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{"Sample_ID":"PT116","chr":"chr1","posStart":31673263,"posEnd":145104261,"length":113430999,"numProbe":16370,"log2ratio.Mean.adj":-0.19904,"log2ratio.SD":0.2041,"log2ratio.Median.adj":-0.1891,"log2ratio.MAD":0.18103,"log2mBAF.Mean":0.28421,"log2mBAF.SD":0.16639,"log2mBAF.Median":0.31415,"log2mBAF.MAD":0.13231,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":769,"gene":"A3GALT2,ABCA4,ABCD3,ACADM,ACOT11,ACTG1P4,ADAM30,ADC,ADORA3,ADPRHL2,AGBL4,AGL,AGO1,AGO3,AGO4,AHCYL1,AK2,AK4,AK5,AKIRIN1,AKNAD1,AKR1A1,AKR7A2P1,ALG14,ALG6,ALX3,AMIGO1,AMPD1,AMPD2,AMY1A,AMY1B,AMY1C,AMY2A,AMY2B,ANGPTL3,ANKRD13C,ANKRD20A12P,AP4B1,AP4B1-AS1,ARHGAP29,ARTN,ASB17,ATG4C,ATP1A1,ATP1A1OS,ATP5F1,ATP6V0B,ATPAF1,ATXN7L2,B4GALT2,BAI2,BARHL2,BCAR3,BCAS2,BCL10,BCL2L15,BEND5,BEST4,BMP8A,BMP8B,BRDT,BSDC1,BSND,BTBD19,BTBD8,BTF3L4,C1orf109,C1orf122,C1orf123,C1orf141,C1orf146,C1orf162,C1orf168,C1orf173,C1orf177,C1orf180,C1orf185,C1orf194,C1orf210,C1orf216,C1orf228,C1orf50,C1orf52,C1orf87,C1orf94,C8A,C8B,CACHD1,CAP1,CAPZA1,CASQ2,CC2D1B,CCBL2,CCDC163P,CCDC17,CCDC18,CCDC23,CCDC24,CCDC28B,CCDC30,CD101,CD2,CD53,CD58,CDC14A,CDC20,CDC7,CDCA8,CDCP2,CDKN2C,CELSR2,CEPT1,CHI3L2,CHIA,CHIAP2,CITED4,CLCA1,CLCA2,CLCA3P,CLCA4,CLCC1,CLDN19,CLSPN,CMPK1,CNN3,COL11A1,COL16A1,COL24A1,COL8A2,COL9A2,CPT2,CRYZ,CSDE1,CSF1,CSF3R,CSMD2,CTBS,CTH,CTPS1,CTTNBP2NL,CYB561D1,CYB5RL,CYMP,CYP2J2,CYP4A11,CYP4A22,CYP4B1,CYP4X1,CYP4Z1,CYP4Z2P,CYR61,DAB1,DBT,DCDC2B,DCLRE1B,DDAH1,DDX20,DENND2C,DENND2D,DEPDC1,DHCR24,DIO1,DIRAS3,DLEU2L,DLGAP3,DMAP1,DMBX1,DMRTA2,DMRTB1,DNAJA1P5,DNAJB4,DNAJC6,DNALI1,DNASE2B,DNTTIP2,DOCK7,DPH2,DPH5,DPYD,DPYD-AS1,DR1,DRAM2,EBNA1BP2,ECHDC2,EDN2,EFCAB14,EFCAB14-AS1,EFCAB7,EIF2B3,EIF3I,ELAVL4,ELOVL1,ELTD1,EMBP1,EPHA10,EPHX4,EPS15,EPS8L3,ERI3,ERMAP,EVA1B,EVI5,EXO5,EXTL2,F3,FAAH,FABP3,FAF1,FAM102B,FAM151A,FAM159A,FAM167B,FAM183A,FAM19A3,FAM212B,FAM229A,FAM46C,FAM69A,FAM72B,FAM72D,FAM73A,FCGR1B,FGGY,FHL3,FLJ27354,FLJ31662,FLJ39739,FNBP1L,FNDC5,FNDC7,FOXD2,FOXD2-AS1,FOXD3,FOXE3,FOXJ3,FPGT,FPGT-TNNI3K,FRRS1,FUBP1,GADD45A,GBP1,GBP1P1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCLM,GDAP2,GEMIN8P4,GFI1,GIPC2,GJA4,GJA9,GJA9-MYCBP,GJB3,GJB4,GJB5,GLIS1,GLMN,GNAI3,GNAT2,GNG12,GNG12-AS1,GNG5,GNL2,GPBP1L1,GPR61,GPR88,GPSM2,GPX7,GRIK3,GSTM1,GSTM2,GSTM3,GSTM4,GSTM5,GTF2B,GUCA2A,GUCA2B,HAO2,HCRTR1,HDAC1,HEATR8-TTC4,HECTD3,HENMT1,HEYL,HFM1,HHLA3,HIAT1,HIPK1,HIST2H2BA,HIVEP3,HMGB4,HMGCS2,HOOK1,HPCA,HPCAL4,HPDL,HS2ST1,HSD3B1,HSD3B2,HSD3BP4,HSD52,HSPB11,HYI,IFI44,IFI44L,IGSF3,IL12RB2,IL23R,INADL,INPP5B,INSL5,IPO13,IPP,IQCC,ITGB3BP,JAK1,JUN,KANK4,KCNA10,KCNA2,KCNA3,KCNC4,KCND3,KCNQ4,KDM4A,KDM4A-AS1,KHDRBS1,KIAA0319L,KIAA0754,KIAA1107,KIAA1324,KIAA1522,KIF2C,KLF17,KNCN,KPNA6,KTI12,L1TD1,LAMTOR5,LCK,LDLRAD1,LEPR,LEPRE1,LEPROT,LHX8,LINC00466,LINC00622,LINC00623,LINC00853,LMO4,LOC100128787,LOC100129046,LOC100129138,LOC100129269,LOC100129620,LOC100129924,LOC100130000,LOC100130557,LOC100131060,LOC100131564,LOC100286793,LOC100505768,LOC100506343,LOC100507564,LOC100507634,LOC149086,LOC284551,LOC339442,LOC339524,LOC400752,LOC402779,LOC440600,LOC643355,LOC643441,LOC646626,LOC653160,LOC653513,LOC728431,LOC728875,LOC729041,LOC729930,LOC729970,LOC729987,LPAR3,LPHN2,LPPR4,LPPR5,LRIF1,LRIG2,LRP8,LRRC39,LRRC40,LRRC41,LRRC42,LRRC7,LRRC8B,LRRC8C,LRRC8D,LRRIQ3,LSM10,LURAP1,MAB21L3,MACF1,MAGI3,MAGOH,MAN1A2,MANEAL,MAP7D1,MARCKSL1,MAST2,MCOLN2,MCOLN3,MEAF6,MED8,MFSD2A,MGC27382,MGC34796,MIER1,MIR101-1,MIR1262,MIR137,MIR137HG,MIR186,MIR197,MIR2682,MIR30C1,MIR30E,MIR3117,MIR320B1,MIR3605,MIR3659,MIR3671,MIR4254,MIR4255,MIR4256,MIR4422,MIR4423,MIR4711,MIR4781,MIR4794,MIR548AA1,MIR548AP,MIR548D1,MIR553,MIR5581,MIR5584,MIR760,MIR761,MIR942,MKNK1,MKNK1-AS1,MMACHC,MOB3C,MOV10,MPL,MROH7,MRPL37,MRPS15,MSH4,MTF1,MTF2,MTMR9LP,MUTYH,MYBPHL,MYCBP,MYCL1,MYSM1,NASP,NBPF4,NBPF6,NBPF7,NBPF8,NBPF9,NCDN,NDUFS5,NEGR1,NEGR1-IT1,NEXN,NFIA,NFYC,NGF,NHLH2,NKAIN1,NOTCH2,NRAS,NRD1,NSUN4,NT5C1A,NTNG1,ODF2L,OLFM3,OLFML3,OMA1,ORC1,OSBPL9,OSCP1,OVGP1,OXCT2,PABPC4,PALMD,PARS2,PCSK9,PDE4B,PDE4DIP,PDZK1IP1,PEF1,PFN1P2,PGCP1,PGM1,PHC2,PHGDH,PHTF1,PIFO,PIGK,PIK3R3,PIN1P1,PKN2,PLK3,PODN,POMGNT1,POU3F1,PPAP2B,PPCS,PPIAL4A,PPIAL4B,PPIAL4C,PPIAL4G,PPIE,PPIEL,PPIH,PPM1J,PPT1,PRDX1,PRKAA2,PRKACB,PRMT6,PROK1,PRPF38A,PRPF38B,PSMA5,PSMB2,PSRC1,PTBP2,PTCH2,PTGER3,PTGFR,PTGFRN,PTP4A2,PTPN22,PTPRF,RAB3B,RABGGTB,RAD54L,RAP1A,RAVER2,RBBP4,RBM15,RBMXL1,REG4,RHBDL2,RHOC,RIMKLA,RIMS3,RLF,RNF11,RNF19B,RNF220,RNPC3,RNU6-6,ROR1,RPAP2,RPE65,RPF1,RPL5,RPS15AP10,RPS8,RRAGC,RSBN1,RSPO1,RTCA,RWDD3,S100PBP,S1PR1,SAMD13,SARS,SASS6,SCARNA2,SCMH1,SCP2,SEC22B,SELRC1,SEP15,SERBP1,SERINC2,SF3A3,SFPQ,SGIP1,SH3D21,SH3GLB1,SIKE1,SKINTL,SLC16A1,SLC16A4,SLC1A7,SLC22A15,SLC25A24,SLC25A3P1,SLC2A1,SLC2A1-AS1,SLC30A7,SLC35A3,SLC35D1,SLC44A3,SLC44A5,SLC5A9,SLC6A17,SLC6A9,SLFNL1,SLFNL1-AS1,SMAP2,SMIM12,SNIP1,SNORA55,SNORA66,SNORD21,SNORD38A,SNORD38B,SNORD45A,SNORD45B,SNORD45C,SNORD46,SNORD55,SNRNP40,SNX7,SORT1,SPAG17,SPATA6,SPOCD1,SRG7,SRGAP2D,SRSF11,SSBP3,SSX2IP,ST3GAL3,ST6GALNAC3,ST6GALNAC5,ST7L,STIL,STK40,STRIP1,STXBP3,SYCP1,SYDE2,SYNC,SYPL2,SYT6,SZT2,TACSTD2,TAF13,TAL1,TBX15,TCEANC2,TCTEX1D1,TCTEX1D4,TEKT2,TESK2,TEX38,TFAP2E,TGFBR3,THRAP3,TIE1,TINAGL1,TM2D1,TMCO2,TMED5,TMEM125,TMEM167B,TMEM234,TMEM39B,TMEM48,TMEM53,TMEM54,TMEM56,TMEM56-RWDD3,TMEM59,TMEM61,TMEM69,TNNI3K,TOE1,TRABD2B,TRAPPC3,TRIM33,TRIM45,TRIM62,TRIT1,TRMT13,TSHB,TSPAN1,TSPAN2,TSSK3,TTC22,TTC39A,TTC4,TTF2,TTLL7,TXLNA,TXNDC12,TYW3,UBE2U,UBL4B,UOX,UQCRH,UROD,USP1,USP24,USP33,UTP11L,VANGL1,VAV3,VAV3-AS1,VCAM1,VTCN1,WARS2,WDR3,WDR47,WDR63,WDR65,WDR77,WDR78,WLS,WNT2B,YARS,YBX1,YIPF1,YRDC,ZBTB8A,ZBTB8B,ZBTB8OS,ZC3H12A,ZCCHC11,ZCCHC17,ZFP69,ZFP69B,ZFYVE9,ZMPSTE24,ZMYM1,ZMYM4,ZMYM6,ZMYM6NB,ZMYND12,ZNF326,ZNF362,ZNF644,ZNF684,ZNF691,ZNF697,ZNHIT6,ZRANB2,ZRANB2-AS1,ZRANB2-AS2,ZSCAN20,ZSWIM5,ZYG11A,ZYG11B,ZZZ3"}
{"Sample_ID":"PT116","chr":"chr1","posStart":145394955,"posEnd":162439902,"length":17044948,"numProbe":2418,"log2ratio.Mean.adj":0.54652,"log2ratio.SD":0.2515,"log2ratio.Median.adj":0.5383,"log2ratio.MAD":0.25486,"log2mBAF.Mean":0.51264,"log2mBAF.SD":0.11875,"log2mBAF.Median":0.5265,"log2mBAF.MAD":0.11341,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":435,"gene":"ACP6,ADAM15,ADAMTS4,ADAMTSL4,ADAR,AIM2,ANKRD34A,ANKRD35,ANP32E,ANXA9,APCS,APH1A,APOA1BP,APOA2,AQP10,ARHGAP30,ARHGEF11,ARHGEF2,ARNT,ASH1L,ASH1L-AS1,ATF6,ATP1A2,ATP1A4,ATP8B2,B4GALT3,BCAN,BCL9,BGLAP,BNIPL,BOLA1,C1orf111,C1orf189,C1orf192,C1orf204,C1orf226,C1orf43,C1orf51,C1orf54,C1orf56,C1orf61,C1orf68,C1orf85,C2CD4D,CA14,CADM3,CASQ1,CCDC19,CCT3,CD160,CD1A,CD1B,CD1C,CD1D,CD1E,CD244,CD48,CD5L,CD84,CDC42SE1,CELF3,CERS2,CGN,CHD1L,CHRNB2,CHTOP,CKS1B,CLK2,COPA,CRABP2,CRCT1,CREB3L4,CRNN,CRP,CRTC2,CTSK,CTSS,CYCSP52,DAP3,DARC,DCAF8,DCST1,DCST2,DEDD,DENND4B,DPM3,DUSP12,DUSP23,ECM1,EFNA1,EFNA3,EFNA4,ENSA,ETV3,ETV3L,F11R,FAM189B,FAM63A,FCER1A,FCER1G,FCGR1A,FCGR1C,FCGR2A,FCGR2B,FCGR2C,FCGR3A,FCGR3B,FCRL1,FCRL2,FCRL3,FCRL4,FCRL5,FCRL6,FCRLA,FCRLB,FDPS,FLAD1,FLG,FLG2,FLJ39739,FMO5,GABPB2,GATAD2B,GBA,GBAP1,GJA5,GJA8,GNRHR2,GOLPH3L,GON4L,GPATCH4,GPR89A,GPR89B,GPR89C,HAPLN2,HAX1,HCN3,HDGF,HFE2,HIST2H2AA3,HIST2H2AA4,HIST2H2AB,HIST2H2AC,HIST2H2BC,HIST2H2BE,HIST2H2BF,HIST2H3A,HIST2H3C,HIST2H3D,HIST2H4A,HIST2H4B,HORMAD1,HRNR,HSPA6,HSPA7,HYDIN2,IFI16,IGSF8,IGSF9,IL6R,ILF2,INSRR,INTS3,IQGAP3,ISG20L2,ITGA10,ITLN1,ITLN2,IVL,JTB,KCNJ10,KCNJ9,KCNN3,KIAA0907,KIRREL,KLHDC9,KPRP,KRTCAP2,LAMTOR2,LCE1A,LCE1B,LCE1C,LCE1D,LCE1E,LCE1F,LCE2A,LCE2B,LCE2C,LCE2D,LCE3A,LCE3B,LCE3C,LCE3D,LCE3E,LCE4A,LCE5A,LCE6A,LELP1,LENEP,LINC00568,LINC00623,LINC00624,LINC00869,LINGO4,LIX1L,LMNA,LOC100131825,LOC100132111,LOC100505633,LOC100505666,LOC388692,LOC645166,LOC646268,LOC728989,LOR,LRRC71,LY9,LYSMD1,MCL1,MEF2D,MEX3A,MIR190B,MIR4257,MIR4258,MIR4654,MIR5087,MIR5187,MIR554,MIR555,MIR556,MIR765,MIR9-1,MIR92B,MLLT11,MNDA,MPZ,MRPL24,MRPL9,MRPS21,MSTO1,MSTO2P,MTMR11,MTX1,MUC1,NBPF11,NBPF14,NBPF15,NBPF16,NBPF24,NBPF8,NCSTN,NDUFS2,NES,NHLH1,NIT1,NOS1AP,NPR1,NR1I3,NTRK1,NUDT17,NUP210L,OAZ3,OLFML2B,OR10J1,OR10J3,OR10J5,OR10K1,OR10K2,OR10R2,OR10T2,OR10X1,OR10Z1,OR6K2,OR6K3,OR6K6,OR6N1,OR6N2,OR6P1,OR6Y1,OTUD7B,PAQR6,PBXIP1,PCP4L1,PDIA3P,PDZK1,PDZK1P1,PEA15,PEAR1,PEX11B,PEX19,PFDN2,PGLYRP3,PGLYRP4,PI4KB,PIAS3,PIGM,PIP5K1A,PKLR,PLEKHO1,PMF1,PMF1-BGLAP,PMVK,POGZ,POLR3C,POLR3GL,POU5F1P4,PPIAL4A,PPIAL4B,PPIAL4C,PPIAL4D,PPIAL4E,PPIAL4F,PPOX,PRCC,PRKAB2,PRPF3,PRR9,PRUNE,PSMB4,PSMD4,PVRL4,PYGO2,PYHIN1,RAB13,RAB25,RBM8A,RFX5,RHBG,RIIAD1,RIT1,RNF115,RORC,RPL31P11,RPRD2,RPS27,RPTN,RRNAD1,RUSC1,RUSC1-AS1,RXFP4,S100A1,S100A10,S100A11,S100A12,S100A13,S100A14,S100A16,S100A2,S100A3,S100A4,S100A5,S100A6,S100A7,S100A7A,S100A7L2,S100A8,S100A9,SCAMP3,SCARNA4,SCNM1,SDHC,SELENBP1,SEMA4A,SEMA6C,SETDB1,SF3B4,SH2D1B,SH2D2A,SHC1,SHE,SLAMF1,SLAMF6,SLAMF7,SLAMF8,SLAMF9,SLC25A44,SLC27A3,SLC39A1,SLC50A1,SMCP,SMG5,SNAPIN,SNORA42,SNX27,SPRR1A,SPRR1B,SPRR2A,SPRR2B,SPRR2C,SPRR2D,SPRR2E,SPRR2F,SPRR2G,SPRR3,SPRR4,SPTA1,SSR2,SUMO1P3,SV2A,SYT11,TAGLN2,TARS2,TCHH,TCHHL1,TDRD10,TDRKH,THBS3,THEM4,THEM5,TMEM79,TMOD4,TNFAIP8L2,TNFAIP8L2-SCNM1,TOMM40L,TPM3,TRIM46,TSACC,TSTD1,TTC24,TUFT1,TXNIP,UBAP2L,UBE2Q1,UBQLN4,UFC1,USF1,USP21,VANGL2,VHLL,VPS45,VPS72,VSIG8,YY1AP1,ZBTB7B,ZNF687"}
{"Sample_ID":"PT116","chr":"chr1","posStart":162440134,"posEnd":179683856,"length":17243723,"numProbe":3465,"log2ratio.Mean.adj":0.62586,"log2ratio.SD":0.26144,"log2ratio.Median.adj":0.6086,"log2ratio.MAD":0.25456,"log2mBAF.Mean":0.51374,"log2mBAF.SD":0.12115,"log2mBAF.Median":0.52627,"log2mBAF.MAD":0.11735,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":143,"gene":"ABL2,ADCY10,ALDH9A1,ANGPTL1,ANKRD36BP1,ANKRD45,ASTN1,ATP1B1,AXDND1,BLZF1,C1orf105,C1orf110,C1orf112,C1orf220,CACYBP,CCDC181,CD247,CENPL,CREG1,DARS2,DCAF6,DDR2,DNM3,DNM3OS,DPT,DUSP27,F5,FAM20B,FAM5B,FAM78B,FASLG,FMO1,FMO2,FMO3,FMO4,FMO6P,FMO9P,GAS5,GAS5-AS1,GORAB,GPA33,GPR161,GPR52,HSD17B7,ILDR2,KIAA0040,KIFAP3,KLHL20,LINC00626,LMX1A,LOC100505795,LOC100505918,LOC100506023,LOC284688,LOC400794,LOC440700,LOC730102,LOC730159,LRRC52,MAEL,METTL11B,METTL13,METTL18,MGST3,MIR1295A,MIR1295B,MIR199A2,MIR214,MIR3119-1,MIR3119-2,MIR3120,MIR3658,MIR4424,MIR488,MIR557,MIR921,MPC2,MPZL1,MROH9,MRPS14,MYOC,NME7,NPHS2,NUF2,PAPPA2,PBX1,PIGC,POGK,POU2F1,PRDX6,PRRC2C,PRRX1,RABGAP1L,RALGPS2,RASAL2,RASAL2-AS1,RC3H1,RCSD1,RFWD2,RGS4,RGS5,RXRG,SCARNA3,SCYL3,SEC16B,SELE,SELL,SELP,SERPINC1,SFT2D2,SLC19A2,SLC9C2,SNORD44,SNORD47,SNORD74,SNORD75,SNORD76,SNORD77,SNORD78,SNORD79,SNORD80,SNORD81,SOAT1,SUCO,TADA1,TBX19,TDRD5,TEX35,TIPRL,TMCO1,TNFSF18,TNFSF4,TNN,TNR,TOP1P1,TOR3A,UAP1,UCK2,UHMK1,VAMP4,XCL1,XCL2,ZBTB37"}
{"Sample_ID":"PT116","chr":"chr1","posStart":179687259,"posEnd":186599524,"length":6912266,"numProbe":1200,"log2ratio.Mean.adj":0.55766,"log2ratio.SD":0.23136,"log2ratio.Median.adj":0.53135,"log2ratio.MAD":0.23714,"log2mBAF.Mean":0.50265,"log2mBAF.SD":0.12343,"log2mBAF.Median":0.51641,"log2mBAF.MAD":0.12318,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":56,"gene":"ACBD6,APOBEC4,ARPC5,C1orf21,C1orf27,CACNA1E,CEP350,COLGALT2,DHX9,EDEM3,FAM129A,FAM163A,FLJ23867,GLUL,GM140,HMCN1,IER5,IVNS1ABP,KIAA1614,LAMC1,LAMC2,LHX4,LINC00272,LOC100288079,LOC100527964,LOC284648,MIR3121,MIR548F1,MR1,NCF2,NMNAT2,NPL,OCLM,PDC,PRG4,QSOX1,RGL1,RGS16,RGS8,RGSL1,RNASEL,RNF2,RNU6-72,SHCBP1L,SMG7,SMG7-AS1,STX6,SWT1,TEDDM1,TOR1AIP1,TOR1AIP2,TPR,TRMT1L,TSEN15,XPR1,ZNF648"}
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{"Sample_ID":"PT116","chr":"chr1","posStart":243501056,"posEnd":249210707,"length":5709652,"numProbe":1133,"log2ratio.Mean.adj":0.33917,"log2ratio.SD":0.2138,"log2ratio.Median.adj":0.34705,"log2ratio.MAD":0.19548,"log2mBAF.Mean":0.29929,"log2mBAF.SD":0.13665,"log2mBAF.Median":0.32055,"log2mBAF.MAD":0.13163,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":82,"gene":"ADSS,AHCTF1,AKT3,C1orf100,C1orf101,C1orf229,CNST,COX20,DESI2,EFCAB2,GCSAML,GCSAML-AS1,HNRNPU,HNRNPU-AS1,KIF26B,LOC149134,LOC255654,LOC339529,LYPD8,MIR3124,MIR3916,MIR4677,NLRP3,OR11L1,OR13G1,OR14A16,OR14C36,OR14I1,OR1C1,OR2AK2,OR2B11,OR2C3,OR2G2,OR2G3,OR2G6,OR2L13,OR2L1P,OR2L2,OR2L3,OR2L5,OR2L8,OR2M1P,OR2M2,OR2M3,OR2M4,OR2M5,OR2M7,OR2T1,OR2T10,OR2T11,OR2T12,OR2T2,OR2T27,OR2T29,OR2T3,OR2T33,OR2T34,OR2T35,OR2T4,OR2T5,OR2T6,OR2T8,OR2W3,OR2W5,OR6F1,PGBD2,SCCPDH,SDCCAG8,SH3BP5L,SMYD3,TFB2M,TRIM58,VN1R5,ZBTB18,ZNF124,ZNF496,ZNF669,ZNF670,ZNF670-ZNF695,ZNF672,ZNF692,ZNF695"}
