Table S3. RAE Analysis of Well-Differentiated Liposarcoma

Table S3. RAE analysis of well-differentiated liposarcoma

Model Chromosome Region start Region end Size q value freqX0* # genes Genes Amp 1 145009467 145122002 112536 0.097 21.8 2 PRKAB2,PDIA3P Amp 1 145224467 146188434 963968 0.029 23.6 10 CHD1L,BCL9,ACP6,GJA5,GJA8,GPR89B,GPR89C,PDZK1P1,RP11-94I2.2,NBPF11 Amp 1 147475854 148412469 936616 0.034 23.6 20 PPIAL4A,FCGR1A,HIST2H2BF,HIST2H3D,HIST2H2AA4,HIST2H2AA3,HIST2H3A,HIST2H3C,HIST2H4B,HIST2H4A,HIST2H2BE, HIST2H2AC,HIST2H2AB,BOLA1,SV2A,SF3B4,MTMR11,OTUD7B,VPS45,PLEKHO1 Amp 1 148582896 153398462 4815567 1.5E-05 49.1 152 PRPF3,RPRD2,TARS2,ECM1,ADAMTSL4,MCL1,ENSA,GOLPH3L,HORMAD1,CTSS,CTSK,ARNT,SETDB1,LASS2,ANXA9, FAM63A,PRUNE,BNIPL,C1orf56,CDC42SE1,MLLT11,GABPB2,SEMA6C,TNFAIP8L2,LYSMD1,SCNM1,TMOD4,VPS72, PIP5K1A,PSMD4,ZNF687,PI4KB,RFX5,SELENBP1,PSMB4,POGZ,CGN,TUFT1,SNX27,TNRC4,MRPL9,OAZ3,TDRKH,LINGO4, RORC,THEM5,THEM4,S100A10,S100A11,TCHHL1,TCHH,RPTN,HRNR,FLG,FLG2,CRNN,LCE5A,CRCT1,LCE3E,LCE3D,LCE3C,LCE3B, LCE3A,LCE2D,LCE2C,LCE2B,LCE2A,LCE4A,KPRP,LCE1F,LCE1E,LCE1D,LCE1C,LCE1B,LCE1A,SMCP,IVL,SPRR4,SPRR1A,SPRR3, SPRR1B,SPRR2D,SPRR2A,SPRR2B,SPRR2E,SPRR2F,SPRR2C,SPRR2G,LELP1,LOR,PGLYRP3,PGLYRP4,S100A9,S100A12,S100A8, S100A7A,S100A7L2,S100A7,S100A6,S100A5,S100A4,S100A3,S100A2,S100A16,S100A14,S100A13,S100A1,C1orf77,SNAPIN,ILF2, NPR1,INTS3,SLC27A3,GATAD2B,DENND4B,CRTC2,SLC39A1,CREB3L4,JTB,RAB13,RPS27,NUP210L,TPM3,C1orf189,C1orf43,UBAP2L,HAX1, AQP10,ATP8B2,IL6R,SHE,TDRD10,UBE2Q1,CHRNB2,ADAR,KCNN3,PMVK,PBXIP1,PYGO2,SHC1,CKS1B,FLAD1,LENEP,ZBTB7B,DCST2, DCST1,ADAM15,EFNA4,EFNA3,EFNA1,RAG1AP1,DPM3

Amp 1 153700678 153894854 194177 0.027 25.5 2 ASH1L,MSTO1 Amp 1 154108857 154183585 74729 0.016 25.5 7 SYT11,RIT1,KIAA0907,SNORA42,SCARNA4,RXFP4,ARHGEF2 Amp 1 155214884 155356571 141688 0.040 23.6 2 ARHGEF11,ETV3L Amp 1 155520004 155720600 200597 0.040 25.5 0 [Nearest:FCRL5] Amp 1 156067709 164154281 8086573 1.9E-06 43.6 120 CD5L,KIRREL,CD1D,CD1A,CD1C,CD1B,CD1E,OR10T2,OR10K2,OR10K1,OR10R2,OR6Y1,OR10X1,OR10Z1,SPTA1,OR6K2,OR6K3,OR6K6, OR6N1,OR6N2,MNDA,PYHIN1,IFI16,AIM2,CADM3,DARC,FCER1A,OR10J3,OR10J1,OR10J5,APCS,CRP,DUSP23,FCRL6,SLAMF8,VSIG8, CCDC19,TAGLN2,IGSF9,SLAMF9,PIGM,KCNJ10,KCNJ9,IGSF8,ATP1A2,ATP1A4,CASQ1,PEA15,WDR42A,PEX19,COPA,SUMO1P3,NCSTN, NHLH1,VANGL2,SLAMF6,CD84,SLAMF1,CD48,SLAMF7,LY9,CD244,ITLN1,ITLN2,F11R,RP11- 544M22.4,USF1,ARHGAP30,PVRL4,KLHDC9,PFDN2,NIT1,DEDD,UFC1,USP21,PPOX,B4GALT3,ADAMTS4,NDUFS2,FCER1G,APOA2,TOMM40L,N R1I3,PCP4L1,MPZ,SDHC,hCG_1776980,C1orf192,FCGR2A,HSPA6,FCGR3A,FCGR2C,FCGR3B,FCGR2B,RPL31P11,FCRLA,FCRLB,DUSP12,ATF6,OL FML2B,NOS1AP,C1orf111,C1orf226,SH2D1B,UHMK1,UAP1,DDR2,HSD17B7,C1orf110,RGS4,RGS5,NUF2,PBX1,LMX1A,RXRG,LRRC52,MGST3,A LDH9A1,TMCO1,UCK2

