Kim et al. TabS2 MCR MET MCRs Recurrence

Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Amplified Genes in MET Correlated mRNA expression data in MET CDC14A GPR88 EXTL2 CGI-30 FLJ25070 AMY1A 1p21.2-p13.3 100.53-107.4 6,87 3 (3) PRMT6 CDC14A AMY1A SEC22L1 HFE2 RBM8A PEX11B ITGA10 POLR3C 1q21.1 142.56-143.88 1,32 3 (3) CD160 PRKAB2 FMO5 RBM8A POLR3C PRKAB2 143.98-144.99 1,01 3 (3) 146.83-147.08 0,25 2 (3) FLJ23221 MRPS21 147.36-147.43 0,07 2 (3) MCL1 ENSA GPP34R MCL1 147.58-147.6 0,01 2 (3) CTSK ARNT 1q23.1 154.96-155.39 0,43 2 (3) CD1D CD1C SPTA1 CD1C 156.37-156.5 0,12 3 (3) APCS CRP APCS CRP 156.61-156.65 0,04 3 (3) SLAMF8 SLAMF8 156.76-156.81 0,05 2 (3) PIGM PIGM 156.82-156.9 0,08 2 (3) KCNJ10 ATP1A2 KCNJ10 ATP1A2 1q23.2 157.47-157.9 0,43 2 (3) CD48 LOC257106 CD48 LOC257106 157.95-158.02 0,06 2 (3) B4GALT3 FCER1G NR1I3 158.11-158.36 0,26 3 (3) SDHC FCGR2A FCGR3A 158.41-158.66 0,25 2 (3) FREB DUSP12 ATF6 FREB DUSP12 1q23.3 159.26-159.49 0,23 2 (3) UAP1 DDR2 HSD17B7 DDR2 HSD17B7 159.77-161.27 1,5 3 (3) RGS4 RGS5 CDCA1 RGS4 RGS5 1q24.2 166.22-166.42 0,21 3 (3) F5 SELL SELE F5 SELL 166.49-166.62 0,13 3 (3) MGC9084 KIFAP3 MGC9084 KIFAP3

2p25.1 8.95-10.51 1,56 2 (3) LOC129642 DDEF2 ITGB1BP1 YWHAQ TFCP2L2 RRM2 LOC129642 DDEF2 ITGB1BP1 TFCP2L2 RRM2 10.53-11.62 1,09 3 (3) ODC1 ATP6V1C2 ROCK2 ATP6V1C2 ROCK2 GREB1 2p25.1-p24.3 11.91-12.81 0,9 4 (4) LPIN1 TRIB2 LPIN1 2p24.3 14.72-14.73 0 3 (4) NSE1 15.68-16.01 0,33 4 (4) DDX1 16.03-16.65 0,62 3 (4) MYCN DKFZP566A1524 2p24.1-p23.3 20.81-23.91 3,1 3 (3) FLJ21820 APOB APOB 2p23.3 24.06-24.34 0,28 5 (5) UBXD4 FKBP1B FLJ21945 TP53I3 ITSN2 UBXD4 FLJ21945 ITSN2 24.93-25.37 0,44 4 (5) MGC11266 RBJ DNMT3A DNMT3A 25.55-25.87 0,32 4 (5) DTNB ASXL2 ASXL2 25.89-26.32 0,43 2 (5) NULL LOC150946 HADHB NULL LOC150946 HADHB 26.33-26.86 0,54 3 (5) HADHA KIAA1724 KCNK3 26.9-26.98 0,08 2 (5) C2orf18 27.06-27.19 0,13 2 (5) DPYSL5 FLJ21839 DPYSL5 27.2-27.21 0,01 2 (5) EMILIN1 27.24-27.29 0,05 4 (5) CGREF1 ABHD1 27.33-27.45 0,11 2 (5) SLC5A6 SLC30A3 SLC5A6 27.46-27.52 0,05 2 (5) GTF3C2 EIF2B4 PPM1G 3p22.2 37.01-37.16 0,15 3 (3) MLH1 LRRFIP2 37.16-37.26 0,1 2 (3) 37.4-38.02 0,62 2 (3) APRG1 CTDSPL CTDSPL 38.18-39.08 0,9 2 (3) OSR1 ACVR2B OSR1 ACVR2B 39.11-39.11 0,01 3 (3) KIAA1449 GORASP1 KIAA1449 3q13.31-q13.32 117-118.88 1,88 3 (3) 3q13.32-q13.33 120.1-120.7 0,6 3 (3) IGSF11 CDGAP FLJ10902 C3orf1 3q13.33 122.83-122.97 0,14 4 (4) HCLS1 GOLGB1 IQCB1 123.28-123.39 0,11 2 (4) CD86 CASR CD86 3q21.2 125.79-126.28 0,5 2 (3) TRAD ITGB5 HEG TRAD 126.65-127.59 0,95 3 (3) SNX4 SLC41A3 3q21.3-q22.1 131.05-133.86 2,81 3 (3) ATP2C1 HT001 FLJ31265 CPNE4 FLJ31265 3q22.1 134.78-135.01 0,23 2 (3) H41 SRPRB H41 SRPRB 135.03-135.68 0,65 3 (3) SLCO2A1 RYK AMOTL2 ANAPC13 RYK ANAPC13 3q22.2 135.74-136 0,26 3 (3) 3q22.2-q22.3 137.17-137.45 0,28 3 (3) PPP2R3A PCCB PCCB 3q22.3-q23 139.47-140.58 1,12 3 (3) HSPC056 COPB2 3q23 140.72-142.18 1,46 3 (3) RBP1 FLJ10618 RBP1 FLJ10618 142.66-143.13 0,46 3 (3) ATP1B3 143.15-143.77 0,61 3 (3) TFDP2 1-Sep ATR ATR 3q23-q24 144.2-148.59 4,39 3 (3) SR140 CHST2 SLC9A9 PLOD2 PLSCR1 SR140 PLOD2 3q24 149.28-149.9 0,62 3 (3) AGTR1 149.98-150.19 0,21 3 (3) CPA3 GYG GYG 3q24-q25.1 150.23-151.08 0,85 3 (3) SMARCA3 CP TM4SF4 TAZ COMMD2 RNF13 SMARCA3 CP COMMD2 3q25.1 151.17-151.61 0,44 3 (3) PFN2 KIAA0669 PFN2 151.62-152.41 0,79 3 (3) SERP1 eIF2A SELT SIAH2 GPR105 SERP1 eIF2A SIAH2 152.53-152.93 0,41 2 (3) GPR86 MGC72001 3q26.1 161.56-161.7 0,14 2 (3) TSBF1 TSBF1 161.77-162.42 0,65 2 (3) LOC90133 CGI-07 166.39-168.94 2,55 3 (3) SLITRK3 SERPINI1 3q26.2 169.21-170.7 1,49 3 (3) GOLPH4 EVI1 GOLPH4 171.15-171.3 0,14 3 (3) TLOC1 PHC3 171.56-171.62 0,06 3 (3) SKIL CLDN11 SKIL 171.66-172.09 0,43 3 (3) FLJ37228 EIF5A2 3q26.2-q26.31 172.19-173.31 1,12 3 (3) TNIK FAD104 FAD104 3q26.31-q26.32 173.57-177.8 4,24 3 (3) TNFSF10 3q26.32 178.22-178.39 0,16 3 (3) IRA1 NULL IRA1 NULL 180.22-180.44 0,23 3 (3) PIK3CA KCNMB3 PIK3CA 180.55-180.6 0,05 3 (3) MFN1 3q26.32-q26.33 180.6-181 0,4 4 (4) GNB4 BAF53A NDUFB5 USP13 NULL BAF53A NDUFB5 USP13 3q26.33 181.8-182.18 0,38 3 (4) TTC14 FXR1 TTC14 FXR1 182.18-184.17 1,99 4 (4) TIM14 ATP11B RP42 3q27.1 184.45-184.84 0,38 3 (3) B3GNT5 DRE1 B3GNT5 DRE1 185.03-185.13 0,1 3 (3) PSARL ABCC5 PSARL ABCC5 185.39-185.91 0,52 2 (3) ABCF3 ALG3 THPO MAGEF1 3q27.1-q27.2 185.93-186.28 0,35 3 (3) 3q27.2 186.39-186.69 0,3 3 (3) EHHADH MGC15397 186.71-187.02 0,31 3 (3) LIPH SENP2 LIPH 3q27.2-q27.3 187.25-187.92 0,67 3 (3) ETV5 FETUB HRG KNG1 KNG1 