{"Sample_ID":"PT116","chr":"chr3","posStart":76317,"posEnd":197813975,"length":197737659,"numProbe":38140,"log2ratio.Mean.adj":-0.20454,"log2ratio.SD":0.19929,"log2ratio.Median.adj":-0.1937,"log2ratio.MAD":0.18043,"log2mBAF.Mean":0.28831,"log2mBAF.SD":0.16747,"log2mBAF.Median":0.31894,"log2mBAF.MAD":0.13422,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":1276,"gene":"A4GNT,AADAC,AADACL2,ABCC5,ABCC5-AS1,ABCF3,ABHD10,ABHD14A,ABHD14A-ACY1,ABHD14B,ABHD5,ABHD6,ABI3BP,ABTB1,ACAA1,ACAD11,ACAD9,ACAP2,ACOX2,ACPL2,ACPP,ACTL6A,ACTR8,ACTRT3,ACVR2B,ACVR2B-AS1,ACY1,ADAMTS9,ADAMTS9-AS2,ADCY5,ADIPOQ,ADIPOQ-AS1,ADPRH,AGTR1,AHSG,ALAS1,ALCAM,ALDH1L1,ALDH1L1-AS1,ALDH1L1-AS2,ALG1L,ALG1L2,ALG3,ALS2CL,AMIGO3,AMOTL2,AMT,ANAPC13,ANKRD18DP,ANKRD28,ANKUB1,ANO10,AP2M1,APEH,APOD,APPL1,ARF4,ARGFX,ARHGAP31,ARHGEF26,ARHGEF26-AS1,ARHGEF3,ARHGEF3-AS1,ARIH2,ARIH2OS,ARL13B,ARL14,ARL6,ARL6IP5,ARL8B,ARMC8,ARPC4,ARPC4-TTLL3,ARPP21,ASB14,ASTE1,ATG3,ATG7,ATP11B,ATP13A3,ATP13A4,ATP13A5,ATP1B3,ATP2B2,ATP2C1,ATP6V1A,ATR,ATRIP,ATXN7,AZI2,B3GALNT1,B3GNT5,B4GALT4,BAP1,BBX,BCHE,BCL6,BDH1,BFSP2,BHLHE40,BHLHE40-AS1,BOC,BPESC1,BRK1,BRPF1,BSN,BSN-AS2,BTD,BTLA,C3orf14,C3orf17,C3orf18,C3orf20,C3orf22,C3orf27,C3orf30,C3orf33,C3orf35,C3orf36,C3orf37,C3orf38,C3orf43,C3orf49,C3orf52,C3orf55,C3orf58,C3orf62,C3orf65,C3orf67,C3orf70,C3orf72,C3orf79,C3orf80,CACNA1D,CACNA2D2,CACNA2D3,CACNA2D3-AS1,CADM2,CADM2-AS2,CADPS,CAMK1,CAMK2N2,CAMKV,CAMP,CAND2,CAPN7,CASR,CAV3,CBLB,CCBP2,CCDC12,CCDC13,CCDC13-AS1,CCDC14,CCDC174,CCDC36,CCDC37,CCDC39,CCDC50,CCDC51,CCDC54,CCDC58,CCDC66,CCDC71,CCDC80,CCK,CCNL1,CCR1,CCR2,CCR3,CCR4,CCR5,CCR8,CCR9,CCRL1,CCRL2,CD200,CD200R1,CD200R1L,CD47,CD80,CD86,CD96,CDC25A,CDCP1,CDHR4,CDV3,CELSR3,CEP19,CEP63,CEP70,CEP97,CGGBP1,CHCHD4,CHCHD6,CHDH,CHL1,CHMP2B,CHRD,CHST13,CHST2,CIDEC,CIDECP,CISH,CLASP2,CLCN2,CLDN1,CLDN11,CLDN16,CLDN18,CLDND1,CLEC3B,CLRN1,CLRN1-AS1,CLSTN2,CMC1,CMSS1,CMTM6,CMTM7,CMTM8,CNBP,CNOT10,CNTN3,CNTN4,CNTN4-AS2,CNTN6,COL6A4P1,COL6A4P2,COL6A5,COL6A6,COL7A1,COL8A1,COLQ,COMMD2,COPB2,COPG1,COX17,CP,CPA3,CPB1,CPN2,CPNE4,CPNE9,CPOX,CRBN,CRELD1,CRTAP,CRYBG3,CRYGS,CSPG5,CSRNP1,CSTA,CT64,CTDSPL,CTNNB1,CX3CR1,CXCR6,CYB561D2,CYP8B1,DAG1,DALRD3,DAZL,DBR1,DCBLD2,DCLK3,DCP1A,DCUN1D1,DENND6A,DGKG,DHFRL1,DHX30,DHX36,DIRC2,DLEC1,DLG1,DLG1-AS1,DNAH1,DNAH12,DNAJB11,DNAJB8,DNAJB8-AS1,DNAJC13,DNAJC19,DNASE1L3,DOCK3,DPH3,DPPA2,DPPA2P3,DPPA4,DRD3,DTX3L,DUSP7,DVL3,DYNC1LI1,DZIP1L,DZIP3,EAF1,EAF2,EBLN2,ECE2,ECT2,EDEM1,EEFSEC,EFCAB12,EFCC1,EFHB,EGFEM1P,EGOT,EHHADH,EHHADH-AS1,EIF1B,EIF1B-AS1,EIF2A,EIF2B5,EIF4A2,EIF4E3,EIF4G1,EIF5A2,ELP6,EMC3,ENTPD3,ENTPD3-AS1,EOGT,EOMES,EPHA3,EPHA6,EPHB1,EPHB3,EPM2AIP1,ERC2,ERC2-IT1,ESRG,ESYT3,ETV5,EXOG,EXOSC7,FAIM,FAM107A,FAM131A,FAM162A,FAM172BP,FAM194A,FAM198A,FAM19A1,FAM19A4,FAM208A,FAM212A,FAM3D,FAM43A,FAM86DP,FAM86HP,FAM86JP,FANCD2,FANCD2OS,FBLN2,FBXL2,FBXO40,FBXO45,FBXW12,FETUB,FEZF2,FGD5,FGD5-AS1,FGD5P1,FGF12,FHIT,FILIP1L,FLJ20518,FLJ22763,FLJ25363,FLJ34208,FLJ42393,FLJ46066,FLNB,FNDC3B,FOXL2,FOXP1,FRG2C,FRMD4B,FSTL1,FXR1,FYCO1,FYTTD1,GABRR3,GADL1,GALNT15,GAP43,GATA2,GBE1,GCSAM,GFM1,GHRL,GHRLOS,GHSR,GK5,GLB1,GLT8D1,GLYCTK,GMNC,GMPPB,GMPS,GNAI2,GNAT1,GNB4,GNL3,GOLGA4,GOLGB1,GOLIM4,GORASP1,GP5,GP9,GPD1L,GPR128,GPR149,GPR15,GPR156,GPR160,GPR171,GPR27,GPR62,GPR87,GPX1,GRAMD1C,GRIP2,GRK7,GRM2,GRM7,GSK3B,GTDC2,GTF2E1,GTPBP8,GUCA1C,GXYLT2,GYG1,H1FOO,H1FX,H1FX-AS1,HACL1,HCLS1,HDAC11,HEG1,HEMK1,HES1,HESX1,HGD,HHATL,HHLA2,HIGD1A,HLTF,HLTF-AS1,HPS3,HRASLS,HRG,HRH1,HSPBAP1,HTR1F,HTR3C,HTR3D,HTR3E,HYAL1,HYAL2,HYAL3,IFRD2,IFT122,IFT57,IFT80,IGF2BP2,IGSF10,IGSF11,IGSF11-AS1,IL12A,IL17RB,IL17RC,IL17RD,IL17RE,IL1RAP,IL20RB,IL5RA,ILDR1,IMPDH2,IMPG2,IP6K1,IP6K2,IQCB1,IQCF1,IQCF2,IQCF3,IQCF4,IQCF5,IQCF6,IQCG,IQCJ,IQCJ-SCHIP1,IQSEC1,IRAK2,ISY1,ISY1-RAB43,ITGA9,ITGB5,ITIH1,ITIH3,ITIH4,ITPR1,JAGN1,KALRN,KAT2B,KBTBD12,KBTBD8,KCNAB1,KCNAB1-AS1,KCNAB1-AS2,KCNH8,KCNMB2,KCNMB2-IT1,KCNMB3,KCTD6,KIAA0226,KIAA1143,KIAA1257,KIAA1407,KIAA1524,KIAA2018,KIF15,KIF9,KIF9-AS1,KLF15,KLHDC8B,KLHL18,KLHL24,KLHL40,KLHL6,KNG1,KPNA1,KPNA4,KRBOX1,KY,LAMB2,LAMB2P1,LAMP3,LARS2,LARS2-AS1,LEKR1,LEPREL1,LHFPL4,LIMD1,LIMD1-AS1,LINC00312,LINC00488,LINC00578,LINC00606,LINC00620,LINC00635,LINC00636,LINC00691,LINC00692,LINC00693,LINC00696,LINC00698,LINC00852,LIPH,LMCD1,LMCD1-AS1,LMLN,LMOD3,LNP1,LOC100009676,LOC100128164,LOC100129480,LOC100129550,LOC100131551,LOC100131635,LOC100132146,LOC100287639,LOC100287879,LOC100289361,LOC100302640,LOC100498859,LOC100505687,LOC100507032,LOC100507389,LOC100507391,LOC100507537,LOC101243545,LOC152217,LOC152225,LOC201617,LOC201651,LOC220729,LOC253573,LOC255025,LOC339862,LOC339874,LOC339894,LOC344595,LOC344887,LOC401052,LOC401074,LOC401109,LOC440970,LOC646168,LOC646498,LOC646903,LOC647323,LOC653712,LOC730091,LOC90246,LPP,LPP-AS2,LRCH3,LRIG1,LRRC15,LRRC2,LRRC2-AS1,LRRC31,LRRC33,LRRC34,LRRC3B,LRRC58,LRRFIP2,LRRIQ4,LRRN1,LRTM1,LSAMP,LSAMP-AS3,LSG1,LSM3,LSMEM2,LTF,LUST,LXN,LYZL4,LZTFL1,MAATS1,MAGEF1,MAGI1,MAGI1-AS1,MANF,MAP3K13,MAP4,MAP6D1,MAPKAPK3,MASP1,MB21D2,MBD4,MBNL1,MBNL1-AS1,MCCC1,MCF2L2,MCM2,MECOM,MED12L,METTL6,MFI2,MFI2-AS1,MFN1,MFSD1,MGC2889,MGLL,MINA,MIR1224,MIR1226,MIR1248,MIR128-2,MIR1284,MIR1324,MIR135A1,MIR138-1,MIR15B,MIR16-2,MIR191,MIR198,MIR26A1,MIR3136,MIR3714,MIR3919,MIR3921,MIR3938,MIR425,MIR4270,MIR4271,MIR4272,MIR4273,MIR4442,MIR4443,MIR4444-1,MIR4446,MIR4787,MIR4788,MIR4789,MIR4790,MIR4791,MIR4792,MIR4793,MIR4795,MIR4796,MIR4797,MIR5002,MIR5092,MIR5186,MIR5193,MIR548A2,MIR548A3,MIR548AC,MIR548G,MIR548H2,MIR548I1,MIR551B,MIR563,MIR564,MIR567,MIR568,MIR5688,MIR569,MIR5692C1,MIR570,MIR5704,MIR711,MIR885,MIR922,MIR944,MIRLET7G,MITF,MKRN2,MLF1,MLH1,MME,MOBP,MON1A,MORC1,MRAS,MRPL3,MRPL47,MRPS22,MRPS25,MSL2,MST1,MST1R,MTMR14,MUC13,MUC20,MUC4,MUSTN1,MYD88,MYH15,MYL3,MYLK,MYLK-AS1,MYNN,MYRIP,NAA50,NAALADL2,NAALADL2-AS3,NAT6,NBEAL2,NCBP2,NCEH1,NCK1,NCKIPSD,NDUFAF3,NDUFB4,NDUFB5,NEK10,NEK11,NEK4,NFKBIZ,NGLY1,NICN1,NISCH,NIT2,NKIRAS1,NKTR,NLGN1,NMD3,NME6,NME9,NMNAT3,NPHP3,NPHP3-ACAD11,NPHP3-AS1,NPRL2,NR1D2,NR1I2,NR2C2,NRADDP,NSUN3,NT5DC2,NUDT16,NUDT16P1,NUP210,NUP210P1,NXPE3,OGG1,OPA1,OPA1-AS1,OR5AC2,OR5H1,OR5H14,OR5H15,OR5H2,OR5H6,OR5K1,OR5K2,OR5K3,OR5K4,OSBPL10,OSBPL10-AS1,OSBPL11,OSTN,OTOL1,OXNAD1,OXSM,OXSR1,OXTR,P2RY1,P2RY12,P2RY13,P2RY14,P4HTM,PA2G4P4,PAK2,PAQR9,PARL,PARP14,PARP15,PARP3,PARP9,PBRM1,PCBP4,PCCB,PCNP,PCOLCE2,PCYT1A,PDCD10,PDCD6IP,PDCL3P4,PDE12,PDHB,PDIA5,PDZRN3,PEX5L,PFKFB4,PFN2,PHC3,PHF7,PHLDB2,PIGX,PIGZ,PIK3CA,PIK3CB,PIK3R4,PISRT1,PLA1A,PLCD1,PLCH1,PLCL2,PLCXD2,PLD1,PLOD2,PLS1,PLSCR1,PLSCR2,PLSCR4,PLSCR5,PLXNA1,PLXNB1,PLXND1,POC1A,PODXL2,POGLUT1,POLQ,POLR2H,POPDC2,POU1F1,PP2D1,PPARG,PPM1L,PPM1M,PPP1R2,PPP2R3A,PPP4R2,PRICKLE2,PRICKLE2-AS1,PRICKLE2-AS2,PRICKLE2-AS3,PRKAR2A,PRKCD,PRKCI,PROK2,PROS1,PRR23A,PRR23B,PRR23C,PRRT3,PRRT3-AS1,PRSS42,PRSS45,PRSS46,PRSS50,PSMD2,PSMD6,PSMD6-AS2,PTH1R,PTPLB,PTPN23,PTPRG,PTPRG-AS1,PTX3,PVRL3,PVRL3-AS1,PXK,PYDC2,QARS,QRICH1,QTRTD1,RAB43,RAB5A,RAB6B,RAB7A,RABL3,RAD18,RAD54L2,RAF1,RAP2B,RARB,RARRES1,RASA2,RASSF1,RBM15B,RBM5,RBM6,RBMS3,RBP1,RBP2,RETNLB,RFC4,RFT1,RFTN1,RHO,RHOA,RNF123,RNF13,RNF168,RNF7,RNU6-69,ROBO1,ROBO2,ROPN1,ROPN1B,RPL14,RPL15,RPL22L1,RPL24,RPL29,RPL32,RPL32P3,RPL35A,RPL39L,RPN1,RPP14,RPSA,RPUSD3,RRP9,RSRC1,RTP1,RTP2,RTP3,RTP4,RUVBL1,RYBP,RYK,SACM1L,SAMD7,SATB1,SCAP,SCARNA7,SCHIP1,SCN10A,SCN11A,SCN5A,SDHAP1,SDHAP2,SEC13,SEC22A,SEC22C,SEC61A1,SEC62,SELK,SELT,SEMA3B,SEMA3F,SEMA3G,SEMA5B,SENP2,SENP5,SENP7,SERP1,SERPINI1,SERPINI2,SETD2,SETD5,SETD5-AS1,SETMAR,SFMBT1,SGOL1,SGOL1-AS1,SH3BP5,SH3BP5-AS1,SHISA5,SHOX2,SHQ1,SI,SIAH2,SIDT1,SKIL,SLC12A8,SLC15A2,SLC22A13,SLC22A14,SLC25A20,SLC25A26,SLC25A36,SLC25A38,SLC26A6,SLC2A2,SLC33A1,SLC35A5,SLC35G2,SLC38A3,SLC41A3,SLC4A7,SLC51A,SLC6A1,SLC6A1-AS1,SLC6A11,SLC6A20,SLC6A6,SLC7A14,SLC9A9,SLC9A9-AS1,SLC9C1,SLCO2A1,SLITRK3,SLMAP,SMARCC1,SMC4,SMIM4,SNAR-I,SNORA4,SNORA58,SNORA6,SNORA62,SNORA63,SNORA7A,SNORA7B,SNORA81,SNORD19,SNORD19B,SNORD2,SNORD66,SNORD69,SNRK,SNRK-AS1,SNTN,SNX4,SOX14,SOX2,SOX2-OT,SPATA12,SPATA16,SPCS1,SPICE1,SPINK8,SPSB4,SPTSSB,SRGAP3,SRPRB,SS18L2,SSR3,SST,SSUH2,ST3GAL6,ST3GAL6-AS1,ST6GAL1,STAB1,STAC,STAG1,STT3B,STX19,STXBP5L,SUCLG2,SUCNR1,SUMF1,SUSD5,SYN2,SYNPR,SYNPR-AS1,TADA3,TAGLN3,TAMM41,TATDN2,TBC1D23,TBC1D5,TBCCD1,TBL1XR1,TCAIM,TCTA,TCTEX1D2,TDGF1,TERC,TEX264,TF,TFDP2,TFG,TFRC,TGFBR2,TGM4,THOC7,THPO,THRB,THRB-AS1,THUMPD3,TIGIT,TIMMDC1,TIMP4,TIPARP,TIPARP-AS1,TKT,TLR9,TM4SF1,TM4SF18,TM4SF19,TM4SF19-TCTEX1D2,TM4SF4,TMA7,TMCC1,TMEM108,TMEM110,TMEM110-MUSTN1,TMEM115,TMEM14E,TMEM158,TMEM207,TMEM212,TMEM30C,TMEM39A,TMEM40,TMEM41A,TMEM42,TMEM43,TMEM44,TMEM44-AS1,TMEM45A,TMEM89,TMF1,TMIE,TMPPE,TMPRSS7,TNFSF10,TNIK,TNK2,TNNC1,TOMM70A,TOP2B,TOPAZ1,TOPBP1,TP63,TPRA1,TPRG1,TPRG1-AS2,TPRXL,TRA2B,TRAIP,TRAK1,TRANK1,TRAT1,TREX1,TRH,TRIM42,TRIM59,TRIM71,TRMT10C,TRNT1,TRPC1,TSC22D2,TSEN2,TTC14,TTC21A,TTLL3,TUSC2,TWF2,TXNRD3,TXNRD3NB,U2SURP,UBA3,UBA5,UBA7,UBE2E1,UBE2E2,UBP1,UBXN7,UCN2,ULK4,UMPS,UPK1B,UQCRC1,UROC1,USP13,USP19,USP4,UTS2B,VENTXP7,VEPH1,VGLL3,VGLL4,VHL,VILL,VIPR1,VPRBP,VPS8,VWA5B2,WDR48,WDR49,WDR52,WDR52-AS1,WDR53,WDR5B,WDR6,WDR82,WNT5A,WNT7A,WWTR1,WWTR1-AS1,XCR1,XIRP1,XPC,XRN1,XXYLT1,XYLB,YEATS2,ZBBX,ZBED2,ZBTB11,ZBTB20,ZBTB20-AS1,ZBTB38,ZBTB47,ZCWPW2,ZDHHC19,ZDHHC23,ZDHHC3,ZFYVE20,ZIC1,ZIC4,ZKSCAN7,ZMAT3,ZMYND10,ZNF148,ZNF197,ZNF35,ZNF385D,ZNF445,ZNF501,ZNF502,ZNF589,ZNF619,ZNF620,ZNF621,ZNF639,ZNF654,ZNF660,ZNF662,ZNF717,ZNF80,ZNF860,ZPLD1,ZXDC"}
{"Sample_ID":"PT116","chr":"chr4","posStart":73508,"posEnd":46188778,"length":46115271,"numProbe":9524,"log2ratio.Mean.adj":0.02585,"log2ratio.SD":0.21113,"log2ratio.Median.adj":0.0189,"log2ratio.MAD":0.17554,"log2mBAF.Mean":0.82655,"log2mBAF.SD":0.09866,"log2mBAF.Median":0.84794,"log2mBAF.MAD":0.08692,"log2ratio.p.value":0.227,"log2mBAF.p.value":0,"p.value":0,"CNV":"LOH","numGene":258,"gene":"ABCA11P,ABLIM2,ACOX3,ADD1,ADRA2C,AFAP1,AFAP1-AS1,ANAPC4,APBB2,ARAP2,ATP5I,ATP8A1,BEND4,BLOC1S4,BOD1L1,BST1,C1QTNF7,C4orf19,C4orf48,C4orf6,CC2D2A,CCDC149,CCDC96,CCKAR,CD38,CHRNA9,CLNK,CLRN2,CPEB2,CPLX1,CPZ,CRIPAK,CRMP1,CTBP1,CTBP1-AS1,CYTL1,DCAF16,DCAF4L1,DEFB131,DGKQ,DHX15,DOK7,DRD5,DTHD1,EVC,EVC2,FAM114A1,FAM184B,FAM193A,FAM200B,FAM53A,FAM86EP,FBXL5,FGFBP1,FGFBP2,FGFR3,FGFRL1,FLJ13197,FLJ35424,FLJ36777,GABRG1,GAK,GBA3,GNPDA2,GPR125,GPR78,GRK4,GRPEL1,GRXCR1,GUF1,HAUS3,HGFAC,HMX1,HS3ST1,HTRA3,HTT,HTT-AS1,IDUA,JAKMIP1,KCNIP4,KCNIP4-IT1,KCTD8,KIAA0232,KIAA1239,KLB,KLF3,KLHL5,LAP3,LCORL,LDB2,LETM1,LGI2,LIAS,LIMCH1,LOC100129917,LOC100129931,LOC100130872,LOC100133461,LOC100505912,LOC100507266,LOC152742,LOC285484,LOC285540,LOC285547,LOC285548,LOC344967,LOC401127,LOC402160,LOC441009,LOC650293,LOC93622,LRPAP1,LYAR,MAEA,MAN2B2,MED28,MFSD10,MFSD7,MIR218-1,MIR3138,MIR378D1,MIR4274,MIR4275,MIR4798,MIR4800,MIR4801,MIR4802,MIR5091,MIR548AJ2,MIR548AX,MIR548I2,MIR572,MIR573,MIR574,MIR943,MRFAP1,MRFAP1L1,MSANTD1,MSX1,MXD4,MYL5,N4BP2,NAT8L,NCAPG,NELFA,NKX3-2,NOP14,NOP14-AS1,NSG1,NSUN7,OTOP1,PACRGL,PCDH7,PCGF3,PDE6B,PDS5A,PGM2,PHOX2B,PI4K2B,PIGG,POLN,PPARGC1A,PPP2R2C,PROM1,PSAPL1,PTTG2,QDPR,RAB28,RBM47,RBPJ,RELL1,RFC1,RGS12,RHOH,RNF212,RNF4,RPL9,S100P,SCARNA22,SEL1L3,SEPSECS,SH3BP2,SH3TC1,SHISA3,SLBP,SLC26A1,SLC2A9,SLC30A9,SLC34A2,SLIT2,SLIT2-IT1,SMIM14,SMIM20,SOD3,SORCS2,SPON2,STIM2,STK32B,STX18,TACC3,TADA2B,TAPT1,TAPT1-AS1,TBC1D1,TBC1D14,TBC1D19,TLR1,TLR10,TLR6,TMED11P,TMEM128,TMEM129,TMEM156,TMEM175,TMEM33,TNIP2,TRMT44,UBE2K,UCHL1,UGDH,UGDH-AS1,USP17L10,USP17L11,USP17L12,USP17L13,USP17L15,USP17L17,USP17L18,USP17L19,USP17L20,USP17L21,USP17L22,USP17L24,USP17L25,USP17L26,USP17L27,USP17L28,USP17L29,USP17L30,USP17L5,USP17L6P,USP17L9P,UVSSA,WDR1,WDR19,WFS1,WHSC1,YIPF7,ZBTB49,ZCCHC4,ZFYVE28,ZNF141,ZNF518B,ZNF595,ZNF718,ZNF721,ZNF732,ZNF876P"}
{"Sample_ID":"PT116","chr":"chr4","posStart":46193045,"posEnd":46840133,"length":647089,"numProbe":49,"log2ratio.Mean.adj":-1.11169,"log2ratio.SD":0.33312,"log2ratio.Median.adj":-1.14375,"log2ratio.MAD":0.32602,"log2mBAF.Mean":0.65477,"log2mBAF.SD":0.14991,"log2mBAF.Median":0.6529,"log2mBAF.MAD":0.10042,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":2,"gene":"COX7B2,GABRA2"}