Amp 1 164857764 165399992 542229 0.026 25.5 7 FMO9P,POGK,TADA1L,ILDR2,MAEL,GPA33,DUSP27 Amp 1 167007682 171482622 4474941 1.6E-07 36.4 33 ATP1B1,NME7,BLZF1,C1orf114,SLC19A2,F5,SELP,SELL,SELE,C1orf156,C1orf112,SCYL3,KIFAP3,GORAB,PRRX1,C1orf129,FMO3,FMO6P,FMO2, FMO1,FMO4,TOP1P1,BAT2D1,MYOC,VAMP4,METTL13,DNM3,C1orf105,PIGC,C1orf9,FASLG,TNFSF18,TNFSF4

Amp 1 171812441 172242030 429590 0.0086 27.3 14 SLC9A11,ANKRD45,KLHL20,CENPL,DARS2,GAS5,SNORD47,SNORD80,SNORD78,SNORD76,SNORD74,ZBTB37,SERPINC1,RC3H1 Amp 1 172326170 172454962 128793 0.049 21.8 1 RABGAP1L Amp 1 172571475 172688677 117203 0.047 21.8 2 RABGAP1L,GPR52 Amp 1 172729145 173129536 400392 0.015 25.5 1 RABGAP1L Amp 1 173246578 173270799 24222 0.039 21.8 2 CACYBP,MRPS14 Amp 1 173442996 174176595 733600 0.0050 25.5 1 TNR Amp 1 174610694 174683039 72346 0.098 20 0 [Nearest:PAPPA2] Amp 1 176189757 176257679 67923 0.037 23.6 1 SEC16B Amp 1 176700160 177016348 316189 0.082 23.6 4 RASAL2,C1orf49,C1orf220,RALGPS2 Del 1 184303737 184407743 104007 0.018 9.1 1 HMCN1 Del 1 196061571 199158666 3097096 0.011 9.1 13 C1orf53,LHX9,NEK7,ATP6V1G3,PTPRC,NR5A2,FAM58B,ZNF281,KIF14,DDX59,CAMSAP1L1,GPR25,C1orf106 Del 1 199873365 200405230 531866 0.051 9.1 11 NAV1,IPO9,SHISA4,LMOD1,TIMM17A,RNPEP,ELF3,GPR37L1,ARL8A,PTPN7,PTPRV Del 1 201044387 201189356 144970 0.021 10.9 4 LOC148709,RABIF,KLHL12,ADIPOR1 Del 1 201426970 205657885 4230916 8.3E-05 14.5 62 CHIT1,BTG2,FMOD,PRELP,OPTC,ATP2B4,SNORA77,LAX1,ZC3H11A,SNRPE,C1orf157,SOX13,ETNK2,REN,KISS1,GOLT1A,PLEKHA6, PPP1R15B,PIK3C2B,MDM4,LRRN2,NFASC,CNTN2,TMEM81,RBBP5,DSTYK,TMCC2,NUAK2,KLHDC8A,LEMD1,PCTK3,MFSD4,ELK4, SLC45A3,NUCKS1,RAB7L1,SLC41A1,PM20D1,SLC26A9,FAM72A,AVPR1B,C1orf186,CTSE,SRGAP2,IKBKE,RASSF5,LGTN,DYRK3, MAPKAPK2,IL10,IL19,IL20,IL24,FAIM3,PIGR,FCAMR,C1orf116,YOD1,PFKFB2,C4BPB,C4BPA,CD55 Del 1 205858189 209222078 3363890 0.021 10.9 18 CR1,CR1L,CD46,CD34,PLXNA2,LOC642587,CAMK1G,LAMB3,G0S2,HSD11B1,TRAF3IP3,C1orf74,IRF6,C1orf107,SYT14,SERTAD4, HHAT,KCNH1 Del 1 209572983 209637355 64373 0.021 10.9 