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Definitions

• RNA splicing a highly regulated molecular event orchestrated by the spliceosome, results in the removal of intronic sequences from pre-mRNA to generate mature mRNA.
• Dysregulation of RNA splicing has been identified as a causative defect in several diseases.
• dysregulated splicing has been proposed to play an important role in tumorigenesis and resistance to therapy; however, the molecular causes of dysregulated splicing in cancer have remained elusive.
• SF3B1 is a protein involved in RNA splicing. It forms part of the U2 snRNP complex which binds to the pre-mRNA at a region containing the branchpoint site and is involved in early recognition and stabilization of the spliceosome at the 3' splice site (3'ss).
• a thorough and systematic analysis of the effects of SF3B 1 mutations is needed to define their effects on RNA splicing in cells and may lead to novel therapeutic approaches for SF3B 1 mutant cancers.
• the methods described herein involve detecting or quantifying the expression of one or more splice variants in a cell containing a neomorphic mutant SF3B1 protein.
• Various embodiments of the invention include detecting or quantifying splice variants to determine whether a patient has a cancer with one or more neomorphic SF3B1 mutations. Additional embodiments include measuring the amount of a splice variant to evaluate the effects of a compound on a mutant SF3B1 protein. Further embodiments include methods of treating a patient who has cancer cells with a neomorphic mutant SF3B 1 protein.
• Various embodiments encompass a method of detecting one or more splice variants selected from rows 1-790 of Table 1 in a biological sample, comprising:
• nucleic acid probes capable of specifically hybridizing to the one or more splice variants
• the one or more nucleic acid probes capable of specifically hybridizing to the one or more splice variants each comprise a label.
• the method of detecting one or more splice variants selected from rows 1-790 of Table 1 in a biological sample further comprises contacting the biological sample with one or more additional nucleic acid probes, wherein the additional probes are each labeled with a molecular barcode.
• Embodiments further encompass a method of modulating the activity of a neomorphic mutant SF3B1 protein in a target cell, comprising applying an SF3B 1- modulating compound to the target cell, wherein the target cell has been determined to express one or more aberrant splice variants selected from rows 1-790 of Table 1 at a level that is increased or decreased relative to the level in a cell not having the neomorphic mutant SF3B 1 protein.
• Embodiments also encompass a method for evaluating the ability of a compound to modulate the activity of a neomorphic mutant SF3B1 protein in a target cell, comprising the steps of:
• the method for evaluating the ability of a compound to modulate the activity of a neomorphic mutant SF3B1 protein in a target cell further comprises the step of measuring the expression level of one or more splice variants selected from row 1-790 of Table 1 before step (b).
• the neomorphic mutant SF3B1 protein is selected from K700E, K666N, R625C, G742D, R625H, E622D, H662Q, K666T, K666E, K666R, G740E, Y623C, T663I, K741N, N626Y, T663P, H662R, G740V, D781E, or R625L.
• the neomorphic mutant SF3B 1 protein is selected from E622D, E622K, E622Q, E622V, Y623C, Y623H, Y623S, R625C, R625G, R625H, R625L, R625P, R625S, N626D, N626H, N626I, N626S, N626Y, H662D, H662L, H662Q, H662R, H662Y, T663I, T663P, K666E, K666M, K666N, K666Q, K666R, K666S, K666T, K700E, V701A, V701F, V701I, I704F, I704N, I704S, I704V, G740E, G740K, G740R, G740V, K741N, K741Q, K
• the step of measuring the expression level of one or more splice variants comprises using an assay to quantify nucleic acid selected from nucleic acid barcoding (e.g. NanoString®), RT-PCR, microarray, nucleic acid sequencing, nanoparticle probes (e.g. SmartFlareTM), and in situ hybridization (e.g. RNAscope®).
• nucleic acid barcoding e.g. NanoString®
• RT-PCR e.g. NanoString®
• microarray e.g. NanoString®
• nucleic acid sequencing e.g. SmartFlareTM
• nanoparticle probes e.g. SmartFlareTM
• in situ hybridization e.g. RNAscope®
• the step of measuring the expression level of one or more splice variants comprises measuring the number of copies of the one or more splice variant RNAs in the target cell.
• the compound is selected from a small molecule, an antibody, an antisense molecule, an aptamer, an RNA molecule, and a peptide.
• the small molecule is selected from pladienolide and a pladienolide analog.
• the pladienolide analog is selected from pladienolide B, pladienolide D, E7107, a compound of formula 1 :
• the target cell is obtained from a patient suspected of having myelodysplastic syndrome, chronic lymphocytic leukemia, chronic myelomonocytic leukemia, or acute myeloid leukemia.
• the target cell is obtained from a sample selected from blood or a blood fraction or is a cultured cell derived from a cell obtained from a sample chosen from blood or a blood fraction.
• the target cell is a lymphocyte.
• the target cell is obtained from a solid tumor.
• the target cell is a breast tissue cell, pancreatic cell, lung cell, or skin cell.
• one or more of the aberrant variants are selected from rows 1, 7, 9, 10, 13, 15, 16, 18, 21, 24, 27, 28, 30, 31, 33, 34, 48, 51, 62, 65, 66, 71, 72, 81, 84, 89, 91, 105, 107, 121, 135, 136, 152, 178, 235, 240, 247, 265, 267, 272, 276, 279, 282, 283, 286, 292, 295, 296, 298, 302, 306, 329, 330, 331, 343, 350, 355, 356, 360, 364, 372, 378, 390, 391, 423, 424, 425, 426, 431, 433, 438, 439, 443, 445, 447, 448, 451, 452, 458, 459, 460, 462, 468
• one or more of the aberrant variants are selected from rows 21, 31, 51, 81, 118, 279, 372, 401, 426, 443, 528, 543, 545, 548 or 566 of Table 1.
• Embodiments further encompass a method for treating a patient with a neoplastic disorder, comprising administering a therapeutically effective amount of an SF3B1 -modulating compound to the patient, wherein a cell from the patient has been determined to:
• a) contain a neomorphic mutant SF3B1 protein; and b) express one or more aberrant splice variants selected from rows 1-790 of Table 1 at a level that is increased or decreased relative to the level in a cell not having the neomorphic mutant SF3B1 protein.
• FIG. 1 is a schematic diagram depicting modes of alternative splicing.
• Fig. 2 is a graph depicting levels of gene expression for abnormally spliced genes across different cancers in patient samples.
• Fig. 3 is a schematic diagram showing the locations of certain neomorphic mutations in the SF3B 1 protein and corresponding coding regions of the SF3B1 gene.
• Fig. 4 is a graph depicting levels of aberrant splice variants detected in RNA isolated from pancreatic, lung cancer, and Nalm-6 isogenic cell lines using a NanoString® assay. Data are represented as the mean of three replicates.
• Fig. 5 is a set of western blot images that confirm overexpression of SF3B1 proteins in 293FT cells.
• Fig. 6 is a graph depicting levels of aberrant splice variants in RNA isolated from 293FT cells expressing wild type SF3B 1 (SF3B 1 WT ) or mutant SF3B 1 proteins, as measured in a NanoString® assay. Data are represented as the mean of three replicates.
• Fig. 7 is a set of western blot images that confirm overexpression of SF3B1 proteins in 293FT cells.
• Fig. 8 is a graph depicting levels of aberrant splice variants in RNA isolated from 293FT cells expressing SF3B 1 WT or mutant SF3B1 proteins, as measured in a NanoString® assay.
• FIG. 9 A depicts a set of western blot images showing expression of SF3B1 alleles before and after shRNA-knockdown in Pane 05.04 cells.
• Fig. 9B depicts a graph showing levels of SF3B1 RNA detected by qPCR in Pane 05.04 cells before and after shRNA-knockdown of all SF3B1 alleles ("SF3B1 PAN ) or SF3Bl WT or mutant SF3B 1 (SFSBl ⁇ 1 alleles.
• Solid black, outlined, and gray bars indicate SF3B 1 PAN , SF3B1 WT , and SFSB l ⁇ allele-specific qPCR data, respectively.
• FIG. 10A depicts a set of western blot images showing expression of SF3B1 alleles before and after shRNA-knockdown in Pane 10.05 cells.
• Fig. 10B depicts a graph showing levels of SF3B 1 RNA detected by qPCR in Pane 10.05 cells before and after shRNA- knockdown of SF3B1 alleles.
• Solid black, outlined, and gray bars indicate SF3B 1 PAN , SF3B1 WT , and SFSB l ⁇ allele- specific qPCR data, respectively.
• Figs. 11 A and 1 IB are a set of graphs depicting levels of splice variants in Pane 05.04 (Fig. 11 A) and Pane 10.05 cells (Fig. 1 IB) before and after shRNA- knockdown of SF3B1 alleles, as measured in a NanoString® assay. Data are represented as mean of three biological replicates.
• Fig. 12 is a set of graphs depicting growth curves of Pane 05.04 cells before (circles) and after (squares) shRNA-knockdown of SF3B1 alleles.
• Fig. 13 is a set of graphs depicting growth curves of Pane 10.05 cells before (circles) and after (squares) shRNA-knockdown of SF3B1 alleles.