{"Sample_ID":"PT116","chr":"chr4","posStart":46840944,"posEnd":130767899,"length":83926956,"numProbe":13155,"log2ratio.Mean.adj":-0.56315,"log2ratio.SD":0.26463,"log2ratio.Median.adj":-0.529,"log2ratio.MAD":0.2427,"log2mBAF.Mean":0.7703,"log2mBAF.SD":0.11333,"log2mBAF.Median":0.79216,"log2mBAF.MAD":0.09865,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":409,"gene":"AASDH,ABCG2,ADAD1,ADAMTS3,ADH1A,ADH1B,ADH1C,ADH4,ADH5,ADH6,ADH7,AFF1,AFM,AFP,AGPAT9,AGXT2L1,AIMP1,ALB,ALPK1,AMBN,AMTN,ANK2,ANKRD17,ANKRD50,ANTXR2,ANXA3,ANXA5,AP1AR,AREG,ARHGAP24,ARHGEF38,ARHGEF38-IT1,ARL9,ARSJ,ART3,ATOH1,ATP10D,BANK1,BBS12,BBS7,BDH2,BMP2K,BMP3,BMPR1B,BTC,C4orf17,C4orf21,C4orf22,C4orf26,C4orf29,C4orf3,C4orf32,C4orf33,C4orf36,C4orf40,CABS1,CAMK2D,CASP6,CCDC109B,CCDC158,CCNA2,CCNG2,CCNI,CCSER1,CDKL2,CDS1,CENPC1,CENPE,CEP135,CEP170P1,CETN4P,CFI,CHIC2,CISD2,CLOCK,CNGA1,CNOT6L,COL25A1,COMMD8,COPS4,COQ2,CORIN,COX18,COX7B2,CSN1S1,CSN1S2AP,CSN1S2BP,CSN2,CSN3,CWH43,CXCL1,CXCL10,CXCL11,CXCL13,CXCL2,CXCL3,CXCL5,CXCL6,CXCL9,CXXC4,CYP2U1,DANCR,DAPP1,DCK,DCUN1D4,DDIT4L,DKK2,DMP1,DNAJB14,DSPP,EGF,EIF4E,ELOVL6,EMCN,EMCN-IT3,ENAM,ENOPH1,ENPEP,EPGN,EPHA5,EREG,ERVMER34-1,EXOC1,EXOSC9,FABP2,FAM13A,FAM13A-AS1,FAM175A,FAM47E,FAM47E-STBD1,FAT4,FDCSP,FGF2,FGF5,FIP1L1,FLJ14186,FLJ20021,FRAS1,FRYL,FTLP10,G3BP2,GABRA4,GABRB1,GAR1,GC,GDEP,GIMD1,GK2,GNRHR,GPRIN3,GRID2,GRSF1,GSTCD,GSX2,H2AFZ,HADH,HELQ,HERC3,HERC5,HERC6,HNRNPD,HNRPDL,HOPX,HPGDS,HPSE,HSD17B11,HSD17B13,HSPA4L,HTN1,HTN3,IBSP,IGFBP7,IGJ,IL2,IL21,IL8,INTS12,INTU,KDR,KIAA1109,KIAA1211,KIT,KLHL8,LAMTOR3,LARP1B,LARP7,LEF1,LEF1-AS1,LIN54,LINC00575,LNX1,LNX1-AS1,LNX1-AS2,LOC100144602,LOC100505702,LOC100505875,LOC100506035,LOC100506746,LOC100507053,LOC152578,LOC255130,LOC256880,LOC285419,LOC401134,LOC441025,LOC550112,LOC550113,LOC644145,LOC644248,LOC645513,LOC728040,LPHN3,LRIT3,LRRC66,MAD2L1,MANBA,MAPK10,MEPE,METAP1,METTL14,MFSD8,MIR1243,MIR1973,MIR2054,MIR302A,MIR302B,MIR302C,MIR302D,MIR367,MIR3684,MIR4449,MIR4450,MIR4451,MIR5705,MIR575,MIR577,MMRN1,MOB1B,MRPL1,MRPS18C,MTHFD2L,MTTP,MUC7,MYOZ2,NAA11,NAAA,NAP1L5,NDNF,NDST3,NDST4,NEUROG2,NFKB1,NFXL1,NIPAL1,NKX6-1,NMU,NOA1,NPFFR2,NPNT,NUDT6,NUDT9,NUP54,OCIAD1,OCIAD2,ODAM,OSTC,PAICS,PAPSS1,PAQR3,PARM1,PCNAP1,PDCL2,PDE5A,PDGFRA,PDHA2,PDLIM5,PF4,PF4V1,PGRMC2,PHF17,PIGY,PITX2,PKD2,PLA2G12A,PLAC8,PLK4,POLR2B,PP12613,PPA2,PPAT,PPBP,PPBPP2,PPEF2,PPM1K,PPP3CA,PRDM5,PRDM8,PRKG2,PROL1,PRSS12,PTPN13,PYURF,QRFPR,RAP1GDS1,RASGEF1B,RASL11B,RASSF6,RCHY1,REST,RPL21P44,RPL34,RPL34-AS1,RRH,RUFY3,SCARB2,SCD5,SCFD2,SCLT1,SDAD1,SEC24B,SEC24B-AS1,SEC24D,SEC31A,SEPT11,SGCB,SGMS2,SHROOM3,SLAIN2,SLC10A4,SLC10A6,SLC25A31,SLC39A8,SLC4A4,SLC9B1,SLC9B2,SMARCAD1,SMR3A,SMR3B,SNCA,SNHG8,SNORA24,SNORA26,SOWAHB,SPARCL1,SPATA18,SPATA5,SPINK2,SPP1,SPRY1,SRD5A3,SRD5A3-AS1,SRP72,STAP1,STATH,STBD1,STPG2,SULT1B1,SULT1E1,SYNPO2,SYT14L,TACR3,TBCK,TEC,TECRL,TET2,THAP6,THAP9,THAP9-AS1,THEGL,TIFA,TIGD2,TMEM150C,TMEM155,TMEM165,TMPRSS11A,TMPRSS11B,TMPRSS11BNL,TMPRSS11D,TMPRSS11E,TMPRSS11F,TMPRSS11GP,TNIP3,TRAM1L1,TRMT10A,TRPC3,TSPAN5,TXK,UBA6,UBE2D3,UGT2A1,UGT2A2,UGT2A3,UGT2B10,UGT2B11,UGT2B15,UGT2B17,UGT2B28,UGT2B4,UGT2B7,UGT8,UNC5C,USO1,USP46,USP53,UTP3,WDFY3,WDFY3-AS2,YTHDC1,ZAR1"}
{"Sample_ID":"PT116","chr":"chr4","posStart":130774012,"posEnd":137744172,"length":6970161,"numProbe":999,"log2ratio.Mean.adj":-0.68365,"log2ratio.SD":0.26964,"log2ratio.Median.adj":-0.6555,"log2ratio.MAD":0.26835,"log2mBAF.Mean":0.75536,"log2mBAF.SD":0.1311,"log2mBAF.Median":0.78612,"log2mBAF.MAD":0.10655,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":2,"gene":"PABPC4L,PCDH10"}
{"Sample_ID":"PT116","chr":"chr4","posStart":137745250,"posEnd":190917893,"length":53172644,"numProbe":10358,"log2ratio.Mean.adj":-0.55381,"log2ratio.SD":0.26673,"log2ratio.Median.adj":-0.5238,"log2ratio.MAD":0.24463,"log2mBAF.Mean":0.77206,"log2mBAF.SD":0.11567,"log2mBAF.Median":0.79559,"log2mBAF.MAD":0.09615,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":217,"gene":"AADAT,ABCE1,ACSL1,ADAM29,AGA,ANAPC10,ANKRD37,ANP32C,ANXA10,ANXA2P1,ARFIP1,ARHGAP10,ASB5,ASIC5,C4orf27,C4orf45,C4orf46,C4orf47,C4orf51,CASP3,CBR4,CCDC110,CCDC111,CCRN4L,CDKN2AIP,CEP44,CLCN3,CLDN22,CLDN24,CLGN,CPE,CTSO,CYP4V2,DCHS2,DCLK2,DCTD,DDX60,DDX60L,DKFZP434I0714,EDNRA,ELF2,ELMOD2,ENPP6,ETFDH,F11,FAM149A,FAM160A1,FAM198B,FAM218A,FAM92A1P2,FAT1,FBXO8,FBXW7,FGA,FGB,FGG,FHDC1,FLJ38576,FNIP2,FREM3,FRG1,FSTL5,GAB1,GALNT7,GALNTL6,GK3P,GLRA3,GLRB,GPM6A,GRIA2,GUCY1A3,GUCY1B3,GUSBP5,GYPA,GYPB,GYPE,HAND2,HELT,HHIP,HHIP-AS1,HMGB2,HPGD,IL15,ING2,INPP4B,IRF2,KIAA0922,KIAA1430,KLHL2,KLKB1,LINC00290,LINC00499,LINC00616,LOC100129858,LOC100505545,LOC100505989,LOC100506013,LOC100506085,LOC100506122,LOC100506229,LOC152586,LOC285441,LOC285501,LOC339975,LOC340017,LOC389247,LOC401164,LOC728175,LOC731424,LRAT,LRBA,LRP2BP,LSM6,MAB21L2,MAML3,MAP9,MARCH1,MFAP3L,MGARP,MGC45800,MGST2,MIR1305,MIR3140,MIR3688-1,MIR3688-2,MIR3945,MIR4276,MIR4453,MIR4799,MIR5684,MIR578,MLF1IP,MMAA,MND1,MSMO1,MTNR1A,NAA15,NAF1,NBLA00301,NDUFC1,NEIL3,NEK1,NPY1R,NPY2R,NPY5R,NR3C2,OTUD4,PALLD,PCDH18,PDGFC,PDLIM3,PET112,PLRG1,POU4F2,PPID,PRMT10,PRSS48,RAB33B,RAPGEF2,RBM46,RNF150,RNF175,RPS3A,RWDD4,RXFP1,SAP30,SCOC,SCRG1,SETD7,SFRP2,SH3D19,SH3RF1,SLC10A7,SLC25A4,SLC7A11,SLC7A11-AS1,SLED1,SMAD1,SMARCA5,SNORD73A,SNX25,SORBS2,SPATA4,SPCS3,SPOCK3,STOX2,TBC1D9,TDO2,TENM3,TIGD4,TKTL2,TLL1,TLR2,TLR3,TMA16,TMEM144,TMEM154,TMEM184C,TMEM192,TNRC18P1,TRAPPC11,TRIM2,TRIM60,TRIM61,TRIML1,TRIML2,TTC29,UCP1,UFSP2,USP38,VEGFC,WDR17,WWC2,WWC2-AS2,ZFP42,ZNF330,ZNF827"}
{"Sample_ID":"PT116","chr":"chr5","posStart":38139,"posEnd":52942197,"length":52904059,"numProbe":10094,"log2ratio.Mean.adj":0.02565,"log2ratio.SD":0.19678,"log2ratio.Median.adj":0.0257,"log2ratio.MAD":0.1791,"log2mBAF.Mean":0.45823,"log2mBAF.SD":0.14511,"log2mBAF.Median":0.48606,"log2mBAF.MAD":0.11179,"log2ratio.p.value":0.011,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":192,"gene":"ADAMTS12,ADAMTS16,ADCY2,AGXT2,AHRR,AMACR,ANKH,ANKRD33B,ANXA2R,BASP1,BRD9,BRIX1,C1QTNF3,C1QTNF3-AMACR,C5orf22,C5orf28,C5orf34,C5orf38,C5orf42,C5orf49,C5orf51,C5orf55,C6,C7,C9,CAPSL,CARD6,CCDC127,CCDC152,CCL28,CCT5,CDH10,CDH12,CDH18,CDH6,CDH9,CEP72,CLPTM1L,CMBL,CT49,CTNND2,DAB2,DAP,DNAH5,DNAJC21,DROSHA,EGFLAM,EGFLAM-AS4,EMB,EXOC3,FAM105A,FAM105B,FAM134B,FAM173B,FASTKD3,FBXL7,FBXO4,FGF10,FLJ33360,FST,FYB,GDNF,GHR,GOLPH3,GUSBP1,HCN1,HMGCS1,IL7R,IRX1,IRX2,IRX4,ISL1,ITGA1,ITGA2,KIAA0947,LIFR,LMBRD2,LOC100130744,LOC100132356,LOC100505738,LOC100505806,LOC100506548,LOC100506688,LOC100652772,LOC153684,LOC255167,LOC257396,LOC285577,LOC285692,LOC285696,LOC340094,LOC340107,LOC340113,LOC401177,LOC442132,LOC642366,LOC643401,LOC646719,LOC648987,LOC728613,LOC729506,LPCAT1,LRRC14B,LSP1P3,MARCH11,MARCH6,MED10,MIR3650,MIR4277,MIR4278,MIR4279,MIR4454,MIR4456,MIR4457,MIR4458,MIR4635,MIR4636,MIR4637,MIR580,MOCS2,MROH2B,MRPL36,MRPS30,MTMR12,MTRR,MYO10,NADKD1,NDUFS4,NDUFS6,NIM1,NIPBL,NKD2,NNT,NPR3,NSUN2,NUP155,OSMR,OXCT1,PAIP1,PAPD7,PARP8,PDCD6,PDZD2,PELO,PLCXD3,PLEKHG4B,PMCHL1,PP7080,PRDM9,PRKAA1,PRLR,PTGER4,RAD1,RAI14,RANBP3L,RICTOR,ROPN1L,RPL37,RXFP3,SDHA,SDHAP3,SEMA5A,SEPP1,SKP2,SLC12A7,SLC1A3,SLC45A2,SLC6A18,SLC6A19,SLC6A3,SLC9A3,SNORD123,SNORD72,SPEF2,SRD5A1,SUB1,TARS,TAS2R1,TERT,TPPP,TRIO,TRIP13,TTC23L,TTC33,UBE2QL1,UGT3A1,UGT3A2,WDR70,ZDHHC11,ZFR,ZNF131,ZNF622"}
{"Sample_ID":"PT116","chr":"chr5","posStart":52942463,"posEnd":180690937,"length":127748475,"numProbe":25003,"log2ratio.Mean.adj":0.18777,"log2ratio.SD":0.19138,"log2ratio.Median.adj":0.18375,"log2ratio.MAD":0.18021,"log2mBAF.Mean":0.14927,"log2mBAF.SD":0.14566,"log2mBAF.Median":0.17357,"log2mBAF.MAD":0.12723,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":832,"gene":"AACSP1,ABLIM3,ACOT12,ACSL6,ACTBL2,ADAM19,ADAMTS19,ADAMTS2,ADAMTS6,ADRA1B,ADRB2,AFAP1L1,AFF4,AGGF1,AGXT2L2,ALDH7A1,ANKDD1B,ANKHD1,ANKHD1-EIF4EBP3,ANKRA2,ANKRD31,ANKRD32,ANKRD34B,ANKRD55,ANXA6,AP3B1,AP3S1,APBB3,APC,AQPEP,ARAP3,ARHGAP26,ARHGAP26-AS1,ARHGEF28,ARHGEF37,ARL10,ARL14EPL,ARL15,ARRDC3,ARRDC3-AS1,ARSB,ARSI,ARSK,ATG10,ATG12,ATOX1,ATP10B,ATP6AP1L,ATP6V0E1,B4GALT7,BDP1,BHMT,BHMT2,BNIP1,BOD1,BRD8,BTF3,BTNL3,BTNL8,BTNL9,C1QTNF2,C5orf15,C5orf20,C5orf24,C5orf27,C5orf30,C5orf45,C5orf46,C5orf47,C5orf48,C5orf52,C5orf54,C5orf56,C5orf58,C5orf60,C5orf63,C5orf64,CAMK2A,CAMK4,CAMLG,CANX,CARTPT,CAST,CATSPER3,CBY3,CCDC112,CCDC125,CCDC69,CCNB1,CCNG1,CCNH,CCNI2,CCNJL,CCNO,CD14,CD180,CD74,CDC20B,CDC23,CDC25C,CDC42SE2,CDHR2,CDK7,CDKL3,CDKN2AIPNL,CDO1,CDX1,CENPH,CENPK,CEP120,CETN3,CHD1,CHSY3,CKMT2,CLINT1,CLK4,CLTB,CMYA5,CNOT6,CNOT8,COL23A1,COL4A3BP,COMMD10,COX7C,CPEB4,CPLX2,CREBRF,CRHBP,CRSP8P,CSF1R,CSF2,CSNK1A1,CSNK1G3,CTNNA1,CTXN3,CWC27,CXCL14,CXXC5,CYFIP2,CYSTM1,DBN1,DCP2,DCTN4,DDX4,DDX41,DDX46,DEPDC1B,DHFR,DHX29,DIAPH1,DIMT1,DMGDH,DMXL1,DNAJC18,DND1,DOCK2,DOK3,DPYSL3,DRD1,DTWD2,DUSP1,EBF1,ECSCR,EDIL3,EFCAB9,EFNA5,EGR1,EIF4E1B,EIF4EBP3,ELL2,ELOVL7,ENC1,EPB41L4A,EPB41L4A-AS1,ERAP1,ERAP2,ERBB2IP,ERCC8,ERGIC1,ESM1,ETF1,F12,F2R,F2RL1,F2RL2,FABP6,FAF2,FAM114A2,FAM13B,FAM151B,FAM153A,FAM153B,FAM153C,FAM159B,FAM169A,FAM170A,FAM172A,FAM174A,FAM193B,FAM196B,FAM53C,FAM71B,FAM81B,FAT2,FAXDC2,FBLL1,FBN2,FBXL17,FBXL21,FBXO38,FBXW11,FCHO2,FCHSD1,FEM1C,FER,FGF1,FGF18,FGFR4,FLJ11235,FLJ16171,FLJ33630,FLJ35946,FLJ38109,FLJ42709,FLT4,FNDC9,FNIP1,FOXD1,FOXI1,FSTL4,FTMT,G3BP1,GABRA1,GABRA6,GABRB2,GABRG2,GABRP,GALNT10,GAPT,GCNT4,GDF9,GEMIN5,GFM2,GFPT2,GFRA3,GIN1,GLRA1,GLRX,GM2A,GMCL1P1,GNB2L1,GNPDA1,GPBP1,GPR150,GPR151,GPR98,GPRIN1,GPX3,GPX8,GRAMD3,GRIA1,GRK6,GRM6,GRPEL2,GRXCR2,GTF2H2,GTF2H2B,GTF2H2C,GTF2H2D,GUSBP3,GUSBP9,GZMA,GZMK,H2AFY,HAND1,HAPLN1,HARS,HARS2,HAVCR1,HAVCR2,HBEGF,HDAC3,HEIH,HEXB,HIGD2A,HINT1,HK3,HMGCR,HMGXB3,HMHB1,HMMR,HMP19,HNRNPA0,HNRNPAB,HNRNPH1,HOMER1,HP07349,HRH2,HSD17B4,HSPA4,HSPA9,HSPB3,HTR1A,HTR4,IGIP,IK,IL12B,IL13,IL17B,IL3,IL31RA,IL4,IL5,IL6ST,IL9,IPO11,IPO11-LRRC70,IQGAP2,IRF1,IRGM,ISOC1,ITK,JAKMIP2,JAKMIP2-AS1,JMY,KCNIP1,KCNMB1,KCNN2,KCTD16,KDM3B,KIAA0141,KIAA0825,KIAA1024L,KIAA1191,KIF20A,KIF2A,KIF3A,KIF4B,KLHL3,LARP1,LARS,LCP2,LEAP2,LECT2,LHFPL2,LINC00461,LINC00847,LIX1,LMAN2,LMNB1,LNPEP,LOC100131067,LOC100133050,LOC100268168,LOC100272216,LOC100289230,LOC100289673,LOC100303749,LOC100505658,LOC100505841,LOC100507387,LOC100996485,LOC202181,LOC257358,LOC285593,LOC285626,LOC285627,LOC285629,LOC340073,LOC340074,LOC389332,LOC441081,LOC553103,LOC643201,LOC644936,LOC647859,LOC728342,LOC728554,LOC729080,LOX,LRRC70,LRRTM2,LSM11,LTC4S,LYRM7,LYSMD3,MAML1,MAN2A1,MAP1B,MAP3K1,MAPK9,MARCH3,MARVELD2,MAST4,MAT2B,MATR3,MBLAC2,MCC,MCCC2,MCIDAS,MCTP1,MED7,MEF2C,MEGF10,MFAP3,MGAT1,MGAT4B,MGC32805,MIER3,MIR103A1,MIR103B1,MIR1229,MIR1244-1,MIR1244-2,MIR1244-3,MIR1289-2,MIR143,MIR143HG,MIR145,MIR146A,MIR218-2,MIR2277,MIR3141,MIR3142,MIR340,MIR3607,MIR3655,MIR3660,MIR3661,MIR378E,MIR3912,MIR3936,MIR3977,MIR4280,MIR4281,MIR4460,MIR4461,MIR449A,MIR449B,MIR449C,MIR4633,MIR4634,MIR4638,MIR4803,MIR4804,MIR5197,MIR548AO,MIR5687,MIR581,MIR583,MIR585,MIR874,MIR9-2,MRPL22,MRPS27,MRPS36,MSH3,MSX2,MTRNR2L2,MTX3,MXD3,MYOT,MYOZ3,MZB1,N4BP3,NAIP,NBPF22P,NCRUPAR,NDFIP1,NDST1,NDUFA2,NDUFAF2,NDUFS4,NEURL1B,NEUROG1,NHP2,NIPAL4,NKX2-5,NLN,NME5,NMUR2,NOP16,NPM1,NPY6R,NR2F1,NR3C1,NREP,NREP-AS1,NRG2,NSA2,NSD1,NUDCD2,NUDT12,OCLN,OR2V1,OR2V2,OR2Y1,OTP,P4HA2,PAIP2,PAM,PANK3,PAPD4,PART1,PCBD2,PCDH1,PCDH12,PCDHA1,PCDHA10,PCDHA11,PCDHA12,PCDHA13,PCDHA2,PCDHA3,PCDHA4,PCDHA5,PCDHA6,PCDHA7,PCDHA8,PCDHA9,PCDHAC1,PCDHAC2,PCDHB1,PCDHB10,PCDHB11,PCDHB12,PCDHB13,PCDHB14,PCDHB15,PCDHB16,PCDHB17,PCDHB18,PCDHB19P,PCDHB2,PCDHB3,PCDHB4,PCDHB5,PCDHB6,PCDHB7,PCDHB8,PCDHB9,PCDHGA1,PCDHGA10,PCDHGA11,PCDHGA12,PCDHGA2,PCDHGA3,PCDHGA4,PCDHGA5,PCDHGA6,PCDHGA7,PCDHGA8,PCDHGA9,PCDHGB1,PCDHGB2,PCDHGB3,PCDHGB4,PCDHGB5,PCDHGB6,PCDHGB7,PCDHGB8P,PCDHGC3,PCDHGC4,PCDHGC5,PCSK1,PCYOX1L,PDE4D,PDE6A,PDE8B,PDGFRB,PDLIM4,PDLIM7,PFDN1,PFN3,PGGT1B,PHAX,PHF15,PIK3R1,PITX1,PJA2,PKD2L2,PLAC8L1,PLK2,PMCHL2,POC5,POLK,POLR3G,POU4F3,POU5F2,PPAP2A,PPARGC1B,PPIC,PPIP5K2,PPP1R2P3,PPP2CA,PPP2R2B,PPP2R2B-IT1,PPWD1,PRDM6,PRELID1,PRELID2,PROB1,PROP1,PRR16,PRR7,PRR7-AS1,PRRC1,PSD2,PTCD2,PTTG1,PURA,PWWP2A,RAB24,RAB3C,RAB9BP1,RAD17,RAD50,RANBP17,RAPGEF6,RARS,RASA1,RASGEF1C,RASGRF2,RBM22,RBM27,REEP2,REEP5,RELL2,RFESD,RGMB,RGS14,RGS7BP,RHOBTB3,RIOK2,RMND5B,RNF130,RNF138P1,RNF14,RNF145,RNF180,RNF44,RNU5D-1,RNU5E-1,RPL26L1,RPS14,RPS23,RUFY1,S100Z,SAP30L,SAR1B,SCAMP1,SCARNA18,SCGB3A1,SCGB3A2,SEC24A,SEMA6A,SEPT8,SERF1A,SERF1B,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{"Sample_ID":"PT116","chr":"chr7","posStart":91509551,"posEnd":134192487,"length":42682937,"numProbe":6830,"log2ratio.Mean.adj":-0.21276,"log2ratio.SD":0.20888,"log2ratio.Median.adj":-0.1979,"log2ratio.MAD":0.19407,"log2mBAF.Mean":0.28825,"log2mBAF.SD":0.16132,"log2mBAF.Median":0.30887,"log2mBAF.MAD":0.13414,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":350,"gene":"AASS,ACHE,ACN9,ACTL6B,AGFG2,AHCYL2,AKAP9,AKR1B1,ALKBH4,ANKIB1,ANKRD7,AP1S1