1 TRAF5 Del 1 210865589 214238939 3373351 0.018 9.1 16 FAM71A,BATF3,NSL1,TATDN3,C1orf227,FLVCR1,VASH2,ANGEL2,RPS6KC1,PROX1,SMYD2,PTPN14,CENPF,KCNK2,KCTD3,USH2A Del 1 214325747 214853588 527842 0.048 9.1 2 USH2A,ESRRG Del 1 214991000 215614604 623605 0.052 9.1 1 ESRRG Del 1 215685071 224858883 9173813 0.017 9.1 52 GPATCH2,SPATA17,RRP15,TGFB2,LYPLAL1,SLC30A10,EPRS,BPNT1,IARS2,RAB3GAP2,AURKAPS1,MARK1,C1orf115,MOSC2,MOSC1, HLX,DUSP10, HHIPL2,TAF1A,MIA3,AIDA,C1orf58,FAM177B,DISP1,TLR5,SUSD4,C1orf65,CAPN2,TP53BP2,FBXO28, DEGS1,NVL,CNIH4,WDR26,CNIH3,DNAH14,LBR,ENAH,SRP9,EPHX1,TMEM63A,LEFTY1,PYCR2,LEFTY2,C1orf55,H3F3A, LOC440926,ACBD3,MIXL1,LIN9,PARP1,C1orf95 Del 1 224904583 225768637 864055 0.0062 9.1 4 ITPKB,PSEN2,CABC1,CDC42BPA Del 1 225979138 234424821 8445684 0.00010 12.7 66 JMJD4,SNAP47,MPN2,WNT9A,WNT3A,ARF1,C1orf35,MRPL55,GUK1,GJC2,C1orf69,OBSCN,TRIM11,TRIM17,HIST3H3,HIST3H2A, HIST3H2BB,DUSP5P,RHOU,RAB4A,SPHAR,C1orf96,ACTA1,NUP133,ABCB10,TAF5L,URB2,GALNT2,PGBD5,COG2,AGT,CAPN9, C1orf198,TTC13,ARV1,FAM89A,TRIM67,C1orf131,GNPAT,EXOC8,C1orf124,EGLN1,TSNAX,DISC1,DISC2,SIPA1L2,KIAA1383,C1orf57, PCNXL2,KIAA1804,KCNK1,SLC35F3,C1orf31,TARBP1,IRF2BP2,TOMM20,SNORA14B,RBM34,ARID4B,GGPS1,TBCE,B3GALNT2, GNG4,LYST,NID1,GPR137B Del 1 238117512 238361689 244178 0.021 9.1 2 CHRM3,FMN2 Del 1 238441116 238783361 342246 0.021 9.1 2 FMN2,GREM2 Del 1 238967345 239083421 116077 0.021 9.1 1 RGS7 Del 1 239360147 239492605 132459 0.021 9.1 1 RGS7 Del 1 240054897 240104800 49904 0.020 9.1 1 EXO1 Del 1 241442091 241560407 118317 0.022 9.1 2 CEP170,SDCCAG8 Del 1 242692737 243906301 1213565 0.021 9.1 6 C1orf101,PPPDE1,FAM36A,HNRNPU,EFCAB2,KIF26B Del 1 246862029 247185356 323328 2.6E-08 18.2 8 OR2T35,OR2T27,OR14I1,LOC646627,SH3BP5L,ZNF672,ZNF692,PGBD2 Del 4 21911407 22194542 283136 0.078 9.1 1 GPR125 Amp 7 141985598 142192030 206433 0.0011 25.5 3 PRSS1,TRY6,PRSS2 Del 8 146024157 146264846 240690 0.00015 12.7 6 ZNF7,COMMD5,ZNF250,ZNF16,TMED10P,C8orf33 Del 9 194193 256045 61853 0.00015 5.5 2 C9orf66,DOCK8 Del 10 135124875 135271770 146896 0.0033 1.8 3 LOC619207,CYP2E1,SYCE1 Del 11 200300 1844960 1644661 0.00046 12.7 59 RIC8A,SIRT3,PSMD13,NLRP6,ATHL1,IFITM5,IFITM2,IFITM1,IFITM3,B4GALNT4,PKP3,SIGIRR,ANO9,PTDSS2,RNH1,HRAS,LRRC56, C11orf35,RASSF7,PHRF1,IRF7,MUPCDH,SCT,DRD4,DEAF1,TMEM80,EPS8L2,TALDO1,PDDC1,CEND1,SLC25A22,LRDD,RPLP2, SNORA52,PNPLA2,EFCAB4A,CD151,POLR2L,TSPAN4,CHID1,AP2A2,MUC6,MUC2,MUC5B,TOLLIP,BRSK2,HCCA2,DUSP8, LOC338651,KRTAP5-1,KRTAP5-2,KRTAP5-3,KRTAP5-4,KRTAP5-5,KRTAP5-6,CTSD,SYT8,TNNI2,LSP1 