosage forms of the disclosure, including conventional and controlled-release parenteral dosage forms.

[0070] Pharmaceutical compositions comprising a NTRK1 inhibitor can also be formulated to be suitable for oral administration, for example as discrete dosage forms, such as, but not limited to, tablets (including without limitation scored or coated tablets), pills, caplets, capsules, chewable tablets, powder packets, cachets, troches, wafers, aerosol sprays, or liquids, such as but not limited to, syrups, elixirs, solutions or suspensions in an aqueous liquid, a non-aqueous liquid, an oil-in-water emulsion, or a water-in-oil emulsion. Such compositions contain a predetermined amount of the pharmaceutically acceptable salt of the disclosed compounds, and may be prepared by methods of pharmacy well known to those skilled in the art. See generally, Remington: The Science and Practice of Pharmacy, 21st Ed., Lippincott, Williams, and Wilkins, Philadelphia PA. (2005).

[0071] Conventional dosage forms generally provide rapid or immediate drug release from the formulation. Depending on the pharmacology and pharmacokinetics of the drug, use of conventional dosage forms can lead to wide fluctuations in the concentrations of the drug in a patient's blood and other tissues. These fluctuations can impact a number of parameters, such as dose frequency, onset of action, duration of efficacy, maintenance of therapeutic blood levels, toxicity, side effects, and the like. Advantageously, controlled-release formulations can be used to control a drug's onset of action, duration of action, plasma levels within the therapeutic window, and peak blood levels. In particular, controlled- or extended-release dosage forms or formulations can be used to ensure that the maximum effectiveness of a drug is achieved while minimizing potential adverse effects and safety concerns, which can occur both from under-dosing a drug (i.e., going below the minimum therapeutic levels) as well as exceeding the toxicity level for the drug. In some embodiments, the NTRK1 inhibitor can be administered in a sustained release formulation.

[0072] Controlled-release pharmaceutical products have a common goal of improving drug therapy over that achieved by their non-controlled release counterparts. Ideally, the use of an optimally designed controlled-release preparation in medical treatment is characterized by a minimum of drug substance being employed to cure or control the condition in a minimum amount of time. Advantages of controlled-release formulations include: 1) extended activity of the drug; 2) reduced dosage frequency; 3) increased patient compliance; 4) usage of less total drug; 5) reduction in local or systemic side effects; 6) minimization of drug accumulation; 7) reduction in blood level fluctuations; 8) improvement in efficacy of treatment; 9) reduction of potentiation or loss of drug activity; and 10) improvement in speed of control of diseases or conditions. Kim, Cherng-ju, Controlled Release Dosage Form Design, 2 (Technomic Publishing, Lancaster, Pa.: 2000).

[0073] Most controlled-release formulations are designed to initially release an amount of drug (active ingredient) that promptly produces the desired therapeutic effect, and gradually and continually release other amounts of drug to maintain this level of therapeutic or prophylactic effect over an extended period of time. In order to maintain this constant level of drug in the body, the drug must be released from the dosage form at a rate that will replace the amount of drug being metabolized and excreted from the body. Controlled-release of an active ingredient can be stimulated by various conditions including, but not limited to, pH, ionic strength, osmotic pressure, temperature, enzymes, water, and other physiological conditions or compounds.

[0074] A variety of known controlled- or extended-release dosage forms, formulations, and devices can be adapted for use with the salts and compositions of the disclosure. Examples include, but are not limited to, those described in U.S. Pat. Nos. : 3,845,770; 3,916,899; 3,536,809; 3,598,123; 4,008,719; 5674,533; 5,059,595; 5,591 ,767; 5, 120,548; 5,073,543; 5,639,476; 5,354,556; 5,733,566; and 6,365, 185 B l ; each of which is incorporated herein by reference. These dosage forms can be used to provide slow or controlled-release of one or more active ingredients using, for example,

hydroxypropylmethyl cellulose, other polymer matrices, gels, permeable membranes, osmotic systems (such as OROS^® (Alza Corporation, Mountain View, Calif. USA)), or a combination thereof to provide the desired release profile in varying proportions.

[0075] The methods described herein can further comprise administering a second agent and/or treatment to the subject, e.g. as part of a combinatorial therapy. Non-limiting examples of a second agent and/or treatment can include radiation therapy, surgery, gemcitabine, cisplastin, paclitaxel, carboplatin, bortezomib, AMG479, vorinostat, rituximab, temozolomide, rapamycin, ABT-737, PI- 103; alkylating agents such as thiotepa and CYTOXAN® cyclosphosphamide; alkyl sulfonates such as busulfan, improsulfan and piposulfan; aziridines such as benzodopa, carboquone, meturedopa, and uredopa; ethylenimines and methylamelamines including altretamine, triethylenemelamine, trietylenephosphoramide, triethiylenethiophosphoramide and trimethylolomelamine; acetogenins (especially bullatacin and bullatacinone); a camptothecin (including the synthetic analogue topotecan); bryostatin; callystatin; CC-1065 (including its adozelesin, carzelesin and bizelesin synthetic analogues); cryptophycins (particularly cryptophycin 1 and cryptophycin 8); dolastatin; duocarmycin (including the synthetic analogues, KW-2189 and CB 1 -TM1); eleutherobin;

pancratistatin; a sarcodictyin; spongistatin; nitrogen mustards such as chlorambucil, chlornaphazine, cholophosphamide, estramustine, ifosfamide, mechlorethamine, mechlorethamine oxide

hydrochloride, melphalan, novembichin, phenesterine, prednimustine, trofosfamide, uracil mustard; nitrosureas such as carmustine, chlorozotocin, fotemustine, lomustine, nimustine, and ranimnustine; antibiotics such as the enediyne antibiotics (e.g., calicheamicin, especially calicheamicin gammal l and calicheamicin omegall (see, e.g., Agnew, Chem. Intl. Ed. Engl., 33: 183-186 (1994)); dynemicin, including dynemicin A; bisphosphonates, such as clodronate; an esperamicin; as well as

neocarzinostatin chromophore and related chromoprotein enediyne antiobiotic chromophores), aclacinomysins, actinomycin, authramycin, azaserine, bleomycins, cactinomycin, carabicin, caminomycin, carzinophilin, chromomycinis, dactinomycin, daunorubicin, detorubicin, 6-diazo-5- oxo-L-norleucine, ADRIAMYCIN® doxorubicin (including morpholino-doxorubicin,

cyanomorpholino-doxorubicin, 2-pyrrolino-doxorubicin and deoxydoxorubicin), epirubicin, esorubicin, idarubicin, marcellomycin, mitomycins such as mitomycin C, mycophenolic acid, nogalamycin, olivomycins, peplomycin, potfiromycin, puromycin, quelamycin, rodorubicin, streptonigrin, streptozocin, tubercidin, ubenimex, zinostatin, zorubicin; anti-metabolites such as methotrexate and 5-fluorouracil (5-FU); folic acid analogues such as denopterin, methotrexate, pteropterin, trimetrexate; purine analogs such as fludarabine, 6-mercaptopurine, thiamiprine, thioguanine; pyrimidine analogs such as ancitabine, azacitidine, 6-azauridine, carmofur, cytarabine, dideoxyuridine, doxifluridine, enocitabine, floxuridine; androgens such as calusterone,

dromostanolone propionate, epitiostanol, mepitiostane, testolactone; anti-adrenals such as

aminoglutethimide, mitotane, trilostane; folic acid replenisher such as frolinic acid; aceglatone;

aldophosphamide glycoside; aminolevulinic acid; eniluracil; amsacrine; bestrabucil; bisantrene;

edatraxate; defofamine; demecolcine; diaziquone; elformithine; elliptinium acetate; an epothilone; etoglucid; gallium nitrate; hydroxyurea; lentinan; lonidainine; maytansinoids such as maytansine and ansamitocins; mitoguazone; mitoxantrone; mopidanmol; nitraerine; pentostatin; phenamet;

pirarubicin; losoxantrone; podophyllinic acid; 2-ethylhydrazide; procarbazine; PSK® polysaccharide complex (JHS Natural Products, Eugene, Oreg.); razoxane; rhizoxin; sizofuran; spirogermanium; tenuazonic acid; triaziquone; 2,2',2"-trichlorotriethylamine; trichothecenes (especially T-2 toxin, verracurin A, roridin A and anguidine); urethan; vindesine; dacarbazine; mannomustine; mitobronitol; mitolactol; pipobroman; gacytosine; arabinoside ("Ara-C"); cyclophosphamide; thiotepa; taxoids, e.g., TAXOL® paclitaxel (Bristol-Myers Squibb Oncology, Princeton, N.J.), ABRAXANE® Cremophor- free, albumin-engineered nanoparticle formulation of paclitaxel (American Pharmaceutical Partners, Schaumberg, 111.), and TAXOTERE® doxetaxel (Rhone-Poulenc Rorer, Antony, France);

chloranbucil; GEMZAR® gemcitabine; 6-thioguanine; mercaptopurine; methotrexate; platinum analogs such as cisplatin, oxalip latin and carboplatin; vinblastine; platinum; etoposide (VP- 16);

ifosfamide; mitoxantrone; vincristine; NAVELBINE.RTM. vinorelbine; novantrone; teniposide; edatrexate; daunomycin; aminopterin; xeloda; ibandronate; irinotecan (Camptosar, CPT-11)

(including the treatment regimen of irinotecan with 5-FU and leucovorin); topoisomerase inhibitor RFS 2000; difluoromethylornithine (DMFO); retinoids such as retinoic acid; capecitabine;

combretastatin; leucovorin (LV); oxaliplatin, including the oxaliplatin treatment regimen (FOLFOX); lapatinib (Tykerb.RTM.); inhibitors of PKC-alpha, Raf, H-Ras, EGFR (e.g., erlotinib (Tarceva®)) and VEGF-A that reduce cell proliferation and pharmaceutically acceptable salts, acids or derivatives of any of the above.

[0076] In addition, the methods of treatment can further include the use of radiation or radiation therapy. Further, the methods of treatment can further include the use of surgical treatments.

[0077] In certain embodiments, an effective dose of a composition comprising a NTRK1 inhibitor as described herein can be administered to a patient once. In certain embodiments, an effective dose of a composition comprising a NTRK1 inhibitor can be administered to a patient repeatedly. For systemic administration, subjects can be administered a therapeutic amount of a composition comprising a NTRKl inhibitor, such as, e.g. 0.1 mg/kg, 0.5 mg/kg, 1.0 mg/kg, 2.0 mg/kg, 2.5 mg/kg, 5 mg/kg, 10 mg/kg, 15 mg/kg, 20 mg/kg, 25 mg/kg, 30 mg/kg, 40 mg/kg, 50 mg/kg, or more.

[0078] In some embodiments, after an initial treatment regimen, the treatments can be administered on a less frequent basis. For example, after treatment biweekly for three months, treatment can be repeated once per month, for six months or a year or longer. Treatment according to the methods described herein can reduce levels of a marker or symptom of a condition, e.g. tumor and/or cancer cell growth by at least 10%, at least 15%, at least 20%, at least 25%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80 % or at least 90% or more.