,AP4M1,ARF5,ARMC10,ARPC1A,ARPC1B,ASB15,ASB4,ASNS,ASZ1,ATP5J2,ATP5J2-PTCD1,ATP6V1F,ATXN7L1,AZGP1,AZGP1P1,BAIAP2L1,BCAP29,BET1,BHLHA15,BRI3,BUD31,C7orf43,C7orf60,C7orf61,C7orf66,C7orf76,CADPS2,CALCR,CALU,CAPZA2,CASD1,CAV1,CAV2,CBLL1,CCDC132,CCDC136,CCDC71L,CDHR3,CDK6,CEP41,CFTR,CHCHD3,CLDN15,CNPY4,COG5,COL1A2,COL26A1,COPG2,COPS6,CPA1,CPA2,CPA4,CPA5,CPED1,CPSF4,CTTNBP2,CUX1,CYP3A4,CYP3A43,CYP3A5,CYP3A7,CYP3A7-CYP3AP1,CYP51A1,DLD,DLX5,DLX6,DLX6-AS1,DNAJB9,DNAJC2,DOCK4,DPY19L2P2,DUS4L,DYNC1I1,EFCAB10,EIF3IP1,EPHB4,EPO,EXOC4,FAM133B,FAM133DP,FAM185A,FAM200A,FAM3C,FAM71F1,FAM71F2,FBXL13,FBXO24,FEZF1,FEZF1-AS1,FIS1,FLJ40288,FLJ43663,FLJ45340,FLNC,FOXP2,FSCN3,GAL3ST4,GATAD1,GATS,GCC1,GIGYF1,GJC3,GNB2,GNG11,GNGT1,GPC2,GPR22,GPR37,GPR85,GRM8,HBP1,HEPACAM2,HILPDA,HYAL4,HYALP1,IFRD1,IMMP2L,IMPDH1,ING3,IQUB,IRF5,KCND2,KCP,KLF14,KLHDC10,KPNA7,KRIT1,LAMB1,LAMB4,LAMTOR4,LEP,LHFPL3,LHFPL3-AS1,LHFPL3-AS2,LMOD2,LMTK2,LOC100130705,LOC100216545,LOC100216546,LOC100289187,LOC100289561,LOC100506136,LOC100630923,LOC154872,LOC401397,LOC407835,LOC646329,LRCH4,LRGUK,LRRC17,LRRC4,LRRD1,LRRN3,LRWD1,LSMEM1,MBLAC1,MCM7,MDFIC,MEPCE,MEST,MESTIT1,MET,METTL2B,MGC16142,MGC27345,MGC72080,MIR106B,MIR129-1,MIR182,MIR183,MIR25,MIR29A,MIR29B1,MIR335,MIR3609,MIR3666,MIR4285,MIR4467,MIR4652,MIR4653,MIR4658,MIR489,MIR5090,MIR591,MIR592,MIR593,MIR653,MIR93,MIR96,MKLN1,MLL5,MOGAT3,MOSPD3,MTERF,MUC12,MUC17,MYH16,MYL10,NAA38,NAMPT,NAPEPLD,NAT16,NDUFA5,NPTX2,NRCAM,NRF1,NYAP1,OCM2,OPN1SW,OR2AE1,ORAI2,ORC5,PAX4,PCOLCE,PCOLCE-AS1,PDAP1,PDK4,PEG10,PEX1,PIK3CG,PILRA,PILRB,PLOD3,PLXNA4,PMPCB,PMS2P1,PNPLA8,PODXL,POLR2J,POLR2J2,POLR2J3,PON1,PON2,PON3,POP7,POT1,PPP1R35,PPP1R3A,PPP1R9A,PRKAR2B,PRKRIP1,PRRT4,PSMC2,PTCD1,PTPRZ1,PUS7,PVRIG,RABL5,RASA4,RASA4B,RBM28,RBM48,RELN,RINT1,RNA5SP244,RNF133,RNF148,RPL19P12,SAMD9,SAMD9L,SAP25,SERPINE1,SGCE,SH2B2,SHFM1,SLC12A9,SLC13A1,SLC25A13,SLC26A3,SLC26A4,SLC26A4-AS1,SLC26A5,SLC35B4,SMKR1,SMO,SMURF1,SND1,SND1-IT1,SPAM1,SPDYE2,SPDYE2L,SPDYE3,SPDYE6,SRPK2,SRRT,SSMEM1,ST7,ST7-AS1,ST7-AS2,ST7-OT3,ST7-OT4,STAG3,STRIP2,SYPL1,TAC1,TAF6,TAS2R16,TECPR1,TES,TFEC,TFPI2,TFR2,THAP5,TMEM130,TMEM168,TMEM209,TMEM229A,TNPO3,TPI1P2,TRIM4,TRIM56,TRIP6,TRRAP,TSC22D4,TSGA13,TSPAN12,TSPAN33,UBE2H,UFSP1,UPK3BL,VGF,WASL,WNT16,WNT2,ZAN,ZC3HC1,ZCWPW1,ZKSCAN1,ZKSCAN5,ZNF277,ZNF3,ZNF394,ZNF655,ZNF789,ZNF800,ZNHIT1,ZSCAN21,ZSCAN25"}
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{"Sample_ID":"PT116","chr":"chr8","posStart":176818,"posEnd":11691142,"length":11514325,"numProbe":4752,"log2ratio.Mean.adj":-1.05438,"log2ratio.SD":0.32955,"log2ratio.Median.adj":-1.0338,"log2ratio.MAD":0.35093,"log2mBAF.Mean":0.66329,"log2mBAF.SD":0.14863,"log2mBAF.Median":0.68702,"log2mBAF.MAD":0.13081,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":93,"gene":"AGPAT5,ANGPT2,ARHGEF10,BLK,C8orf12,C8orf42,C8orf74,CLDN23,CLN8,CSMD1,DEFA1,DEFA10P,DEFA11P,DEFA1B,DEFA3,DEFA4,DEFA5,DEFA6,DEFA8P,DEFA9P,DEFB1,DEFB103A,DEFB103B,DEFB104A,DEFB104B,DEFB105A,DEFB105B,DEFB106A,DEFB106B,DEFB107A,DEFB107B,DEFB109P1B,DEFB4A,DEFB4B,DEFT1P,DEFT1P2,DLGAP2,ERI1,ERICH1,ERICH1-AS1,FAM167A,FAM66B,FAM66E,FAM86B3P,FAM90A10P,FAM90A7P,FBXO25,FDFT1,GATA4,KBTBD11,LINC00208,LINC00599,LOC100287015,LOC100652791,LOC157273,LOC286083,LOC349196,MCPH1,MFHAS1,MIR124-1,MIR1322,MIR4659A,MIR4659B,MIR4660,MIR548I3,MIR596,MIR597,MIR598,MSRA,MTMR9,MYOM2,NEIL2,PINX1,PPP1R3B,PRSS55,RP1L1,RPL23AP53,SGK223,SLC35G5,SOX7,SPAG11A,SPAG11B,TDH,TNKS,USP17L1P,USP17L3,USP17L4,USP17L8,XKR5,XKR6,ZNF596,ZNF705B,ZNF705G"}
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{"Sample_ID":"PT116","chr":"chr9","posStart":204201,"posEnd":141027939,"length":140823739,"numProbe":27063,"log2ratio.Mean.adj":-0.20835,"log2ratio.SD":0.20055,"log2ratio.Median.adj":-0.1969,"log2ratio.MAD":0.18362,"log2mBAF.Mean":0.28877,"log2mBAF.SD":0.16449,"log2mBAF.Median":0.31665,"log2mBAF.MAD":0.13375,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":955,"gene":"AAED1,ABCA1,ABCA2,ABHD17B,ABL1,ABO,ACER2,ACO1,ACTL7A,ACTL7B,ADAMTS13,ADAMTSL1,ADAMTSL2,AGPAT2,AGTPBP1,AIF1L,AK1,AK3,AK8,AKAP2,AKNA,ALAD,ALDH1A1,ALDH1B1,ALDOB,ALG2,AMBP,ANAPC2,ANGPTL2,ANKRD18A,ANKRD18B,ANKRD19P,ANKRD20A1,ANKRD20A2,ANKRD20A3,ANKRD20A4,ANKS6,ANP32B,ANXA1,ANXA2P2,APBA1,APTX,AQP3,AQP7,AQP7P1,AQP7P3,ARHGEF39,ARID3C,ARPC5L,ARRDC1,ASB6,ASPN,ASS1,ASTN2,ATP6V1G1,ATP8B5P,AUH,B4GALT1,BAAT,BAG1,BANCR,BARHL1,BARX1,BICD2,BNC2,BRD3,BSPRY,C5,C8G,C9orf106,C9orf114,C9orf116,C9orf117,C9orf123,C9orf129,C9orf131,C9orf135,C9orf139,C9orf142,C9orf152,C9orf153,C9orf156,C9orf16,C9orf163,C9orf169,C9orf170,C9orf171,C9orf172,C9orf173,C9orf24,C9orf3,C9orf37,C9orf40,C9orf41,C9orf43,C9orf47,C9orf50,C9orf53,C9orf57,C9orf62,C9orf64,C9orf66,C9orf69,C9orf72,C9orf78,C9orf84,C9orf85,C9orf89,C9orf9,C9orf91,C9orf92,C9orf96,CA9,CAAP1,CACFD1,CACNA1B,CAMSAP1,CARD9,CBWD3,CBWD5,CBWD6,CCBL1,CCDC107,CCDC171,CCDC180,CCIN,CCL19,CCL21,CCL27,CD274,CD72,CDC14B,CDC26,CDC37L1,CDK20,CDK5RAP2,CDK9,CDKN2A,CDKN2B,CDKN2B-AS1,CEL,CELP,CENPP,CEP78,CER1,CERCAM,CHMP5,CIZ1,CKS2,CLIC3,CLTA,CNTFR,CNTLN,CNTNAP3,CNTNAP3B,CNTRL,COL15A1,COL27A1,COL5A1,COQ4,CORO2A,CRAT,CRB2,CREB3,CTNNAL1,CTSL1,CTSL1P8,CTSL2,CTSL3P,CYLC2,DAB2IP,DAPK1,DBC1,DBH,DCAF10,DCAF12,DCTN3,DDX31,DDX58,DEC1,DENND1A,DENND4C,DFNB31,DIRAS2,DKFZP434A062,DMRT1,DMRT2,DMRT3,DMRTA1,DNAI1,DNAJA1,DNAJB5,DNAJC25,DNAJC25-GNG10,DNLZ,DNM1,DOCK8,DOLK,DOLPP1,DPM2,DPP7,ECM2,EDF1,EGFL7,EHMT1,ELAVL2,ENDOG,ENG,ENHO,ENTPD2,ENTPD8,EPB41L4B,EQTN,ERCC6L2,ERMP1,ERP44,EXD3,EXOSC2,EXOSC3,FAM102A,FAM120A,FAM120AOS,FAM122A,FAM129B,FAM154A,FAM163B,FAM166A,FAM166B,FAM189A2,FAM201A,FAM205A,FAM205B,FAM206A,FAM214B,FAM219A,FAM221B,FAM225A,FAM225B,FAM27A,FAM27B,FAM27C,FAM69B,FAM73B,FAM74A1,FAM74A2,FAM74A3,FAM74A4,FAM78A,FAM95B1,FAM95C,FANCC,FANCG,FBP1,FBP2,FBXO10,FBXW2,FBXW5,FCN1,FCN2,FGD3,FIBCD1,FKBP15,FKTN,FLJ35024,FLJ35282,FLJ40292,FLJ41200,FNBP1,FOCAD,FOXB2,FOXD4L2,FOXD4L3,FOXD4L4,FOXD4L5,FOXD4L6,FOXE1,FP588,FPGS,FREM1,FRMD3,FRMPD1,FRRS1L,FSD1L,FUBP3,FUT7,FXN,GABBR2,GADD45G,GALNT12,GALT,GAPVD1,GARNL3,GAS1,GBA2,GBGT1,GCNT1,GDA,GFI1B,GGTA1P,GKAP1,GLDC,GLE1,GLIPR2,GLIS3,GLIS3-AS1,GLT6D1,GNA14,GNAQ,GNE,GNG10,GOLGA1,GOLGA2,GOLM1,GPR107,GPR144,GPR21,GPSM1,GRHPR,GRIN1,GRIN3A,GSN,GTF3C4,GTF3C5,HABP4,HAUS6,HDHD3,HEMGN,HIATL1,HIATL2,HINT2,HNRNPK,HRCT1,HSD17B3,HSDL2,HSPA5,IARS,IDNK,IER5L,IFNA1,IFNA10,IFNA13,IFNA14,IFNA16,IFNA17,IFNA2,IFNA21,IFNA22P,IFNA4,IFNA5,IFNA6,IFNA7,IFNA8,IFNB1,IFNE,IFNK,IFNW1,IFT74,IGFBPL1,IKBKAP,IL11RA,IL33,INIP,INPP5E,INSL4,INSL6,INVS,IPPK,ISCA1,IZUMO3,JAK2,KANK1,KCNT1,KCNV2,KDM4C,KGFLP1,KGFLP2,KIAA0020,KIAA0368,KIAA1045,KIAA1161,KIAA1432,KIAA1958,KIAA1984,KIAA1984-AS1,KIAA2026,KIF12,KIF24,KIF27,KLF4,KLF9,KLHL9,LAMC3,LCN1,LCN10,LCN12,LCN15,LCN2,LCN6,LCN8,LCN9,LCNL1,LHX2,LHX3,LHX6,LINC00032,LINC00092,LINC00094,LINC00474,LINC00475,LINC00476,LINC00583,LINGO2,LMX1B,LOC100128076,LOC100128361,LOC100128505,LOC100128593,LOC100129034,LOC100129316,LOC100129722,LOC100130954,LOC100132077,LOC100132352,LOC100132781,LOC100133920,LOC100272217,LOC100288842,LOC100289019,LOC100289341,LOC100499484,LOC100499484-C9ORF174,LOC100505478,LOC100506100,LOC100506190,LOC100506422,LOC100506599,LOC100506710,LOC100506834,LOC100507244,LOC100507299,LOC100507346,LOC158376,LOC158434,LOC158435,LOC253039,LOC286238,LOC286297,LOC286359,LOC286367,LOC286370,LOC340508,LOC340515,LOC389705,LOC389765,LOC389791,LOC392364,LOC401497,LOC401557,LOC415056,LOC440173,LOC440896,LOC441454,LOC441455,LOC441461,LOC494127,LOC494558,LOC642236,LOC642929,LOC643648,LOC653501,LPAR1,LPPR1,LRRC19,LRRC26,LRRC37A5P,LRRC8A,LRSAM1,LURAP1L,MAMDC2,MAMDC4,MAN1B1,MAPKAP1,MED22,MED27,MEGF9,MELK,MGC21881,MIR101-2,MIR126,MIR147A,MIR181A2,MIR181A2HG,MIR181B2,MIR199B,MIR204,MIR219-2,MIR2278,MIR23B,MIR24-1,MIR27B,MIR2861,MIR2964A,MIR3074,MIR31,MIR3134,MIR3152,MIR3153,MIR3154,MIR31HG,MIR32,MIR3621,MIR3651,MIR3689A,MIR3689B,MIR3689C,MIR3689D1,MIR3689D2,MIR3689E,MIR3689F,MIR3910-1,MIR3910-2,MIR3911,MIR3960,MIR4289,MIR4290,MIR4291,MIR4292,MIR4473,MIR4474,MIR4475,MIR4476,MIR4478,MIR4479,MIR4540,MIR455,MIR4665,MIR4667,MIR4668,MIR4669,MIR4670,MIR4672,MIR4673,MIR4674,MIR491,MIR548H3,MIR548Q,MIR600,MIR600HG,MIR601,MIR602,MIR7-1,MIR873,MIR876,MIRLET7A1,MIRLET7D,MIRLET7DHG,MIRLET7F1,MLANA,MLLT3,MOB3B,MORN5,MPDZ,MRPL41,MRPL50,MRPS2,MRRF,MSANTD3,MSANTD3-TMEFF1,MSMP,MTAP,MURC,MUSK,MVB12B,NAA35,NACC2,NAIF1,NAMA,NANS,NCBP1,NCS1,NDOR1,NDUFA8,NDUFB6,NEK6,NELFB,NFIB,NFIL3,NFX1,NINJ1,NIPSNAP3A,NIPSNAP3B,NMRK1,NOL6,NOL8,NOTCH1,NOXA1,NPDC1,NPR2,NR4A3,NR5A1,NR6A1,NRARP,NRON,NSMF,NTMT1,NTNG2,NTRK2,NUDT2,NUP188,NUP214,NUTMF,NUTMG,NXNL2,OBP2A,OBP2B,ODF2,OGN,OLFM1,OLFML2A,OMD,OR13C2,OR13C3,OR13C4,OR13C5,OR13C8,OR13C9,OR1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{"Sample_ID":"PT116","chr":"chr11","posStart":199256,"posEnd":132998331,"length":132799076,"numProbe":26691,"log2ratio.Mean.adj":-0.20745,"log2ratio.SD":0.20342,"log2ratio.Median.adj":-0.1981,"log2ratio.MAD":0.18495,"log2mBAF.Mean":0.28364,"log2mBAF.SD":0.16664,"log2mBAF.Median":0.31195,"log2mBAF.MAD":0.13849,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":1447,"gene":"AAMDC,AASDHPPT,ABCC8,ABCG4,ABTB2,ACAT1,ACCS,ACCSL,ACER3,ACP2,ACRV1,ACTN3,ACY3,ADAMTS15,ADAMTS8,ADM,ADRBK1,AGBL2,AHNAK,AIP,AKIP1,ALDH3B1,ALDH3B2,ALG1L9P,ALG8,ALG9,ALKBH3,ALKBH8,ALX4,AMBRA1,AMICA1,AMOTL1,AMPD3,ANAPC15,ANGPTL5,ANKK1,ANKRD13D,ANKRD42,ANKRD49,ANO1,ANO3,ANO5,ANO9,AP2A2,AP5B1,APBB1,API5,APIP,APLNR,APLP2,APOA1,APOA4,APOA5,APOC3,AQP11,ARAP1,ARCN1,ARFGAP2,ARFIP2,ARHGAP1,ARHGAP20,ARHGAP32,ARHGAP42,ARHGEF12,ARHGEF17,ARL14EP,ARL2,ARL2-SNX15,ARNTL,ARRB1,ART1,ART5,ASCL2,ASCL3,ASRGL1,ATG13,ATG16L2,ATG2A,ATHL1,ATL3,ATM,ATP5L,B3GAT3,B3GNT1,B3GNT6,B4GALNT4,BACE1,BACE1-AS,BAD,BANF1,BARX2,BATF2,BBOX1,BBS1,BCL9L,BCO2,BDNF,BDNF-AS,BEST1,BET1L,BIRC2,BIRC3,BLID,BRMS1,BRSK2,BSCL2,BSX,BTBD10,BTBD18,BTG4,BUD13,C11orf1,C11orf16,C11orf21,C11orf24,C11orf30,C11orf31,C11orf34,C11orf35,C11orf40,C11orf42,C11orf44,C11orf45,C11orf48,C11orf49,C11orf52,C11orf53,C11orf54,C11orf57,C11orf58,C11orf63,C11orf65,C11orf68,C11orf70,C11orf71,C11orf73,C11orf74,C11orf80,C11orf82,C11orf83,C11orf84,C11orf85,C11orf86,C11orf87,C11orf88,C11orf91,C11orf92,C11orf93,C11orf94,C11orf95,C11orf96,C1QTNF4,C1QTNF5,C2CD2L,C2CD3,CABP2,CABP4,CADM1,CALCA,CALCB,CAPN1,CAPN5,CAPRIN1,CARD16,CARD17,CARD18,CARNS1,CARS,CASP1,CASP12,CASP4,CASP5,CAT,CATSPER1,CBL,CCDC15,CCDC153,CCDC179,CCDC34,CCDC67,CCDC73,CCDC81,CCDC82,CCDC83,CCDC84,CCDC85B,CCDC86,CCDC87,CCDC88B,CCDC89,CCDC90B,CCKBR,CCND1,CCS,CD151,CD248,CD3D,CD3E,CD3G,CD44,CD5,CD59,CD6,CD81,CD82,CDC42BPG,CDC42EP2,CDCA5,CDHR5,CDK2AP2,CDKN1C,CDON,CELF1,CEND1,CEP164,CEP57,CFL1,CHEK1,CHID1,CHKA,CHORDC1,CHRDL2,CHRM1,CHRM4,CHRNA10,CHST1,CKAP5,CLCF1,CLDN25,CLMP,CLNS1A,CLP1,CLPB,CNGA4,CNIH2,CNTF,CNTN5,COA4,COMMD9,COPB1,CORO1B,COX8A,CPSF7,CPT1A,CREB3L1,CREBZF,CRTAM,CRY2,CRYAB,CSNK2A3,CSRP3,CST6,CSTF3,CSTF3-AS1,CTNND1,CTR9,CTSC,CTSD,CTSF,CTSW,CTTN,CUL5,CWC15,CWF19L2,CXCR5,CYB561A3,CYB5R2,CYP2R1,DAGLA,DAK,DBX1,DCDC1,DCDC5,DCHS1,DCPS,DCUN1D5,DDB1,DDB2,DDI1,DDX10,DDX25,DDX6,DEAF1,DEFB108B,DENND5A,DEPDC7,DGAT2,DGKZ,DHCR7,DIXDC1,DKFZP434K028,DKFZp686K1684,DKFZp779M0652,DKK3,DLAT,DLG2,DNAJB13,DNAJC24,DNAJC4,DNHD1,DOC2GP,DPAGT1,DPF2,DPP3,DRAP1,DRD2,DRD4,DSCAML1,DTX4,DUSP8,DYNC2H1,E2F8,EED,EEF1G,EFCAB4A,EFEMP2,EHBP1L1,EHD1,EHF,EI24,EIF1AD,EIF3F,EIF3M,EIF4G2,ELF5,ELMOD1,ELP4,EML3,ENDOD1,EPS8L2,ESAM,ESRRA,ETS1,EXPH5,EXT2,F2,FADD,FADS1,FADS2,FADS3,FAM111A,FAM111B,FAM118B,FAM160A2,FAM168A,FAM180B,FAM181B,FAM76B,FAM86C1,FAM86C2P,FAM89B,FAM99A,FAM99B,FANCF,FAR1,FAT3,FAU,FBXO3,FCHSD2,FDX1,FDXACB1,FEN1,FERMT3,FEZ1,FGF19,FGF3,FGF4,FIBIN,FIBP,FJX1,FKBP2,FLI1,FLI1-AS1,FLJ39051,FLJ42102,FLRT1,FNBP4,FOLH1,FOLH1B,FOLR1,FOLR2,FOLR3,FOLR4,FOSL1,FOXR1,FOXRED1,FRMD8,FSHB,FTH1,FUT4,FXYD2,FXYD6,FXYD6-FXYD2,FZD4,GAB2,GAL,GAL3ST3,GALNT18,GANAB,GAS2,GDPD4,GDPD5,GIF,GLYAT,GLYATL1,GLYATL2,GNG3,GPHA2,GPR137,GPR152,GPR83,GRAMD1B,GRIA4,GRIK4,GRM5,GRM5-AS1,GSTP1,GTF2H1,GUCY1A2,GUCY2EP,GVINP1,GYLTL1B,H19,H2AFX,HARBI1,HBB,HBBP1,HBD,HBE1,HBG1,HBG2,HEPACAM,HEPHL1,HEPN1,HINFP,HIPK3,HMBS,HNRNPKP3,HNRNPUL2,HNRNPUL2-BSCL2,HPS5,HPX,HRAS,HRASLS2,HRASLS5,HSD17B12,HSPA8,HSPB2,HSPB2-C11orf52,HTATIP2,HTR3A,HTR3B,HYLS1,HYOU1,IFITM1,IFITM10,IFITM2,IFITM3,IFITM5,IFT46,IGF2,IGF2-AS,IGHMBP2,IGSF22,IL10RA,IL18,IL18BP,ILK,IMMP1L,INCENP,INPPL1,INS,INS-IGF2,INSC,INTS4,INTS5,IPO7,IRF7,JRKL,JRKL-AS1,KAT5,KBTBD3,KBTBD4,KCNA4,KCNC1,KCNE3,KCNJ1,KCNJ11,KCNJ5,KCNK4,KCNK7,KCNQ1,KCNQ1DN,KCNQ1OT1,KCTD14,KCTD21,KDELC2,KDM2A,KDM4D,KDM4E,KIAA1377,KIAA1549L,KIAA1731,KIF18A,KIRREL3,KIRREL3-AS2,KIRREL3-AS3,KLC2,KLHL35,KRT8P41,KRTAP5-1,KRTAP5-10,KRTAP5-11,KRTAP5-2,KRTAP5-3,KRTAP5-4,KRTAP5-5,KRTAP5-6,KRTAP5-7,KRTAP5-8,KRTAP5-9,LAMTOR1,LAYN,LDHA,LDHAL6A,LDHC,LDLRAD3,LGALS12,LGR4,LIN7C,LINC00167,LINC00294,LINC00301,LIPT2,LMO1,LMO2,LOC100126784,LOC100129216,LOC100130348,LOC100130987,LOC100131626,LOC100132078,LOC100133315,LOC100288346,LOC100289388,LOC100499227,LOC100506082,LOC100506233,LOC100506305,LOC100506368,LOC100507205,LOC100507300,LOC100507384,LOC100652768,LOC100996455,LOC101054525,LOC143666,LOC221122,LOC254100,LOC255512,LOC283143,LOC283194,LOC283214,LOC283299,LOC338651,LOC341056,LOC440028,LOC440040,LOC441601,LOC494141,LOC643037,LOC643733,LOC643923,LOC644656,LOC646813,LOC649133,LOC650368,LOC729013,LPXN,LRFN4,LRP4,LRP4-AS1,LRP5,LRRC10B,LRRC32,LRRC4C,LRRC55,LRRC56,LRRN4CL,LRTOMT,LSP1,LTBP3,LUZP2,LYVE1,MACROD1,MADD,MALAT1,MAML2,MAP3K11,MAP4K2,MAP6,MAPK8IP1,MARK2,MCAM,MDK,ME3,MED17,MED19,MEN1,METTL12,METTL15,MFRP,MICAL2,MICALCL,MIR100,MIR100HG,MIR1237,MIR125B1,MIR1260B,MIR129-2,MIR1304,MIR130A,MIR1343,MIR139,MIR1908,MIR192,MIR194-2,MIR210,MIR210HG,MIR3160-1,MIR3160-2,MIR3162,MIR3165,MIR3167,MIR326,MIR34B,MIR34C,MIR3654,MIR3656,MIR3664,MIR3680-1,MIR3680-2,MIR3920,MIR3973,MIR4298,MIR4299,MIR4300,MIR4301,MIR4485,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{"Sample_ID":"PT116","chr":"chr11","posStart":133002178,"posEnd":134940416,"length":1938239,"numProbe":576,"log2ratio.Mean.adj":-0.46227,"log2ratio.SD":0.26235,"log2ratio.Median.adj":-0.4213,"log2ratio.MAD":0.2599,"log2mBAF.Mean":0.77681,"log2mBAF.SD":0.10427,"log2mBAF.Median":0.79664,"log2mBAF.MAD":0.09067,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":15,"gene":"ACAD8,B3GAT1,GLB1L2,GLB1L3,IGSF9B,JAM3,LOC100128239,LOC283174,LOC283177,MIR4697,NCAPD3,OPCML,SPATA19,THYN1,VPS26B"}