Del 11 3585368 6105831 2520464 0.0080 41.8 77 TRPC2,ART5,ART1,CHRNA10,NUP98,FRAG1,RHOG,STIM1,RRM1,OR52B4,TRIM21,OR52K2,OR52K1,OR52M1,C11orf40,OR52I2, OR52I1,TRIM68,OR51D1,OR51E1,OR51E2,OR51F1,OR52R1,OR51F2,OR51S1,OR51T1,OR51A7,OR51G2,OR51G1,OR51A4,OR51A2, MMP26,OR51L1,OR52J3,OR52E2,OR52A4,OR52A5,OR52A1,OR51V1,HBB,HBD,HBBP1,HBG1,HBG2,HBE1,OR51B4,OR51B2, OR51B5,OR51B6,OR51M1,OR51Q1,OR51I1,OR51I2,OR52D1,UBQLN3,UBQLNL,OR52H1,OR52B6,TRIM6,TRIM6- TRIM34,TRIM34,TRIMP1,TRIM5,TRIM22,OR56B1,OR52N4,OR52N5,OR52N1,OR52N2,OR52E6,OR52E8,OR52E4,OR56A3,OR52L1,OR56A4,OR 56A1,OR56B4 Del 11 21080944 35610142 14529199 2.5E-05 18.2 55 NELL1,ANO5,SLC17A6,FANCF,GAS2,SVIP,LUZP2,ANO3,MUC15,SLC5A12,FIBIN,BBOX1,CCDC34,LGR4,LIN7C,BDNFOS,BDNF, KIF18A,METT5D1,KCNA4,FSHB,C11orf46,MPPED2,DCDC1,DNAJC24,IMMP1L,ELP4,PAX6,RCN1,WT1,WIT1,EIF3M,CCDC73,PRRG4, QSER1,DEPDC7,TCP11L1,CSTF3,HIPK3,C11orf41,CD59,FBXO3,LMO2,CAPRIN1,NAT10,ABTB2,CAT,ELF5,EHF,APIP,PDHX,CD44, SLC1A2,DKFZP586H2123,FJX1 Del 11 36115488 36662689 547202 0.075 9.1 7 LDLRAD3,COMMD9,FLJ14213,TRAF6,RAG1,RAG2,C11orf74 Amp 12 56084979 56106676 21698 0.056 20 0 [Nearest:INHBC] Amp 12 56135099 61001541 96587 4.0E-117 94.5 1 CTDSP2 Amp 12 56135099 61001541 4866443 4.0E-117 94.5 29 INHBE,GLI1,ARHGAP9,MARS,DDIT3,MBD6,DCTN2,KIF5A,PIP4K2C,DTX3,GEFT,SLC26A10,B4GALNT1,OS9,AGAP2,TSPAN31, CDK4,9-Mar,CYP27B1,METTL1,FAM119B,TSFM,AVIL,CTDSP2,XRCC6BP1,LRIG3,SLC16A7,FAM19A2,USP15 Amp 12 61035406 61054010 18605 0.043 18.2 1 USP15 Amp 12 61108058 61186965 78908 0.015 18.2 1 MON2 Amp 12 61652819 61661575 8757 0.083 18.2 0 [Nearest:PPM1H] Amp 12 62731258 63181490 450233 5.4E-08 40 5 SRGAP1,C12orf66,C12orf56,XPOT,TBK1 Amp 12 63267869 63346598 78730 0.010 20 1 RASSF3 Amp 12 63382272 78071183 190700 9.4E-61 52.7 1 HMGA2 Amp 12 63382272 78071183 51891 4.4E-133 98.2 1 CPM Amp 12 63382272 78071183 14688912 4.4E-133 98.2 58 GNS,WIF1,LEMD3,MSRB3,HMGA2,LLPH,TMBIM4,IRAK3,HELB,GRIP1,CAND1,DYRK2,IFNG,IL26,IL22,MDM1,RAP1B,hCG_1757335, NUP107,SLC35E3,MDM2,CPM,CPSF6,LYZ,YEATS4,FRS2,CCT2,LRRC10,BEST3,RAB3IP,CNOT2,KCNMB4, PTPRB,PTPRR,TSPAN8,LGR5,ZFC3H1,THAP2,TMEM19,RAB21,TBC1D15,TPH2,TRHDE,KCNC2,CAPS2,GLIPR1L1, GLIPR1L2,GLIPR1,KRR1,PHLDA1,NAP1L1,BBS10,OSBPL8,ZDHHC17,CSRP2,E2F7,NAV3,SYT1 Amp 