3q27.3 187.98-188.58 0,6 3 (3) EIF4A2 RFC4 ACDC SIAT1 EIF4A2 RFC4 3q27.3-q28 188.87-190.83 1,96 3 (3) SST NULL TP73L 3q28 191.31-191.71 0,41 3 (3) CLDN1 IL1RAP IL1RAP 192.47-192.6 0,13 2 (3) URP C3orf6 URP 3q28-q29 193.34-195.03 1,69 3 (3) FGF12 OPA1 FGF12 OPA1 3q29 195.54-195.89 0,35 3 (3) CPN2 LRRC15 AFURS1 FLJ90022 196.48-197.26 0,79 3 (3) CENTB2 APOD TFRC CENTB2 APOD 197.28-197.41 0,13 3 (3) ZDHHC19 197.77-197.8 0,03 3 (3) MGC64882 LOC200933 MGC64882 LOC200933 197.92-197.93 0,01 2 (3) FLJ20522 197.96-198.08 0,13 3 (3) PAK2 SENP5 SENP5 198.15-198.26 0,11 3 (3) NCBP2 DLG1 198.35-198.89 0,54 3 (3) KIAA0226 KIAA0226 199.09-199.17 0,09 3 (3) LRCH3 LRCH3 5p13.3-p13.2 34.23-34.99 0,76 3 (3) RAI14 LOC134218 RAI14 5p13.2 35.03-35.06 0,03 3 (3) AGXT2 AGXT2 35.09-35.9 0,81 2 (3) PRLR FLJ23577 IL7R FLJ23577 IL7R 36.22-36.93 0,71 2 (3) SKP2 FLJ30596 SKP2 FLJ30596 37.14-38.44 1,3 2 (3) FLJ13231 NUP155 FLJ39155 FLJ13231 FLJ39155 5p13.1 38.52-38.97 0,46 2 (3) LIFR MGC39830 LIFR MGC39830 39.14-40.8 1,65 3 (3) FYB DAB2 PRKAA1 PRKAA1 41.03-41.34 0,31 3 (3) FLJ40243 C6 5q33.2-q33.3 154.18-156.28 2,1 3 (3) C5orf4 SGCD LOC91937 5q33.3 156.63-156.99 0,36 1 (3) CYFIP2 CYFIP2 SOX30 157.12-157.15 0,03 2 (3) LSM11 LSM11 159.37-159.61 0,24 3 (3) KIAA1935 FLJ14166 5q33.3-q34 159.76-161.21 1,45 3 (3) SLU7 PTTG1 GABRA1 PTTG1 5q34 161.43-162.8 1,37 3 (3) GABRG2 CCNG1 5q35.1 167.65-167.91 0,26 2 (4) KIBRA PANK3 168.35-170.66 2,31 4 (4) FLJ20364 DOCK2 LCP2 DOCK2 LCP2 171.4-171.57 0,17 1 (4) STK10 6p24.1 11.82-12.13 0,31 2 (3) C6orf105 HIVEP1 12.4-13.43 1,02 3 (3) TBC1D7 6p23 13.68-13.7 0,02 3 (3) SIRT5 SIRT5 13.72-15.35 1,63 3 (3) NOL7 CD83 JARID2 JARID2 7p22.1 5.04-5.12 0,08 2 (3) DKFZP434J154 KIAA1856 5.84-5.92 0,08 2 (3) JTV1 6.14-6.19 0,05 2 (3) MGC12966 RAC1 6.22-7.06 0,84 3 (3) LOC221955 KDELR2 ZDHHC4 C7orf28B C1GALT1 7p21.3 7.4-7.78 0,39 4 (4) FLJ20323 RPA3 GLCCI1 RPA3 GLCCI1 7.93-10.92 2,99 3 (4) ICA1 11.19-12.5 1,31 4 (4) KIAA0960 ARL4A KIAA0960 ARL4A 7p21.2-p21.1 13.7-16.08 2,38 3 (3) ETV1 MEOX2 ETV1 7p21.1-p15.3 17.7-19.51 1,81 3 (3) SNX13 HDAC9 7p15.3 19.95-20.14 0,2 2 (4) 20.23-20.46 0,23 4 (4) ABCB5 20.47-21.92 1,45 4 (4) DNAH11 NULL 21.93-22.75 0,82 4 (4) RAPGEF5 IL6 LOC54543 DRCTNNB1A RAPGEF5 22.99-23.06 0,07 