{"Sample_ID":"PT116","chr":"chr12","posStart":197841,"posEnd":133778796,"length":133580956,"numProbe":27191,"log2ratio.Mean.adj":-0.22615,"log2ratio.SD":0.20545,"log2ratio.Median.adj":-0.21235,"log2ratio.MAD":0.18347,"log2mBAF.Mean":0.28313,"log2mBAF.SD":0.16664,"log2mBAF.Median":0.31272,"log2mBAF.MAD":0.1328,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":1182,"gene":"A2M,A2M-AS1,A2ML1,A2MP1,AAAS,AACS,ABCB9,ABCC9,ABCD2,ACACB,ACAD10,ACADS,ACRBP,ACSM4,ACSS3,ACTR6,ACVR1B,ACVRL1,ADAM1A,ADAMTS20,ADCY6,ADIPOR2,AEBP2,AGAP2,AICDA,AKAP3,ALDH1L2,ALDH2,ALG10,ALG10B,ALKBH2,ALX1,AMDHD1,AMHR2,AMIGO2,AMN1,ANAPC5,ANAPC7,ANKLE2,ANKRD13A,ANKRD33,ANKRD52,ANKS1B,ANO2,ANO4,ANO6,ANP32D,APAF1,APOBEC1,APOF,APOLD1,APPL2,AQP2,AQP5,AQP6,ARF3,ARHGAP9,ARHGDIB,ARHGEF25,ARID2,ARL1,ARL6IP4,ARNTL2,ARPC3,ART4,ASB8,ASCL1,ASCL4,ASIC1,ASUN,ATF1,ATF7,ATF7IP,ATN1,ATP2A2,ATP2B1,ATP5B,ATP5G2,ATP6V0A2,ATXN2,ATXN7L3B,AVIL,AVPR1A,B3GNT4,B4GALNT1,B4GALNT3,BAZ2A,BBS10,BCAT1,BCDIN3D,BCDIN3D-AS1,BCL2L14,BCL7A,BEST3,BHLHE41,BICD1,BIN2,BLOC1S1,BLOC1S1-RDH5,BRAP,BRI3BP,BTBD11,BTG1,C12orf10,C12orf23,C12orf29,C12orf36,C12orf39,C12orf4,C12orf40,C12orf42,C12orf43,C12orf44,C12orf45,C12orf49,C12orf5,C12orf50,C12orf52,C12orf54,C12orf56,C12orf57,C12orf60,C12orf61,C12orf65,C12orf66,C12orf68,C12orf71,C12orf73,C12orf74,C12orf75,C12orf76,C12orf77,C1QL4,C1R,C1RL,C1RL-AS1,C1S,C2CD5,C3AR1,CABP1,CACNA1C,CACNA1C-AS1,CACNA1C-AS4,CACNA1C-IT3,CACNA2D4,CACNB3,CALCOCO1,CAMKK2,CAND1,CAPRIN2,CAPS2,CAPZA3,CASC1,CBX5,CCDC38,CCDC41,CCDC42B,CCDC53,CCDC59,CCDC60,CCDC62,CCDC63,CCDC64,CCDC65,CCDC77,CCDC91,CCDC92,CCER1,CCND2,CCNT1,CCT2,CD163,CD163L1,CD27,CD27-AS1,CD4,CD63,CD69,CD9,CDCA3,CDK17,CDK2,CDK2AP1,CDK4,CDKN1B,CELA1,CEP290,CERS5,CHD4,CHFR,CHPT1,CHST11,CIT,CKAP4,CLEC12A,CLEC12B,CLEC1A,CLEC1B,CLEC2A,CLEC2B,CLEC2D,CLEC4A,CLEC4C,CLEC4D,CLEC4E,CLEC6A,CLEC7A,CLEC9A,CLECL1,CLIP1,CLLU1,CLLU1OS,CLSTN3,CMAS,CMKLR1,CNOT2,CNPY2,CNTN1,COL2A1,COPS7A,COPZ1,COQ10A,COQ5,CORO1C,COX14,COX6A1,CPM,CPNE8,CPSF6,CRADD,CREBL2,CRY1,CS,CSAD,CSRNP2,CSRP2,CTDSP2,CUX2,CYP27B1,DAO,DAZAP2,DBX2,DCD,DCN,DCP1B,DCTN2,DDIT3,DDN,DDX11,DDX11-AS1,DDX12P,DDX23,DDX47,DDX51,DDX54,DDX55,DENND5B,DENND5B-AS1,DENR,DEPDC4,DERA,DGKA,DHH,DHX37,DIABLO,DIP2B,DNAH10,DNAJC14,DNAJC22,DNM1L,DPPA3,DPY19L2,DRAM1,DSTNP2,DTX1,DTX3,DUSP16,DUSP6,DYNLL1,DYRK2,DYRK4,E2F7,EEA1,EFCAB4B,EID3,EIF2B1,EIF4B,ELK3,EMG1,EMP1,ENDOU,ENO2,EP400,EP400NL,EPS8,EPYC,ERBB3,ERC1,ERGIC2,ERP27,ERP29,ESPL1,ESYT1,ETNK1,ETV6,FAIM2,FAM101A,FAM109A,FAM186A,FAM186B,FAM19A2,FAM216A,FAM222A,FAM222A-AS1,FAM60A,FAM66C,FAM71C,FAM86FP,FAM90A1,FAR2,FBRSL1,FBXL14,FBXO21,FBXW8,FGD4,FGD6,FGF23,FGF6,FGFR1OP2,FICD,FIGNL2,FKBP11,FKBP4,FLJ12825,FLJ13224,FLJ31485,FLJ37505,FLJ41278,FMNL3,FOXJ2,FOXM1,FOXN4,FRS2,FZD10,GABARAPL1,GALNT4,GALNT6,GALNT8,GALNT9,GAPDH,GAS2L3,GATC,GCN1L1,GDF11,GDF3,GIT2,GLI1,GLIPR1,GLIPR1L1,GLIPR1L2,GLS2,GLT1D1,GLT8D2,GLTP,GLYCAM1,GNB3,GNN,GNPTAB,GNS,GOLGA2P5,GOLGA3,GOLT1B,GPD1,GPN3,GPR133,GPR162,GPR182,GPR19,GPR84,GPRC5A,GPRC5D,GRASP,GRIN2B,GRIP1,GSG1,GTF2H3,GTSF1,GUCY2C,GXYLT1,GYS2,H1FNT,H2AFJ,H3F3C,HAL,HCAR1,HCAR2,HCAR3,HCFC2,HDAC7,HEBP1,HECTD4,HELB,HIGD1C,HIP1R,HIST4H4,HMGA2,HNF1A,HNF1A-AS1,HNRNPA1,HNRNPA1P10,HOTAIR,HOXC-AS5,HOXC10,HOXC11,HOXC12,HOXC13,HOXC4,HOXC5,HOXC6,HOXC8,HOXC9,HPD,HRK,HSD17B6,HSP90B1,HSPB8,HTR7P1,HVCN1,IAPP,IFFO1,IFLTD1,IFNG,IFT81,IGF1,IGFBP6,IKBIP,IKZF4,IL22,IL23A,IL26,IL31,ING4,INHBC,INHBE,IPO8,IQCD,IQSEC3,IRAK3,IRAK4,ISCU,ITFG2,ITGA5,ITGA7,ITGB7,ITPR2,KANSL2,KCNA1,KCNA5,KCNA6,KCNC2,KCNH3,KCNJ8,KCNMB4,KCTD10,KDM2B,KDM5A,KERA,KIAA1033,KIAA1467,KIAA1551,KIF21A,KIF5A,KITLG,KLHL42,KLRAP1,KLRB1,KLRC1,KLRC2,KLRC3,KLRC4,KLRC4-KLRK1,KLRD1,KLRF1,KLRF2,KLRG1,KLRK1,KNTC1,KRAS,KRR1,KRT1,KRT18,KRT19P2,KRT2,KRT3,KRT4,KRT5,KRT6A,KRT6B,KRT6C,KRT7,KRT71,KRT72,KRT73,KRT74,KRT75,KRT76,KRT77,KRT78,KRT79,KRT8,KRT80,KRT81,KRT82,KRT83,KRT84,KRT85,KRT86,KSR2,LACRT,LAG3,LALBA,LARP4,LDHB,LEMD3,LEPREL2,LETMD1,LGR5,LHX5,LIMA1,LIN7A,LINC00173,LINC00477,LINC00485,LINC00507,LINC00592,LINC00612,LINC00615,LLPH,LMBR1L,LMO3,LOC100128554,LOC100129361,LOC100130075,LOC100130238,LOC100130776,LOC100131138,LOC100190940,LOC100240734,LOC100240735,LOC100271702,LOC100287314,LOC100287944,LOC100292680,LOC100335030,LOC100499405,LOC100505978,LOC100506314,LOC100506393,LOC100506451,LOC100506668,LOC100506844,LOC100507066,LOC100507091,LOC100507206,LOC100507250,LOC100507377,LOC100507424,LOC100652999,LOC101055625,LOC116437,LOC144486,LOC144742,LOC255411,LOC256021,LOC283332,LOC283335,LOC283403,LOC283440,LOC338758,LOC338799,LOC338817,LOC374443,LOC387895,LOC389634,LOC400027,LOC400043,LOC400084,LOC440117,LOC574538,LOC642846,LOC643339,LOC643711,LOC643770,LOC728084,LOC728739,LOH12CR1,LOH12CR2,LPAR5,LPCAT3,LRCOL1,LRIG3,LRMP,LRP1,LRP6,LRRC10,LRRC23,LRRC43,LRRIQ1,LRRK2,LRTM2,LTA4H,LTBR,LUM,LYRM5,LYZ,M6PR,MAGOHB,MANSC1,MANSC4,MAP1LC3B2,MAP3K12,MAPKAPK5,MAPKAPK5-AS1,MARCH9,MARS,MBD6,MCRS1,MDM1,MDM2,MED13L,MED21,METAP2,METTL1,METTL20,METTL21B,METTL25,METTL7A,METTL7B,MFAP5,MFSD5,MGAT4C,MGP,MGST1,MIP,MIR1178,MIR1228,MIR1244-1,MIR1244-2,MIR1244-3,MIR1251,MIR1252,MIR1279,MIR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{"Sample_ID":"PT116","chr":"chr15","posStart":20161372,"posEnd":102398060,"length":82236689,"numProbe":17100,"log2ratio.Mean.adj":-0.2032,"log2ratio.SD":0.20008,"log2ratio.Median.adj":-0.1914,"log2ratio.MAD":0.18147,"log2mBAF.Mean":0.289,"log2mBAF.SD":0.1629,"log2mBAF.Median":0.31782,"log2mBAF.MAD":0.12926,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":822,"gene":"AAGAB,ABHD17C,ABHD2,ACAN,ACSBG1,ACTC1,ADAL,ADAM10,ADAMTS17,ADAMTS7,ADAMTSL3,ADPGK,ADPGK-AS1,AEN,AGBL1,AGPHD1,AGSK1,AKAP13,ALDH1A2,ALDH1A3,ALPK3,ANKDD1A,ANKRD34C,ANKRD63,ANP32A,ANP32A-IT1,ANP32AP1,ANPEP,ANXA2,AP3B2,AP3S2,AP4E1,APBA2,APH1B,AQP9,AQR,ARHGAP11A,ARHGAP11B,ARID3B,ARIH1,ARNT2,ARPP19,ARRDC4,ASB7,ASB9P1,ATP10A,ATP8B4,ATPBD4,ATPBD4-AS1,AVEN,B2M,BAHD1,BBS4,BCL2A1,BCL2L10,BLM,BLOC1S6,BMF,BNC1,BNIP2,BTBD1,BUB1B,C15orf26,C15orf27,C15orf32,C15orf37,C15orf38,C15orf38-AP3S2,C15orf39,C15orf40,C15orf41,C15orf43,C15orf48,C15orf52,C15orf53,C15orf54,C15orf56,C15orf57,C15orf59,C15orf60,C15orf61,C15orf62,C2CD4A,C2CD4B,CA12,CALML4,CAPN3,CASC4,CASC5,CATSPER2,CATSPER2P1,CCDC33,CCNB2,CCNDBP1,CCPG1,CD276,CDAN1,CELF6,CEP152,CERS3,CGNL1,CHAC1,CHD2,CHEK2P2,CHP1,CHRFAM7A,CHRM5,CHRNA3,CHRNA5,CHRNA7,CHRNB4,CHST14,CHSY1,CIB1,CIB2,CILP,CKMT1A,CKMT1B,CLK3,CLN6,CLPX,COMMD4,COPS2,CORO2B,COX5A,CPEB1,CPLX3,CRABP1,CRTC3,CSK,CSNK1A1P1,CSNK1G1,CSPG4,CT60,CT62,CTDSPL2,CTSH,CTXN2,CXADRP2,CYFIP1,CYP11A1,CYP19A1,CYP1A1,CYP1A2,DAPK2,DCAF13P3,DENND4A,DET1,DIS3L,DISP2,DKFZP434L187,DLL4,DMXL2,DNAJA4,DNAJC17,DNM1P35,DNM1P41,DNM1P46,DPP8,DTWD1,DUOX1,DUOX2,DUOXA1,DUOXA2,DUT,DYX1C1,DYX1C1-CCPG1,EDC3,EFTUD1,EFTUD1P1,EHD4,EID1,EIF2AK4,EIF3J,ELL3,EMC4,EMC7,EPB42,ETFA,EXD1,FAH,FAM103A1,FAM154B,FAM169B,FAM174B,FAM189A1,FAM214A,FAM219B,FAM227B,FAM63B,FAM81A,FAM96A,FAM98B,FAN1,FANCI,FBN1,FBXL22,FBXO22,FBXO22-AS1,FEM1B,FES,FGF7,FLJ10038,FLJ27352,FLJ42289,FMN1,FOXB1,FRMD5,FSD2,FSIP1,FURIN,GABARAPL3,GABPB1,GABPB1-AS1,GABRA5,GABRB3,GABRG3,GALK2,GANC,GATM,GATM-AS1,GCHFR,GCNT3,GCOM1,GDPGP1,GJD2,GLCE,GLDN,GNB5,GOLGA6A,GOLGA6B,GOLGA6C,GOLGA6D,GOLGA6L1,GOLGA6L10,GOLGA6L4,GOLGA6L5,GOLGA6L6,GOLGA6L7P,GOLGA6L9,GOLGA8A,GOLGA8B,GOLGA8CP,GOLGA8DP,GOLGA8EP,GOLGA8F,GOLGA8G,GOLGA8I,GOLGA8O,GOLGA8S,GOLGA8T,GPR176,GRAMD2,GREM1,GTF2A2,HAPLN3,HAUS2,HCN4,HDC,HDDC3,HDGFRP3,HERC1,HERC2,HERC2P10,HERC2P2,HERC2P3,HERC2P7,HERC2P9,HEXA,HEXA-AS1,HIGD2B,HMG20A,HMGN2P46,HOMER2,HSP90AB4P,HSP90B2P,HYPK,IDH2,IDH3A,IGDCC3,IGDCC4,IGF1R,IL16,IMP3,INO80,IPW,IQCH,IQCH-AS1,IQGAP1,IREB2,ISG20,ISL2,ISLR,ISLR2,ITGA11,ITPKA,IVD,JMJD7,JMJD7-PLA2G4B,KATNBL1,KBTBD13,KIAA0101,KIAA1024,KIAA1199,KIF23,KIF7,KLF13,KLHL25,KNSTRN,LACTB,LARP6,LCMT2,LCTL,LDHAL6B,LEO1,LINC00052,LINC00277,LINC00593,LINC00597,LINGO1,LINS,LIPC,LMAN1L,LOC100128714,LOC100130855,LOC100131089,LOC100144604,LOC100287399,LOC100288637,LOC100289656,LOC100505648,LOC100505679,LOC100506874,LOC100507118,LOC100507217,LOC100507472,LOC100996331,LOC145783,LOC145820,LOC145837,LOC145845,LOC253044,LOC254559,LOC283663,LOC283683,LOC283688,LOC283692,LOC283693,LOC283710,LOC283731,LOC283761,LOC338963,LOC388152,LOC390660,LOC400456,LOC440243,LOC440288,LOC440297,LOC440300,LOC440311,LOC503519,LOC642423,LOC645212,LOC645752,LOC646214,LOC646278,LOC646938,LOC727849,LOC727915,LOC727924,LOC729739,LOC729911,LOC91450,LOC91948,LOXL1,LOXL1-AS1,LPCAT4,LRRC28,LRRC49,LRRC57,LRRK1,LTK,LYSMD2,LYSMD4,MAGEL2,MAN2A2,MAN2C1,MAP1A,MAP2K1,MAP2K5,MAPK6,MAPKBP1,MCTP2,MEF2A,MEGF11,MEIS2,MESDC1,MESDC2,MESP1,MESP2,MEX3B,MFAP1,MFGE8,MGA,MGC15885,MIR1179,MIR1233-1,MIR1233-2,MIR1266,MIR1272,MIR1276,MIR1282,MIR1469,MIR147B,MIR184,MIR190A,MIR211,MIR2116,MIR3175,MIR3529,MIR3942,MIR4310,MIR4311,MIR4312,MIR4313,MIR4508,MIR4509-1,MIR4509-2,MIR4509-3,MIR4510,MIR4511,MIR4513,MIR4514,MIR4515,MIR4712,MIR4713,MIR4714,MIR4715,MIR4716,MIR5003,MIR5094,MIR548H4,MIR549,MIR626,MIR627,MIR628,MIR629,MIR630,MIR631,MIR7-2,MIR9-3,MKRN3,MNS1,MORF4L1,MPI,MRPL42P5,MRPL46,MRPS11,MTFMT,MTHFS,MTMR10,MYEF2,MYO1E,MYO5A,MYO5C,MYO9A,MYZAP,NARG2,NBEAP1,NDN,NDNL2,NDUFAF1,NDUFAF4P1,NEDD4,NEIL1,NEO1,NF1P2,NGRN,NIPA1,NIPA2,NMB,NOP10,NOX5,NPAP1,NPTN,NR2E3,NR2F2,NRG4,NTRK3,NTRK3-AS1,NUSAP1,NUTM1,OAZ2,OCA2,ODF3L1,OIP5,OIP5-AS1,ONECUT1,OR4F13P,OR4F15,OR4F6,OR4M2,OR4N3P,OR4N4,OTUD7A,PAK6,PAQR5,PAR-SN,PAR1,PAR4,PAR5,PARP16,PARP6,PATL2,PCSK6,PDCD7,PDE8A,PDIA3,PEAK1,PEX11A,PGBD4,PGPEP1L,PHGR1,PIAS1,PIF1,PIGB,PIN4P1,PKM,PLA2G4B,PLA2G4D,PLA2G4E,PLA2G4F,PLCB2,PLEKHO2,PLIN1,PML,POLG,POLR2M,POTEB,PPCDC,PPIB,PPIP5K1,PPP1R14D,PRC1,PRKXP1,PRTG,PSMA4,PSTPIP1,PTPLAD1,PTPN9,PWRN1,PWRN2,PYGO1,RAB11A,RAB27A,RAB8B,RAD51,RASGRF1,RASGRP1,RASL12,RBPMS2,RCCD1,RCN2,REREP3,RFX7,RGMA,RHCG,RHOV,RLBP1,RMDN3,RNF111,RNU6-28,RORA,RPAP1,RPL4,RPLP1,RPP25,RPS17,RPS17L,RPS27L,RPUSD2,RSL24D1,RTF1,RYR3,SCAMP2,SCAMP5,SCAND2P,SCAPER,SCARNA14,SCARNA15,SCG3,SCG5,SEC11A,SECISBP2L,SEMA4B,SEMA6D,SEMA7A,SENP8,SERF2,SERF2-C15ORF63,SERINC4,SH2D7,SH3GL3,SHC4,SHF,SIN3A,SKOR1,SLC12A1,SLC12A6,SLC24A1,SLC24A5,SLC27A2,SLC28A1,SLC28A2,SLC30A4,SLC51B,SLCO3A1,SLTM,SMAD3,SMAD6,SNAP23,SNAPC5,SNORD107,SNORD108,SNORD109A,SNORD109B,SNORD115-1,SNORD115-10,SNORD115-11,SNORD115-12,SNORD115-13,SNORD115-14,SNORD115-15,SNORD115-16,SNORD115-17,SNORD115-18,SNORD115-19,SNORD115-2,SNORD115-20,SNORD115-21,SNORD115-22,SNORD115-23,SNORD115-24,SNORD115-25,SNORD115-26,SNORD115-27,SNORD115-28,SNORD115-29,SNORD115-3,SNORD115-30,SNORD115-31,SNORD115-32,SNORD115-33,SNORD115-34,SNORD115-35,SNORD115-36,SNORD115-37,SNORD115-38,SNORD115-39,SNORD115-4,SNORD115-40,SNORD115-41,SNORD115-42,SNORD115-43,SNORD115-44,SNORD115-45,SNORD115-47,SNORD115-48,SNORD115-5,SNORD115-6,SNORD115-7,SNORD115-8,SNORD115-9,SNORD116-1,SNORD116-10,SNORD116-11,SNORD116-12,SNORD116-13,SNORD116-14,SNORD116-15,SNORD116-16,SNORD116-17,SNORD116-18,SNORD116-19,SNORD116-2,SNORD116-20,SNORD116-21,SNORD116-22,SNORD116-23,SNORD116-24,SNORD116-25,SNORD116-26,SNORD116-27,SNORD116-28,SNORD116-29,SNORD116-3,SNORD116-4,SNORD116-5,SNORD116-6,SNORD116-7,SNORD116-8,SNORD116-9,SNORD16,SNORD18A,SNORD18B,SNORD18C,SNORD64,SNRPA1,SNRPN,SNUPN,SNURF,SNX1,SNX22,SNX33,SORD,SPATA5L1,SPATA8,SPESP1,SPG11,SPG21,SPINT1,SPPL2A,SPRED1,SPTBN5,SQRDL,SRP14,ST20,ST20-MTHFS,ST8SIA2,STARD5,STARD9,STOML1,STRA6,STRC,SV2B,SYNM,TARSL2,TBC1D21,TBC1D2B,TCF12,TEX9,TGM5,TGM7,THAP10,THBS1,THSD4,TICRR,TIPIN,TJP1,TLE3,TLN2,TM2D3,TM6SF1,TMC3,TMCO5A,TMCO5B,TMED3,TMEM202,TMEM62,TMEM87A,TMOD2,TMOD3,TNFAIP8L3,TP53BP1,TPM1,TRIM69,TRIP4,TRPM1,TRPM7,TSPAN3,TTBK2,TTC23,TTLL13,TUBGCP4,TUBGCP5,TYRO3,TYRO3P,UACA,UBAP1L,UBE2Q2,UBE2Q2P1,UBE2Q2P2,UBE2Q2P3,UBE3A,UBL7,UBR1,ULK3,ULK4P1,ULK4P2,ULK4P3,UNC13C,UNC45A,USP3,USP50,USP8,VIMP,VPS13C,VPS18,VPS33B,VPS39,VWA9,WDR61,WDR72,WDR73,WDR76,WDR93,WHAMM,WHAMMP1,WHAMMP2,WHAMMP3,ZFAND6,ZFP106,ZFYVE19,ZNF280D,ZNF592,ZNF609,ZNF710,ZNF770,ZNF774,ZSCAN2,ZSCAN29,ZWILCH"}