12 78101964 78132029 30066 0.086 20 1 SYT1 Amp 12 78214100 78233561 19462 0.045 18.2 1 SYT1 Amp 12 78306130 78481096 174967 0.0022 23.6 1 SYT1 Amp 12 78615059 78632312 17254 0.082 20 0 [Nearest:PAWR] Amp 12 78774686 78854174 79489 0.036 21.8 1 PPP1R12A Amp 12 79019913 84002916 4983004 7.3E-08 80 11 MYF6,MYF5,LIN7A,ACSS3,PPFIA2,CCDC59,C12orf26,TMTC2,SLC6A15,TSPAN19,LRRIQ1 Amp 12 84201600 84341455 139856 0.019 25.5 1 ALX1 Amp 12 84522553 84563669 41117 0.079 18.2 0 [Nearest:RASSF9] Amp 12 84729285 84834258 104974 0.00035 29.1 2 RASSF9,NTS Amp 12 85001809 85084638 82830 0.034 21.8 1 MGAT4C Amp 12 85520358 85722596 202239 0.012 25.5 1 MGAT4C Amp 12 85756662 91719498 380868 4.2E-20 54.5 0 [Nearest:DCN] Amp 12 85756662 91719498 5962837 4.2E-20 81.8 20 MGAT4C,C12orf50,C12orf29,CEP290,TMTC3,KITLG,DUSP6,WDR51B,GALNT4,ATP2B1,C12orf12,EPYC,KERA,LUM,DCN,BTG1, CLLU1OS,C12orf74,PLEKHG7,EEA1 Amp 12 91809546 91830035 20490 0.100 20 1 EEA1 Amp 12 92257746 92309645 51900 0.080 20 2 NUDT4,NUDT4P1 Amp 12 92337342 92373716 36375 0.031 21.8 1 UBE2N Amp 12 92480737 92498943 18207 0.043 21.8 1 SOCS2 Amp 12 93245910 93296810 50901 0.048 21.8 1 CCDC41 Amp 12 93329703 93336742 7040 0.056 21.8 1 CCDC41 Amp 12 93429970 93544225 114256 0.026 25.5 1 TMCC3 Amp 12 93678214 94512305 834092 2.4E-05 47.3 6 NDUFA12,NR2C1,FGD6,VEZT,METAP2,USP44 Amp 12 94543179 94571351 28173 0.080 20 0 [Nearest:NTN4] Amp 12 94606858 94655857 49000 0.097 20 1 NTN4 Amp 12 94704314 95567848 863535 1.8E-10 43.6 9 NTN4,SNRPF,CCDC38,AMDHD1,HAL,LTA4H,ELK3,PCTK2,C12orf63 Amp 12 95591978 95657864 65887 0.0070 23.6 1 C12orf63 Amp 12 95684604 95701256 16653 0.049 21.8 0 [Nearest:C12orf63] Amp 12 98422338 98558687 136350 0.069 20 1 ANKS1B Amp 12 98968955 98988530 19576 0.066 18.2 1 UHRF1BP1L Amp 12 99804838 99819553 14716 0.085 18.2 1 ANO4 Del 12 100270022 100300991 30970 0.068 7.3 1 UTP20 Amp 12 101743060 101817806 74747 0.052 20 1 PAH Del 12 131896929 132031511 134583 0.018 10.9 3 GOLGA3,CHFR,ZNF605 Del 12 132128126 132289090 160965 0.0013 12.7 4 ZNF84,ZNF140,ZNF10,ZNF268 Del 13 50837545 50887128 49584 0.0085 10.9 1 INTS6 Del 13 94645059 94870258 225200 0.018 10.9 1 ABCC4 Del 18 75863391 76048654 185264 0.0038 10.9 3 C18orf22,ADNP2,PARD6G Del 22 15464955 49565816 34100862 9.7E-06 43.6 435 Redacted for size

* approximate frequency of copy number alteration, see Taylor et al . (2010; ref.6)