[0079] The dosage of a composition as described herein can be determined by a physician and adjusted, as necessary, to suit observed effects of the treatment. With respect to duration and frequency of treatment, it is typical for skilled clinicians to monitor subjects in order to determine when the treatment is providing therapeutic benefit, and to determine whether to increase or decrease dosage, increase or decrease administration frequency, discontinue treatment, resume treatment, or make other alterations to the treatment regimen. The dosing schedule can vary from once a week to daily depending on a number of clinical factors, such as the subject's sensitivity to the NTRK1 inhibitor. The desired dose or amount of activation can be administered at one time or divided into subdoses, e.g., 2-4 subdoses and administered over a period of time, e.g., at appropriate intervals through the day or other appropriate schedule. In some embodiments, administration can be chronic, e.g., one or more doses and/or treatments daily over a period of weeks or months. Examples of dosing and/or treatment schedules are administration daily, twice daily, three times daily or four or more times daily over a period of 1 week, 2 weeks, 3 weeks, 4 weeks, 1 month, 2 months, 3 months, 4 months, 5 months, or 6 months, or more. A composition comprising a NTRK1 inhibitor can be administered over a period of time, such as over a 5 minute, 10 minute, 15 minute, 20 minute, or 25 minute period.

[0080] The dosage ranges for the administration of a NTRK1 inhibitor, according to the methods described herein depend upon, for example, the form of the NTRK1 inhibitor, its potency, and the extent to which symptoms, markers, or indicators of a condition described herein are desired to be reduced, for example the percentage reduction desired for tumor and/or cancer cell growth rate. The dosage should not be so large as to cause adverse side effects. Generally, the dosage will vary with the age, condition, and sex of the patient and can be determined by one of skill in the art. The dosage can also be adjusted by the individual physician in the event of any complication.

[0081] The efficacy of a NTRKl inhibitor in, e.g. the treatment of a condition described herein, or to induce a response as described herein (e.g. a reduction in tumor and/or cancer cell growth rate) can be determined by the skilled clinician. However, a treatment is considered "effective treatment," as the term is used herein, if one or more of the signs or symptoms of a condition described herein are altered in a beneficial manner, other clinically accepted symptoms are improved, or even ameliorated, or a desired response is induced e.g., by at least 10% following treatment according to the methods described herein. Efficacy can be assessed, for example, by measuring a marker, indicator, symptom, and/or the incidence of a condition treated according to the methods described herein or any other measurable parameter appropriate, e.g. tumor growth. Efficacy can also be measured by a failure of an individual to worsen as assessed by hospitalization, or need for medical interventions (i.e., progression of the disease is halted). Methods of measuring these indicators are known to those of skill in the art and/or are described herein. Treatment includes any treatment of a disease in an individual or an animal (some non-limiting examples include a human or an animal) and includes: (1) inhibiting the disease, e.g., preventing a worsening of symptoms (e.g. pain or inflammation); or (2) relieving the severity of the disease, e.g., causing regression of symptoms. An effective amount for the treatment of a disease means that amount which, when administered to a subject in need thereof, is sufficient to result in effective treatment as that term is defined herein, for that disease. Efficacy of an agent can be determined by assessing physical indicators of a condition or desired response, (e.g. tumor growth or size). It is well within the ability of one skilled in the art to monitor efficacy of administration and/or treatment by measuring any one of such parameters, or any combination of parameters. Efficacy can be assessed in animal models of a condition described herein, for example treatment of cancer. When using an experimental animal model, efficacy of treatment is evidenced when a statistically significant change in a marker is observed, e.g. tumor growth and/or survival.

[0082] In vitro and animal model assays are provided herein which allow the assessment of a given dose of an inhibitor of NTRKl kinase activity. By way of non-limiting example, the effects of a dose of an inhibitor of NTRKl kinase activity can be assessed by the growth and/or survival of a cancer cell line. For example, the cells of a cancer cell line can be contacted with a dose of an inhibitor of NTRKl kinase activity in vitro and their growth, activity, and/or viability measured to determine the efficacy of the dose. Such assays are known to one of skill in the art.

[0083] The efficacy of a given dosage combination can also be assessed in an animal model, e.g. a mouse model of cancer. For example, a dose of an inhibitor of NTRKl kinase activity can be administered to a mouse having cancer (e.g. induced and/or cause by introducing cancer cells (e.g. from a human tumor sample) into the mouse) and the growth of the tumor and/or the survival of the mouse measured to determine efficacy. Such assays are known to one of skill in the art.

[0084] In one aspect, described herein is a method of identifying an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of NTRK1, e.g. a genetic fusion of CHTOP and NTRK1 or ARHGEF2 and NTRK1 , the method comprising contacting a NTRK1 fusion peptide, e.g. a CHTOP-NTRK1 or ARHGEF2-NTRK1 polypeptide with a candidate agent detecting the level of kinase activity of the polypeptide wherein a decreased level of kinase activity in the presence of the candidate agent, as compared to a reference level, indicates the candidate agent is an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of NTRK1 , e.g. a genetic fusion of CHTOP and NTRK1 or ARHGEF2 and NTRK1. In some embodiments, a decreased level can be a level that is statistically significantly less than the reference level. In some embodiments, a decreased level can be a level that is at least 10% less than the reference level, e.g. 10% less, 20% less, 30% less, 50% less, 75% less, 80% less, 90% less or lower. In some embodiments, the reference level can be the level of kinase activity of a polypeptide contacted with a control, e.g. buffer, or which is not contacted.

[0085] In the context of the screening methods described herein, inhibiting the proliferation and survival of a cancer call refers to measuring or detecting any aspect of cell division, cell metabolism, growth, structure, and/or propagation which is indicative of either a healthy, viable, and/or dividing cell or a dead, nonviable and/or nonproliferative cell. Colorimetric, luminescent, radiometric, and/or fluorometric assays known in the art can be used. In some embodiments, the cancer cell can be a brain cancer cell, e.g. a glioblastoma cell.

[0086] In some embodiments, the polypeptide that is contacted is isolated, e.g. present in a non- cellular solution or on a substrate or matrix. In some embodiments, the polypeptide that is contacted is present in a cell. In some embodiments, the cancer cell can be a brain cancer cell, e.g. a glioblastoma cell. As used herein, the term "contacting" refers to any suitable means for delivering, or exposing, an agent to at least one polypeptide molecule. Exemplary delivery methods include, but are not limited to, direct delivery to cell culture medium, delivery to an in vitro scaffold in which cells are seeded, e.g., via perfusion or injection, or other delivery method well known to one skilled in the art. Kinase activity can be measured and/or determined as described elsewhere herein.

[0087] As used herein, a "candidate agent" refers to any entity which is normally not present or not present at the levels being administered to a cell, tissue or subject. A candidate agent can be selected from a group comprising: chemicals; small organic or inorganic molecules; nucleic acid sequences; nucleic acid analogues; proteins; peptides; aptamers; peptidomimetic, peptide derivative, peptide analogs, antibodies; intrabodies; biological macromolecules, extracts made from biological materials such as bacteria, plants, fungi, or animal cells or tissues; naturally occurring or synthetic compositions or functional fragments thereof. In some embodiments, the candidate agent is any chemical, entity or moiety, including without limitation synthetic and naturally-occurring non-proteinaceous entities. In certain embodiments the candidate agent is a small molecule having a chemical moiety. For example, chemical moieties include unsubstituted or substituted alkyl, aromatic, or heterocyclyl moieties including macrolides, leptomycins and related natural products or analogues thereof. Candidate agents can be known to have a desired activity and/or property, or can be selected from a library of diverse compounds.

[0088] Candidate compounds and agents can be screened for their ability to inhibit NTRK1 activity in vitro. The inhibition of NTRK1 kinase activity can also be monitored in vivo. Candidate agents are typically first screened for their ability to inhibit NTRK1 kinase activity in vitro and those candidate agents with such inhibitory effects are identified. Those agents are then tested for efficacy with respect to inhibition of NTRK1 kinase activity in an in vivo assay.

[0089] Generally, compounds can be tested at any concentration that can modulate kinase activity relative to a control over an appropriate time period. In some embodiments, compounds are tested at concentration in the range of about O. lnM to about lOOOmM. In one embodiment, the compound is tested in the range of about 0.1 μΜ to about 20μΜ, about 0.1 μΜ to about 10μΜ, or about 0.1 μΜ to about 5μΜ.

[0090] Depending upon the particular embodiment being practiced, the candidate or test agents can be provided free in solution, or can be attached to a carrier, or a solid support, e.g., beads. A number of suitable solid supports can be employed for immobilization of the candidate agents. Examples of suitable solid supports include agarose, cellulose, dextran (commercially available as, e.g., Sephadex, Sepharose) carboxymethyl cellulose, polystyrene, polyethylene glycol (PEG), filter paper, nitrocellulose, ion exchange resins, plastic films, polyaminemethylvinylether maleic acid copolymer, glass beads, amino acid copolymer, ethylene-maleic acid copolymer, nylon, silk, etc. Additionally, for the methods described herein, test compounds can be screened individually, or in groups. Group screening is particularly useful where hit rates for effective test compounds are expected to be low such that one would not expect more than one positive result for a given group.

[0091] Methods for developing small molecule, polymeric and genome based libraries are described, for example, in Ding, et al. J Am. Chem. Soc. 124: 1594-1596 (2002) and Lynn, et al., J. Am. Chem. Soc. 123: 8155-8156 (2001). Commercially available compound libraries can be obtained from, e.g., ArQule (Woburn, MA), Invitrogen (Carlsbad, CA), Ryan Scientific (Mt. Pleasant, SC), and Enzo Life Sciences (Farmingdale, NY). These libraries can be screened for the ability of members to inhibit NTRK1 kianse activity using e.g. methods described herein.

[0092] In some embodiments, the candidate agents can be naturally occurring proteins or their fragments. Such candidate agents can be obtained from a natural source, e.g., a cell or tissue lysate. Libraries of polypeptide agents can also be prepared, e.g., from a cDNA library commercially available or generated with routine methods. The candidate agents can also be peptides, e.g., peptides of from about 5 to about 30 amino acids, with from about 5 to about 20 amino acids being preferred and from about 7 to about 15 being particularly preferred. The peptides can be digests of naturally occurring proteins, random peptides, or "biased" random peptides. In some methods, the candidate agents are polypeptides or proteins. Peptide libraries, e.g. combinatorial libraries of peptides or other compounds can be fully randomized, with no sequence preferences or constants at any position. Alternatively, the library can be biased, i.e., some positions within the sequence are either held constant, or are selected from a limited number of possibilities. For example, in some cases, the nucleotides or amino acid residues are randomized within a defined class, for example, of hydrophobic amino acids, hydrophilic residues, sterically biased (either small or large) residues, towards the creation of cysteines, for cross-linking, prolines for SH-3 domains, serines, threonines, tyrosines or histidines for phosphorylation sites, or to purines.

[0093] The candidate agents can also be nucleic acids. Nucleic acid candidate agents can be naturally occurring nucleic acids, random nucleic acids, or "biased" random nucleic acids. For example, digests of prokaryotic or eukaryotic genomes can be similarly used as described above for proteins.

[0094] The candidate agent can function directly in the form in which it is administered.