• Figs. 14A and 14B are a set of images of culture plates showing colony formation of Pane 05.04 cells (Fig. 14A) and Pane 10.05 (Fig. 14B) cells before and after shRNA-knockdown of SF3B1 alleles.
• Fig. 16B depicts upper panels, a pair of graphs showing the levels of EIF4A1 pre-mRNA (squares) and SLC25A19 mature RNA (inverted triangles) in Nalm-6 SF3 B 1 K7OOK cdls Q eft pand and NALM _ 6 SF 3 B 1 K7OOE CDL S ⁇ RIGHT PAND TREATED WITH varying concentrations of E7107, as measured by qPCR.
• Fig. 16B depicts upper panels, a pair of graphs showing the levels of EIF4A1 pre-mRNA (squares) and SLC25A19 mature RNA (inverted triangles) in Nalm-6 SF3 B 1 K7OOK cdls Q eft pand and NALM _ 6 SF 3 B 1 K7OOE CDL S ⁇ RIGHT PAND TREATED WITH varying concentrations of E7107, as measured by qPCR.
• 16B depicts lower panels, a pair of graphs showing the levels of abnormally spliced isoforms of abnormally spliced genes COASY (triangles) and ZDHHC16 (diamonds) in Nalm-6 SF3B1 K700K cells (left panel) and Nalm-6 SF3B 1 K700E cells (right panel) treated with varying concentrations of E7107, as measured by qPCR.
• Fig. 17 is a set of graphs depicting levels of splice variants in Nalm-6 SF3 B 1 K7OOK AND NALM _ 6 SF 3 B 1 K7OOE cells after treatment of ce ii s w i t E7107 for two or six hours, as measured in a NanoString® assay. Data are expressed as fold change from
• Fig. 18 is a set of graphs depicting levels of splice variants in Nalm-6 SF3 B 1 K7OOK and Na i m _ 6 SF3 B 1 K7OOE cells after treatment of ce ii s w i t E7107 for six hours, as measured by RNA-Seq analysis.
• Fig. 19 is a set of graphs depicting levels of splice variants in Nalm-6 SF3 B 1 K7OOK AND NALM _ 6 SF 3 B 1 K7OOE cells after treatment of C ells with the numbered compounds indicated above the graphs, as measured by RNA-Seq analysis.
• Fig. 20 depict the levels of EIF4A1 pre-mRNA (squares) and
• FIG. 20 depict the levels of abnormally spliced isoforms of abnormally spliced genes COASY (triangles) and ZDHHC16 (diamonds) in Nalm-6 SF3 B 1 K7OOK cdls Q eft pand and NALM _ 6 SF 3 B 1 K7OOE CDL S ⁇ RIGHT PANEL ⁇ DETECTED AT certain times after treatment with E7107.
• Open circles show the concentration of E7107 (in ⁇ g/ml [right vertical axis]) as determined by mass spectrometry of tumor samples.
• Fig. 21 is a set of graphs depicting levels of canonical and aberrant splice variants in Nalm-6 SF3B1 K700K - and Nalm-6 SF3Bl K700E -xenograft tumors (left and right sets of panels, respectively) at certain timepoints after treatment of xenograft mice with E7107, as measured in a NanoString® assay. Data are represented as mean of three replicates.
• inverted triangles 1.25 mg/kg
• triangles 2.5 mg/kg
• squares 5 mg/kg.
• Fig. 24 is a graph depicting survival rates in 10-animal cohorts of Nalm-6 SF3Bl K700E -xenograft mice following treatment with E7107, with an untreated cohort shown by the solid black line.
• dashed line 1.25 mg/kg
• gray line 2.5 mg/kg
• dotted line 5 mg/kg.
• the methods of the invention provide assays for measuring the amount of a splice variant in a cell, thereby determining whether a patient has a cancer with a neomorphic SF3B 1 mutation.
• at least one of the measured splice variants is an aberrant splice variant associated with a neomorphic mutation in an SF3B 1 protein.
• the measurement of a splice variant in a cell may be used to evaluate the ability of a compound to modulate a mutant neomorphic SF3B1 protein in a cell.
• mutant SF3B1 protein includes SF3B1 proteins that differ in amino acid sequence from the human wild type SF3B1 protein set forth in SEQ ID NO: 1200 (GenBank Accession Number NP_036565, Version
• mutant SF3B1 proteins are "neomorphic" mutants, which refers to mutant SF3B1 proteins that are associated with differential expression of aberrant splice variants.