{"Sample_ID":"PT116","chr":"chr16","posStart":101263,"posEnd":5282314,"length":5181052,"numProbe":869,"log2ratio.Mean.adj":0.0583,"log2ratio.SD":0.20735,"log2ratio.Median.adj":0.0587,"log2ratio.MAD":0.17643,"log2mBAF.Mean":0.15225,"log2mBAF.SD":0.13809,"log2mBAF.Median":0.17263,"log2mBAF.MAD":0.11721,"log2ratio.p.value":0.029,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":221,"gene":"ABCA17P,ABCA3,ADCY9,ALG1,AMDHD2,ANKS3,ARHGDIG,ATP6V0C,AXIN1,BAIAP3,BRICD5,C16orf11,C16orf13,C16orf59,C16orf71,C16orf89,C16orf90,C16orf91,C16orf96,C1QTNF8,CACNA1H,CASKIN1,CCDC154,CCDC64B,CCDC78,CCNF,CDIP1,CEMP1,CHTF18,CLCN7,CLDN6,CLDN9,CLUAP1,CORO7,CORO7-PAM16,CRAMP1L,CREBBP,DECR2,DNAJA3,DNASE1,DNASE1L2,E4F1,ECI1,EME2,ERVK13-1,FAHD1,FAM173A,FAM195A,FAM86A,FBXL16,FLJ39639,FLJ42627,FLYWCH1,FLYWCH2,GFER,GLIS2,GLYR1,GNG13,GNPTG,HAGH,HAGHL,HBA1,HBA2,HBM,HBQ1,HBZ,HCFC1R1,HMOX2,HN1L,HS3ST6,IFT140,IGFALS,IL32,ITFG3,JMJD8,KCTD5,KREMEN2,LINC00235,LINC00254,LINC00514,LMF1,LOC100128770,LOC100134368,LOC100507501,LOC440335,LOC652276,LUC7L,MAPK8IP3,MEFV,MEIOB,METRN,MGRN1,MIR1225,MIR3176,MIR3177,MIR3178,MIR3180-5,MIR3677,MIR4516,MIR4717,MIR5587,MIR662,MIR940,MLST8,MMP25,MPG,MRPL28,MRPS34,MSLN,MSRB1,MTRNR2L4,NAA60,NAGPA,NAGPA-AS1,NARFL,NDUFB10,NHLRC4,NLRC3,NME3,NME4,NMRAL1,NOXO1,NPRL3,NPW,NTHL1,NTN3,NUBP2,NUDT16L1,OR1F1,OR1F2P,OR2C1,PAM16,PAQR4,PDIA2,PDPK1,PGP,PIGQ,PKD1,PKMYT1,POLR3K,PPL,PRR25,PRSS21,PRSS22,PRSS27,PRSS30P,PRSS33,PRSS41,PTX4,RAB11FIP3,RAB26,RAB40C,RGS11,RHBDF1,RHBDL1,RHOT2,RNF151,RNPS1,ROGDI,RPL3L,RPS2,RPUSD1,SEC14L5,SEPT12,SLC9A3R2,SLX4,SNHG9,SNORA10,SNORA64,SNORA78,SNORD60,SNRNP25,SOLH,SOX8,SPSB3,SRL,SRRM2,SRRM2-AS1,SSTR5,SSTR5-AS1,STUB1,SYNGR3,TBC1D24,TBL3,TCEB2,TELO2,TFAP4,THOC6,TIGD7,TMEM204,TMEM8A,TNFRSF12A,TPSAB1,TPSB2,TPSD1,TPSG1,TRAF7,TRAP1,TSC2,TSR3,UBALD1,UBE2I,UBN1,UNKL,VASN,WDR24,WDR90,WFIKKN1,ZG16B,ZNF174,ZNF200,ZNF205,ZNF205-AS1,ZNF213,ZNF263,ZNF500,ZNF597,ZNF598,ZNF75A,ZSCAN10,ZSCAN32"}
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{"Sample_ID":"PT116","chr":"chr16","posStart":64338819,"posEnd":90149922,"length":25811104,"numProbe":7007,"log2ratio.Mean.adj":-0.48161,"log2ratio.SD":0.25217,"log2ratio.Median.adj":-0.4456,"log2ratio.MAD":0.22521,"log2mBAF.Mean":0.77686,"log2mBAF.SD":0.1026,"log2mBAF.Median":0.79221,"log2mBAF.MAD":0.09235,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":298,"gene":"AARS,ACD,ACSF3,ADAD2,ADAMTS18,ADAT1,AFG3L1P,AGRP,ANKRD11,AP1G1,APRT,ATMIN,ATP2C2,ATP6V0D1,ATXN1L,B3GNT9,BANP,BCAR1,BCMO1,BEAN1,C16orf3,C16orf46,C16orf55,C16orf70,C16orf74,C16orf86,C16orf95,CA5A,CA7,CALB2,CBFA2T3,CBFB,CCDC79,CDH1,CDH11,CDH13,CDH15,CDH16,CDH3,CDH5,CDK10,CDT1,CDYL2,CENPBD1,CENPN,CENPT,CES2,CES3,CES4A,CFDP1,CHMP1A,CHST4,CHST5,CHST6,CHTF8,CIRH1A,CKLF,CKLF-CMTM1,CLEC18A,CLEC18B,CLEC18C,CLEC3A,CMC2,CMIP,CMTM1,CMTM2,CMTM3,CMTM4,CNTNAP4,COG4,COG8,COTL1,COX4I1,CPNE7,CRISPLD2,CTCF,CTRB1,CTRB2,CTRL,CTU2,CYB5B,CYBA,DBNDD1,DDX19A,DDX19B,DDX28,DEF8,DHODH,DHX38,DNAAF1,DPEP1,DPEP2,DPEP3,DUS2L,DYNC1LI2,DYNLRB2,E2F4,EDC4,ELMO3,EMC8,ENKD1,ESRP2,EXOC3L1,EXOSC6,FA2H,FAM65A,FAM92B,FAM96B,FANCA,FBXL8,FBXO31,FENDRR,FHOD1,FLJ30679,FOXC2,FOXF1,FOXL1,FTSJD1,FUK,GABARAPL2,GALNS,GAN,GAS8,GCSH,GFOD2,GINS2,GLG1,GSE1,HAS3,HP,HPR,HSBP1,HSD11B2,HSD17B2,HSDL1,HSF4,HTA,HYDIN,IL17C,IL34,IRF8,IST1,JPH3,KARS,KCNG4,KCTD19,KIAA0513,KIAA0895L,KLHDC4,KLHL36,LCAT,LDHD,LINC00304,LINC00311,LOC100128881,LOC100129617,LOC100130015,LOC100130894,LOC100287036,LOC100505865,LOC100506060,LOC100506083,LOC100506172,LOC146513,LOC283867,LOC283922,LOC400548,LOC400558,LOC732275,LRRC29,LRRC36,MAF,MAP1LC3B,MARVELD3,MBTPS1,MC1R,MIR140,MIR1538,MIR1910,MIR1972-1,MIR1972-2,MIR3182,MIR328,MIR4719,MIR4720,MIR4722,MIR5093,MIR5189,MLKL,MLYCD,MON1B,MPHOSPH6,MTHFSD,MTSS1L,MVD,NAE1,NECAB2,NFAT5,NFATC3,NIP7,NOB1,NOL3,NQO1,NRN1L,NUDT7,NUTF2,OSGIN1,PABPN1L,PARD6A,PDF,PDP2,PDPR,PDXDC2P,PHLPP2,PIEZO1,PKD1L2,PKD1L3,PLA2G15,PLCG2,PLEKHG4,PMFBP1,PRDM7,PRMT7,PSKH1,PSMB10,PSMD7,RANBP10,RFWD3,RLTPR,RNF166,RPL13,RRAD,SDR42E1,SF3B3,SLC12A4,SLC22A31,SLC38A8,SLC7A5,SLC7A6,SLC7A6OS,SLC9A5,SMPD3,SNAI3,SNAI3-AS1,SNORA70D,SNORD111,SNORD111B,SNORD68,SNORD71,SNTB2,SPATA2L,SPG7,SPIRE2,ST3GAL2,SYCE1L,TAF1C,TANGO6,TAT,TCF25,TERF2,TERF2IP,THAP11,TK2,TLDC1,TMED6,TMEM170A,TMEM208,TMEM231,TPPP3,TRADD,TRAPPC2L,TSNAXIP1,TUBB3,TXNL4B,USP10,VAC14,VAT1L,VPS4A,VPS9D1,WDR59,WFDC1,WWOX,WWP2,ZC3H18,ZCCHC14,ZDHHC1,ZDHHC7,ZFHX3,ZFP1,ZFP90,ZFPM1,ZNF19,ZNF23,ZNF276,ZNF469,ZNF778,ZNF821,ZNRF1"}
{"Sample_ID":"PT116","chr":"chr17","posStart":53011,"posEnd":19581009,"length":19527999,"numProbe":4418,"log2ratio.Mean.adj":-1.00477,"log2ratio.SD":0.34079,"log2ratio.Median.adj":-0.9827,"log2ratio.MAD":0.34982,"log2mBAF.Mean":0.67355,"log2mBAF.SD":0.14567,"log2mBAF.Median":0.69202,"log2mBAF.MAD":0.13656,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":379,"gene":"ABR,ACADVL,ACAP1,ADORA2B,ADPRM,AIPL1,ALDH3A2,ALKBH5,ALOX12,ALOX12B,ALOX12P2,ALOX15,ALOX15B,ALOX15P1,ALOXE3,ANKFY1,ARHGAP44,ARHGEF15,ARRB2,ASGR1,ASGR2,ASPA,ATP1B2,ATP2A3,ATPAF2,AURKB,B9D1,BCL6B,BHLHA9,C17orf100,C17orf107,C17orf49,C17orf59,C17orf61-PLSCR3,C17orf74,C17orf76-AS1,C17orf85,C17orf97,C1QBP,CAMKK1,CAMTA2,CCDC144A,CCDC144B,CCDC42,CD68,CDRT1,CDRT15,CDRT15P1,CDRT15P2,CDRT4,CDRT7,CENPV,CHD3,CHRNB1,CHRNE,CLDN7,CLEC10A,CLUH,CNTROB,COPS3,COX10,COX10-AS1,CRK,CTC1,CTDNEP1,CTNS,CXCL16,CYB5D1,CYB5D2,DBIL5P,DERL2,DHRS7C,DHX33,DLG4,DNAH2,DNAH9,DPH1,DRG2,DVL2,EFNB3,EIF4A1,EIF5A,ELAC2,ELP5,EMC6,ENO3,EPN2,EPN2-AS1,EPN2-IT1,EVPLL,FAM101B,FAM106A,FAM106CP,FAM211A,FAM57A,FAM64A,FAM83G,FBXO39,FBXW10,FGF11,FLCN,FLII,FOXO3B,FXR2,GABARAP,GAS7,GEMIN4,GGT6,GID4,GLOD4,GLP2R,GLTPD2,GP1BA,GPS2,GRAP,GRAPL,GSG2,GUCY2D,HES7,HIC1,HS3ST3A1,HS3ST3B1,INCA1,INPP5K,ITGAE,KCNAB3,KCTD11,KDM6B,KIAA0753,KIF1C,KRBA2,KRT16P1,KRT16P2,LGALS9C,LINC00324,LINC00670,LINC00675,LLGL1,LOC100128288,LOC100130950,LOC100506388,LOC100506713,LOC284009,LOC284023,LOC339166,LOC339240,LOC728392,LRRC48,LSMD1,MAGOH2,MAP2K4,MAPK7,MED11,MED31,MED9,MEIS3P1,METTL16,MFAP4,MFSD6L,MGC12916,MINK1,MIR1180,MIR1253,MIR1288,MIR132,MIR195,MIR212,MIR22,MIR22HG,MIR3183,MIR324,MIR33B,MIR3676,MIR4314,MIR4520A,MIR4520B,MIR4521,MIR4731,MIR497,MIR497HG,MIR744,MIS12,MNT,MPDU1,MPRIP,MYBBP1A,MYH1,MYH10,MYH13,MYH2,MYH3,MYH4,MYH8,MYO15A,MYO1C,MYOCD,NCOR1,NDEL1,NEURL4,NLGN2,NLRP1,NT5M,NTN1,NUP88,NXN,ODF4,OR1A1,OR1A2,OR1D2,OR1D4,OR1D5,OR1E1,OR1E2,OR1G1,OR3A1,OR3A2,OR3A3,OR3A4P,OVCA2,P2RX1,P2RX5,P2RX5-TAX1BP3,PAFAH1B1,PELP1,PEMT,PER1,PFAS,PFN1,PHF23,PIGL,PIK3R5,PIK3R6,PIRT,PITPNA,PITPNA-AS1,PITPNM3,PLD2,PLD6,PLSCR3,PMP22,POLR2A,PRPF8,PRPSAP2,PSMB6,RABEP1,RAI1,RANGRF,RAP1GAP2,RASD1,RCVRN,RILP,RNASEK,RNASEK-C17orf49,RNF112,RNF167,RNF222,RNMTL1,RPA1,RPAIN,RPH3AL,RPL26,RPL29P2,RTN4RL1,SAT2,SCARF1,SCARNA21,SCIMP,SCO1,SENP3,SENP3-EIF4A1,SERPINF1,SERPINF2,SGSM2,SHBG,SHISA6,SHMT1,SHPK,SLC13A5,SLC16A11,SLC16A13,SLC25A11,SLC25A35,SLC2A4,SLC35G6,SLC43A2,SLC47A1,SLC52A1,SLC5A10,SMCR5,SMCR7,SMCR8,SMCR9,SMG6,SMTNL2,SMYD4,SNORA48,SNORA59A,SNORA59B,SNORA67,SNORD10,SNORD49A,SNORD49B,SNORD65,SNORD91A,SNORD91B,SOX15,SPAG7,SPATA22,SPDYE4,SPEM1,SPNS2,SPNS3,SREBF1,SRR,STX8,TAX1BP3,TBC1D26,TBC1D28,TEKT1,TEKT3,TIMM22,TLCD2,TM4SF5,TMEM102,TMEM107,TMEM220,TMEM220-AS1,TMEM256,TMEM88,TMEM95,TNFRSF13B,TNFSF12,TNFSF12-TNFSF13,TNFSF13,TNK1,TOM1L2,TOP3A,TP53,TRAPPC1,TRIM16,TRIM16L,TRPV1,TRPV2,TRPV3,TSR1,TTC19,TUSC5,TVP23B,TVP23C,TVP23C-CDRT4,TXNDC17,UBB,UBE2G1,USP32P1,USP32P2,USP43,USP6,VAMP2,VMO1,VPS53,WDR16,WDR81,WRAP53,WSCD1,XAF1,YBX2,YWHAE,ZBTB4,ZFP3,ZMYND15,ZNF18,ZNF232,ZNF286A,ZNF286B,ZNF287,ZNF594,ZNF624,ZSWIM7,ZZEF1"}
{"Sample_ID":"PT116","chr":"chr17","posStart":19603060,"posEnd":19795774,"length":192715,"numProbe":26,"log2ratio.Mean.adj":-0.1185,"log2ratio.SD":0.4133,"log2ratio.Median.adj":0.00695,"log2ratio.MAD":0.4152,"log2mBAF.Mean":0.43441,"log2mBAF.SD":0.20836,"log2mBAF.Median":0.47363,"log2mBAF.MAD":0.12802,"log2ratio.p.value":0.92,"log2mBAF.p.value":0,"p.value":0,"CNV":"LOH","numGene":3,"gene":"ALDH3A1,SLC47A2,ULK2"}
{"Sample_ID":"PT116","chr":"chr17","posStart":19804247,"posEnd":21368138,"length":1563892,"numProbe":132,"log2ratio.Mean.adj":-0.70068,"log2ratio.SD":0.30641,"log2ratio.Median.adj":-0.654,"log2ratio.MAD":0.31891,"log2mBAF.Mean":0.7401,"log2mBAF.SD":0.09369,"log2mBAF.Median":0.74111,"log2mBAF.MAD":0.1003,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":15,"gene":"AKAP10,C17orf103,CCDC144CP,CCDC144NL,CDRT15L2,DHRS7B,KCNJ12,KCNJ18,KRT16P3,LGALS9B,LOC100287072,MAP2K3,SPECC1,TMEM11,USP22"}
{"Sample_ID":"PT116","chr":"chr17","posStart":21374579,"posEnd":30039942,"length":8665364,"numProbe":516,"log2ratio.Mean.adj":0.13617,"log2ratio.SD":0.16651,"log2ratio.Median.adj":0.13355,"log2ratio.MAD":0.1559,"log2mBAF.Mean":0.14504,"log2mBAF.SD":0.14072,"log2mBAF.Median":0.1552,"log2mBAF.MAD":0.12896,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":99,"gene":"ABHD15,ADAP2,ALDOC,ANKRD13B,ATAD5,BLMH,C17orf51,CORO6,CPD,CRLF3,CRYBA1,DHRS13,DPRXP4,EFCAB5,ERAL1,EVI2A,EVI2B,FAM222B,FAM27L,FLJ36000,FLOT2,FOXN1,GIT1,GOSR1,IFT20,KIAA0100,KRT18P55,KSR1,LGALS9,LRRC37BP1,LYRM9,MIR144,MIR193A,MIR3184,MIR365B,MIR423,MIR451A,MIR451B,MIR4522,MIR4523,MIR4723,MIR4724,MIR4725,MIR4732,MIR4733,MTRNR2L1,MYO18A,NARR,NEK8,NF1,NLK,NOS2,NSRP1,NUFIP2,OMG,PHF12,PIGS,PIPOX,POLDIP2,PPY2,PROCA1,PYY2,RAB11FIP4,RAB34,RNF135,RPL23A,SARM1,SDF2,SEBOX,SEZ6,SGK494,SH3GL1P2,SLC13A2,SLC46A1,SLC6A4,SNORD42A,SNORD42B,SNORD4A,SNORD4B,SPAG5,SPAG5-AS1,SSH2,SUPT6H,SUZ12P1,TAOK1,TBC1D29,TBC1D3P5,TEFM,TIAF1,TLCD1,TMEM199,TMEM97,TMIGD1,TNFAIP1,TP53I13,TRAF4,UNC119,VTN,WSB1"}
{"Sample_ID":"PT116","chr":"chr17","posStart":30040819,"posEnd":32529159,"length":2488341,"numProbe":599,"log2ratio.Mean.adj":0.23244,"log2ratio.SD":0.2008,"log2ratio.Median.adj":0.2288,"log2ratio.MAD":0.18236,"log2mBAF.Mean":0.17863,"log2mBAF.SD":0.12438,"log2mBAF.Median":0.20299,"log2mBAF.MAD":0.10022,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":18,"gene":"AA06,ARGFXP2,ASIC2,C17orf75,CDK5R1,COPRS,LRRC37B,MIR632,MYO1D,PSMD11,RHBDL3,RHOT1,SH3GL1P1,SPACA3,SUZ12,TMEM98,UTP6,ZNF207"}