Alternatively, the candidate agent can be modified or utilized intracellularly to produce a form that modulates the desired activity, e.g. introduction of a nucleic acid sequence into a cell and its transcription resulting in the production of an inhibitor of NTRK1 kinase activity within the cell.

[0095] For convenience, the meaning of some terms and phrases used in the specification, examples, and appended claims, are provided below. Unless stated otherwise, or implicit from context, the following terms and phrases include the meanings provided below. The definitions are provided to aid in describing particular embodiments, and are not intended to limit the claimed invention, because the scope of the invention is limited only by the claims. Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. If there is an apparent discrepancy between the usage of a term in the art and its definition provided herein, the definition provided within the specification shall prevail.

[0096] For convenience, certain terms employed herein, in the specification, examples and appended claims are collected here.

[0097] The terms "decrease", "reduced", "reduction", or "inhibit" are all used herein to mean a decrease by a statistically significant amount. In some embodiments, "reduce," "reduction" or "decrease" or "inhibit" typically means a decrease by at least 10% as compared to a reference level (e.g. the absence of a given treatment) and can include, for example, a decrease by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%>, at least about 95%, at least about 98%, at least about 99% , or more. As used herein, "reduction" or "inhibition" does not encompass a complete inhibition or reduction as compared to a reference level. "Complete inhibition" is a 100%) inhibition as compared to a reference level. A decrease can be preferably down to a level accepted as within the range of normal for an individual without a given disorder.

[0098] The terms "increased", "increase", "enhance", or "activate" are all used herein to mean an increase by a statically significant amount. In some embodiments, the terms "increased", "increase", "enhance", or "activate" can mean an increase of at least 10% as compared to a reference level, for example an increase of at least about 20%, or at least about 30%, or at least about 40%, or at least about 50%), or at least about 60%, or at least about 70%, or at least about 80%, or at least about 90% or up to and including a 100%) increase or any increase between 10-100%) as compared to a reference level, or at least about a 2-fold, or at least about a 3 -fold, or at least about a 4-fold, or at least about a 5-fold or at least about a 10-fold increase, or any increase between 2-fold and 10-fold or greater as compared to a reference level. In the context of a marker or symptom, a "increase" is a statistically significant increase in such level.

[0099] As used herein, a "subject" means a human or animal. Usually the animal is a vertebrate such as a primate, rodent, domestic animal or game animal. Primates include chimpanzees, cynomologous monkeys, spider monkeys, and macaques, e.g., Rhesus. Rodents include mice, rats, woodchucks, ferrets, rabbits and hamsters. Domestic and game animals include cows, horses, pigs, deer, bison, buffalo, feline species, e.g., domestic cat, canine species, e.g., dog, fox, wolf, avian species, e.g., chicken, emu, ostrich, and fish, e.g., trout, catfish and salmon. In some embodiments, the subject is a mammal, e.g., a primate, e.g., a human. The terms, "individual," "patient" and "subject" are used interchangeably herein.

[00100] Preferably, the subject is a mammal. The mammal can be a human, non-human primate, mouse, rat, dog, cat, horse, or cow, but is not limited to these examples. Mammals other than humans can be advantageously used as subjects that represent animal models of cancer. A subject can be male or female.

[00101] As used herein, the term "cancer'Or "tumor" refers to an uncontrolled growth of cells which interferes with the normal functioning of the bodily organs and systems. A subject that has a cancer or a tumor is a subject having objectively measurable cancer cells present in the subject's body. Included in this definition are benign and malignant cancers, as well as dormant tumors or micrometastases. Cancers which migrate from their original location and seed vital organs can eventually lead to the death of the subject through the functional deterioration of the affected organs.

[00102] The term "agent" refers generally to any entity which is normally not present or not present at the levels being administered to a cell, tissue or subject. An agent can be selected from a group including but not limited to: polynucleotides; polypeptides; small molecules; and antibodies or antigen-binding fragments thereof. A polynucleotide can be RNA or DNA, and can be single or double stranded, and can be selected from a group including, for example, nucleic acids and nucleic acid analogues that encode a polypeptide. A polypeptide can be, but is not limited to, a naturally- occurring polypeptide, a mutated polypeptide or a fragment thereof that retains the function of interest. Further examples of agents include, but are not limited to a nucleic acid aptamer, peptide - nucleic acid (PNA), locked nucleic acid (LNA), small organic or inorganic molecules; saccharide; oligosaccharides; polysaccharides; biological macromolecules, peptidomimetics; nucleic acid analogs and derivatives; extracts made from biological materials such as bacteria, plants, fungi, or mammalian cells or tissues and naturally occurring or synthetic compositions. An agent can be applied to the media, where it contacts the cell and induces its effects. Alternatively, an agent can be intracellular as a result of introduction of a nucleic acid sequence encoding the agent into the cell and its transcription resulting in the production of the nucleic acid and/or protein environmental stimuli within the cell. In some embodiments, the agent is any chemical, entity or moiety, including without limitation synthetic and naturally-occurring non-proteinaceous entities. In certain embodiments the agent is a small molecule having a chemical moiety selected, for example, from unsubstituted or substituted alkyl, aromatic, or heterocyclyl moieties including macrolides, leptomycins and related natural products or analogues thereof. Agents can be known to have a desired activity and/or property, or can be selected from a library of diverse compounds. As used herein, the term "small molecule" can refer to compounds that are "natural product-like," however, the term "small molecule" is not limited to "natural product-like" compounds. Rather, a small molecule is typically characterized in that it contains several carbon— carbon bonds, and has a molecular weight more than about 50, but less than about 5000 Daltons (5 kD). Preferably the small molecule has a molecular weight of less than 3 kD, still more preferably less than 2 kD, and most preferably less than 1 kD. In some cases it is preferred that a small molecule have a molecular mass equal to or less than 700 Daltons.

[00103] As used herein, the terms "protein" and "polypeptide" are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The terms "protein", and "polypeptide" refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogs, regardless of its size or function. "Protein" and

"polypeptide" are often used in reference to relatively large polypeptides, whereas the term "peptide" is often used in reference to small polypeptides, but usage of these terms in the art overlaps. The terms "protein" and "polypeptide" are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogs of the foregoing. [00104] As used herein, a "functional fragment" of, e.g. NTRK1, is a fragment or segment of that polypeptide which exhibits least 10% of the kinase activity of the reference polypeptide, e.g. at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 75%, at least 90%, at least 100% as strongly, or more strongly. Assays for measuring kinase activity are known in the art and described herein. A functional fragment can comprise conservative substitutions of the sequences disclosed herein.

[00105] Variants of the polypeptides described herein can be obtained by mutations of native nucleotide or amino acid sequences, for example SEQ ID NO: 8 or a nucleotide sequence encoding a peptide comprising SEQ ID NO:8. A "variant," as referred to herein, is a polypeptide substantially homologous to a reference polypeptide described herein (e.g. SEQ ID NO: 8), but which has an amino acid sequence different from that of one of the sequences described herein because of one or a plurality of deletions, insertions or substitutions.

[00106] The variant amino acid or DNA sequence preferably is at least 60%>, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%), at least 98%, at least 99%, or more, identical to the sequence from which it is derived (referred to herein as an "original" sequence). The degree of homology (percent identity) between an original and a mutant sequence can be determined, for example, by comparing the two sequences using freely available computer programs commonly employed for this purpose on the world wide web. The variant amino acid or DNA sequence preferably is at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%), at least 98%, at least 99%, or more, similar to the sequence from which it is derived (referred to herein as an "original" sequence). The degree of similarity (percent similarity) between an original and a mutant sequence can be determined, for example, by using a similarity matrix. Similarity matrices are well known in the art and a number of tools for comparing two sequences using similarity matrices are freely available online, e.g. BLASTp (available on the world wide web at http://blast.ncbi.nlm.nih.gov).

[00107] Alterations of the original amino acid sequence can be accomplished by any of a number of known techniques known to one of skill in the art. Mutations can be introduced, for example, at particular loci by synthesizing oligonucleotides containing a mutant sequence, flanked by restriction sites enabling ligation to fragments of the native sequence. Following ligation, the resulting reconstructed sequence encodes an analog having the desired amino acid insertion, substitution, or deletion. Alternatively, oligonucleotide-directed site-specific mutagenesis procedures can be employed to provide an altered nucleotide sequence having particular codons altered according to the substitution, deletion, or insertion required. Techniques for making such alterations include those disclosed by Walder et al. (Gene 42: 133, 1986); Bauer et al. (Gene 37:73, 1985); Craik

(BioTechniques, January 1985, 12-19); Smith et al. (Genetic Engineering: Principles and Methods, Plenum Press, 1981); and U.S. Pat. Nos. 4,518,584 and 4,737,462, which are herein incorporated by reference in their entireties. In some embodiments, an isolated peptide as described herein can be chemically synthesized and mutations can be incorporated as part of the chemical synthesis process.

[00108] Variants can comprise conservatively substituted sequences, meaning that one or more amino acid residues of an original peptide are replaced by different residues, and that the

conservatively substituted peptide retains a desired biological activity, i.e., the ability to bind heme, that is essentially equivalent to that of the original peptide. Examples of conservative substitutions include substitutions that do not change the overall or local hydrophobic character, substitutions that do not change the overall or local charge, substitutions by residues of equivalent sidechain size, or substitutions by sidechains with similar reactive groups.

[00109] A given amino acid can be replaced by a residue having similar physiochemical characteristics, e.g., substituting one aliphatic residue for another (such as He, Val, Leu, or Ala for one another), or substitution of one polar residue for another (such as between Lys and Arg; Glu and Asp; or Gin and Asn). Other such conservative substitutions, e.g., substitutions of entire regions having similar hydrophobicity characteristics or substitutions of residues with similar sidechain volume are well known. Isolated peptides comprising conservative amino acid substitutions can be tested in any one of the assays described herein to confirm that a desired activity, e.g. the ability to bind heme, is retained, as determined by the assays described elsewhere herein.

[00110] Amino acids can be grouped according to similarities in the properties of their side chains (in A. L. Lehninger, in Biochemistry, second ed., pp. 73-75, Worth Publishers, New York (1975)): (1) non-polar: Ala (A), Val (V), Leu (L), He (I), Pro (P), Phe (F), Trp (W), Met (M); (2) uncharged polar: Gly (G), Ser (S), Thr (T), Cys (C), Tyr (Y), Asn (N), Gin (Q); (3) acidic: Asp (D), Glu (E); (4) basic: Lys (K), Arg (R), His (H). Alternatively, naturally occurring residues can be divided into groups based on common side -chain properties: (1) hydrophobic: Norleucine, Met, Ala, Val, Leu, He, Phe, Trp; (2) neutral hydrophilic: Cys, Ser, Thr, Asn, Gin, Ala, Tyr, His, Pro, Gly; (3) acidic: Asp, Glu; (4) basic: His, Lys, Arg; (5) residues that influence chain orientation: Gly, Pro; (6) aromatic: Trp, Tyr, Phe, Pro, His, or hydroxyproline. Non-conservative substitutions will entail exchanging a member of one of these classes for another class.

