Table S4. RAE analysis of dedifferentiated liposarcoma Model Chromosome Region start Region end Size q value freqX0* # genes genes Amp 1 57809872 60413476 2603605 0.00026 34.6 10 DAB1,RPS26P15,OMA1,TACSTD2,MYSM1,JUN,FGGY,HOOK1,CYP2J2,C1orf87 Amp 1 158619146 158696968 77823 0.053 25 1 VANGL2 Amp 1 158883523 158922841 39319 0.081 23.1 2 SLAMF1,CD48 Amp 1 162042586 162118557 75972 0.072 25 0 [Nearest:NUF2] Amp 1 162272460 162767627 495168 0.017 26.9 0 [Nearest:PBX1] Amp 1 165486554 165532374 45821 0.057 25 1 POU2F1 Amp 1 167138282 167483267 344986 0.024 26.9 2 ATP1B1,NME7 Amp 1 167612872 167708844 95973 0.041 25 3 BLZF1,C1orf114,SLC19A2 Amp 1 167728199 167808161 79963 0.076 21.2 1 F5 Amp 1 168436370 169233893 797524 0.018 26.9 3 GORAB,PRRX1,C1orf129 Amp 1 169462231 170768440 1306210 1.3E-06 38.5 10 FMO1,FMO4,TOP1P1,BAT2D1,MYOC,VAMP4,METTL13,DNM3,C1orf105,PIGC Amp 1 171026247 171291427 265181 0.015 26.9 1 TNFSF18 Del 1 201860394 202299299 438906 0.0047 25 6 ATP2B4,SNORA77,LAX1,ZC3H11A,SNRPE,C1orf157 Del 1 210909187 212021116 1111930 0.017 19.2 8 BATF3,NSL1,TATDN3,C1orf227,FLVCR1,VASH2,ANGEL2,RPS6KC1 Del 1 215937857 216049214 111358 0.079 23.1 1 SPATA17 Del 1 218237257 218367476 130220 0.0063 26.9 3 EPRS,BPNT1,IARS2 Del 1 222100886 222727238 626353 5.2E-05 32.7 5 FBXO28,DEGS1,NVL,CNIH4,WDR26 Del 1 223166548 224519805 1353258 0.0063 26.9 15 DNAH14,LBR,ENAH,SRP9,EPHX1,TMEM63A,LEFTY1,PYCR2,LEFTY2,C1orf55,H3F3A,LOC440926 ,ACBD3,MIXL1,LIN9 Del 1 225283136 225374166 91031 0.054 23.1 1 CDC42BPA Del 1 227278990 229012661 1733672 0.091 21.2 13 RAB4A,SPHAR,C1orf96,ACTA1,NUP133,ABCB10,TAF5L,URB2,GALNT2,PGBD5,COG2,AGT,CAP Del 1 229602259 229673038 70780 0.020 25 1 EGLN1N9 Del 1 233309013 234365436 1056424 0.0014 28.8 10 TOMM20,SNORA14B,RBM34,ARID4B,GGPS1,TBCE,B3GALNT2,GNG4,LYST,NID1 Del 1 234407392 234755921 348530 0.048 23.1 4 GPR137B,ERO1LB,EDARADD,LGALS8 Del 1 239674808 240239705 564898 0.039 23.1 7 FH,KMO,OPN3,CHML,WDR64,EXO1,MAP1LC3C Del 1 240760677 247185356 6424680 8.3E-05 44.2 72 CEP170,SDCCAG8,AKT3,ZNF238,C1orf100,ADSS,C1orf101,PPPDE1,FAM36A,HNRNPU,EFCAB2, KIF26B,SMYD3,TFB2M,C1orf71,SCCPDH,AHCTF1,ZNF695,ZNF670,ZNF669,FLJ45717,ZNF124,V N1R5,ZNF496,NLRP3,OR2B11,OR2W5,OR2C3,C1orf150,OR2G2,OR2G3,OR6F1,OR1C1,OR14A1 6,OR11L1,TRIM58,OR2W3,OR2T8,OR2L13,OR2L8,OR2AK2,OR2L1P,OR2L2,OR2L3,OR2M1P,OR 2M5,OR2M2,OR2M3,OR2M4,OR2T33,OR2T12,OR2M7,OR14C36,OR2T4,OR2T6,OR2T1,OR2T2 ,OR2T3,OR2T5,OR2G6,OR2T29,OR2T34,OR2T10,OR2T11,OR2T35,OR2T27,OR14I1,LOC646627 Del 2 241844891 242579492 734602 0.038 28.8 10 HDLBP,2-Sep,FARP2,STK25,BOK,ING5,GAL3ST2,NEU4,PDCD1,C2orf85,SH3BP5L,ZNF672,ZNF692,PGBD2 Del 3 10016504 10254819 238316 0.028 23.1 7 LOC401052,CIDECP,FANCD2,C3orf24,C3orf10,VHL,IRAK2 Del 3 12604063 12680013 75951 0.083 21.2 1 RAF1 Del 3 41806019 41852414 46396 0.083 19.2 1 ULK4 Del 3 47039911 53977519 6937609 4.0E-07 38.5 150 SETD2,KIF9,KLHL18,PTPN23,SCAP,C3orf75,CSPG5,SMARCC1,DHX30,MAP4,CDC25A,CAMP,ZNF 589,NME6,SPINK8,FBXW12,PLXNB1,CCDC51,CCDC72,ATRIP,TREX1,SHISA5,PFKFB4,UCN2,COL 7A1,UQCRC1,TMEM89,SLC26A6,CELSR3,NCKIPSD,IP6K2,PRKAR2A,SLC25A20,C3orf71,ARIH2,P 4HTM,WDR6,DALRD3,NDUFAF3,IMPDH2,QRICH1,QARS,USP19,LAMB2,LAMB2L,CCDC71,KLH DC8B,LOC646498,CCDC36,C3orf62,USP4,GPX1,RHOA,TCTA,AMT,NICN1,DAG1,BSN,APEH,MST 1,RNF123,AMIGO3,GMPPB,IP6K1,CDH29,C3orf54,UBA7,TRAIP,CAMKV,MST1R,MON1A,RBM6 ,RBM5,SEMA3F,GNAT1,SLC38A3,GNAI2,SEMA3B,C3orf45,IFRD2,HYAL3,NAT6,HYAL1,HYAL2,T USC2,RASSF1,ZMYND10,TUSC4,CYB561D2,TMEM115,CACNA2D2,C3orf18,HEMK1,CISH,MAPK APK3,DOCK3,ARMET,RBM15B,VPRBP,RAD54L2,TEX264,GRM2,IQCF3,IQCF2,IQCF1,RRP9,PARP 3,GPR62,PCBP4,ABHD14B,ABHD14A,ACY1,RPL29,DUSP7,WDR51A,ALAS1,TLR9,TWF2,PPM1M ,WDR82,GLYCTK,DNAH1,BAP1,PHF7,SEMA3G,TNNC1,NISCH,STAB1,NT5DC2,LOC440957,PBR M1,GNL3,GLT8D1,SPCS1,NEK4,ITIH1,ITIH3,ITIH4,MUSTN1,TMEM110,SFMBT1,RFT1,PRKCD,TK Del 3 56229193 58360129 2130937 0.00037 28.8 19 ERC2,CCDC66,C3orf63,ARHGEF3,SPATA12,IL17RD,HESX1,APPL1,ASB14,DNAH12,PDE12,ARF4, FAM116A,SLMAP,FLNB,DNASE1L3,ABHD6,RPP14,PXK Del 3 69268931 69400527 131597 0.044 23.1 1 FRMD4B Del 3 72657187 73277953 620767 0.022 25 4 SHQ1,GLT8D4,PPP4R2,FLJ10213 Del 3 110414130 110683868 269739 0.088 21.2 2 DPPA2,DPPA4 Del 3 139908783 140149821 241039 0.024 23.1 3 PIK3CB,FOXL2,C3orf72 Del 3 171328741 171590705 261965 0.020 23.1 3 PHC3,PRKCI,SKIL Del 3 196481383 199329592 2848210 1.1E-06 51.9 37 ACAP2,PPP1R2,APOD,SDHALP2,MUC20,MUC4,TNK2,SDHALP1,TFRC,ZDHHC19,OSTalpha,PCYT 1A,TCTEX1D2,TM4SF19,UBXN7,RNF168,C3orf43,WDR53,FBXO45,LRRC33,C3orf34,PIGX,PAK2, SENP5,NCBP2,PIGZ,MFI2,DLG1,BDH1,LOC220729,KIAA0226,FYTTD1,LRCH3,IQCG,RPL35A,LML Del 4 39682282 39820681 138400 0.052 23.1 1 N4BP2 Amp 5 1093705 1543862 450158 0.0020 30.8 7 SLC12A7,SLC6A19,SLC6A18,TERT,CLPTM1L,SLC6A3,LPCAT1 Amp 5 1697394 1789892 92499 0.065 25 0 [Nearest:LOC728613] Amp 5 13319637 13466970 147334 0.054 26.9 0 [Nearest:DNAH5] Amp 