{"Sample_ID":"PT116","chr":"chr17","posStart":32529280,"posEnd":49398048,"length":16868769,"numProbe":2364,"log2ratio.Mean.adj":0.13394,"log2ratio.SD":0.18982,"log2ratio.Median.adj":0.1327,"log2ratio.MAD":0.17628,"log2mBAF.Mean":0.14392,"log2mBAF.SD":0.14353,"log2mBAF.Median":0.16696,"log2mBAF.MAD":0.1228,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":450,"gene":"AARSD1,AATF,ABCC3,ABI3,ACACA,ACBD4,ACLY,ACSF2,ADAM11,ANKRD40,AOC2,AOC3,AOC4,AP2B1,ARHGAP23,ARHGAP27,ARL17A,ARL17B,ARL4D,ARL5C,ASB16,ASB16-AS1,ATP5G1,ATP6V0A1,ATXN7L3,B4GALNT2,BECN1,BRCA1,C17orf102,C17orf104,C17orf105,C17orf50,C17orf53,C17orf66,C17orf78,C17orf96,C17orf98,C1QL1,CACNA1G,CACNA1G-AS1,CACNB1,CALCOCO2,CASC3,CBX1,CCDC103,CCDC43,CCL1,CCL11,CCL13,CCL14,CCL15,CCL15-CCL14,CCL16,CCL18,CCL2,CCL23,CCL3,CCL3L1,CCL3L3,CCL4,CCL4L1,CCL4L2,CCL5,CCL7,CCL8,CCR10,CCR7,CCT6B,CD300LG,CDC27,CDC6,CDK12,CDK5RAP3,CHAD,CISD3,CNP,CNTD1,CNTNAP1,COA3,COASY,COL1A1,COPZ2,CRHR1,CRHR1-IT1,CSF3,CWC25,DBF4B,DCAKD,DDX52,DHRS11,DHX58,DHX8,DLX3,DLX4,DNAJC7,DUSP14,DUSP3,EFCAB13,EFTUD2,EIF1,EME1,EPN3,ERBB2,ETV4,EZH1,FAM117A,FAM134C,FAM171A2,FAM215A,FBXL20,FBXO47,FKBP10,FLJ40194,FLJ45513,FMNL1,FNDC8,FZD2,G6PC,G6PC3,GAS2L2,GAST,GFAP,GGNBP2,GHDC,GIP,GJC1,GJD3,GNGT2,GOSR2,GPATCH8,GPR179,GRB7,GRN,GSDMA,GSDMB,HAP1,HCRT,HDAC5,HEXIM1,HEXIM2,HIGD1B,HILS1,HNF1B,HOXB-AS1,HOXB-AS3,HOXB-AS5,HOXB1,HOXB13,HOXB2,HOXB3,HOXB4,HOXB5,HOXB6,HOXB7,HOXB8,HOXB9,HSD17B1,HSPB9,IFI35,IGF2BP1,IGFBP4,IKZF3,ITGA2B,ITGA3,ITGB3,JUP,KANSL1,KANSL1-AS1,KAT2A,KAT7,KCNH4,KIF18B,KLHL10,KLHL11,KPNB1,KRT10,KRT12,KRT13,KRT14,KRT15,KRT16,KRT17,KRT19,KRT20,KRT222,KRT23,KRT24,KRT25,KRT26,KRT27,KRT28,KRT31,KRT32,KRT33A,KRT33B,KRT34,KRT35,KRT36,KRT37,KRT38,KRT39,KRT40,KRT42P,KRT9,KRTAP1-1,KRTAP1-3,KRTAP1-4,KRTAP1-5,KRTAP16-1,KRTAP17-1,KRTAP2-1,KRTAP2-2,KRTAP2-3,KRTAP2-4,KRTAP29-1,KRTAP3-1,KRTAP3-2,KRTAP3-3,KRTAP4-1,KRTAP4-11,KRTAP4-12,KRTAP4-2,KRTAP4-3,KRTAP4-4,KRTAP4-5,KRTAP4-6,KRTAP4-7,KRTAP4-8,KRTAP4-9,KRTAP9-1,KRTAP9-2,KRTAP9-3,KRTAP9-4,KRTAP9-6,KRTAP9-7,KRTAP9-8,KRTAP9-9,LASP1,LEPREL4,LHX1,LIG3,LINC00483,LINC00671,LINC00672,LINC00854,LOC100130581,LOC100131347,LOC100505782,LOC147093,LOC284080,LOC284100,LOC440434,LOC644172,LRRC37A,LRRC37A11P,LRRC37A2,LRRC37A4P,LRRC3C,LRRC46,LRRC59,LSM12,LUC7L3,LYZL6,MAP3K14,MAP3K14-AS1,MAPT,MAPT-AS1,MAPT-IT1,MBTD1,MED1,MED24,MEOX1,MGC57346,MIEN1,MIR10A,MIR1203,MIR152,MIR196A1,MIR2117,MIR2909,MIR3185,MIR4315-1,MIR4315-2,MIR4726,MIR4727,MIR4728,MIR4734,MIR5010,MIR5089,MLLT6,MLX,MMP28,MPP2,MPP3,MRM1,MRPL10,MRPL27,MRPL45,MRPL45P2,MSL1,MYCBPAP,MYL4,MYO19,NAGLU,NAGS,NBR1,NBR2,NEUROD2,NFE2L1,NGFR,NKIRAS2,NLE1,NME1,NME1-NME2,NME2,NMT1,NPEPPS,NR1D1,NSF,NSFP1,NT5C3B,NXPH3,ORMDL3,OSBPL7,PCGF2,PDK2,PEX12,PGAP3,PHB,PHOSPHO1,PIGW,PIP4K2B,PLCD3,PLEKHH3,PLEKHM1,PLXDC1,PNMT,PNPO,PPP1R1B,PPP1R9B,PPY,PRAC,PRR15L,PSMB3,PSMC3IP,PSMD3,PSME3,PTGES3L,PTGES3L-AARSD1,PTRF,PYY,RAB5C,RAD51D,RAD51L3-RFFL,RAMP2,RAMP2-AS1,RAPGEFL1,RARA,RASL10B,RDM1,RFFL,RND2,RPL19,RPL23,RPL27,RPRML,RSAD1,RUNDC1,RUNDC3A,SAMD14,SCRN2,SGCA,SKAP1,SLC25A39,SLC35B1,SLC35G3,SLC4A1,SLFN11,SLFN12,SLFN12L,SLFN13,SLFN14,SLFN5,SMARCE1,SNF8,SNORA21,SNORD124,SNORD7,SNX11,SOCS7,SOST,SP2,SP6,SPAG9,SPATA20,SPATA32,SPOP,SPPL2C,SRCIN1,STAC2,STARD3,STAT3,STAT5A,STAT5B,STH,SYNRG,TAC4,TADA2A,TAF15,TBC1D3,TBC1D3B,TBC1D3C,TBC1D3F,TBC1D3G,TBC1D3H,TBKBP1,TBX21,TCAP,THRA,TMEM101,TMEM106A,TMEM132E,TMEM92,TMEM99,TMUB2,TNS4,TOB1,TOB1-AS1,TOP2A,TTC25,TTLL6,TUBG1,TUBG2,UBE2Z,UBTF,UNC45B,UTP18,VAT1,VPS25,WFIKKN2,WIPF2,WNK4,WNT3,WNT9B,XYLT2,ZNF385C,ZNF652,ZNF830,ZNHIT3,ZPBP2"}
{"Sample_ID":"PT116","chr":"chr17","posStart":49415060,"posEnd":54577027,"length":5161968,"numProbe":1093,"log2ratio.Mean.adj":0.2442,"log2ratio.SD":0.17313,"log2ratio.Median.adj":0.2333,"log2ratio.MAD":0.15612,"log2mBAF.Mean":0.15245,"log2mBAF.SD":0.14181,"log2mBAF.Median":0.17704,"log2mBAF.MAD":0.12882,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":11,"gene":"ANKFN1,C17orf112,CA10,COX11,HLF,KIF2B,MMD,PCTP,STXBP4,TMEM100,TOM1L1"}
{"Sample_ID":"PT116","chr":"chr17","posStart":54578920,"posEnd":67522975,"length":12944056,"numProbe":1968,"log2ratio.Mean.adj":0.15339,"log2ratio.SD":0.18981,"log2ratio.Median.adj":0.14845,"log2ratio.MAD":0.16983,"log2mBAF.Mean":0.13804,"log2mBAF.SD":0.15291,"log2mBAF.Median":0.16364,"log2mBAF.MAD":0.13715,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":157,"gene":"ABCA10,ABCA5,ABCA6,ABCA8,ABCA9,ACE,AKAP1,AMZ2,AMZ2P1,APOH,APPBP2,ARSG,AXIN2,BCAS3,BPTF,BRIP1,BZRAP1,BZRAP1-AS1,C17orf47,C17orf58,C17orf64,C17orf67,C17orf72,C17orf82,CA4,CACNG1,CACNG4,CACNG5,CCDC47,CD79B,CEP112,CEP95,CLTC,COIL,CSH1,CSH2,CSHL1,CUEDC1,CYB561,DCAF7,DDX42,DDX5,DGKE,DHX40,DYNLL2,EFCAB3,EPX,ERN1,FAM20A,FTSJ3,GDPD1,GH1,GH2,GNA13,HEATR6,HELZ,HSF5,ICAM2,INTS2,KCNH6,KPNA2,LIMD2,LINC00674,LOC146880,LOC440461,LOC645638,LOC653653,LOC729683,LPO,LRRC37A3,MAP2K6,MAP3K3,MARCH10,MED13,METTL2A,MILR1,MIR142,MIR21,MIR301A,MIR3064,MIR3614,MIR4315-1,MIR4315-2,MIR4524A,MIR4524B,MIR454,MIR4729,MIR4736,MIR4737,MIR5047,MIR548W,MIR634,MIR635,MKS1,MPO,MRC2,MRPS23,MSI2,MSX2P1,MTMR4,MTVR2,NACA2,NOG,NOL11,OR4D1,OR4D2,PECAM1,PITPNC1,PLEKHM1P,POLG2,PPM1D,PPM1E,PRKAR1A,PRKCA,PRR11,PSMC5,PSMD12,PTRH2,RAD51C,RGS9,RNF126P1,RNF43,RNFT1,RPS6KB1,SCARNA20,SCN4A,SCPEP1,SEPT4,SKA2,SLC16A6,SMARCD2,SMG8,SMURF2,SNORA38B,SNORA76,SNORD104,SRSF1,STRADA,SUPT4H1,TACO1,TANC2,TBC1D3P1-DHX40P1,TBC1D3P2,TBX2,TBX4,TCAM1P,TEX14,TEX2,TLK2,TRIM25,TRIM37,TUBD1,USP32,VEZF1,VMP1,WIPI1,YPEL2"}
{"Sample_ID":"PT116","chr":"chr17","posStart":67523260,"posEnd":70317514,"length":2794255,"numProbe":685,"log2ratio.Mean.adj":0.25279,"log2ratio.SD":0.18281,"log2ratio.Median.adj":0.248,"log2ratio.MAD":0.16316,"log2mBAF.Mean":0.13432,"log2mBAF.SD":0.1422,"log2mBAF.Median":0.15047,"log2mBAF.MAD":0.135,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":5,"gene":"KCNJ16,KCNJ2,KCNJ2-AS1,MAP2K6,SOX9"}
{"Sample_ID":"PT116","chr":"chr17","posStart":70317988,"posEnd":81041077,"length":10723090,"numProbe":2499,"log2ratio.Mean.adj":0.11302,"log2ratio.SD":0.19925,"log2ratio.Median.adj":0.108,"log2ratio.MAD":0.18028,"log2mBAF.Mean":0.15328,"log2mBAF.SD":0.13491,"log2mBAF.Median":0.17831,"log2mBAF.MAD":0.11588,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":235,"gene":"AANAT,AATK,AATK-AS1,ACOX1,ACTG1,AFMID,ALYREF,ANAPC11,ARHGDIA,ARL16,ARMC7,ASPSCR1,ATP5H,AZI1,B3GNTL1,BAHCC1,BAIAP2,BAIAP2-AS1,BIRC5,BTBD17,C17orf62,C17orf70,C17orf77,C17orf80,C17orf89,C17orf99,C1QTNF1,CANT1,CARD14,CASKIN2,CBX2,CBX4,CBX8,CCDC137,CCDC40,CCDC57,CD300A,CD300C,CD300E,CD300LB,CD300LD,CD300LF,CD7,CDC42EP4,CDK3,CDR2L,CHMP6,COG1,CPSF4L,CSNK1D,CYGB,CYTH1,DCXR,DNAH17,DNAI2,DUS1L,EIF4A3,ENDOV,ENGASE,ENPP7,ENTHD2,EVPL,EXOC7,FADS6,FAM104A,FAM195B,FASN,FBF1,FDXR,FLJ45079,FN3K,FN3KRP,FOXJ1,FOXK2,FSCN2,GAA,GALK1,GALR2,GCGR,GGA3,GPR142,GPRC5C,GPS1,GRB2,GRIN2C,H3F3B,HEXDC,HGS,HID1,HN1,ICT1,ITGB4,JMJD6,KCTD2,KIAA0195,KIF19,LGALS3BP,LINC00338,LINC00469,LINC00482,LINC00511,LINC00673,LLGL2,LOC100130370,LOC100131096,LOC100287042,LOC100294362,LOC100507351,LOC100507410,LOC100653515,LOC100996291,LOC100996295,LOC400620,LRRC45,MAFG,MAFG-AS1,METRNL,METTL23,MFSD11,MGAT5B,MGC16275,MIF4GD,MIR1250,MIR3065,MIR3186,MIR338,MIR3615,MIR3678,MIR4316,MIR4730,MIR4738,MIR4739,MIR4740,MIR636,MIR657,MRPL12,MRPL38,MRPS7,MXRA7,MYADML2,MYO15B,NARF,NAT9,NOTUM,NPB,NPLOC4,NPTX1,NT5C,NUP85,OGFOD3,OTOP2,OTOP3,OXLD1,P4HB,PCYT2,PDE6G,PGS1,PPP1R27,PRCD,PRPSAP1,PYCR1,QRICH2,RAB37,RAB40B,RAC3,RBFOX3,RECQL5,RFNG,RHBDF2,RNF157,RNF157-AS1,RNF213,RPL38,RPTOR,SAP30BP,SCARNA16,SDK2,SEC14L1,SECTM1,SEPT9,SGSH,SIRT7,SLC16A3,SLC16A5,SLC25A10,SLC25A19,SLC26A11,SLC38A10,SLC39A11,SLC9A3R1,SMIM5,SMIM6,SNHG16,SNORD1A,SNORD1B,SNORD1C,SOCS3,SPHK1,SRP68,SRSF2,SSTR2,ST6GALNAC1,ST6GALNAC2,STRA13,SUMO2,SYNGR2,TBC1D16,TBCD,TEN1,TEN1-CDK3,TEX19,TIMP2,TK1,TMC6,TMC8,TMEM104,TMEM105,TMEM235,TNRC6C,TRIM47,TRIM65,TSEN54,TSPAN10,TTYH2,UBALD2,UBE2O,UNC13D,UNK,USH1G,USP36,UTS2R,WBP2,WDR45B,ZACN,ZNF750"}
{"Sample_ID":"PT116","chr":"chr19","posStart":267039,"posEnd":59087479,"length":58820441,"numProbe":9527,"log2ratio.Mean.adj":-0.24743,"log2ratio.SD":0.21958,"log2ratio.Median.adj":-0.22915,"log2ratio.MAD":0.18925,"log2mBAF.Mean":0.28089,"log2mBAF.SD":0.16761,"log2mBAF.Median":0.30956,"log2mBAF.MAD":0.13383,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":1631,"gene":"A1BG,A1BG-AS1,ABCA7,ABHD17A,ABHD8,ACER1,ACP5,ACPT,ACSBG2,ACTL9,ACTN4,ADAMTS10,ADAMTSL5,ADAT3,ADCK4,ADM5,AES,AKAP8,AKAP8L,AKT1S1,AKT2,ALDH16A1,ALKBH6,ALKBH7,AMH,ANGPTL4,ANGPTL6,ANKLE1,ANKRD24,ANKRD27,ANO8,AP1M1,AP1M2,AP2A1,AP2S1,AP3D1,APBA3,APC2,APLP1,APOC1,APOC1P1,APOC2,APOC4,APOC4-APOC2,APOE,ARHGAP33,ARHGAP35,ARHGEF1,ARHGEF18,ARID3A,ARMC6,ARRDC2,ARRDC5,ASF1B,ASNA1,ASPDH,ATCAY,ATF5,ATG4D,ATP13A1,ATP1A3,ATP4A,ATP5D,ATP5SL,ATP8B3,AURKC,AXL,AZU1,B3GNT3,B3GNT8,B9D2,BABAM1,BAX,BBC3,BCAM,BCAT2,BCKDHA,BCL2L12,BCL3,BEST2,BIRC8,BLOC1S3,BLVRB,BRD4,BRSK1,BSG,BSPH1,BST2,BTBD2,C19orf10,C19orf12,C19orf18,C19orf21,C19orf24,C19orf25,C19orf26,C19orf33,C19orf35,C19orf38,C19orf40,C19orf43,C19orf44,C19orf45,C19orf47,C19orf48,C19orf52,C19orf53,C19orf54,C19orf55,C19orf57,C19orf59,C19orf60,C19orf66,C19orf67,C19orf69,C19orf70,C19orf71,C19orf73,C19orf77,C19orf80,C19orf81,C2CD4C,C3,C3P1,C5AR1,C5AR2,CA11,CABP5,CACNA1A,CACNG6,CACNG7,CACNG8,CACTIN,CACTIN-AS1,CADM4,CALM3,CALR,CALR3,CAMSAP3,CAPN12,CAPNS1,CAPS,CARD8,CARM1,CASP14,CATSPERD,CATSPERG,CBLC,CC2D1A,CCDC105,CCDC106,CCDC114,CCDC124,CCDC130,CCDC151,CCDC155,CCDC159,CCDC61,CCDC8,CCDC9,CCDC94,CCDC97,CCL25,CCNE1,CD177,CD209,CD22,CD320,CD33,CD37,CD3EAP,CD70,CD79A,CD97,CDC34,CDC37,CDC42EP5,CDKN2D,CEACAM1,CEACAM16,CEACAM18,CEACAM19,CEACAM20,CEACAM21,CEACAM22P,CEACAM3,CEACAM4,CEACAM5,CEACAM6,CEACAM7,CEACAM8,CEBPA,CEBPA-AS1,CEBPG,CELF5,CEP89,CERS1,CERS4,CFD,CGB,CGB1,CGB2,CGB5,CGB7,CGB8,CHAF1A,CHERP,CHMP2A,CHST8,CIB3,CIC,CILP2,CIRBP,CIRBP-AS1,CKM,CLASRP,CLC,CLDND2,CLEC11A,CLEC17A,CLEC4G,CLEC4GP1,CLEC4M,CLIP3,CLPP,CLPTM1,CNFN,CNN1,CNN2,CNOT3,CNTD2,COL5A3,COLGALT1,COMP,COPE,COX6B1,COX6B2,COX7A1,CPAMD8,CPT1C,CRB3,CREB3L3,CRLF1,CRTC1,CRX,CSNK1G2,CSNK1G2-AS1,CTU1,CTXN1,CXCL17,CYP2A13,CYP2A6,CYP2A7,CYP2B6,CYP2B7P1,CYP2F1,CYP2G1P,CYP2S1,CYP4F11,CYP4F12,CYP4F2,CYP4F22,CYP4F24P,CYP4F3,CYP4F8,CYTH2,DACT3,DACT3-AS1,DAND5,DAPK3,DAZAP1,DBP,DCAF15,DDA1,DDX39A,DDX49,DEDD2,DENND1C,DHDH,DHPS,DHX34,DIRAS1,DKFZp434J0226,DKFZp566F0947,DKKL1,DLL3,DMKN,DMPK,DMRTC2,DMWD,DNAAF3,DNAJB1,DNASE2,DNM2,DNMT1,DOCK6,DOHH,DOT1L,DPF1,DPP9,DPRX,DPY19L3,DUS3L,DUXA,DYRK1B,EBI3,ECH1,ECSIT,EEF2,EFNA2,EGLN2,EHD2,EID2,EID2B,EIF3G,EIF3K,ELANE,ELAVL1,ELAVL3,ELL,ELOF1,ELSPBP1,EMC10,EML2,EMP3,EMR1,EMR2,EMR3,EMR4P,EPHX3,EPN1,EPOR,EPS15L1,EPS8L1,ERCC1,ERCC2,ERF,ERVV-1,ERVV-2,ETFB,ETHE1,ETV2,EVI5L,EXOC3L2,EXOSC5,F2RL3,FAM129C,FAM187B,FAM32A,FAM71E1,FAM71E2,FAM83E,FAM90A27P,FAM98C,FARSA,FBL,FBN3,FBXL12,FBXO17,FBXO27,FBXO46,FBXW9,FCAR,FCER2,FCGBP,FCGRT,FCHO1,FDX1L,FEM1A,FFAR1,FFAR2,FFAR3,FGF21,FGF22,FIZ1,FKBP1AP1,FKBP8,FKRP,FLJ22184,FLJ25328,FLJ25758,FLJ26850,FLJ30403,FLT3LG,FOSB,FOXA3,FPR1,FPR2,FPR3,FSD1,FSTL3,FTL,FUT1,FUT2,FUT3,FUT5,FUT6,FUZ,FXYD1,FXYD3,FXYD5,FXYD7,FZR1,GADD45B,GADD45GIP1,GALP,GAMT,GAPDHS,GATAD2A,GCDH,GDF1,GDF15,GEMIN7,GGN,GIPC1,GIPC3,GIPR,GLTSCR1,GLTSCR2,GMFG,GMIP,GNA11,GNA15,GNG7,GNG8,GP6,GPATCH1,GPI,GPR108,GPR32,GPR4,GPX4,GRAMD1A,GRIK5,GRIN2D,GRIN3B,GRWD1,GSK3A,GTF2F1,GTPBP3,GYS1,GZMM,HAMP,HAPLN4,HAS1,HAUS5,HAUS8,HAVCR1P1,HCN2,HCST,HDGFRP2,HIF3A,HIPK4,HKR1,HMG20B,HMHA1,HNRNPL,HNRNPM,HNRNPUL1,HOMER3,HOOK2,HPN,HRC,HSD11B1L,HSD17B14,HSH2D,HSPB6,HSPBP1,ICAM1,ICAM3,ICAM4,ICAM5,IER2,IFI30,IFNL1,IFNL2,IFNL3,IFNL4,IGFL1,IGFL2,IGFL3,IGFL4,IGFLR1,IGLON5,IGSF23,IL11,IL12RB1,IL27RA,IL4I1,ILF3,ILF3-AS1,ILVBL,INSL3,INSR,IRF2BP1,IRF3,IRGC,IRGQ,ISOC2,ISYNA1,ITPKC,IZUMO1,IZUMO2,IZUMO4,JAK3,JOSD2,JSRP1,JUNB,JUND,KANK2,KANK3,KCNA7,KCNC3,KCNJ14,KCNK6,KCNN1,KCNN4,KCTD15,KDELR1,KDM4B,KEAP1,KHSRP,KIAA0355,KIAA1683,KIR2DL1,KIR2DL3,KIR2DL4,KIR2DS4,KIR3DL1,KIR3DL2,KIR3DL3,KIR3DX1,KIRREL2,KISS1R,KLC3,KLF1,KLF16,KLF2,KLHL26,KLK1,KLK10,KLK11,KLK12,KLK13,KLK14,KLK15,KLK2,KLK3,KLK4,KLK5,KLK6,KLK7,KLK8,KLK9,KLKP1,KPTN,KRI1,KRTDAP,KXD1,LAIR1,LAIR2,LDLR,LENG1,LENG8,LENG9,LEUTX,LGALS13,LGALS14,LGALS16,LGALS17A,LGALS4,LGALS7,LGALS7B,LGI4,LHB,LIG1,LILRA1,LILRA2,LILRA3,LILRA4,LILRA5,LILRA6,LILRB1,LILRB2,LILRB3,LILRB4,LILRB5,LILRP2,LIM2,LIN37,LIN7B,LINC00085,LINC00661,LINC00662,LINC00663,LINC00665,LINGO3,LIPE,LMNB2,LMTK3,LOC100128252,LOC100128398,LOC100128568,LOC100128573,LOC100128675,LOC100128682,LOC100129083,LOC100129935,LOC100131094,LOC100131691,LOC100134317,LOC100287177,LOC100287534,LOC100288123,LOC100289650,LOC100379224,LOC100505495,LOC100505622,LOC100505715,LOC100505812,LOC100505835,LOC100506469,LOC100507003,LOC100507373,LOC100507433,LOC100631378,LOC100652909,LOC100996307,LOC101059948,LOC113230,LOC147646,LOC148145,LOC284344,LOC284379,LOC284385,LOC284395,LOC284412,LOC284454,LOC388499,LOC388553,LOC400680,LOC400684,LOC400685,LOC440518,LOC641367,LOC643669,LOC644189,LOC644554,LOC646862,LOC728752,LOC729966,LONP1,LPAR2,LPHN1,LPPR2,LPPR3,LRFN1,LRFN3,LRG1,LRP3,LRRC25,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{"Sample_ID":"PT116","chr":"chr20","posStart":24078128,"posEnd":59871603,"length":35793476,"numProbe":6982,"log2ratio.Mean.adj":0.26407,"log2ratio.SD":0.20264,"log2ratio.Median.adj":0.2561,"log2ratio.MAD":0.19748,"log2mBAF.Mean":0.00757,"log2mBAF.SD":0.10611,"log2mBAF.Median":0.01465,"log2mBAF.MAD":0.10476,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":365,"gene":"AAR2,ABHD12,ACOT8,ACSS1,ACSS2,ACTL10,ACTR5,ADA,ADIG,ADNP,AHCY,APCDD1L,APCDD1L-AS1,APMAP,ARFGEF2,ARHGAP40,ASIP,ASXL1,ATP5E,ATP9A,AURKA,B4GALT5,BCAS1,BCAS4,BCL2L1,BLCAP,BMP7,BPI,BPIFA1,BPIFA2,BPIFA3,BPIFA4P,BPIFB1,BPIFB2