[00111] Particularly preferred conservative substitutions for use in the variants described herein are as follows: Ala into Gly or into Ser; Arg into Lys; Asn into Gin or into His; Asp into Glu or into Asn; Cys into Ser; Gin into Asn; Glu into Asp; Gly into Ala or into Pro; His into Asn or into Gin; He into Leu or into Val; Leu into He or into Val; Lys into Arg, into Gin or into Glu; Met into Leu, into Tyr or into He; Phe into Met, into Leu or into Tyr; Ser into Thr; Thr into Ser; Trp into Tyr or into Phe; Tyr into Phe or into Trp; and/or Phe into Val, into Tyr, into He or into Leu. In general, conservative substitutions encompass residue exchanges with those of similar physicochemical properties (i.e. substitution of a hydrophobic residue for another hydrophobic amino acid). [00112] As used herein an "antibody" refers to IgG, IgM, IgA, IgD or IgE molecules or antigen- specific antibody fragments thereof (including, but not limited to, a Fab, F(ab')₂, Fv, disulphide linked Fv, scFv, single domain antibody, closed conformation multispecific antibody, disulphide-linked scfv, diabody), whether derived from any species that naturally produces an antibody, or created by recombinant DNA technology; whether isolated from serum, B-cells, hybridomas, transfectomas, yeast or bacteria.

[00113] As described herein, an "antigen" is a molecule that is bound by a binding site on an antibody agent. Typically, antigens are bound by antibody ligands and are capable of raising an antibody response in vivo. An antigen can be a polypeptide, protein, nucleic acid or other molecule or portion thereof. The term "antigenic determinant" refers to an epitope on the antigen recognized by an antigen-binding molecule, and more particularly, by the antigen-binding site of said molecule.

[00114] As used herein, the term "antibody reagent" refers to a polypeptide that includes at least one immunoglobulin variable domain or immunoglobulin variable domain sequence and which specifically binds a given antigen. An antibody reagent can comprise an antibody or a polypeptide comprising an antigen-binding domain of an antibody. In some embodiments, an antibody reagent can comprise a monoclonal antibody or a polypeptide comprising an antigen-binding domain of a monoclonal antibody. For example, an antibody can include a heavy (H) chain variable region (abbreviated herein as VH), and a light (L) chain variable region (abbreviated herein as VL). In another example, an antibody includes two heavy (H) chain variable regions and two light (L) chain variable regions. The term "antibody reagent" encompasses antigen-binding fragments of antibodies (e.g., single chain antibodies, Fab and sFab fragments, F(ab')2, Fd fragments, Fv fragments, scFv, and domain antibodies (dAb) fragments (see, e.g. de Wildt et al., Eur J. Immunol. 1996; 26(3):629-39; which is incorporated by reference herein in its entirety)) as well as complete antibodies. An antibody can have the structural features of IgA, IgG, IgE, IgD, IgM (as well as subtypes and combinations thereof). Antibodies can be from any source, including mouse, rabbit, pig, rat, and primate (human and non-human primate) and primatized antibodies. Antibodies also include midibodies, humanized antibodies, chimeric antibodies, and the like.

[00115] The VH and VL regions can be further subdivided into regions of hypervariability, termed "complementarity determining regions" ("CDR"), interspersed with regions that are more conserved, termed "framework regions" ("FR"). The extent of the framework region and CDRs has been precisely defined (see, Kabat, E. A., et al. (1991) Sequences of Proteins of Immunological Interest, Fifth Edition, U.S. Department of Health and Human Services, NIH Publication No. 91- 3242, and Chothia, C. et al. (1987) J. Mol. Biol. 196:901-917; which are incorporated by reference herein in their entireties). Each VH and VL is typically composed of three CDRs and four FRs, arranged from amino-terminus to carboxy-terminus in the following order: FR1 , CDR1 , FR2, CDR2, FR3, CDR3, FR4. [00116] The terms "antigen-binding fragment" or "antigen-binding domain", which are used interchangeably herein are used to refer to one or more fragments of a full length antibody that retain the ability to specifically bind to a target of interest. Examples of binding fragments encompassed within the term "antigen-binding fragment" of a full length antibody include (i) a Fab fragment, a monovalent fragment consisting of the VL, VH, CL and CHI domains; (ii) a F(ab')2 fragment, a bivalent fragment including two Fab fragments linked by a disulfide bridge at the hinge region; (iii) an Fd fragment consisting of the VH and CHI domains; (iv) an Fv fragment consisting of the VL and VH domains of a single arm of an antibody, (v) a dAb fragment (Ward et al., (1989) Nature 341 :544- 546; which is incorporated by reference herein in its entirety), which consists of a VH or VL domain; and (vi) an isolated complementarity determining region (CDR) that retains specific antigen-binding functionality. As used herein, the term "specific binding" refers to a chemical interaction between two molecules, compounds, cells and/or particles wherein the first entity binds to the second, target entity with greater specificity and affinity than it binds to a third entity which is a non-target. In some embodiments, specific binding can refer to an affinity of the first entity for the second target entity which is at least 10 times, at least 50 times, at least 100 times, at least 500 times, at least 1000 times or greater than the affinity for the third nontarget entity.

[00117] Additionally, and as described herein, a recombinant humanized antibody can be further optimized to decrease potential immunogenicity, while maintaining functional activity, for therapy in humans. In this regard, functional activity means a polypeptide capable of displaying one or more known functional activities associated with a recombinant antibody or antibody reagent thereof as described herein. Such functional activities include, e.g. the ability to bind to a genetic fusion as described herein.

[00118] As used herein, the term "nucleic acid" or "nucleic acid sequence" refers to any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analog thereof. The nucleic acid can be either single-stranded or double-stranded. A single-stranded nucleic acid can be one nucleic acid strand of a denatured double- stranded DNA. Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the nucleic acid can be DNA. In another aspect, the nucleic acid can be RNA. Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA. Other suitable nucleic acid molecules are RNA, including mRNA.

[00119] Inhibitors of the expression of a given gene can be an inhibitory nucleic acid. In some embodiments, the inhibitory nucleic acid is an inhibitory RNA (iRNA). Double-stranded RNA molecules (dsRNA) have been shown to block gene expression in a highly conserved regulatory mechanism known as RNA interference (RNAi). The inhibitory nucleic acids described herein can include an RNA strand (the antisense strand) having a region which is 30 nucleotides or less in length, i.e., 15-30 nucleotides in length, generally 19-24 nucleotides in length, which region is substantially complementary to at least part the targeted mRNA transcript. The use of these iRNAs enables the targeted degradation of mRNA transcripts, resulting in decreased expression and/or activity of the target.

[00120] As used herein, the term "iRNA" refers to an agent that contains RNA as that term is defined herein, and which mediates the targeted cleavage of an RNA transcript via an RNA-induced silencing complex (RISC) pathway. In one embodiment, an iRNA as described herein effects inhibition of the expression and/or activity of a NTRK1. In certain embodiments, contacting a cell with the inhibitor (e.g. an iRNA) results in a decrease in the target mRNA level in a cell by at least about 5%, about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90%, about 95%, about 99%, up to and including 100% of the target mRNA level found in the cell without the presence of the iRNA.

[00121] In some embodiments, the iRNA can be a dsRNA. A dsRNA includes two RNA strands that are sufficiently complementary to hybridize to form a duplex structure under conditions in which the dsRNA will be used. One strand of a dsRNA (the antisense strand) includes a region of complementarity that is substantially complementary, and generally fully complementary, to a target sequence. The target sequence can be derived from the sequence of an mRNA formed during the expression of the target. The other strand (the sense strand) includes a region that is complementary to the antisense strand, such that the two strands hybridize and form a duplex structure when combined under suitable conditions. Generally, the duplex structure is between 15 and 30 inclusive, more generally between 18 and 25 inclusive, yet more generally between 19 and 24 inclusive, and most generally between 19 and 21 base pairs in length, inclusive. Similarly, the region of complementarity to the target sequence is between 15 and 30 inclusive, more generally between 18 and 25 inclusive, yet more generally between 19 and 24 inclusive, and most generally between 19 and 21 nucleotides in length, inclusive. In some embodiments, the dsRNA is between 15 and 20 nucleotides in length, inclusive, and in other embodiments, the dsRNA is between 25 and 30 nucleotides in length, inclusive. As the ordinarily skilled person will recognize, the targeted region of an RNA targeted for cleavage will most often be part of a larger RNA molecule, often an mRNA molecule. Where relevant, a "part" of an mRNA target is a contiguous sequence of an mRNA target of sufficient length to be a substrate for RNAi-directed cleavage (i.e., cleavage through a RISC pathway). dsRNAs having duplexes as short as 9 base pairs can, under some circumstances, mediate RNAi-directed RNA cleavage. Most often a target will be at least 15 nucleotides in length, preferably 15-30 nucleotides in length.

[00122] In yet another embodiment, the RNA of an iRNA, e.g., a dsRNA, is chemically modified to enhance stability or other beneficial characteristics. The nucleic acids featured in the invention may be synthesized and/or modified by methods well established in the art, such as those described in "Current protocols in nucleic acid chemistry," Beaucage, S.L. et al. (Edrs.), John Wiley & Sons, Inc., New York, NY, USA, which is hereby incorporated herein by reference. Modifications include, for example, (a) end modifications, e.g., 5' end modifications (phosphorylation, conjugation, inverted linkages, etc.) 3' end modifications (conjugation, DNA nucleotides, inverted linkages, etc.), (b) base modifications, e.g., replacement with stabilizing bases, destabilizing bases, or bases that base pair with an expanded repertoire of partners, removal of bases (abasic nucleotides), or conjugated bases,

(c) sugar modifications (e.g., at the 2' position or 4' position) or replacement of the sugar, as well as

(d) backbone modifications, including modification or replacement of the phosphodiester linkages. Specific examples of RNA compounds useful in the embodiments described herein include, but are not limited to RNAs containing modified backbones or no natural internucleoside linkages. RNAs having modified backbones include, among others, those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified RNAs that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides. In particular embodiments, the modified RNA will have a phosphorus atom in its internucleoside backbone.

[00123] Modified RNA backbones can include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3 '-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, and

boranophosphates having normal 3'-5' linkages, 2'-5' linked analogs of these, and those) having inverted polarity wherein the adjacent pairs of nucleoside units are linked 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed salts and free acid forms are also included. Representative U.S. patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos. 3,687,808; 4,469,863; 4,476,301 ; 5,023,243; 5,177,195; 5,188,897; 5,264,423; 5,276,019;

5,278,302; 5,286,717; 5,321,131 ; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821 ; 5,541,316; 5,550,111 ; 5,563,253; 5,571,799; 5,587,361 ; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170; 6,172,209; 6, 239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423; 6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294; 6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and US Pat RE39464, each of which is herein incorporated by reference

[00124] Modified RNA backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatoms and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones;

formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts. Representative U.S. patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos. 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141 ; 5,235,033; 5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and, 5,677,439, each of which is herein incorporated by reference.

[00125] In other RNA mimetics suitable or contemplated for use in iRNAs, both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an RNA mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar backbone of an RNA is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative U.S. patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos. 5,539,082; 5,714,331 ; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found, for example, in Nielsen et al, Science, 1991, 254, 1497-1500.