• neomorphic SF3B1 mutants include K700E, K666N, R625C, G742D, R625H, E622D, H662Q, K666T, K666E, K666R, G740E, Y623C, T663I, K741N, N626Y, T663P, H662R, G740V, D781E, or R625L.
• neomophic SF3B1 mutants include E622D, E622K, E622Q, E622V, Y623C, Y623H, Y623S, R625C, R625G, R625H, R625L, R625P, R625S, N626D, N626H, N626I, N626S, N626Y, H662D, H662L, H662Q, H662R, H662Y, T663I, T663P, K666E, K666M, K666N, K666Q, K666R, K666S, K666T, K700E, V701A, V701F, V701I, I704F, I704N, I704S, I704V, G740E, G740K, G740R, G740V, K741N, K741Q, K741
• splice variant includes nucleic acid sequences that span a junction either between two exon sequences or across an intron- exon boundary in a gene, where the junction can be alternatively spliced.
• Alternative splicing includes alternate 3' splice site selection ("3'ss”), alternate 5' splice site selection ("5'ss”), differential exon inclusion, exon skipping, and intron retention (Fig. 1).
• Certain splice variants associated with a given genomic location may be referred to as wild type, or "canonical,” variants. These splice variants are most abundantly expressed in cells that do not contain a neomorphic SF3B1 mutant protein.
• Additional splice variants may be referred to as "aberrant" splice variants, which differ from the canonical splice variant and are primarily associated with the presence of a neomorphic SF3B1 mutant protein in a cell.
• Aberrant splice variants may alternatively be referred to as “abnormal” or “noncanonical” splice variants.
• cells with a wild type or non-neomorphic SF3B 1 protein have low or undetected amounts of an aberrant splice variant, while cells with a neomorphic SF3B 1 protein have levels of an aberrant splice variant that are elevated relative to the low or undetected levels in the wild type SF3B 1 cells.
• an aberrant splice variant is a splice variant that is present in a wild type SF3B 1 cell but is differentially expressed in a cell that has a neomorphic SF3B1 mutant, whereby the latter cell has a level of the aberrant splice variant that is elevated or reduced relative to the level in the wild type SF3B 1 cell.
• Different types of cells containing a neomorphic SF3B 1 mutant may have differing levels of expression of certain aberrant splice variants.
• certain aberrant splice variants present in one type of cell containing a neomorphic SF3B1 mutant may not be present in other types of cells containing a neomorphic SF3B1 mutant.
• patients with a neomorphic SF3B1 mutant protein may not express an aberrant splice variant or may express an aberrant splice variant at lower levels, due to low allelic frequency of the neomorphic SF3B1 allele.
• the identity and relative expression levels of aberrant splice variants associated with various types of cells containing neomorphic SF3B1 mutants, such as certain cancer cells will be apparent from the description and examples provided herein.
• the term "evaluating" includes determining the ability of a compound to treat a disease associated with a neomorphic SF3B 1 mutation. In some instances, "evaluating" includes determining whether or to what degree a compound modulates aberrant splicing events associated with a neomorphic SF3B1 protein. Modulation of the activity of an SF3B1 protein may encompass up-regulation or down-regulation of aberrant splice variant expression associated with a neomorphic SF3B 1 protein.
• evaluating includes distinguishing patients that may be successfully treated with a compound that modulates the expression of splice variants associated with a neomorphic SF3B1 protein.
• Splice variants of the invention are listed in Table 1.
• Table 1 provides the genomic location of each canonical ("WT") and aberrant ("Ab.") splice junction, as well as the sequence. Each sequence listed in the table contains 20 nucleotides from each of the 3' and 5' sides of a splice junction (i.e., the splice junction is at the midpoint of the listed nucleotide sequence).
• the "Avg WT %” and “Avg Ab. %” columns provide the average percentage count that the canonical (WT) or aberrant splice variant, respectively, represented out of the total counts of all splice variants that utilize a shared splice site, where the counts were determined as set forth in Example 1.
• the "Log 2 Fold Change” column provides the log 2 of the fold change observed between percentage counts of canonical and aberrant cohorts (see Example 1).
• the "FDR Q- Value” column provides, as a measure of statistical significance, q-values calculated
• the "Event” column indicates the nature of the aberrant splice variant, where “3'ss” indicates alternate 3' splice site selection, “5'ss” indicates alternate 5' splice site selection, “exon incl .” indicates differential exon inclusion, and “exon skip” indicates exon skipping.
• the "Type” column refers to the cancer type of the sample in which the aberrant splice variant was identified, where “Br.” indicates breast cancer, “CLL” indicates chronic lymphocytic leukemia, and “Mel.” indicates melanoma. Table 1.