3 (4) NUPL2 GPNMB GPNMB 23.19-24.39 1,19 2 (4) TRA2A MPP6 TRA2A 24.51-24.61 0,1 3 (4) DFNA5 OSBPL3 DFNA5 OSBPL3 7p15.2 25.41-25.47 0,06 3 (4) 25.66-26.6 0,94 4 (4) NFE2L3 HNRPA2B1 CBX3 KIAA0087 CBX3 26.91-26.93 0,02 3 (4) HOXA1 HOXA2 26.93-27.01 0,07 3 (4) HOXA4 HOXA13 27.65-27.65 0 4 (4) 7p15.2-p15.1 27.92-29.46 1,54 4 (4) CHN2 NULL CHN2 NULL 7p15.1 29.48-29.83 0,35 5 (5) SCRN1 FKBP14 29.89-29.95 0,05 5 (5) Ells1 30-30.02 0,02 3 (5) FKBP14 FKBP14 30.1-30.32 0,23 4 (5) ZNRF2 DKFZp586I1420 ZNRF2 DKFZp586I1420 30.36-31.5 1,14 5 (5) GARS INMT C7orf16 GARS INMT 7p14.3 32.57-32.83 0,25 3 (3) KBTBD2 FKBP9 NT5C3 KBTBD2 32.91-34.74 1,83 2 (3) RP9 B1 NULL BMPER RP9 35.41-35.5 0,09 2 (3) 7p14.2-p14.1 35.72-38.2 2,48 4 (4) ELMO1 UCC1 TRGV9 AMPH TRGV9 AMPH 7p14.1 38.54-39.38 0,85 3 (4) VPS41 C7orf36 39.58-39.76 0,18 3 (4) CDC2L5 41.5-42.73 1,23 4 (4) INHBA GLI3 C7orf25 42.93-43.25 0,33 3 (4) NEDL1 7p13 43.32-43.42 0,1 4 (4) 43.44-43.45 0,02 2 (4) STK17A FLJ10803 43.68-44.01 0,33 4 (4) MRPS24 AEBP1 YKT6 AEBP1 YKT6 44.33-44.44 0,11 3 (4) NPC1L1 DDX56 HNLF OGDH 44.88-44.91 0,03 2 (4) TBRG4 7q22.1 98.27-98.75 0,48 2 (3) SMURF1 PDAP1 ATP5J2 ZFP95 ZFP95 98.97-99.16 0,2 2 (3) TRIM4 99.58-99.71 0,13 2 (3) PILRB PILRB 99.81-100.1 0,29 2 (3) PILRA TRIP6 PILRA 100.58-101.49 0,91 2 (3) AP1S1 AP1S1 101.72-101.9 0,18 3 (3) POLR2J POLR2J2 POLR2J2 7q32.2-q32.3 129.53-130.47 0,94 3 (3) CPA4 TSGA14 COPG2 MKLN1 COPG2 7q33 132.7-133.1 0,41 2 (3) 134.32-134.53 0,21 3 (3) HSPC049 CNOT4 135.11-136.36 1,25 2 (3) 136.37-136.53 0,16 2 (3) DGKI 7q34 138.37-138.71 0,33 2 (4) FLJ25778 LUC7L2 HIPK2 FLJ25778 HIPK2 138.76-139.24 0,48 3 (4) ZC3HDC1 139.24-139.87 0,63 2 (4) KIAA1718 SLC37A3 NDUFB2 139.89-139.98 0,1 3 (4) BRAF 140.16-140.86 0,69 4 (4) MRPS33 FLJ10842 LCHN FLJ10842 LCHN 140.89-140.99 0,1 3 (4) SSBP1 SSBP1 141.41-142.01 0,6 3 (4) TRY1 PRSS2 142.09-142.5 0,41 3 (4) TRPV6 FLJ90586 7q36.1 148.43-148.85 0,42 3 (4) FLJ31413 FLJ31413 KIAA1862 148.97-149.17 0,2 4 (4) KIAA0543 LOC90520 KIAA0543 LOC90520 149.48-149.57 0,09 2 (4) LOC285972 149.7-150.08 0,38 4 (4) HIMAP4 IAN4L1 KCNH2 8q13.1 66.68-66.8 0,12 3 (3) FLJ10511 CHPPR PDE7A FLJ10511 CHPPR PDE7A 67.25-67.57 0,32 2 (3) CRH RRS1 ADHFE1 MGC33510 67.7-67.85 0,15 2 (3) 8q13.2 