[00126] Some embodiments featured in the invention include RNAs with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular— CH₂— NH— CH₂— ,— CH₂-N(CH₃)-0--CH₂--[known as a methylene (methylimino) or MMI backbone], -CH₂-0- N(CH₃)-CH₂-, -CH₂-N(CH₃)-N(CH₃)-CH₂- and -N(CH₃)-CH₂-CH₂-[wherein the native phosphodiester backbone is represented as -0-P-0-CH₂-] of the above-referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above -referenced U.S. Pat. No. 5,602,240. In some embodiments, the RNAs featured herein have morpholino backbone structures of the above- referenced U.S. Pat. No. 5,034,506.

[00127] Modified RNAs can also contain one or more substituted sugar moieties. The iRNAs, e.g., dsRNAs, featured herein can include one of the following at the 2' position: OH; F; 0-, S-, or N- alkyl; 0-, S-, or N-alkenyl; 0-, S- or N-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted Ci to Cio alkyl or C₂ to Cio alkenyl and alkynyl.

Exemplary suitable modifications include 0[(CH₂)_nO] _mCH₃, 0(CH₂)._nOCH₃, 0(CH₂)_nNH₂, 0(CH₂) _nCH₃, 0(CH₂)_nONH₂, and 0(CH₂)_nON[(CH₂)_nCH₃)]₂, where n and m are from 1 to about 10. In other embodiments, dsRNAs include one of the following at the 2' position: Ci to Cio lower alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, CI, Br, CN, CF₃, OCF₃, SOCH₃, S0₂CH₃, ON0₂, N0₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl,

aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an iRNA, or a group for improving the pharmacodynamic properties of an iRNA, and other substituents having similar properties. In some embodiments, the modification includes a 2'-methoxyethoxy (2'-0—

CH₂CH₂OCH₃, also known as 2'-0-(2-methoxyethyl) or 2'-MOE) (Martin et al, Helv. Chim. Acta, 1995, 78:486-504) i.e., an alkoxy-alkoxy group. Another exemplary modification is 2'- dimethylaminooxyethoxy, i.e., a 0(CH₂)₂0N(CH₃)₂ group, also known as 2'-DMAOE, as described in examples herein below, and 2'-dimethylaminoethoxyethoxy (also known in the art as 2'-0- dimethylaminoethoxyethyl or 2'-DMAEOE), i.e., 2'-0--CH₂--0--CH₂--N(CH₂)₂, also described in examples herein below.

[00128] Other modifications include 2'-methoxy (2'-OCH₃), 2'-aminopropoxy (2'- OCH₂CH₂CH₂NH₂) and 2'-fluoro (2'-F). Similar modifications can also be made at other positions on the RNA of an iRNA, particularly the 3' position of the sugar on the 3' terminal nucleotide or in 2'-5' linked dsRNAs and the 5' position of 5' terminal nucleotide. iRNAs may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative U.S. patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference.

[00129] An iRNA can also include nucleobase (often referred to in the art simply as "base") modifications or substitutions. As used herein, "unmodified" or "natural" nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5- methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6- methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5- propynyl uracil and cytosine, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl anal other 8-substituted adenines and guanines, 5- halo, particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7- methylguanine and 7-methyladenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7- daazaadenine and 3-deazaguanine and 3-deazaadenine. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in Modified Nucleosides in Biochemistry, Biotechnology and Medicine, Herdewijn, P. ed. Wiley- VCH, 2008; those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons, 1990, these disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y S., Chapter 15, dsRNA Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., Ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds featured in the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and 0-6 substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2°C (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., Eds., dsRNA Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are exemplary base substitutions, even more particularly when combined with 2'-0- methoxyethyl sugar modifications.

[00130] Representative U.S. patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos. 4,845,205; 5,130,30; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711 ; 5,552,540; 5,587,469; 5,594,121, 5,596,091 ; 5,614,617; 5,681,941 ; 6,015,886; 6,147,200; 6,166,197; 6,222,025; 6,235,887; 6,380,368; 6,528,640; 6,639,062; 6,617,438; 7,045,610; 7,427,672; and 7,495,088, each of which is herein incorporated by reference, and U.S. Pat. No. 5,750,692, also herein incorporated by reference.

[00131] The RNA of an iRNA can also be modified to include one or more locked nucleic acids (LNA). A locked nucleic acid is a nucleotide having a modified ribose moiety in which the ribose moiety comprises an extra bridge connecting the 2' and 4' carbons. This structure effectively "locks" the ribose in the 3'-endo structural conformation. The addition of locked nucleic acids to siRNAs has been shown to increase siRNA stability in serum, and to reduce off-target effects (Elmen, J. et al., (2005) Nucleic Acids Research 33(l):439-447; Mook, OR. et al., (2007) Mol Cane Ther 6(3):833-843; Grunweller, A. et al., (2003) Nucleic Acids Research 31(12):3185-3193). Representative U.S. Patents that teach the preparation of locked nucleic acid nucleotides include, but are not limited to, the following: U.S. Pat. Nos. 6,268,490; 6,670,461 ; 6,794,499; 6,998,484; 7,053,207; 7,084,125; and 7,399,845, each of which is herein incorporated by reference in its entirety.

[00132] Another modification of the RNA of an iRNA featured in the invention involves chemically linking to the RNA one or more ligands, moieties or conjugates that enhance the activity, cellular distribution, pharmacokinetic properties, or cellular uptake of the iRNA. Such moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acid. Sci. USA, 1989, 86: 6553-6556), cholic acid (Manoharan et al, Biorg. Med. Chem. Let., 1994, 4: 1053-1060), a thioether, e.g., beryl-S-tritylthiol (Manoharan et al, Ann. N.Y. Acad. Sci., 1992, 660:306-309; Manoharan et al, Biorg. Med. Chem. Let, 1993, 3:2765-2770), a thiocholesterol (Oberhauser et al, Nucl. Acids Res., 1992, 20:533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al, EMBO J, 1991, 10: 1111-1118; Kabanov et al, FEBS Lett., 1990, 259:327-330; Svinarchuk et al, Biochimie, 1993, 75:49-54), a phospholipid, e.g., di- hexadecyl-rac-glycerol or triethyl-ammonium l,2-di-0-hexadecyl-rac-glycero-3-phosphonate (Manoharan et al, Tetrahedron Lett., 1995, 36:3651-3654; Shea et al, Nucl. Acids Res., 1990, 18:3777-3783), a olyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides &

Nucleotides, 1995, 14:969-973), or adamantane acetic acid (Manoharan et al, Tetrahedron Lett., 1995, 36:3651-3654), a palmityl moiety (Mishra et al, Biochim. Biophys. Acta, 1995, 1264:229-237), or an octadecylamine or hexylamino-carbonyloxycholesterol moiety (Crooke et al, J. Pharmacol. Exp. Ther., 1996, 277:923-937).

[00133] A subject can be one who has been previously diagnosed with or identified as suffering from or having a condition in need of treatment (e.g. for a brain cancer) or one or more complications related to such a condition, and optionally, have already undergone treatment for cancer or the one or more complications related to cancer. Alternatively, a subject can also be one who has not been previously diagnosed as having cancer or one or more complications related to cancer. For example, a subject can be one who exhibits one or more risk factors for cancer or one or more complications related to cancer or a subject who does not exhibit risk factors.

[00134] A "subject in need" of treatment for a particular condition can be a subject having that condition, diagnosed as having that condition, or at risk of developing that condition.

[00135] As used herein, the terms "protein" and "polypeptide" are used interchangeably herein to designate a series of amino acid residues, connected to each other by peptide bonds between the alpha-amino and carboxy groups of adjacent residues. The terms "protein", and "polypeptide" refer to a polymer of amino acids, including modified amino acids (e.g., phosphorylated, glycated, glycosylated, etc.) and amino acid analogs, regardless of its size or function. "Protein" and

"polypeptide" are often used in reference to relatively large polypeptides, whereas the term "peptide" is often used in reference to small polypeptides, but usage of these terms in the art overlaps. The terms "protein" and "polypeptide" are used interchangeably herein when referring to a gene product and fragments thereof. Thus, exemplary polypeptides or proteins include gene products, naturally occurring proteins, homologs, orthologs, paralogs, fragments and other equivalents, variants, fragments, and analogs of the foregoing.

[00136] As used herein, the term "nucleic acid" or "nucleic acid sequence" refers to any molecule, preferably a polymeric molecule, incorporating units of ribonucleic acid, deoxyribonucleic acid or an analog thereof. The nucleic acid can be either single-stranded or double-stranded. A single-stranded nucleic acid can be one nucleic acid strand of a denatured double- stranded DNA. Alternatively, it can be a single-stranded nucleic acid not derived from any double-stranded DNA. In one aspect, the nucleic acid can be DNA. In another aspect, the nucleic acid can be RNA. Suitable nucleic acid molecules are DNA, including genomic DNA or cDNA. Other suitable nucleic acid molecules are RNA, including mRNA.

[00137] As used herein, the terms "treat," "treatment," "treating," or "amelioration" refer to therapeutic treatments, wherein the object is to reverse, alleviate, ameliorate, inhibit, slow down or stop the progression or severity of a condition associated with a disease or disorder, e.g. cancer. The term "treating" includes reducing or alleviating at least one adverse effect or symptom of a condition, disease or disorder associated with a cancer. Treatment is generally "effective" if one or more symptoms or clinical markers are reduced. Alternatively, treatment is "effective" if the progression of a disease is reduced or halted. That is, "treatment" includes not just the improvement of symptoms or markers, but also a cessation of, or at least slowing of, progress or worsening of symptoms compared to what would be expected in the absence of treatment. Beneficial or desired clinical results include, but are not limited to, alleviation of one or more symptom(s), diminishment of extent of disease, stabilized (i.e., not worsening) state of disease, delay or slowing of disease progression, amelioration or palliation of the disease state, remission (whether partial or total), and/or decreased mortality, whether detectable or undetectable. The term "treatment" of a disease also includes providing relief from the symptoms or side-effects of the disease (including palliative treatment).

[00138] As used herein, the term "pharmaceutical composition" refers to the active agent in combination with a pharmaceutically acceptable carrier e.g. a carrier commonly used in the pharmaceutical industry. The phrase "pharmaceutically acceptable" is employed herein to refer to those compounds, materials, compositions, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.

[00139] As used herein, the term "administering," refers to the placement of a compound as disclosed herein into a subject by a method or route which results in at least partial delivery of the agent at a desired site. Pharmaceutical compositions comprising the compounds disclosed herein can be administered by any appropriate route which results in an effective treatment in the subject.

[00140] The term "statistically significant" or "significantly" refers to statistical significance and generally means a two standard deviation (2SD) or greater difference.

[00141] Other than in the operating examples, or where otherwise indicated, all numbers expressing quantities of ingredients or reaction conditions used herein should be understood as modified in all instances by the term "about." The term "about" when used in connection with percentages can mean ±1%.

[00142] As used herein the term "comprising" or "comprises" is used in reference to

compositions, methods, and respective component(s) thereof, that are essential to the method or composition, yet open to the inclusion of unspecified elements, whether essential or not.