5 13620666 13737186 116521 0.043 26.9 0 [Nearest:DNAH5] Amp 5 15649221 15660073 10853 0.054 25 1 FBXL7 Amp 5 24058033 24297675 239643 0.038 26.9 0 [Nearest:CDH10] Amp 5 24480832 24582277 101446 0.075 23.1 1 CDH10 Amp 5 25201868 25258652 56785 0.087 23.1 0 [Nearest:CDH10] Amp 5 25986189 26103823 117635 0.079 23.1 0 [Nearest:CDH9] Amp 6 103477930 103845083 367154 0.087 25 0 [Nearest:GRIK2] Amp 6 113439154 117189663 3750510 0.0054 30.8 17 MARCKS,HDAC2,HS3ST5,FRK,NT5DC1,COL10A1,TSPYL4,TSPYL1,DSE,FAM26F,FAM26E,FAM26 D,RWDD1,RSPH4A,ZUFSP,KPNA5,FAM162B Amp 6 117302727 117338857 36131 0.083 23.1 1 RFX6 Amp 6 117388338 117692206 303869 0.081 25 0 [Nearest:VGLL2] Amp 6 128176607 128529036 352430 0.061 26.9 2 C6orf190,PTPRK Amp 6 128878261 129057937 179677 0.078 25 1 PTPRK Amp 6 134681434 145160649 10479216 0.00018 38.5 42 ALDH8A1,HBS1L,MYB,AHI1,PDE7B,FAM54A,BCLAF1,MAP7,MAP3K5,PEX7,SLC35D3,IL20RA,IL2 2RA2,IFNGR1,OLIG3,TNFAIP3,PERP,KIAA1244,PBOV1,HEBP2,CCDC28A,ECT2L,REPS1,C6orf115 ,HECA,TXLNB,CITED2,NMBR,VTA1,GPR126,HIVEP2,AIG1,ADAT2,PEX3,FUCA2,PHACTR2,LTV1,P LAGL1,HYMAI,SF3B5,STX11,UTRN Amp 6 145988967 146457034 468068 0.029 25 4 EPM2A,FBXO30,SHPRH,GRM1 Amp 6 146998782 147048234 49453 0.036 25 1 C6orf103 Amp 6 147282904 149969228 2686325 0.00049 34.6 10 STXBP5,SAMD5,SASH1,UST,MAP3K7IP2,SUMO4,ZC3H12D,PPIL4,C6orf72,KATNA1 Amp 7 13538028 13699329 161302 0.095 23.1 0 [Nearest:ETV1] Amp 7 16772441 16801091 28651 0.090 25 2 TSPAN13,AGR2 Amp 7 25253943 25955523 701581 0.025 28.8 0 [Nearest:NPVF] Amp 7 27099126 27240566 141441 0.00031 36.5 12 HOXA1,HOXA2,HOXA3,HOXA4,HOXA5,HOXA6,HOXA7,HOXA9,HOXA10,HOXA11,HOXA11AS,H Amp 7 29519225 31543483 2024259 0.088 25 20 CHN2,PRR15,WIPF3,SCRN1,FKBP14,PLEKHA8,C7orf41,ZNRF2,DKFZP586I1420,NOD1,GGCT,GAOXA13 RS,CRHR2,INMT,C7orf67,AQP1,GHRHR,ADCYAP1R1,NEUROD6,CCDC129 Del 7 75205238 75309970 104733 0.049 23.1 3 HIP1,CCL26,CCL24 Amp 7 141720324 142192030 471707 1.1E-06 42.3 3 PRSS1,TRY6,PRSS2 Amp 8 99393649 99532186 138538 0.048 26.9 1 KCNS2 Del 8 145909942 146264846 354905 0.016 23.1 10 ZNF251,ZNF34,RPL8,ZNF517,ZNF7,COMMD5,ZNF250,ZNF16,TMED10P,C8orf33 Del 9 194193 16047005 15852813 0.0077 32.7 51 C9orf66,DOCK8,KANK1,DMRT1,DMRT3,DMRT2,SMARCA2,FLJ35024,VLDLR,KCNV2,KIAA0020, RFX3,GLIS3,SLC1A1,C9orf68,PPAPDC2,CDC37L1,AK3,RCL1,JAK2,INSL6,INSL4,RLN2,RLN1,C9orf 46,CD274,PDCD1LG2,KIAA1432,ERMP1,MLANA,KIAA2026,RANBP6,IL33,TPD52L3,UHRF2,GLD