68.14-68.4 0,26 3 (3) FLJ22490 BIG1 BIG1 68.5-69.31 0,81 2 (3) CPA6 CPA6 8q13.2-q13.3 69.51-71.24 1,73 3 (3) VEST1 NCOA2 NULL VEST1 NULL 8q21.11 74.14-74.87 0,73 2 (4) RPESP RDH10 FLJ11011 RPESP RDH10 FLJ11011 75.02-76.06 1,04 4 (4) TCEB1 GDAP1 LOC83690 TCEB1 GDAP1 8q21.11-q21.12 77.78-79.59 1,81 3 (3) ZFH4 PXMP3 PKIA PKIA 8q21.12 79.74-79.78 0,04 3 (3) CGI-62 CGI-62 8q21.13 81.11-81.56 0,45 2 (5) TPD52 ZBTB10 81.6-81.62 0,02 5 (5) 81.7-82.36 0,66 4 (5) PAG FABP5 82.52-82.7 0,19 3 (5) PMP2 FABP4 PMP2 FABP4 82.73-82.78 0,04 3 (5) IMPA1 FLJ14007 IMPA1 FLJ14007 8q21.2 86.28-86.74 0,47 3 (3) E2F5 CA13 CA2 E2F5 CA13 8q21.3 87.42-90.98 3,56 4 (4) WWP1 CPNE3 CNGB3 MMP16 C8orf1 CNGB3 C8orf1 91.01-91.08 0,07 3 (4) NBS1 91.14-93.04 1,9 3 (4) CALB1 CBFA2T1 CBFA2T1 8q22.1 93.97-94.78 0,82 3 (4) LOC286144 LOC137392 94.81-95 0,19 3 (4) LOC389677 PRO1905 PPM2C LOC389677 PRO1905 PPM2C 95.33-95.9 0,57 3 (4) GEM FLJ20171 FLJ20530 FLJ20530 95.96-97.31 1,35 3 (4) CCNE2 MGC40214 UQCRB UQCRB 97.34-97.69 0,35 4 (4) PTDSS1 SDC2 PTDSS1 SDC2 97.73-98.73 1 4 (4) PGCP LYRIC PGCP 8q22.1-q22.2 99.1-99.12 0,03 4 (4) MATN2 RPL30 MATN2 8q22.2 99.21-99.65 0,44 5 (5) POP1 FLJ13955 KCNS2 POP1 FLJ13955 100.09-100.96 0,86 2 (5) COH1 COX6C COH1 COX6C 8q22.2-q22.3 101.23-101.99 0,76 6 (6) POLR2K LOC157567 8q22.3 102.25-102.28 0,03 3 (5) LOC51123 LOC51123 102.57-102.57 0 5 (5) TFCP2L3 TFCP2L3 103.08-103.29 0,21 5 (5) RRM2B 103.33-103.45 0,12 3 (5) DD5 103.73-104.22 0,49 4 (5) TIEG OAZIN ATP6V1C1 BAALC TIEG BAALC 104.38-104.53 0,15 3 (5) FZD6 FZD6 104.9-105.46 0,56 3 (5) RIMS2 RIMS2 DPYS 8q23.1 106.59-108.27 1,68 5 (5) 8q23.1-q23.3 110.32-114.23 3,91 4 (4) CML66 e(y)2 KCNV1 CSMD3 CML66 e(y)2 KCNV1 8q23.3-q24.11 116.49-117.72 1,23 5 (5) TRPS1 8q24.11 118.03-118.88 0,85 4 (4) SLC30A8 SLC30A8 EXT1 8q24.12 120.64-120.66 0,02 3 (3) ENPP2 121.31-121.61 0,3 2 (3) 8q24.13 124.33-124.4 0,07 2 (4) ZHX1 ATAD2 ATAD2 124.58-124.79 0,21 2 (4) FBXO32 ANXA13 FBXO32 125.58-125.66 0,07 3 (4) MTSS1 125.72-126.32 0,6 3 (4) KIAA0196 126.37-127 0,63 4 (4) 8q24.21 127.63-128.22 0,58 2 (4) NSE2 NSE2 128.82-128.91 0,09 2 (4) MYC MYC 129.18-130.92 1,74 4 (4) PVT1 PVT1 131.13-131.4 0,26 3 (4) DDEF1 DDEF1 8q24.22 132.98-133.08 0,1 5 (7) KIAA0143 133.2-134.12 0,92 