[00143] The term "consisting of refers to compositions, methods, and respective components thereof as described herein, which are exclusive of any element not recited in that description of the embodiment. [00144] As used herein the term "consisting essentially of refers to those elements required for a given embodiment. The term permits the presence of elements that do not materially affect the basic and novel or functional characteristic(s) of that embodiment.

[00145] The singular terms "a," "an," and "the" include plural referents unless context clearly indicates otherwise. Similarly, the word "or" is intended to include "and" unless the context clearly indicates otherwise. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of this disclosure, suitable methods and materials are described below. The abbreviation, "e.g." is derived from the Latin exempli gratia, and is used herein to indicate a non-limiting example. Thus, the abbreviation "e.g." is synonymous with the term "for example."

[00146] Definitions of common terms in cell biology and molecular biology can be found in "The Merck Manual of Diagnosis and Therapy", 19th Edition, published by Merck Research Laboratories, 2006 (ISBN 0-911910-19-0); Robert S. Porter et al. (eds.), The Encyclopedia of Molecular Biology, published by Blackwell Science Ltd., 1994 (ISBN 0-632-02182-9); Benjamin Lewin, Genes X, published by Jones & Bartlett Publishing, 2009 (ISBN-10: 0763766321); Kendrew et al. (eds.), , Molecular Biology and Biotechnology: a Comprehensive Desk Reference, published by VCH Publishers, Inc., 1995 (ISBN 1-56081-569-8) and Current Protocols in Protein Sciences 2009, Wiley Intersciences, Coligan et al., eds.

[00147] Unless otherwise stated, the present invention was performed using standard procedures, as described, for example in Sambrook et al., Molecular Cloning: A Laboratory Manual (3 ed.), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., USA (2001); Davis et al., Basic Methods in Molecular Biology, Elsevier Science Publishing, Inc., New York, USA (1995); or Methods in Enzymology: Guide to Molecular Cloning Techniques Vol.152, S. L. Berger and A. R. Kimmel Eds., Academic Press Inc., San Diego, USA (1987); Current Protocols in Protein Science (CPPS) (John E. Coligan, et. al., ed., John Wiley and Sons, Inc.), Current Protocols in Cell Biology (CPCB) (Juan S. Bonifacino et. al. ed., John Wiley and Sons, Inc.), and Culture of Animal Cells: A Manual of Basic Technique by R. Ian Freshney, Publisher: Wiley-Liss; 5th edition (2005), Animal Cell Culture Methods (Methods in Cell Biology, Vol. 57, Jennie P. Mather and David Barnes editors, Academic Press, 1st edition, 1998) which are all incorporated by reference herein in their entireties.

[00148] Other terms are defined herein within the description of the various aspects of the invention.

[00149] All patents and other publications; including literature references, issued patents, published patent applications, and co-pending patent applications; cited throughout this application 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 technology described herein. 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 representation as to the contents of these documents is based on the information available to the applicants and does not constitute any admission as to the correctness of the dates or contents of these documents.

[00150] The description of embodiments of the disclosure is not intended to be exhaustive or to limit the disclosure to the precise form disclosed. While specific embodiments of, and examples for, the disclosure are described herein for illustrative purposes, various equivalent modifications are possible within the scope of the disclosure, as those skilled in the relevant art will recognize. For example, while method steps or functions are presented in a given order, alternative embodiments may perform functions in a different order, or functions may be performed substantially concurrently. The teachings of the disclosure provided herein can be applied to other procedures or methods as appropriate. The various embodiments described herein can be combined to provide further embodiments. Aspects of the disclosure can be modified, if necessary, to employ the compositions, functions and concepts of the above references and application to provide yet further embodiments of the disclosure. Moreover, due to biological functional equivalency considerations, some changes can be made in protein structure without affecting the biological or chemical action in kind or amount. These and other changes can be made to the disclosure in light of the detailed description. All such modifications are intended to be included within the scope of the appended claims.

[00151] Specific elements of any of the foregoing embodiments can be combined or substituted for elements in other embodiments. Furthermore, while advantages associated with certain embodiments of the disclosure have been described in the context of these embodiments, other embodiments may also exhibit such advantages, and not all embodiments need necessarily exhibit such advantages to fall within the scope of the disclosure.

[00152] The technology described herein is further illustrated by the following examples which in no way should be construed as being further limiting.

[00153] Some embodiments of the technology described herein can be defined according to any of the following numbered paragraphs:

1. A method of treating cancer in a subject in need thereof the method comprising:

administering an inhibitor of NTRK1 kinase activity to a subject determined to have a genetic fusion of NTRK1 and a second gene.

2. The method of paragraph 1, wherein the second gene is CHTOP or ARHGEF2.

3. The method of any of paragraphs 1-2, wherein the genetic fusion comprises NTRK1 as the 3' fusion partner.

4. The method of any of paragraphs 1-3, wherein the genetic fusion comprises a chromosomal rearrangement. The method of any of paragraphs 1-4, wherein the subject is determined to have a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl by detecting the presence of a CHTOP-NTRK1 or ARHGEF2 -NTRKl fusion protein.

The method of paragraph 5, wherein the fusion protein has the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 3.

The method of any of paragraphs 5-6, wherein the presence of the fusion protein is detected using an immunoassay.

The method of any of paragraphs 1-4, wherein the subject is determined to have a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl by detecting the presence of a nucleic acid encoding a CHTOP-NTRK1 or ARHGEF2-NTRK1 fusion protein.

The method of paragraph 8, wherein the nucleic acid has the sequence of SEQ ID NO: 2 or SEQ ID NO: 4.

The method of any of paragraphs 8-9, wherein the presence of the nucleic acid is detected using a method selected from the group consisting of:

karyotyping; PCR; RT-PCR; sequencing; and FISH.

The method of any of paragraphs 1-12, wherein the inhibitor of NTRKl kinase activity is selected from the group consisting of:

AZD7451 ; Crizotinib; ARRY-470; CEP-701 ; AG 879; GW 441756; and Ro 08-2750. The method of any of paragraphs 1-11, wherein the cancer is a brain cancer.

The method of any of paragraphs 1-12, wherein the brain cancer is a glioblastoma.

The method of any of paragraphs 1-13, further comprising the step of assaying a sample obtained from the subject to detect the presence or absence of a genetic fusion of NTRKl and a second gene.

A method of identifying an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl , the method comprising:

contacting a CHTOP-NTRK1 or ARHGEF2 -NTRKl polypeptide with a candidate agent;

detecting the level of kinase activity of the polypeptide;

wherein a decreased level of kinase activity in the presence of the candidate agent, as compared to a reference level, indicates the candidate agent is an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl .

The method of paragraph 15, wherein the cancer cell is a brain cancer cell.

The method of paragraph 15, wherein the cancer cell is a glioblastoma cell.

EXAMPLES [00154] Anchored multiplex PCR for targeted next-generation sequencing

[00155] Targeted next-generation sequencing (NGS) is an important approach for both research and clinical applications. Described herein is the discovery of therapeutically important novel gene fusions: MSN-ROS1, ARHGEF2-NTRK1 , and CHTOP-NTRK1 using a method termed anchored multiplex polymerase chain reaction (AMP). AMP offers a rapid, economical, and scalable target enrichment solution in a single tube format for greater than 300 amplicons. The assay is designed for low nucleic acid input (25 ng DNA) and low quality formalin-fixed paraffin-embedded (FFPE) specimens, delivering robust performance across various clinical sample types. The utility of AMP for the detection of gene rearrangements, single nucleotide variants, insertions/deletions, and copy number changes from clinical FFPE specimens is demonstrated herein. Relying on a core set of standard molecular biology reagents, AMP may be highly scalable yet easily implemented within less than one working day for targeted applications in RNA-Seq, genomic DNA sequencing, clinical genotyping, and confirmation sequencing.

[00156] Next-generation sequencing has been instrumental in the advancement of genomic research and clinical molecular diagnostics in recent years. While the cataloguing of complete genomes and their variation is an important endeavor for reference building and discovery, the use of whole human genome sequencing outside of this context is impractical with respect to cost and efficiency¹. Certain applications such as cancer genotyping for somatic mutations require selective deep sequencing to achieve the desired analytical sensitivity for clinical utility². At the present time, clinical sequencing is most feasible for assays based on targeted gene panels or whole exomes. The emerging need for a rapid and focused confirmation sequencing strategy to validate variants remains to be addressed. Currently, there is need for a rapid and efficient technique for gene rearrangement detection by next generation sequencing.

[00157] AMP addresses the escalating demand within molecular diagnostics for gene

rearrangement testing of the ALK, RET, and ROSl genes, all of which are associated with response to targeted therapy in lung cancer ^3~6. For rearrangement testing, fluorescence in situ hybridization (FISH) shows limited scalability for high- volume multi-target testing and requires diagnostic expertise. Immunohistochemistry (IHC) is used to detect expressed fusion genes as a surrogate marker for gene rearrangement; however, the technique relies on the availability of good quality antibodies and qualitative scoring. Both FISH and IHC do not provide specific fusion partner breakpoint details which may be the underlying explanation for heterogeneous treatment responses ⁴'⁷'⁸. Reverse transcription-PCR on the other hand may yield such information but requires knowledge of all fusion partner variants for primer design and demonstrates limited scalability in the setting of multiple heterologous partners and their involved exons. For example, ROSl rearrangements in lung cancer pose a challenge due to potential involvement with at least seven different fusion partners and variable splicing ⁹. [00158] The initial motivation for AMP was to tackle all the current deficiencies of clinical gene rearrangement detection noted above by employing a targeted RNA-Seq strategy. Briefly, double- stranded cDNA undergoes end-repair, adenylation, and ligation, as previously described¹⁰, with a novel universal half- functional adapter. The resulting half-functional library by itself is insufficient for downstream bridge amplification, emulsion PCR, or sequencing. The library is rendered fully functional at the end of two rounds of low-cycle, nested PCR which are utilized for target enrichment. The second PCR step uses nested primers which are 5' tagged with a common sequencing adapter (Fig. 6). In combination with the first half- functional universal adapter, the resulting target amplicons are functionalized for clonal amplification (e.g. emulsion PCR or bridge PCR) and sequencing. Non- target fragments remain half- functional/inconsequential and do not need to be eliminated from the library. Libraries are quantitated and processed for MiSeq or Ion Torrent sequencing (Fig. 1).

[00159] One powerful advantage of AMP is the anchoring of target-specific nested primers on one side while the other end is randomly ligated with the half- functional universal adapter. In contrast to other routine PCR techniques, AMP enables enrichment of a target region with knowledge of only one of its ends, avoiding the need to flank both ends with primers. We exploited this feature of AMP for targeted RNA-Seq detection of gene rearrangements using total nucleic acid derived from clinical FFPE material (Fig. 6). Gene fusion detection via targeted RNA-Seq offers several advantages over genomic DNA sequencing, including expressed fusion transcript sequence information, a smaller target window, potentially easier unique alignment, and confident fusion calls with deeper coverage. A single-tube 23-plex AMP panel was designed to amplify the kinase domains of ALK, RET, ROS1, MUSK, and the CTBP1 housekeeping gene as an internal control (Fig. 4). Amplification of these target transcripts from the target-specific anchored end allows detection of nearly all potentially expressed fusion partners on the other end. The unknown partner may be located 5' upstream or 3' downstream of the targeted, anchored end of the transcript.