• chr7 chr7: GGACTGAGATTT GGACTGAGGATT
• chr20 chr20: ACACACAGCCCT ACACACAGGTGC
• chrl7 chrl7: TTGTGAAATCAT TTGTGAAAGTTT
• chrl7 chrl7: CCCCCGAACCTA CCCCCGAAATGA
• chr20 chr20: GGGCTACATCCC GGGCTACATACC
• chr2 chr2: ACCTGGGGCCCT ACCTGGGGATCA
• chrl7 chrl7: AGGCTATGTGTT AGGCTATGAACA
• chrl2 chrl2: TAGCAATGATGT TAGCAATGAGCA
• chrl2 chrl2: CAATGCCGGCCC CAATGCCGGGCA
• chr22 chr22: ATTCAAAGCCCC ATTCAAAGGCTC
• chr20 chr20: ACGGAGAGGCTC ACGGAGAGGTAC
• chr6 chr6: TCATTCAAGTCA TCATTCAAGTTG
• chrl chrl: TAAACGAGTTTT TAAACGAGGTAT
• chrl chrl: AGGAGAAGTCTG AGGAGAAGCCCC
• chr8 chr8: ATCCAAAGCCAG ATCCAAAGCTTA
• chrl 9 chrl9: TCACCAAGCCTC TCACCAAGGTGC
• chrl4 chrl4: AACCAGAGTGTT AACCAGAGCTCC
• chrl 9 chrl9: GGTTCCTTGTCA GGTTCCTTACCG
• chrl chrl: TACAACAGGTTT TACAACAGCTCC
• chr9 chr9: TCCTAAAGCCTC TCCTAAAGATAA
• chrl l chrl l: ACAGCTAATTCT ACAGCTAAGCAA
• chrl2 chrl2: TGCCCTGGATTT TGCCCTGGGTCA
• chr20 chr20: TGGGCCAGGCCC TGGGCCAGTGAC
• chrl2 chrl2: CCAAACAGGGAC CCAAACAGGTCA
• CAGTTATAAACT CAGTTATAAACT
• chrl4 chrl4: CTAGAGTGAGTT CTAGAGTGCTTA
• chrl6 chrl6: AACTCAAGATGT AACTCAAGATGG
• chrl7 chrl7: AGCACCAGATAA AGCACCAGTTGC
• GGATCCTTCACC GGATCCTTCACC
• chrl6 chrl6: CGTGTCTGTCTT CGTGTCTGGACC
• chr3 chr3: TGTTCCTCTTTT TGTTCCTCATAC
• chrl4 chrl4: GGAGAAAGCCTT GGAGAAAGCTGT
• chrl8 chrl8: AATTGGAAATAT AATTGGAAGAGT
• chrl chrl: ACTACAAAGGTG ACTACAAAACAG
• chr6 chr6: TGAGACCGCTTG TGAGACCGGTGC
• chr2 chr2: TAATTCAGGGTC TAATTCAGGCAA
• CAAGATAGATAT CAAGATAGATAT
• chr2 chr2: TATAGCAGGTGG TATAGCAGAACT
• chrl 5 chrl5: AGGCAAAGCCCA AGGCAAAGGTAA
• chrl chrl: CTGTAGAGATGT CTGTAGAGTCCG
• chr2 chr2: TCTGACAGATAC TCTGACAGTGAG
• chr5 chr5: TCCATCTGTTTT TCCATCTGCCGG
• chrX chrX: GTTTCCAGGTTG GTTTCCAGGTGG
• chrX chrX: GGAAGCAGGTGG GTTTCCAGGTGG
• chr20 chr20: AGTCCCAGCTGC AGTCCCAGGGGT
• chrl8 chrl8: AAAGAAAGTGTA AAAGAAAGAACA
• chrl2 chrl2: ATTACCAGGCAC CAGTACAGGCAC
• chrl4 chrl4: TGCTGCATTTTG TGCTGCATGTAC
• chrl7 chrl7: ATGAACATATCC ATGAACATATCC
• GAATCTCTTATC GAATCTCTTATC
• chrl chrl: ATTGATGGTTCC ATTGATGGTTTA
• chr5 chr5: CTCTCTGGTTTC CTCTCTGGGGAA
• chrl2 chrl2: GCCGACGGGGAA GCCGACGGTTTA
• chrlO chrlO: GTGGACATCGTT GTGGACATAAAC
• chrl l chrl l: GCATGGCACCTC GCATGGCAGTCC
• chrl9 chrl9: AAGAGAGATTTT AAGAGAGAAGCT
• chr22 chr22: TGCATTCTCATC TGCATTCTTTGG