7 (7) KCNQ3 CGI-72 SLA SLA 134.27-134.64 0,37 6 (7) WISP1 WISP1 8q24.22-q24.23 135.85-139.22 3,38 4 (4) KHDRBS3 LOC51059 KHDRBS3 LOC51059 8q24.3 141.17-141.66 0,48 3 (4) EIF2C2 EIF2C2 141.74-141.78 0,04 4 (4) PTK2 PTK2 141.8-141.96 0,16 2 (4) 142.51-143.84 1,33 2 (4) PTP4A3 FLJ31164 PTP4A3 9q31.2-q31.3 110.21-111.4 1,2 3 (3) POLYDOM EDG2 LTB4DH 9q33.3 126.17-126.25 0,08 4 (4) C9orf28 C9orf28 9q34.3-q34.3 137.27- (TERMINUS) TERMINUS 3 (3) MAN1B1 DPP7 DPP7 COBRA1 COBRA1 10p15.1 3.81-4.88 1,07 2 (3) COPEB COPEB 5.48-5.77 0,28 3 (3) NET1 C10orf18 NET1 5.78-6.06 0,28 3 (3) GDI2 FBXO18 IL15RA 6.19-6.25 0,06 3 (3) RBM17 6.4-6.51 0,11 3 (3) PRKCQ 10p15.1-p14 6.67-7.24 0,58 3 (3) SFMBT2 11q14.2 86.65-87.69 1,05 3 (3) CTSC CTSC 14q11.2 20.74-20.89 0,15 2 (3) HNRPC SUPT16H 21.02-21.99 0,97 2 (3) C14orf92 TRD@ 22.31-22.38 0,06 2 (3) SLC7A7 SLC7A7 MMP14 22.44-22.63 0,19 2 (3) RBM23 SKB1 JUB ACIN1 C14orf119 RBM23 22.83-22.86 0,03 3 (3) BCL2L2 PABPN1 14q22.1 52.15-52.18 0,03 3 (3) DKFZp762F0713 ERO1L ERO1L ERO1L ERO1L 14q22.1-q22.2 52.26-52.31 0,05 3 (3) PSMC6 14q22.2-q22.3 54.38-54.59 0,21 3 (3) GCH1 C14orf32 14q22.3 54.67-54.81 0,14 3 (3) LGALS3 DLG7 DLG7 16p13.13 10.53-10.95 0,41 3 (3) EMP2 NUBP1 DEXI KIAA0350 11.26-11.75 0,5 2 (3) SOCS1 LITAF ZC3HDC7 LITAF 16p13.11 14.98-15.41 0,44 3 (3) KIAA0251 NTAN1 RRN3 RRN3 15.58-15.64 0,06 3 (3) BC008967 LKAP NDE1 BC008967 NDE1 15.87-16.15 0,28 3 (3) FLJ31153 ABCC6 FLJ31153 ABCC6 16p12.3 17.1-18.52 1,41 2 (4) 18.7-19.03 0,33 2 (4) RPS15A ARL6IP SMG1 LOC162073 19.04-19.42 0,38 2 (4) LOC51760 MIR16 LOC51760 19.64-20.46 0,82 4 (4) MGC35048 GPRC5B 16p12.1 21.74-22 0,26 3 (3) UQCRC2 LOC146174 LOC146174 22.13-22.22 0,09 3 (3) EEF2K POLR3E EEF2K 22.26-22.98 0,72 2 (3) CDR2 CDR2 23.33-23.37 0,04 2 (3) COG7 NULL 23.5-23.6 0,09 2 (3) PLK1 PLK1 25.19-27.14 1,96 2 (3) NSE1 NSE1 16q22.1 66.68-66.82 0,14 2 (3) NFATC3 NFATC3 67.13-67.24 0,11 2 (3) ZFP90 CDH3 ZFP90 67.33-67.71 0,38 3 (3) CDH1 FLJ12688 FLJ20400 FLJ12688 68.16-68.3 0,14 2 (3) NFAT5 NFAT5 NQO1 17p13.1 8.47-8.72 0,25 2 (3) 9.5-10.34 0,84 3 (3) NULL RCV1 GAS7 MYH1 NULL MYH1 20q13.12 42.56-42.95 0,39 2 (3) TDE1 YWHAB 43.53-43.91 0,38 3 (3) WFDC2 PTE1 WFDC2 44.07-44.62 0,55 3 (3) MMP9 SLC13A3 MMP9 SLC13A3 20q13.2 