[00160] Known FISH-positive ROS1 fusion cases were tested and revealed multiple partners, including CD74 exon 6, SLC34A2 exon 13, and EZR exon 10, fused to ROS1 exon 34 as the most frequent fusion variants. Interestingly, a small fraction of alternative splicing events were also detected, such as the in-frame CD74 exon6-ROSl exon35 and SLC34A2 exonl3-ROSl exon32 fusion transcripts. Similarly, this assay successfully detected EML4-ALK, SDC-ALK, and KIF5B- RET fusions in lung cancer, and CCDC6-RET and NOCA4-RET in thyroid cancer, all detected with a minimal set of anchored primers targeting the kinase domains of the three genes from the 3' end of the fusion transcripts (Fig 2A).

[00161] A 137-plex expanded rearrangement AMP panel was developed for discovery to detect possible fusions with 14 additional receptor tyrosine kinase genes, and revealed an FGFR3-TACC3 fusion in glioblastoma (targeted from the 5' end of the fusion transcript) and ETV6-NTRK3 fusion in a case of secretory breast carcinoma (Fig. 4). [00162] Further, a novel in-frame gene rearrangement involving exon 9 of the Moesin encoding gene (MSN) and exon 34 of the ROSl gene (Fig 2A) was detected in a lung cancer case which was also detected by a hybrid selection assay targeting the consensus breakpoint intronic region of ROSl (data not shown)¹¹. Additionally, two novel in-frame fusions that were detected in three glioblastoma tumors as a result of screening a total of 115 cases: ARHGEF2-NTRK1 (1 case) and CHTOP-NTRK1 (2 cases) (Figs. 7A-7B). These gene fusions were confirmed by FISH and RT-PCR, respectively, and more importantly represent potential therapeutic targets with small-molecule inhibitors¹².

[00163] As a clinical gene rearrangement assay, AMP also demonstrated superior performance with respect to clinical sensitivity and specificity when compared to standard clinical FISH assays. Using TNA extracted from 319 FFPE samples, the targeted RNA-Seq assay detected 55 of 56 FISH positive cases, with a clinical sensitivity of 98.2%. All 274 negative FISH cases were negative by the targeted RNA-Seq assay, resulting in a clinical specificity of 100%). Indeterminate FISH cases were not included in the calculations (Table 2). One discrepant case was clinically reported as

indeterminate by FISH based on an unusual but abnormal pattern of tandem ROSl gene copies with one copy showing an imbalance between the 5' and 3' signals (data not shown). AMP definitively detected a CD74-ROS1 rearrangement in this case, suggesting that targeted RNA-Seq may be more specific than FISH. Unusual ALK and ROSl FISH cases showing individual 5' (green only) probe signals upstream of the receptor tyrosine kinase gene present a diagnostic challenge for the clinical lab. Evaluation of these indeterminate cases with the AMP assay did not show any typical ALK and ROSl fusion gene transcripts (data not shown), indicating the possibility of atypical structural changes detected by FISH that are not related to the known crizotinib-sensitive ALK and ROSl gene rearrangements.

[00164] Of note, the green-only ALK FISH case (data not shown) did not show increased ALK expression by immunohistochemistry (typically expected in an ALK-rearranged tumor) but instead harbored a KRAS mutation detected by genotyping (usually mutually exclusive of ALK

rearrangement). Similarly, the green-only ROSl FISH case (data not shown) showed no response to crizotinib after 8 weeks of treatment indicating the biological absence of a canonical ROSl rearrangement.

[00165] Because AMP works with any double-stranded starting nucleic acid, its utility for targeted sequencing of genomic DNA was determined. Assay performance was evaluated by assessing the sequence on-target specificity rate and minimum coverage across target bases with two targeted gDNA assays: a 626-amplicon assay for all coding regions of 18 important tumor suppressor genes, and a 96-amplicon assay for cancer hotspot mutations and all coding regions of three tumor suppressor genes TP53, PTEN, and CDKN2A (Fig. 2D, Fig. 4). A bi-template (plus and minus strands) sequencing approach was employed when targeting >200bp exons. To avoid conventional PCR, the plus and minus primers were segregated into two reactions, effectively yielding a 313-plex reaction per tube for the 626-amplicon assay and a 48-plex reaction per tube for the 96-amplicon assay.

[00166] Different PCR conditions were assessed using the 626-amplicon assay on a non-tumor FFPE sample (Fig. 3). PCR amplification bias among extreme GC -content amplicons was greatly improved by using a slower ramping rate during PCR¹³. Therefore, a 20% ramping rate was set for all PCR amplifications. Tetramethyl ammonium chloride (TMAC) to improve amplification of A-T rich targets ¹⁴'¹⁵ was tested, as were three different polymerases: Platinum Taq™, OneTaq™ and Phusion HF™. Platinum Taq polymerase resulted in the highest rate of mapped (99.5% to human genome) and on-target (88%) reads, with 97% of targeted bases sequenced at more than 100-fold coverage and 94% at more than 500-fold for the 626-amplicon assay (Fig. 2B). The majority of targeted bases showed even coverage: 93.1% within 5-fold above and below the average (25-fold range) and 83.9% within 3.2-fold above and below the average (10-fold range). OneTaq™ and Phusion HF™ yielded poorer performance while addition of TMAC to Platinum Taq™ showed only minor improvement in uniformity (94.3% coverage within 25-fold and 86.5% within 10-fold) (Fig. 3). Of note, these enrichment metrics were achieved with one primer design, synthesis, and pooling attempt without any further optimizations.

[00167] To evaluate the robustness of the AMP method for limited amounts of starting material, the sequencing results of AMP libraries generated with total input amounts of 200, 100, 50, 10 and 5 ng of an FFPE tumor DNA sample divided across a two-tube assay were analyzed. The 96-amplicon hotspot plus tumor suppressor assay was utilized for testing. Alignment percentages and on-target reads were similar for the five libraries. While minimum target coverage for the first three libraries were 100% at >100X and -96% at >500X, it decreased for the 10-ng library (91% and 75%, respectively) and even further for the 5-ng library (82% and 61%, respectively) (Fig. 3). The raw read pileup for EGFR exon 20 showed adequate library complexity with few duplicates for samples with 50-ng or higher input. In contrast, lower library complexity and higher duplication rates were observed for the 10-ng and 5-ng input samples (Fig. 8). These results indicate that an adapter ligation approach for AMP optimally requires 25 ng of minimal DNA input per reaction.

[00168] Next, the ability of AMP to detect known single nucleotide variants, indels, and copy number change previously genotyped with clinical assays¹⁶ was determined. Using the 96-amplicon AMP hotspot mutation assay, all expected single nucleotide variants, insertions (3- and 12-bp in ERBB2), and deletions (15- and 18-bp in EGFR) previously genotyped in a clinical laboratory were identified (Fig. 2C, Fig. 3). The use of minimal cycling for the PCR steps in AMP maintains linear amplification across targets. As a result, an EGFR gene amplification was identified by its excessive read coverage relative to the inter-sample average EGFR read depth as well as relative to the read coverage of an intra-sample reference control target (Fig. 9). The results indicate the capability of AMP to preserve allelic abundance for copy number detection. [00169] Various target enrichment methods for NGS have been described and compared, each associated with its own advantages and disadvantages¹. For example, microdroplet-based PCR may achieve a high level of multiplexing and uniformity¹⁷; however, it requires special instrumentation and a large amount of input template (> 1 μg DNA) which is often not available in clinical specimens. The molecular inversion probe approach is based on an initial long hybridization step and suffers from low target evenness with only 58% of targets within a 10-fold abundance range¹⁸. Hybridization-capture based target enrichment has demonstrated high scalability from hundreds of genes ¹⁹ to the human exome²⁰. This method generally requires lengthy hybridization, a relatively large amount of starting material, and specialized bait design/synthesis/optimization. Although operational in terms of medium

21 22 23

level scalability, other methods such as AmpliSeq , TruSeq Amplicon , Haloplex , and Nested Patch PCR²⁴ all suffer from strategies that target the two ends flanking a region of interest, yielding sequencing read pileups that are blunted on both ends. As a result, the lack of unique sequencing start sites may introduce systematic errors and preclude confident variant calling based on random sequence sampling.

[00170] Anchored multiplex PCR (AMP) is described herein as a novel enrichment method for targeted RNA and DNA next generation sequencing. Its robust utility for detection of gene fusions, point mutations, insertion/deletions, and copy number changes from low amounts of clinical FFPE RNA and DNA samples is demonstrated herein.

[00171] A unique advantage of this system compared to other PCR methods is the ability to assess for unique reads based on randomly distributed sequencing start sites on the end ligated with the universal half-functional adapter. As a result, sequence read complexity based on random start sites may be assessed in contrast to other PCR based enrichment techniques described above. By targeting sequences based on a one-sided nested primer approach, AMP offers the distinctive ability to agnostically detect gene rearrangements by simply targeting one of the consistently involved fusion partners. Based on a core set of standard molecular biology reagents, AMP utilizes routine primers that may be quickly designed and synthesized as part of a facile, custom targeted sequencing solution for which library construction could be completed in less than one working day (Fig. 10). The method described herein is economical and easily accessible for such applications as confirmation sequencing for larger scale methods like whole exome or genome sequencing. AMP is scalable for targeted applications in RNA-Seq, genomic DNA sequencing, and clinical genotyping.

[00172] METHODS

[00173] Study samples and nucleic acids extraction. Samples submitted for genotyping in Diagnostic Molecular Pathology Laboratory, Massachusetts General Hospital (MGH), were used in this study. Total nucleic acids containing total RNA and genomic DNA were extracted from formalin- fixed paraffin-embedded biopsies, using the Agencourt FORMAPURE™ Kit for FFPE Tissue (Beckman Coulter, Indianapolis, IN). ALK, RET, ROS1, and PPARG FISH results were available for comparison based on assays performed as previously described ⁴'⁵. In addition, SNaPshot™ point mutation results were available for comparison based on genotyping performed as previously described¹⁶. The study was approved by the MGH IRB and Partners Healthcare Human Research Committee.