• chr9 chr9: GCCACGAGACAT GCCACGAGTATT
• chrl5 chrl5: AACCAAGAGTAG AACCAAGAGTGT
• chr9 CCGACTTGCTCA CCGACTTGTGAT
• chr6 chr6: GCACAGAAGTGT GCACAGAAATGA
• chrl l chrl l: TTGCCAGACCTT TTGCCAGAGGAA
• chrl3 chrl3: CAGTAAAGGGGG CAGTAAAGCCTG
• chrl6 chrl6: ACTATCAAGGGC ACTATCAAGTCT
• chr2 chr2: AGTTACAGTATA AGTTACAGTGTC
• chrX GTGGAGAGGGTC GTGGAGAGGTAT
• chrl chrl: CACCTCAGTGAC CACCTCAGGAGG
• chrl 5 chrl5: ATTTGAAAGTGT AACCAAGAGTGT
• chrl l chrl l: CCTGGCGGCCCC CCTGGCGGGTCT
• chrl l chrl l: ACGTGCAGTACC ACGTGCAGGTGG
• chrl9 chrl9: TCCTCTGGTCCT TCCTCTGGTTCG
• chr22 chr22: CAGAGCAGGGGA CAGAGCAGATGC
• chr9 chr9: CTGTGAAGGCCC CTGTGAAGATCT
• chrl chrl: GAGTAAATTCTC GAGTAAATATGA
• chrl9 chrl9: CTGTGCAGACTT CTGTGCAGCCTG
• chr2 chr2: AGAAAGAGCTCC AGAAAGAGCTCC
• chr2 chr2: CCTGAATGATGT CCTGAATGGCTC
• chrl2 chrl2: AATGCAAGTTTG AATGCAAGGAAT
• chrl6 chrl6: CCTACGGGTCTG CCTACGGGCCCT
• GGCTCCCATTCT GGCTCCCATTCT
• chrl chrl: GGTTAAAGAGTG GGTTAAAGGCCA
• CTGCACTTATAA CTGCACTTATAA
• chrl chrl: ATATTCAGTGTT ATATTCAGACCC
• chr22 chr22: GAACCCAGTATT GAACCCAGAGAG
• chr6 chr6: TCCTTTAGGTTG TCATTCAAGTTG
• chrl chrl: ATCAAAAGTTTT ATCAAAAGTTCC
• chrl l chrl l: CAAGTTCGGACT CAAGTTCGGGGT
• chrl2 chrl2: TCTCCACGGCCT TCTCCACGGTAA
• chrl4 chrl4: TCCAGAAGGGGT CCTGCCTGGGGT
• chrl chrl: CCCCCAAGTCCT CCCCCAAGTGAT
• chrl l chrl l: CCTCCTCACCCC CCTCCTCAGCAT
• chrl2 chrl2: TCAACAAGATGA TCAACAAGGAGA
• chrl6 chrl6: GCTTCCAGTCTG GCTTCCAGGCCA
• chrl7 chrl7: AAGACAAGCTTT AAGACAAGGTCC
• chrl7 chrl7: AACCTCGGCTTC AACCTCGGGGGC
• chr21 chr21: TGAGGATTGTGT TGAGGATTGCAC
• chr6 chr6: TCATTCAATCTG TCATTCAAGTTG
• chrX chrX: CCGAAATGTCTC CCGAAATGCGCC
• chrl7 chrl7: TCCTGTCGGCCT AGGTTTCAGCCT
• chrl5 chrl5: AAAACCAGCCTT AAAACCAGGCTC
• chr2 chr2: TAATTCAGCCAA TAATTCAGGCAA
• chr7 chr7: GATATGTTCATT GATATGTTTCTT
• chr3 chr3: CCCCTCAGCCTT CCCCTCAGGAAA
• chr8 chr8: GACGCCTGCCCT GACGCCTGTCAC
• chrl7 chrl7: CACACCGGAAGA CATGCACGAAGA
• chrl6 chrl6: ACAGACAGTGTC ACAGACAGATCC
• chrl9 chrl9: TTCCCCAGATCT TTCCCCAGGCCC
• chrl chrl: GGAGAGCAGCCC GGAGAGCAGCAA
• chr2 chr2: TGCATAAGCTTC TGCATAAGATCC
• chr3 chr3: TGGTAGTGGGTC TACTACAGGGTC
• chr4 chr4: AAAACACATTAT AAAACACAGGTA
• chr7 chr7: ACGCAGCAATGG ACGCAGCAGAAC
• chr8 chr8: GGTCCTGGGAAG ATGACTATGAAG
• chrl7 chrl7: AAAACAAGCCTT AAAACAAGCTGG
• AGCTCGGACCAA AGCTCGGACCAA