,BPIFB3,BPIFB4,BPIFB6,C20orf111,C20orf112,C20orf144,C20orf173,C20orf197,C20orf203,C20orf24,C20orf85,CASS4,CBFA2T2,CBLN4,CCM2L,CD40,CDH22,CDH26,CDH4,CDK5RAP1,CEBPB,CEP250,CHD6,CHMP4B,CNBD2,COMMD7,COX4I2,CPNE1,CSE1L,CST7,CSTF1,CTCFL,CTNNBL1,CTSA,CTSZ,CYP24A1,DBNDD2,DDX27,DEFB115,DEFB116,DEFB118,DEFB119,DEFB121,DEFB122,DEFB123,DEFB124,DHX35,DLGAP4,DNMT3B,DNTTIP1,DOK5,DPM1,DSN1,DUSP15,DYNLRB1,E2F1,EDEM2,EDN3,EIF2S2,EIF6,ELMO2,EMILIN3,ENTPD6,EPB41L1,EPPIN,EPPIN-WFDC6,ERGIC3,EYA2,FAM182A,FAM182B,FAM209A,FAM209B,FAM210B,FAM217B,FAM65C,FAM83C,FAM83D,FITM2,FLJ33581,FOXS1,FRG1B,GCNT7,GDAP1L1,GDF5,GGT7,GHRH,GINS1,GNAS,GNAS-AS1,GSS,GTSF1L,HCK,HM13,HM13-AS1,HMGB3P1,HNF4A,ID1,IFT52,ITCH,JPH2,KCNB1,KCNG1,KCNK15,KCNS1,KIAA1755,KIF3B,L3MBTL1,LBP,LINC00028,LINC00489,LINC00494,LINC00651,LINC00657,LOC100131496,LOC100134868,LOC100287792,LOC100505783,LOC100506384,LOC149950,LOC284751,LOC284757,LOC284798,LOC284801,LOC339568,LOC388796,LOC79015,LPIN3,MAFB,MANBAL,MAP1LC3A,MAPRE1,MATN4,MC3R,MIR296,MIR298,MIR3193,MIR3194,MIR3616,MIR3646,MIR4325,MIR4532,MIR4533,MIR4755,MIR4756,MIR499A,MIR499B,MIR5095,MIR644A,MIR645,MIR663A,MKRN7P,MLLT10P1,MMP24,MMP9,MOCS3,MROH8,MTRNR2L3,MYBL2,MYH7B,MYL9,MYLK2,NANP,NCOA3,NCOA5,NCOA6,NCOR1P1,NDRG3,NECAB3,NELFCD,NEURL2,NFATC2,NFS1,NINL,NNAT,NPEPL1,OCSTAMP,PABPC1L,PARD6B,PCIF1,PCK1,PDRG1,PFDN4,PHACTR3,PHF20,PI3,PIGT,PIGU,PKIG,PLAGL2,PLCG1,PLTP,PMEPA1,POFUT1,PPP1R16B,PPP1R3D,PPP4R1L,PREX1,PROCR,PSIMCT-1,PTGIS,PTPN1,PTPRT,PXMP4,PYGB,R3HDML,RAB22A,RAE1,RALGAPB,RALY,RBL1,RBM12,RBM38,RBM39,RBPJL,REM1,RIMS4,RNF114,ROMO1,RPN2,RPRD1B,RTFDC1,SALL4,SAMHD1,SCAND1,SDC4,SEMG1,SEMG2,SERINC3,SGK2,SLA2,SLC12A5,SLC13A3,SLC2A10,SLC32A1,SLC35C2,SLC9A8,SLMO2,SLMO2-ATP5E,SLPI,SNAI1,SNHG11,SNORA39,SNORA60,SNORA71A,SNORA71B,SNORA71C,SNORA71D,SNORD12,SNORD12B,SNORD12C,SNTA1,SNX21,SOGA1,SPAG4,SPATA2,SPATA25,SPINT3,SPINT4,SPO11,SRC,SRSF6,STAU1,STK4,STK4-AS1,STX16,STX16-NPEPL1,SULF2,SUMO1P1,SUN5,SYCP2,SYNDIG1,SYS1,SYS1-DBNDD2,TFAP2C,TGIF2,TGIF2-C20orf24,TGM2,TLDC2,TM9SF4,TMEM189,TMEM189-UBE2V1,TNNC2,TOMM34,TOP1,TOX2,TP53INP2,TP53RK,TP53TG5,TPX2,TRPC4AP,TSHZ2,TSPY26P,TTI1,TTLL9,TTPAL,TUBB1,UBE2C,UBE2V1,UQCC,VAPB,VSTM2L,VSX1,WFDC10A,WFDC10B,WFDC11,WFDC12,WFDC13,WFDC2,WFDC3,WFDC5,WFDC6,WFDC8,WFDC9,WISP2,XKR7,YWHAB,ZBP1,ZFAS1,ZFP64,ZHX3,ZMYND8,ZNF217,ZNF334,ZNF335,ZNF337,ZNF341,ZNF663,ZNF831,ZNFX1,ZSWIM1,ZSWIM3"}
{"Sample_ID":"PT116","chr":"chr20","posStart":59871744,"posEnd":62912463,"length":3040720,"numProbe":672,"log2ratio.Mean.adj":0.16152,"log2ratio.SD":0.20957,"log2ratio.Median.adj":0.1629,"log2ratio.MAD":0.20178,"log2mBAF.Mean":0.01028,"log2mBAF.SD":0.08966,"log2mBAF.Median":0.0145,"log2mBAF.MAD":0.08487,"log2ratio.p.value":0,"log2mBAF.p.value":0.013,"p.value":0,"CNV":"gain","numGene":88,"gene":"ABHD16B,ADRM1,ARFGAP1,ARFRP1,BHLHE23,BIRC7,C20orf166,C20orf166-AS1,C20orf195,C20orf201,CABLES2,CDH4,CHRNA4,COL20A1,COL9A3,DIDO1,DNAJC5,DPH3P1,EEF1A2,FLJ16779,GATA5,GID8,GMEB2,GTPBP5,HAR1A,HAR1B,HELZ2,HRH3,KCNQ2,LAMA5,LIME1,LINC00029,LINC00176,LINC00659,LOC100127888,LOC100144597,LOC63930,LSM14B,MIR1-1,MIR124-3,MIR1257,MIR133A2,MIR1914,MIR3196,MIR4326,MIR4758,MIR647,MIR941-1,MIR941-2,MIR941-3,MIR941-4,MRGBP,MYT1,NKAIN4,NPBWR2,NTSR1,OGFR,OPRL1,OSBPL2,PCMTD2,PPDPF,PRPF6,PSMA7,PTK6,RBBP8NL,RGS19,RPS21,RTEL1,RTEL1-TNFRSF6B,SAMD10,SLC17A9,SLC2A4RG,SLCO4A1,SOX18,SRMS,SS18L1,STMN3,TAF4,TCEA2,TCFL5,TNFRSF6B,TPD52L2,UCKL1,UCKL1-AS1,YTHDF1,ZBTB46,ZGPAT,ZNF512B"}
{"Sample_ID":"PT116","chr":"chr21","posStart":14640400,"posEnd":43318856,"length":28678457,"numProbe":7111,"log2ratio.Mean.adj":0.02624,"log2ratio.SD":0.19781,"log2ratio.Median.adj":0.0251,"log2ratio.MAD":0.17287,"log2mBAF.Mean":0.4606,"log2mBAF.SD":0.14209,"log2mBAF.Median":0.48338,"log2mBAF.MAD":0.11084,"log2ratio.p.value":0.017,"log2mBAF.p.value":0,"p.value":0,"CNV":"gain","numGene":201,"gene":"ABCC13,ADAMTS1,ADAMTS5,ANKRD20A11P,APP,ATP5J,ATP5O,B3GALT5,BACE2,BACH1,BRWD1,BRWD1-AS1,BRWD1-IT2,BTG3,C21orf119,C21orf15,C21orf37,C21orf49,C21orf54,C21orf59,C21orf62,C21orf88,C21orf91,C21orf91-OT1,C2CD2,CBR1,CBR3,CBR3-AS1,CCT8,CHAF1B,CHODL,CHODL-AS1,CLDN14,CLDN17,CLDN8,CLIC6,CRYZL1,CXADR,CYYR1,D21S2088E,DNAJC28,DONSON,DOPEY2,DSCAM,DSCAM-AS1,DSCAM-IT1,DSCR10,DSCR3,DSCR4,DSCR6,DSCR8,DSCR9,DYRK1A,ERG,ETS2,EVA1C,FAM3B,GABPA,GART,GRIK1,GRIK1-AS1,GRIK1-AS2,HLCS,HMGN1,HSPA13,HUNK,IFNAR1,IFNAR2,IFNGR2,IGSF5,IL10RB,ITSN1,JAM2,KCNE1,KCNE2,KCNJ15,KCNJ6,KRTAP11-1,KRTAP13-1,KRTAP13-2,KRTAP13-3,KRTAP13-4,KRTAP15-1,KRTAP19-1,KRTAP19-2,KRTAP19-3,KRTAP19-4,KRTAP19-5,KRTAP19-6,KRTAP19-7,KRTAP19-8,KRTAP20-1,KRTAP20-2,KRTAP20-3,KRTAP20-4,KRTAP21-1,KRTAP21-2,KRTAP21-3,KRTAP22-1,KRTAP22-2,KRTAP23-1,KRTAP24-1,KRTAP25-1,KRTAP26-1,KRTAP27-1,KRTAP6-1,KRTAP6-2,KRTAP6-3,KRTAP7-1,KRTAP8-1,LCA5L,LINC00111,LINC00112,LINC00113,LINC00114,LINC00158,LINC00159,LINC00160,LINC00161,LINC00189,LINC00307,LINC00308,LINC00310,LINC00314,LINC00317,LINC00320,LINC00323,LINC00478,LINC00479,LINC00515,LINC00649,LIPI,LOC100133286,LOC100288432,LOC100506385,LOC100506403,LOC339622,LOC388813,LTN1,MAP3K7CL,MIR125B2,MIR155,MIR155HG,MIR3156-3,MIR3197,MIR4327,MIR4759,MIR4760,MIR5009,MIR802,MIR99A,MIRLET7C,MIS18A,MORC3,MRAP,MRPL39,MRPS6,MX1,MX2,N6AMT1,NCAM2,NRIP1,OLIG1,OLIG2,PAXBP1,PAXBP1-AS1,PCP4,PIGP,PLAC4,POTED,PRDM15,PSMG1,RBM11,RCAN1,RIPK4,RNU6-67,RUNX1,RUNX1-IT1,RWDD2B,SAMSN1,SAMSN1-AS1,SCAF4,SETD4,SH3BGR,SIM2,SLC5A3,SMIM11,SNORA80,SOD1,SON,SYNJ1,TCP10L,TIAM1,TMEM50B,TMPRSS15,TMPRSS2,TTC3,URB1,USP16,USP25,WRB"}
{"Sample_ID":"PT116","chr":"chr21","posStart":43319043,"posEnd":48084989,"length":4765947,"numProbe":1281,"log2ratio.Mean.adj":-0.05544,"log2ratio.SD":0.21129,"log2ratio.Median.adj":-0.0619,"log2ratio.MAD":0.18636,"log2mBAF.Mean":0.44449,"log2mBAF.SD":0.14189,"log2mBAF.Median":0.46888,"log2mBAF.MAD":0.1056,"log2ratio.p.value":0.006,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":92,"gene":"ABCG1,ADARB1,AGPAT3,AIRE,C21orf128,C21orf2,C21orf33,C21orf58,C21orf67,C21orf90,C2CD2,CBS,COL18A1,COL18A1-AS1,COL18A1-AS2,COL6A1,COL6A2,CRYAA,CSTB,DIP2A,DIP2A-IT1,DNMT3L,FAM207A,FTCD,HSF2BP,ICOSLG,ITGB2,ITGB2-AS1,KRTAP10-1,KRTAP10-10,KRTAP10-11,KRTAP10-12,KRTAP10-2,KRTAP10-3,KRTAP10-4,KRTAP10-5,KRTAP10-6,KRTAP10-7,KRTAP10-8,KRTAP10-9,KRTAP12-1,KRTAP12-2,KRTAP12-3,KRTAP12-4,LINC00162,LINC00163,LINC00313,LINC00319,LOC100129027,LOC284837,LOC642852,LRRC3,LRRC3-AS1,LSS,MCM3AP,MCM3AP-AS1,NDUFV3,PCBP3,PCNT,PDE9A,PDXK,PFKL,PKNOX1,POFUT2,PRMT2,PTTG1IP,PWP2,RRP1,RRP1B,RSPH1,S100B,SIK1,SLC19A1,SLC37A1,SPATC1L,SSR4P1,SUMO3,TFF1,TFF2,TFF3,TMPRSS3,TRAPPC10,TRPM2,TSPEAR,U2AF1,UBASH3A,UBE2G2,UMODL1,WDR4,YBEY,ZBTB21,ZNF295-AS1"}
{"Sample_ID":"PT116","chr":"chr22","posStart":16918335,"posEnd":19690250,"length":2771916,"numProbe":582,"log2ratio.Mean.adj":-0.52421,"log2ratio.SD":0.22855,"log2ratio.Median.adj":-0.4924,"log2ratio.MAD":0.20267,"log2mBAF.Mean":0.0597,"log2mBAF.SD":0.1138,"log2mBAF.Median":0.06543,"log2mBAF.MAD":0.10341,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":45,"gene":"ANKRD62P1-PARP4P3,ATP6V1E1,BCL2L13,BID,C22orf39,CCT8L2,CDC45,CECR1,CECR2,CECR3,CECR5,CECR5-AS1,CECR6,CECR7,CLDN5,CLTCL1,DGCR10,DGCR11,DGCR14,DGCR2,DGCR5,DGCR6,DGCR9,FLJ41941,GAB4,GGT3P,GSC2,HIRA,HSFY1P1,IL17RA,LOC150185,MICAL3,MIR3198-1,MIR648,MRPL40,PEX26,PRODH,SLC25A1,SLC25A18,TPTEP1,TSSK2,TUBA8,UFD1L,USP18,XKR3"}
{"Sample_ID":"PT116","chr":"chr22","posStart":19691502,"posEnd":20784550,"length":1093049,"numProbe":181,"log2ratio.Mean.adj":-0.73527,"log2ratio.SD":0.24755,"log2ratio.Median.adj":-0.74565,"log2ratio.MAD":0.29244,"log2mBAF.Mean":0.06813,"log2mBAF.SD":0.11484,"log2mBAF.Median":0.07995,"log2mBAF.MAD":0.1098,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":30,"gene":"ARVCF,C22orf29,COMT,DGCR6L,DGCR8,GNB1L,GP1BB,LOC150197,LOC284865,LOC388849,LOC729444,MIR1286,MIR1306,MIR185,MIR3618,MIR4761,PI4KAP1,RANBP1,RIMBP3,RTN4R,SCARF2,SEPT5,SEPT5-GP1BB,TANGO2,TBX1,TMEM191B,TRMT2A,TXNRD2,ZDHHC8,ZNF74"}
{"Sample_ID":"PT116","chr":"chr22","posStart":20789074,"posEnd":38719189,"length":17930116,"numProbe":4415,"log2ratio.Mean.adj":-0.5311,"log2ratio.SD":0.2149,"log2ratio.Median.adj":-0.5098,"log2ratio.MAD":0.20682,"log2mBAF.Mean":0.05757,"log2mBAF.SD":0.11316,"log2mBAF.Median":0.05639,"log2mBAF.MAD":0.10723,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":268,"gene":"ADORA2A,ADORA2A-AS1,ADRBK2,AIFM3,ANKRD54,AP1B1,AP1B1P1,APOL1,APOL2,APOL3,APOL4,APOL5,APOL6,ASCC2,ASPHD2,BAIAP2L2,BCR,BCRP2,BCRP3,BPIFC,C1QTNF6,C22orf15,C22orf23,C22orf24,C22orf28,C22orf31,C22orf42,C22orf43,CABIN1,CABP7,CACNG2,CARD10,CCDC116,CCDC117,CCDC157,CDC42EP1,CES5AP1,CHCHD10,CHEK2,CRKL,CRYBA4,CRYBB1,CRYBB2,CRYBB2P1,CRYBB3,CSF2RB,CSNK1E,CYTH4,DDT,DDTL,DEPDC5,DERL3,DRG1,DUSP18,EIF3D,EIF3L,EIF4ENIF1,ELFN2,EMID1,EWSR1,FAM211B,FBXO7,FBXW4P1,FOXRED2,GAL3ST1,GALR3,GAS2L1,GATSL3,GCAT,GGA1,GGT1,GGT5,GGTLC2,GNAZ,GSTT1,GSTT2,GSTT2B,GSTTP1,GSTTP2,GUCD1,GUSBP11,H1F0,HIC2,HMGXB4,HMOX1,HORMAD2,HPS4,HSCB,IFT27,IGLL1,IGLL3P,IGLL5,IL2RB,INPP5J,ISX,KCTD17,KIAA1656,KIAA1671,KLHL22,KREMEN1,LARGE,LGALS1,LGALS2,LIF,LIMK2,LOC100128531,LOC100506195,LOC100506241,LOC284889,LOC339666,LOC391322,LOC400891,LOC648691,LOC96610,LRP5L,LZTR1,MAFF,MAPK1,MB,MCM5,MED15,MFNG,MIAT,MICALL1,MIF,MIR130B,MIR301B,MIR3199-1,MIR3199-2,MIR3200,MIR3653,MIR3909,MIR3928,MIR4534,MIR4764,MIR548J,MIR650,MIR658,MIR659,MMP11,MN1,MORC2,MORC2-AS1,MPST,MTFP1,MTMR3,MYH9,MYO18B,NCF4,NEFH,NF2,NIPSNAP1,NOL12,OSBP2,OSM,P2RX6,P2RX6P,PATZ1,PDXP,PES1,PI4KA,PI4KAP2,PICK1,PIK3IP1,PISD,PITPNB,PIWIL3,PLA2G3,PLA2G6,POLR2F,POM121L10P,POM121L1P,POM121L4P,POM121L8P,POM121L9P,PPIL2,PPM1F,PRAME,PRR14L,PVALB,RAB36,RAC2,RASD2,RASL10A,RBFOX2,RFPL1,RFPL1S,RFPL2,RFPL3,RFPL3S,RGL4,RHBDD3,RIMBP3B,RIMBP3C,RNF185,RNF215,RTDR1,SCARF2,SDC4P,SDF2L1,SEC14L2,SEC14L3,SEC14L4,SEC14L6,SELM,SERPIND1,SEZ6L,SF3A1,SFI1,SGSM1,SH3BP1,SLC16A8,SLC2A11,SLC35E4,SLC5A1,SLC5A4,SLC7A4,SMARCB1,SMTN,SNAP29,SNORD125,SNRPD3,SOX10,SPECC1L,SRRD,SSTR3,SUSD2,SYN3,TBC1D10A,TCN2,TEX33,TFIP11,THAP7,THAP7-AS1,THOC5,TIMP3,TMEM184B,TMEM191A,TMEM191C,TMEM211,TMPRSS6,TOM1,TOP1P2,TOP3B,TPST2,TRIOBP,TST,TTC28,TTC28-AS1,TUBA3FP,TUG1,TXN2,UBE2L3,UPB1,UQCR10,VPREB1,VPREB3,XBP1,YDJC,YPEL1,YWHAH,ZDHHC8P1,ZMAT5,ZNF280A,ZNF280B,ZNF70,ZNRF3,ZNRF3-AS1"}
{"Sample_ID":"PT116","chr":"chr22","posStart":38732824,"posEnd":39538214,"length":805391,"numProbe":112,"log2ratio.Mean.adj":-0.25198,"log2ratio.SD":0.21888,"log2ratio.Median.adj":-0.22985,"log2ratio.MAD":0.2235,"log2mBAF.Mean":0.28363,"log2mBAF.SD":0.13413,"log2mBAF.Median":0.28171,"log2mBAF.MAD":0.11956,"log2ratio.p.value":0.004,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":23,"gene":"APOBEC3A,APOBEC3A_B,APOBEC3B,APOBEC3C,APOBEC3D,APOBEC3F,APOBEC3G,APOBEC3H,CBX6,CBX7,CBY1,DDX17,DMC1,DNAL4,FAM227A,GTPBP1,JOSD1,KCNJ4,KDELR3,LOC400927,NPTXR,SUN2,TOMM22"}
{"Sample_ID":"PT116","chr":"chr22","posStart":39542292,"posEnd":51178090,"length":11635799,"numProbe":3021,"log2ratio.Mean.adj":-0.56522,"log2ratio.SD":0.22953,"log2ratio.Median.adj":-0.5482,"log2ratio.MAD":0.21498,"log2mBAF.Mean":0.05493,"log2mBAF.SD":0.1223,"log2mBAF.Median":0.05657,"log2mBAF.MAD":0.11668,"log2ratio.p.value":0,"log2mBAF.p.value":0,"p.value":0,"CNV":"loss","numGene":177,"gene":"A4GALT,ACO2,ACR,ADM2,ADSL,ALG12,ARFGAP3,ARHGAP8,ARSA,ATF4,ATP5L2,ATXN10,BIK,BRD1,C22orf26,C22orf34,C22orf46,CACNA1I,CBX7,CCDC134,CDPF1,CELSR1,CENPM,CERK,CHADL,CHKB,CHKB-CPT1B,CN5H6.4,CPT1B,CRELD2,CSDC2,CYB5R3,CYP2D6,CYP2D7P1,DENND6B,DESI1,DNAJB7,EFCAB6,EFCAB6-AS1,ENTHD1,EP300,FAM109B,FAM118A,FAM19A5,FAM83F,FBLN1,FLJ46257,GRAMD4,GRAP2,GTSE1,HDAC10,IL17REL,KIAA0930,KIAA1644,KLHDC7B,L3MBTL2,LDOC1L,LINC00207,LINC00229,LINC00634,LMF2,LOC100128946,LOC100130899,LOC100144603,LOC100271722,LOC100506472,LOC100506714,LOC150381,LOC284933,LOC388906,LOC730668,LOC90834,MAPK11,MAPK12,MAPK8IP2,MCAT,MCHR1,MEI1,MGAT3,MIOX,MIR1249,MIR1281,MIR3201,MIR33A,MIR3619,MIR4535,MIR4762,MIR4763,MIR4766,MIRLET7A3,MIRLET7B,MIRLET7BHG,MKL1,MLC1,MOV10L1,MPPED1,NAGA,NCAPH2,NDUFA6,NDUFA6-AS1,NFAM1,NHP2L1,NUP50,ODF3B,PACSIN2,PANX2,PARVB,PARVG,PDGFB,PHF21B,PHF5A,PIM3,PKDREJ,PLXNB2,PMM1,PNPLA3,PNPLA5,POLDIP3,POLR3H,PPARA,PPP6R2,PRR5,PRR5-ARHGAP8,RANGAP1,RBX1,RIBC2,RNU12,RNU86,RPL3,RPS19BP1,RRP7A,RRP7B,SAMM50,SBF1,SCO2,SCUBE1,SELO,SEPT3,SERHL,SERHL2,SGSM3,SHANK3,SHISA8,SLC25A17,SMC1B,SMCR7L,SMDT1,SNORD43,SNORD83A,SNORD83B,SREBF2,ST13,SULT4A1,SYCE3,SYNGR1,TAB1,TBC1D22A,TCF20,TEF,TNFRSF13C,TNRC6B,TOB2,TRABD,TRMU,TSPO,TTC38,TTLL1,TTLL12,TUBGCP6,TYMP,UPK3A,WBP2NL,WNT7B,XPNPEP3,XRCC6,ZBED4,ZC3H7B"}