[00174] Anchored Multiplex Polymerase Chain Reaction. Library construction for AMP (Fig. 1) starts with RNA or total nucleic acid (DNA and RNA mix) as input, without the need for ribosomal RNA or genomic DNA depletion. First and second strand complementary DNA (cDNA) synthesis was performed using a combination of Superscript III™ (Life Technologies, Carlsbad, CA), DNA Polymerase I (Enzymatics, Beverly, MA), and RNAse H (Enzymatics). Double-stranded cDNA was cleaned with Ampure XP SPRI™ beads (Beckman Coulter). Either double-stranded cDNA or alternatively genomic DNA underwent end-repair (End-Repair Mix, Enzymatics), adenylation (Klenow Exo-, Enzymatics; Taq Polymerase, Life Technologies), and ligation (T4 DNA Ligase, Enzymatics) with a novel universal half- functional adapter. SPRI-cleaned ligated libraries were put through two rounds of nested PCR at 10 to 14 cycles each for target enrichment (Platinum Taq™ Polymerase, Life Technologies). The first round of PCR was performed using a primer

complementary to the universal adapter and a first pool of up to hundreds of target specific primers (Operon, Huntsville, AL). After SPRI cleanup, a second round of PCR is executed using a 3' nested universal adapter primer downstream of the first adapter primer, and a second pool of 3' nested target specific primers downstream of the respective, initial first pool target primers. These nested primers are each 5' tagged with a common sequencing adapter which in combination with the first half- functional universal adapter, create target amplicons ready for clonal amplification (e.g. emulsion PCR or bridge PCR) and sequencing. Libraries are quantitated using quantitative PCR (Kapa Biosystems, Woburn, MA), normalized, and processed respectively for sequencing on the MiSeq™ (Illumina, San Diego, CA) or Ion Torrent™ Personal Genome Machine (PGM) (Life Technologies) according to the manufacturers' standard protocol. Upfront library construction prior to quantitation by qPCR can be typically accomplished in 6-8 hours.

[00175] Data analysis. Sequence data were processed initially by trimming adapter sequences from the 3' end for both paired-end reads using a shell script. Processed reads with lengths shorter than 50 bp after adapter trimming were discarded. A combination of BWA25 and BLAT26 was used in a hybrid manner to optimize fusion gene alignment and detection. BWA was used first to align nearly perfect reads to the hg¹⁹ reference genome. The unmapped reads from BWA, potentially containing chimeric fusion reads, were then aligned using the BLAT²⁶ algorithm in a 2-step optimized multithreaded process. The first BLAT stage (tileSize 11 and stepSize 16) was used to loosely align the BWA unmapped reads to the hg¹⁹ reference genome. The resulting unmapped reads and the mapped reads with greater than 15 nt unmapped overhangs were then realigned more stringently with a second BLAT stage (tileSize 11 and stepSize 9). Gene fusion variant calling was executed with the following three criteria for the BWA-BLAT hybrid mapped reads: (1) fusion partners must show at least 25 non-overlapping mapped bases on their respective ends of a chimeric read; (2) the two fusion partners must map to different genes; and (3) the unknown partner upstream or downstream of the targeted gene on the anchored end must be minimally represented with 15 uniquely starting reads (reflecting random ligation of the universal adapter).

[00176] To detect point mutations and indels from genomic DNA sequencing, reads were mapped to the human hg¹⁹ reference genome using the BWA short read aligner with default parameters²⁵. BWA unmapped reads were submitted for BLAT mapping using a minimum score of 50 and a minimum identity of 95% to retain the highest quality mapped reads. The resulting PSL mapping files were converted to SAM and then BAM using SAMtools²⁷. The BAM files derived from BWA and BLAT mappings were merged into one single BAM file per sample, processed by SAMtools mpileup, and variant called using VarScan (v2.3.3)²⁸. A minimum of 100X coverage and a minimum of 5% allelic fraction were applied. The resulting variants were filtered against dbSNP and annotated using the Bioconductor Variant Annotation™ package. Overall coverage was calculated using a 21 -bp window for hotspot point mutation targets (±10 bp) and 5-bp intronic flanks for whole exon targets.

[00177] Primer design. A custom primer design engine was developed specifically for efficient AMP primer design based on Primer3²⁹. To maintain applicability for fragmented nucleic acids from such samples as FFPE tissue, primers were designed to yield short amplicons of approximately 90 bp. For targeted RNA-Seq to detect gene fusions, gene specific primers were designed in a tiled fashion against the tyrosine kinase domains and near the exon boundary putatively involved in the rearrangement (data not shown). A set of three primers for house-keeping genes (GAPDH, B2M, CTBP1) were included as an internal control for RNA quality check (Fig. 4). An initial assay targeting ALK, RET, and ROS 1 was designed and implemented for gene fusion detection in lung cancer. Subsequently, a 14-receptor tyrosine kinase gene panel including ALK, ROS1, RET, MUSK, EGFR, FGFR1, FGFR3, INSR, INSRR, MET, NTRK1, NTRK2, NTRK3 and PDGFRA was also designed for both 3' and 5' fusion partner detection (Fig. 4). For targeted gDNA sequencing, a 96- amplicon panel was designed to cover 40 hotspot cancer mutations (shared in common with the clinical SNaPshot assay¹⁶) and the entire coding region of three important tumor suppressor genes (PTEN, TP53 and CDKN2A). Additionally, a gDNA 626-amplicon panel for 18 tumor suppressor genes (Fig. 5) was constructed to demonstrate the scalability of the assay. The gDNA sequencing primers were designed to avoid common single nucleotide variants found in dbSNP and clinically relevant SNPs from the 1000 Genomes Project (20120626 Release). Candidate primers were prioritized to avoid potential homodimerization, heterodimerization, and mispriming with the library construction sequencing adapters and barcodes (IonTorrent 96 barcodes, and Illumina MiSeq 96 forward and 12 reversed indexes).

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[00179] Table 1 : 96-Amplicon Hotspot Mutation Plus Tumor Suppressor AMP Panel. Exon targets were designed to be fully covered for their coding regions. Gene Target Gene Target Gene Target Gene Target exon/hotspots exon/hotspots exon/hotspots exon/hotspots

PTEN Exon 1 CDKN2A Exon 1 EGFR p.G719 ERBB2 p.M774

PTEN Exon 2 CDKN2A Exon 2 EGFR p.E746 GNA11 p.Q209

PTEN Exon 3 CDKN2A Exon 3 EGFR p.T790 GNAS p.R201

PTEN Exon 4 NRAS p.Q61 EGFR p.L858 APC Exon 16

PTEN Exon 5 NRAS p.G12 BRAF p.K601 ALK Exon 20

PTEN Exon 6 IDH1 p.R.132 BRAF p.V600 ALK Exon 21

PTEN Exon 7 CTNNB1 p.A5 GNAQ p.Q209 ALK Exon 22

PTEN Exon 8 CTNNB1 p.T41 NOTCH1 P.P2515 ALK Exon 23

PTEN Exon 9 PIK3CA p.R88 NOTCH1 p.L1679 ALK Exon 24

TP53 Exon 1 PIK3CA p.N345 NOTCH1 P.L1601 ALK Exon 25

TP53 Exon 2 PIK3CA p.C420 NOTCH1 P.L1575 ALK Exon 26

TP53 Exon 3 PIK3CA p.E545 RET p.E632 ALK Exon 27

TP53 Exon 4 PIK3CA p.H1047 RET p.M918 ALK Exon 28

TP53 Exon 5 FGFR3 p.S249 HRAS p.Q61 ALK Exon 29

TP53 Exon 6 FGFR3 p.Y373 HRAS p.G12 MAP2K1 Exon 2

TP53 Exon 7 FGFR3 p.K650 KRAS p.A146 MAP2K1 Exon 2

TP53 Exon 8 FGFR3 p.G697 KRAS p.Q61

TP53 Exon 9 KIT p.Y503 KRAS p.G12

TP53 Exon 10 KIT p.W557 AKT1 p.E17

TP53 Exon 11 KIT p.D816 IDH2 p.R172

[00180] Table 2: Clinical sensitivity and specificity of AMP for gene rearrangement detection compared to fluorescence in situ hybridization (FISH) as a golden standard. A cohort of 319 archived clinical FFPE samples with available FISH results were tested with an AMP R A- Seq assay targeting the receptor tyrosine kinase domains of ALK, RET, ROSl, and PPARG. A clinical sensitivity of 98.2% (55 of 56) and a clinical specificity of 100% were achieved (indeterminate cases not included in calculation). * = One discordant case was a clinical ROSl FISH case that was reported as indeterminate based on an unusual probe pattern (Fig. 6). On the AMP assay, it was confirmed to harbor a CD74-ROS1 gene fusion. ** = Targeted RNA-Seq of one ALK FISH positive case detected RNA expression for all targeted ALK exons 19-22 (normally not expressed in the lung) but did not detect fusion reads. Potentially, there may be a fusion involving a region 5'upstream of ALK exon 19 that needs further evaluation. JOne ALK FISH case and one ROSl FISH case showed indeterminate green probe only results and tested negative by the targeted RNA-seq assay. Of note, the green-only ALK case (data not shown) did not show increased ALK expression by immunohistochemistry (typically expected in an ALK-rearranged tumor) but instead harbored a KRAS mutation detected by genotyping (usually mutually exclusive of ALK rearrangement). Similarly, the green-only ROSl case that we tested (data not shown) showed no response to crizotinib after 8 weeks of treatment indicating the biological absence of a canonical ROSl rearrangement.

Claims

What is claimed herein is:

administering an inhibitor of NTRKl kinase activity to a subject determined to have a genetic fusion of NTRKl and a second gene.

2. The method of claim 1, wherein the second gene is CHTOP or ARHGEF2.

3. The method of any of claims 1-2, wherein the genetic fusion comprises NTRKl as the 3' fusion partner.

4. The method of any of claims 1-3, wherein the genetic fusion comprises a chromosomal

rearrangement.

5. The method of any of claims 1-4, wherein the subject is determined to have a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl by detecting the presence of a CHTOP- NTRK1 or ARHGEF2 -NTRKl fusion protein.

6. The method of claim 5, wherein the fusion protein has the amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 3.

7. The method of any of claims 5-6, wherein the presence of the fusion protein is detected using an immunoassay.

8. The method of any of claims 1-4, wherein the subject is determined to have a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl by detecting the presence of a nucleic acid encoding a CHTOP-NTRK1 or ARHGEF2 -NTRKl fusion protein.

9. The method of claim 8, wherein the nucleic acid has the sequence of SEQ ID NO: 2 or SEQ ID NO: 4.

10. The method of any of claims 8-9, wherein the presence of the nucleic acid is detected using a method selected from the group consisting of:

karyotyping; PCR; RT-PCR; sequencing; and FISH.

11. The method of any of claims 1-12, wherein the inhibitor of NTRKl kinase activity is selected from the group consisting of:

AZD7451 ; Crizotinib; ARRY-470; CEP-701 ; AG 879; GW 441756; and Ro 08-2750.

12. The method of any of claims 1-11, wherein the cancer is a brain cancer.

13. The method of any of claims 1-12, wherein the brain cancer is a glioblastoma.

14. The method of any of claims 1-13, further comprising the step of assaying a sample obtained from the subject to detect the presence or absence of a genetic fusion of NTRKl and a second gene.

15. A method of identifying an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRKl , the method comprising: contacting a CHTOP-NTRKl or ARHGEF2-NTRK1 polypeptide with a candidate agent;

detecting the level of kinase activity of the polypeptide;

wherein a decreased level of kinase activity in the presence of the candidate agent, as compared to a reference level, indicates the candidate agent is an agent that can inhibit the proliferation and survival of a cancer cell comprising a genetic fusion of CHTOP and NTRKl or ARHGEF2 and NTRK1.

16. The method of claim 15, wherein the cancer cell is a brain cancer cell.

17. The method of claim 15, wherein the cancer cell is a glioblastoma cell.