• chrl6 chrl6: GCGCTCAGTTTT GCGCTCAGCTTA
• chr6 chr6: ATATAATGTTTG ATATAATGTGCT
• chrl 5 chrl5: GAAGCTGGGCTG GAAGCTGGTGCC
• chrl7 chrl7: ATCCCACTAACT ACAAAAAGAACT
• chrl7 chrl7: GCATGGAGCCTG GCATGGAGTGTC
• chrl6 chrl6: GGCTCCAGGAAA GGCTCCAGGGCC
• chrl l chrl l: ATCGAAACGCAT ATCGAAACTTTA
• chrlO chrlO: TTTTATAGGTTG TATCTTCGGTTG
• chrl l chrl l: CAGAAAAGTCTC CAGAAAAGGTTC
• chrl2 chrl2: TCCTGCAGCCAT TCCTGCAGGACT
• chrl2 chrl2: GATGGCAGATCA GATGGCAGGTGC
• chrl7 chrl7: AAGAGAAGTTTC AAGAGAAGGTTA
• chrl chrl: TCCTCCTGCAAA TCCTCCTGAACT
• chrl chrl: GCAGCAAGGTGT GCAGCAAGCTCT
• chr2 chr2: TTTCAAAATTTC TTTCAAAAATCT
• chr2 chr2: GGTGGAAACATT GGTGGAAAAATT
• chr3 chr3: GCTATCAGTTAC GCTATCAGGGCT
• chr5 chr5: CTAAGACGCACT CTAAGACGGACC
• chr6 chr6: CTGGGCAGGTGT CTGGGCAGGTGT
• chrX chrX: GGAATCAGTATC GGAATCAGCCTT
• chrX chrX: ATAAAGAGGAGT ATAAAGAGAGGA
• chr6 chr6: CTGCCCAGCCCT CTGCCCAGTACC
• chr2 chr2: GCCGCCAGGCTC TATAGCAGGCTC
• CTGG 159 97760437 97757599 CTGG (309) CTGG (310) 10 40 1.90 4.22E-03 5'ss Br.
• chrl9 chrl9: TGTACCAGCCCA TGTACCAGCTCT
• chrl6 chrl6: ATAAGGAGTTCT ATAAGGAGGTAA
• chr2 chr2: ACATTCAGCTCC AGAAAGAGCTCC
• chrlO chrlO: GGACACAGGACA AGATTCAGGACA
• chrl chrl: TTTTGAAGAGCC TTTTGAAGAATG
• chrl6 chrl6: GCTGGCGGATAA TGATGCAGATAA
• chrl6 chrl6: ATAAGGAGGATG ATAAGGAGGTAA
• chrl4 chrl4: AGGAAGAGGTTG TACGCAGGGTTG
• chrl3 chrl3: GACCTCCATCCA GATATGGGTCCA
• chrl7 chrl7: CAAAAAAGACTT CAAAAAAGTCTG
• chrl6 chrl6: TTAGGAGGCCAT TTAGGAGGGAAT
• chrl2 chrl2: CAAAGCAGGAGA TCAACAAGGAGA
• chrl6 chrl6: ATGCAATGGTTC ATGCAATGGCTC
• chrl7 chrl7: TCCCTGAGGTCT TCCCTGAGCTGC
• chrl8 chrl8: AAAATAAGTTTG AAAATAAGGGTA
• CTATTCCTTTAT CTATTCCTTTAT
• chrl chrl: TGAATTTGTTTT TGAATTTGATAC
• chr2 chr2: AGCAGCAGTTTG AGCAGCAGAAAA
• chr3 chr3: GGCATCAGCTGC GGCATCAGGAGA
• chr4 chr4: AATGGCAGCACC AATGGCAGACAA
• chr5 chr5: AATTTCAGGCCA AATTTCAGTTTG
• chr5 chr5: AAATTAAGTTTT AAATTAAGGAGC
• chr5 chr5: GTATCAAGCATA GTATCAAGGATT
• chr6 chr6: GTCACTGTTTTG GTCACTGTTTAC
• chr7 chr7: CCTCCCAGGAAC ACGCAGCAGAAC
• chrl5 CATCCAACTGGT CATCCAACGCGG
• chrl chrl: CCCCAAAGTCTT CCCCAAAGTACC
• chrl chrl: TGTATTCGTTTG CGGGAAAGTTTG
• chrl 9 chrl9: TTGTGGAGGTCC TTGTGGAGTTCC
• chrl5 CCTACGCAAACT CCTGGCAGAACT
• chrl chrl: GCTCAAAGATCA TAAAAATGATCA
• chr22 chr22: CCGATGGGGAGG CCGATGGGGAGA