C,JMJD2C,C9orf123,PTPRD,TYRP1,C9orf150,MPDZ,NFIB,ZDHHC21,CER1,FREM1,LOC389705,T Del 9 16455531 23807986 7352456 1.5E-08 42.3 39 BNC2,CNTLN,SH3GL2,ADAMTSL1,FAM154A,RRAGA,FAM29A,SCARNA8,ADFP,DENND4C,RPS6, ACER2,SLC24A2,MLLT3,KIAA1797,PTPLAD2,IFNB1,IFNW1,IFNA21,IFNA4,IFNA7,IFNA10,IFNA1 6,IFNA17,IFNA14,IFNA5,KLHL9,IFNA6,IFNA13,IFNA2,IFNA8,IFNA1,IFNE,MTAP,CDKN2A,CDKN2 BAS,CDKN2B,DMRTA1,ELAVL2 Del 9 24053497 25573028 1519532 0.030 23.1 0 [Nearest:TUSC1] Del 9 26736903 31829311 5092409 0.017 26.9 10 C9orf82,PLAA,IFT74,LRRC19,TEK,C9orf11,MOBKL2B,IFNK,C9orf72,LINGO2 Del 9 32375919 32490919 115001 0.051 23.1 2 ACO1,DDX58 Del 9 32803501 32894286 90786 0.052 23.1 0 [Nearest:TMEM215] Del 9 33803335 37898880 4095546 3.5E-06 36.5 73 UBE2R2,UBAP2,WDR40A,UBAP1,KIF24,NUDT2,KIAA1161,C9orf24,C9orf25,DNAI1,ENHO,CNTF R,C9orf23,DCTN3,ARID3C,SIGMAR1,GALT,IL11RA,CCL27,CCL19,CCL21,KIAA1045,DNAJB5,C9or f131,VCP,FANCG,PIGO,STOML2,KIAA1539,UNC13B,LOC158381,RUSC2,FAM166B,TESK1,CD72, SIT1,RMRP,CCDC107,C9orf100,CA9,TPM2,TLN1,CREB3,GBA2,RGP1,MSMP,NPR2,SPAG8,HINT 2,C9orf128,C9orf127,OR13J1,HRCT1,OR2S2,RECK,GLIPR2,CCIN,CLTA,GNE,RNF38,MELK,PAX5, ZCCHC7,GRHPR,ZBTB5,POLR1E,FBXO10,TOMM5,FRMPD1,RG9MTD3,EXOSC3,WDR32,MCART Del 9 38435900 43530076 5094177 0.081 28.8 10 CNTNAP3,FAM75A2,FAM75A1,FAM75A3,FAM74A3,ZNF658,LOC653501,ZNF658B,KGFLP2,AN Amp 9 71552270 71888549 336280 0.098 25 3 PTAR1,C9orf135,MAMDC2 Amp 9 84329796 84853118 523323 0.045 26.9 1 RASEF Amp 9 85635121 85718742 83622 0.083 25 1 KIF27 Amp 9 85901224 87149173 1247950 0.041 26.9 2 SLC28A3,NTRK2 Amp 9 90182693 93177300 2994608 0.0057 28.8 13 SPIN1,NXNL2,LOC286238,C9orf47,S1PR3,SHC3,CKS2,SECISBP2,SEMA4D,GADD45G,DIRAS2,SY Amp 9 93564711 98074124 4509414 0.013 30.8 34 ROR2,SPTLC1,LOC100128076,IARS,NOL8,CENPP,OGN,OMD,ASPN,ECM2,IPPK,BICD2,ZNF484,F GD3,SUSD3,C9orf89,NINJ1,WNK2,C9orf129,FAM120AOS,FAM120A,PHF2,BARX1,PTPDC1,ZNF 169,FAM22F,HIATL1,FBP2,FBP1,C9orf3,FANCC,PTCH1,C9orf102,HSD17B3 Amp 9 99075283 99262711 187429 0.040 26.9 2 KIAA1529,TDRD7 Amp 9 99393409 99647356 253948 0.047 26.9 4 TMOD1,C9orf97,NCBP1,XPA Amp 9 100100965 100238966 138002 0.051 26.9 1 GABBR2 Amp 9 100353031 102993750 2640720 0.017 28.8 16 GABBR2,ANKS6,GALNT12,COL15A1,TGFBR1,ALG2,SEC61B,NR4A3,STX17,ERP44,INVS,TEX10,C 9orf30,TMEFF1,MURC,RP11-35N6.1 Amp 9 103099517 103151635 52119 0.047 26.9 1 RP11-35N6.1 Amp 9 103837411 106370277 2532867 0.014 30.8 5 CYLC2,SMC2,OR13F1,OR13C4,OR13C3