Automated exposition of known and novel multiple myeloma genomic variants using a single sequencing platform

A method of identifying multiple myeloma mutations in a subject in need thereof, comprising:

• a) providing a DNA sequencing library comprising genomic DNA obtained from tumor cells of a subject;
• b) providing a DNA sequencing library comprising genomic DNA obtained from non-tumor cells of the subject;
• c) hybridizing the sequencing library comprising the genomic DNA obtained from the tumor to a set of biotinylated oligonucleotide probes, wherein each biotinylated oligonucleotide probe specifically hybridizes to:
• i) a gene of at least 400 genes selected from the following 465 genes:
• DTNB, DNMT3A, ULK4, TRAK1, DNAH11, CDCA7L, FGFR3, WHSC1, CCND3, CCND1, MAF, MAFB, CKS1B, ANP32E, LTBR, MAP4K4, MYC, CDKN2C, RBI, CDKN2A, NRAS, KRAS, BRAF, PIK3CA, AKT1, TRAF3, CYLD, DKKI, FRZB, DNAH5, XBP1P1, PRDM1, IRF4, TP53, MRE11A, PARP1, DIS3, FAM46C, LRRK2, KDM6A, MLL, HOXA9, KDM6B, FAF1, BIRC2, BIRC3, WWOX, ACTG1, FNDC3A, MAX, TNKS, RPL10, BCL7A, EGR1, SP140, GCET2, HIST1H3G, SNRNP48, BAGE2, MEOX1, FERMT2, PRND, TRIP12, DNAH2, RASA2, PLA2G2D, COBLL1, ATF71P, GSTO2, SLC24A1, AASS, RBM25, ROBO2, THRAP3, ZNF326, GNG7, IF144, STARD13, HAUS3, TTC7B, CDKN1B, RNF151, SLC36A1, FAM153B, OR1L8, PRUNE2, COL4A1, USP50, SAMHD1, CXCR4, CHD2, KRTDAP, PTCH2, FBXO36, ABCC4, UBB, YTHDF2, HUWE1, NLRCS, CDH8, PHOX2B, CDCA2, MOGAT3, PSMD1, EXOG, GRIA2, CCDC144NL, IQSEC1, CKM, SYMPK, DAAM1, PTPRZ1, OR1N2, AGTR2, DUSP28, ADCY8, ACACA, PRIM2, DOLK, CST4, ACSM4, TMCO3, HTR6, OR1S2, NDUFAF3, FAM122C, SLC48A1, HIST1H3H, PNRC11, NALCN, COL11A2, LCE3A, ZNF431, HERC4, TMEM143, CDC27, FXYD6, OR5P3, MALL, PLXDC2, EGFL6, CELSR2, PHKB, IRX2, PRKD2, STXS, TOM1L1, COX7B2, RNF40, PTPRD, MMP7, YAP1, MSRA, K1AA1377, SOX7, FAM167A, RP1L1, XKR6, CSMD2, PDE4DIP, FLG, HMCN1, RGS2, USH2A, OBSCN, RYR2, ANK3, TACC2 , MK167, LRRC4C, FAT3, DYNC2H1, BTG1, EP400, AHNAK2, RYR3, HYDIN, ZFBX3, DNAH9, LAMA1, ZNF208, ZNF257, RYR1, FCGBP, NRXN1, NEB, SCN2A, FRG1B, BSN, ROBO1, KALRN, ANK2, FAT4, TRIO, FAM134B, MYO10, CMYA5, VCAN, FBN2, PKHD1, DST, SYNE1, HECW1, PCLO, PCMTD1, ZFHX4, CSMD3, MLLT3, TRPM3, GJB3, KTI12, DIRAS3, HIST2H3D, HIST2H2BE, HIST2H2AC, HIST3H2A, NAMPTL, RBMXL2, CDC42EP2, KRTAP5-10, FUT4, HIST4H4, ATXN7L3B, PABPC3, SPRY2, GREM1, EID1, IMP3, SOCS1, NACA2, TRAPPC5, RPS28, ZNF493, RPSAP58, FFAR2, EID2B, FAM84A, FOXD4L1, TMEM177, KCNE4, MOV10L1, LRRC3B, RPP14, CGGBP1, H1FX, SLC35G2, CRIPAK, DCAF16, PURA, HIST1H4B, HIST1H2BB, HIST1H3C, HIST1H1C, HIST1H4C, HIST1H2AC, HIST1H1E, HIST1H3E, HIST1H3D, HIST1H2BF, HIST1H4E, HIST1H2AE, HIST1H1D, HIST1H3F, HIST1H4H, HIST1H2BJ, HIST1H2AG, HIST1H2BK, HIST1H2BL, HIST1H2BM, HIST1H2AM, HIST1H2BO, LTB, C2, TBCC, TPBG, CLDN4, PEG10, RNF133, NATI, AQP7, GCNT1, DIRAS2, TMSB4X, CPXCR1, RPA4, TCEAL3, MAGEC3, NOTCH2, EHD1, AKAP6, LRRTM4, VCPIP1, ABCA2, LYPLA2, DTX1, MYOM1, TGFB1, RRBP1, RPRD1B, IGLL5, ZNF148, RNF150, ATM, ARID2, SCAF11, WDR87, SETD2, EXOC4, MAGED1, SLIT3, SLC6A11, ZNF319, ZNF100, ZNF91, ZNF681, ZNF235, ZNF616, ZNF721, KCNH4, GRM7, TJP3, FMN1, TLR5, VDR, ADRA2B, LRRN1, SLIT2, ATR, AICDA, SUPT5H, UNG, CCDC88A, MSH2, NLRP2, PAX5, TCF3, ID2, NFKB1, NFKB2, RELA, PRKACB, PTBP2, APEX1, APEX2, MSH6, TRJM28, SUPT6H, MSH3, MSH5, POLQ, RNF8, RNF168, REV3L, PMS2, PAXIP1, PCNA, MLH1, MLH3, EXO1, XRCC6, XRCC5, LIG4, XRCC4, PRKDC, DCLRE1C, NHEJ1, NBN, RAD50, RBBP8, LIG3, LIG1, XRCC1, BBC3, BCL2L11, PRKCD, BCL2L1, TNFSF13B, RAG1, MDC1, TP53BP1, CHEK2, BLM, R1F1, SAMSN1, LILRB3, U2AF1, SF3B1, SRSF2, NADK, DNAJC11, DENND4B, KCNN3, ARHGEF11, CR1, KIF26B, AGAP5, TMEM216, TECTA, ZCRB1, CLIP1, UPF3A, SYNRG, PNKP, 1DH1, RALGAPA2, NCOA6, CTCFL, EFCAB6, TOMM70A, INTS12, ANKHD1, ZNF318, PLG, TBP, CNTNAP2, ANKRD18B, PCSK5, SHC3, DDX11, HLA-A, HLA-DRB1, ISPD, ALK, ANTXR2, ARID1A, AXL, BA12, BCORL1, BRCA2, CARD11, CCDC155, CDHR1, CHD3, CNKSR2, DCLK2, DICER1, HOXA4, IFG1R, IKBKB, IL6ST, JAK2, KIT, MED12, MED12L, MERTK, MLL5, MTOR, NBEA, NOTCH1, PIK3C2G, PTPN11, PTPN14, ROS1, SKP2, SPOP, ST7, STAT3, TP63, TPTE, XBP1, ZIM3, and ZNF717;
• or
• ii) a sequence from a set of sequences tiled in an unbiased fashion from ˜50 Kb upstream to ˜50 Kb downstream of the IGH locus;
• d) purifying the library comprising the genomic DNA obtained from the tumor cells hybridized to the biotinylated oligonucleotides, wherein the biotinylated oligonucleotides are immobilized via binding to streptavidin-labeled magnetic beads;
• e) sequencing the library comprising the genomic DNA obtained from the tumor cells hybridized to the biotinylated oligonucleotide probes to a maximum average depth of 500×;
• f) hybridizing the sequencing library comprising the genomic DNA obtained from the non-tumor cells to the biotinylated oligonucleotide probes;
• g) purifying the library comprising the genomic DNA obtained from the non-tumor cells hybridized to the biotinylated oligonucleotides, wherein the biotinylated oligonucleotides are immobilized via binding to streptavidin-labeled magnetic beads;
• h) sequencing the library comprising the genomic DNA obtained from the non-tumor cells hybridized to the biotinylated oligonucleotide probes to a maximum average depth of ˜500×;
• and
• i) identifying variants in the genomic DNA obtained from the tumor cells compared to the genomic DNA obtained from the non-tumor cells, thereby identifying individual genetic mutations in multiple myeloma in the subject.