• chr7 chr7: ATTTGATGAGCC ATTTGATGAACT
• chr8 chr8: CACCAGAGACCA CACCAGAGGTTA intron
• chr9 chr9: AGGCATGGCCAT GCGACAAACCAT
• chr2 chr2: AATATGAGCTTT AATATGAGGTCT
• chrl9 chrl9: TCTCGTTGCCCT TCTCGTTGGTGG
• chrl l chrl l: GGAGCCAGGGTT GGAGCCAGAGAT
• chrl chrl: TCTGGAAAGATG TCTGGAAAGTGC
• chrl 9 chrl9: CACCACTGGGCC CACCACTGCCAG
• chr3 chr3: GAGGGCAGCCCC GAGGGCAGTCTG
• chr2 chr2: GGAGGCAGAGGA GGAGGCAGCTTT
• chrlO chrlO: AGTAATAGGAGA AGTAATAGAGCC
• chrl chrl: AGGCCCAGTGGC AGGCCCAGGAAA
• chrl chrl: GCAAACAGTTCT GCAAACAGCTGC
• chr6 chr6: TTCTACAGGTAC TTCTACAGCTAA
• chrl7 chrl7: ACCCACTCCCCT ACCCACTCCTGT
• chrl chrl: AATTCAAGCTTA CAGAGAAGCTTA
• CTTCCTCAAGTC CTTCCTCAAGTC
• chr5 chr5: GCCCAAAGCTCC GCCCAAAGACAA
• chr7 chr7: GCAAACTGTATC GCAAACTGCGGG
• chrl chrl: AAGTGGAGTATG AAGTGGAGTATC
• chr3 chr3: GACTGTTGCATT GACTGTTGGTAT
• chr8 chr8: CCCCTAAGGTGG ATGGCCTTGTGG
• chrX chrX: GCTTCCAGGCCC GCTTCCAGGCTG
• chrl6 chrl6: TGAGCTCGATGG AACTCAAGATGG
• chr6 chr6: ACCAGGAGCATT ACCAGGAGGGGT
• chr6 chr6: TAGATTCTGATT TAGATTCTTTCT
• chr7 chr7: GTTACTAGTTTG GTTACTAGAGGC
• chrl2 chrl2: TGTTTTGCGATT ACAGGAAGGATT intron
• chr4 chr4: CATGGATGATCT CATGGATGCAGT
• chrlO chrlO: ATGTCCAGCTTT ATGTCCAGGTTC
• chrl6 chrl6: GTCGACCTTCTC GTCGACCTCTGG
• chr3 chr3: GGATAGAGACAT GGATAGAGGTTT
• chrl chrl: GGGAACAGAGCC GGGAACAGAATG
• chr20 chr20: AGGTTCCGTGTT CCAACCAGTGTT
• chrl chrl: TGACATCGCTTC TGACATCGCAGC
• chr4 chr4: CCTCGCAGCTCT CCTCGCAGACGT
• chr20 chr20: ATTTCGAGTCTT ATTTCGAGGTGG
• chrX chrX: CCCCAAGGCCGC CCCCAAGGGGCT
• chrl chrl: GATAGATCTTCT GATAGATCTGGC
• chrl chrl: GGAACAGGCCCT GGAACAGGGTTT
• chrlO chrlO: TTGAGCAGGAGG TTGAGCAGGCAA
• chrl2 chrl2: CAGAGAAGTCTT CAGAGAAGGTGC
• chr2 chr2: ATTCAGAGCTTG ATTCAGAGAGTT
• chrl l chrl l: GTCCCGAGGCAT GGGGAAAGGCAT
• chrX chrX: CATGCCATTCGG GATTATAATCGG
• chr9 chr9: ACAGACAGCTTG ACAGACAGCAGC
• chr2 chr2: AATCTAAGATTT AGTGTTTAATTT
• chrl2 chrl2: TTTACACTTTTG TTTACACTGGTC
• chr7 chr7: AGAACATGTTTC GGCTACAGTTTC
• chrlO chrlO: TGCTCCAGTGGT TGCTCCAGGTTC
• chrX chrX: GATTATAACACG GATTATAATCGG
• chr2 chr2: AGCAACAGCACC AGCAACAGCAGG
• chrl7 chrl7: AATGCAAGGCAC GGCACCAGGCAC
• chrl chrl: CCTCCAAGCAGC CCTCCAAGAGGA

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• 2016
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