52-52.22 0,23 3 (3) CYP24A1 ARF1 CYP24A1 ARF1 20q13.2-q13.31 52.26-55.18 2,91 3 (3) PFDN4 DOK5 STK6 CSTF1 BMP7 STK6 CSTF1 BMP7 20q13.31 55.38-55.4 0,02 3 (3) RAE1 RNPC1 RNPC1 55.57-55.66 0,09 2 (3) PCK1 20q13.32 56.24-56.33 0,09 2 (3) RAB22A 56.4-56.86 0,46 3 (3) VAPB NULL GNAS 57.03-57.04 0,01 2 (3) TUBB1 ATP5E TUBB1 20q13.32-q13.33 57.31-57.94 0,63 3 (3) EDN3 C20orf177 20q13.33 58.09-58.33 0,24 4 (4) 59.97-60.31 0,34 2 (4) PSMA7 60.4-60.99 0,59 3 (4) CABLES2 DATF1 CABLES2 DATF1 61.04-61.55 0,51 3 (4) C20orf11 ARFGAP1 KIAA1510 NULL KIAA1510 Xp22.11 23.45-23.83 0,38 3 (3) PRDX4 PRDX4 EIF2S3 23.93-24.39 0,47 2 (3) ZFX EIF2S3 PDK3 PDK3 Xp21.3-p21.1 27.12-37.4 10,27 3 (3) DMD TM4SF10 PRRG1 XK DMD Xp21.1-p11.4 37.45-38.41 0,96 3 (3) TCTE1L TM4SF2 TCTE1L TM4SF2 Xq11.2 65.02-65.02 0 3 (3) Z39IG Z39IG Xq12 66.73-67.54 0,8 3 (3) MGC21416 MGC21416 MCR MET MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Deleted Genes in MET Correlated mRNA expression data in MET 1p32.1-p31.3 60.07-61.86 1,79 3 (3) CYP2J2 MGC34837 NFIA NFIA BBP 2p23.3 24.16-24.78 0,61 2 (3) FLJ21945 TP53I3 ITSN2 NCOA1 FLJ21945 TP53I3 NCOA1 24.93-25.55 0,63 2 (3) MGC11266 RBJ DNMT3A DTNB 26.9-26.98 0,08 3 (3) C2orf18 C2orf18 4q13.2-q13.3 69.34-70.88 1,54 3 (3) UGT2B15 UGT2B4 4q13.3 70.89-71.89 1 3 (3) SULT1E1 IGJ 72.02-72.57 0,55 2 (3) RIPX GRSF1 DCK SLC4A4 RIPX 72.97-73.51 0,54 3 (3) GC 74.29-74.34 0,06 2 (3) FLJ38991 ANKRD17 74.46-74.49 0,03 3 (3) 74.76-74.97 0,21 2 (3) 75.1-75.22 0,12 2 (3) CXCL1 75.42-75.6 0,17 2 (3) FLJ13105 5q13.2 68.57-68.9 0,33 2 (3) CDK7 MRVLDC2 OCLN GTF2H2 CDK7 OCLN 68.91-69.24 0,33 2 (3) SMA5 69.32-69.32 0 3 (3) 70.3-71.44 1,14 2 (3) BIRC1 MAP1B 71.65-72.88 1,23 2 (3) PTCD2 TNPO1 LOC115548 BTF3 ANKRA2 72.9-73.02 0,12 2 (3) FLJ12787 RGNEF 6p24.3 10.52-10.54 0,01 3 (3) FILIP1 SENP6 MYO6 IMPG1 HMGN3 SH3BGRL2 6q14.1 76.06-83.8 7,74 3 (3) C6orf37 C6orf157 SH3BGRL2 C6orf37 6q14.2 83.93-84.11 0,17 3 (3) PGM3 RWDD2 ME1 PGM3 ME1 84.32-84.63 0,31 2 (3) SNAP91 NCB5OR NCB5OR 6q14.3-q15 84.8-87.92 3,12 3 (3) C6orf117 C6orf84 NT5E SYNCRIP CGA ZNF292 C6orf117 C6orf84 SYNCRIP ZNF292 6q15 88-88.14 0,14 2 (3) C6orf162 88.17-88.17 0 2 (3) C6orf165 88.28-89.9 1,63 3 (3) C6orf165 ORC3L CNR1 NULL C6orf165 NULL 90.09-90.2 0,11 3 (3) UBE2J1 NULL RRAGD ANKRD6 UBE2J1 RRAGD ANKRD6 90.33-90.41 0,08 3 (3) MDN1 6q15-q16.1 90.61-94.01 3,4 4 (4) CASP8AP2 MAP3K7 EPHA7 MAP3K7 6q16.1-q16.2 97.86-99.45 1,59 3 (3) MYST3 FBXL4 MYST3 6q16.3 99.97-100.05 0,08 3 (3) C6orf111 C6orf111 6q27 166.8-167.36 0,57 2 (3) RPS6KA2 RNASET2 167.37-167.9 0,54 2 (3) CCR6 168.11-169.67 1,56 2 (3) MLLT4 THBS2 MLLT4 169.92-169.97 0,04 3 (3) PHF10 PHF10 8p23.3 0.17-0.21 0,03 2 (3) 0.35-0.39 0,05 2 (3) FBXO25 0.4-0.42 0,01 3 (3) 1.7-1.97 0,27 2 (3) CLN8 8p23.2-p23.1 2.78-6.25 3,47 3 (3) CSMD1 FLJ12847 8p23.1 6.29-6.35 0,06 2 (3) ANGPT2 6.46-6.59 0,13 2 (3) 6.82-7.74 0,92 2 (3) 8.72-10.56 1,84 3 (3) 3'HEXO KRT6A 11.32-11.6 0,28 2 (3) C8orf13 GATA4 11.73-11.74 0,01 2 (3) FDFT1 8p21.2 23.41-23.45 0,04 3 (4) 23.45-23.49 0,03 2 (4) MSCP MSCP 24.86-25.33 0,47 3 (4) NEFL GNRH1 NEFL 25.37-25.78 0,41 2 (4) CDCA2 26.2-26.31 0,1 3 (4) PPP2R2A BNIP3L PPP2R2A BNIP3L 26.38-27.2 0,82 4 (4) TRIM35 TRIM35 8p21.1 27.44-27.55 0,11 2 (4) SCARA3 27.69-28.01 0,32 3 (4) LOC157570 TOPK ELP3 28.41-28.92 0,52 3 (4) FZD3 FLJ10871 FLJ21616 FLJ21616 28.97-29.25 0,28 4 (4) KIF13B KIF13B 8p12 30.13-30.56 0,42 2 (4) DCTN6 RBPMS DCTN6 RBPMS GTF2E2 30.62-30.66 0,04 2 (4) GSR 30.72-30.97 0,25 3 (4) D8S2298E 31.01-33.02 2,01 4 (4) WRN NRG1 33.47-36.67 3,21 2 (4) LOC84549 36.86-37.84 0,97 2 (4) C8orf2 PROSC BRF2 38.12-38.14 0,02 2 (4) LSM1 38.15-38.39 0,24 2 (4) BAG4 DDHD2 HTPAP FGFR1 HTPAP 8q13.3-q21.11 72.92-74.14 1,22 3 (3) MSC TERF1 RPESP TERF1 RPESP 10q23.1-q23.2 82.27-88.8 6,53 3 (3) DC-TM4F2 PCDH21 KIAA1128 BMPR1A GLUD1 KIAA1128 GLUD1 10q23.2 88.84-88.99 0,14 3 (3) FAM35A FAM35A 89.04-89.06 0,02 3 (3) 10q23.2-q23.31 89.08-90.7 1,61 4 (4) ATAD1 PTEN LIPL3 ACTA2 ATAD1 PTEN ACTA2 10q23.31 90.74-90.77 0,03 3 (5) TNFRSF6 90.96-91.08 0,11 5 (5) LIPA IFIT2 LIPA 91.15-91.33 0,18 2 (5) IFIT1 IFIT5 PANK1 91.45-92.49 1,04 2 (5) MPHOSPH1 10q23.31-q23.32 92.66-93.69 1,02 3 (3) ANKRD1 RNF159 TNKS2 BTAF1 BTAF1 10q26.13 123.23-123.71 0,48 2 (3) FGFR2 124.02-124.12 0,1 2 (3) C10orf87 124.19-124.68 0,49 3 (3) C10orf88 124.73-124.76 0,03 3 (3) C10orf89 ZNFN1A5 ACADSB 124.9-125.5 0,59 3 (3) BUB3 LOC119587 126.48-126.62 0,14 3 (3) KIAA0157 ZRANB1 12p13.2-p13.1 11.81-12.71 0,89 3 (3) LRP6 CREBL2 GPR19 CREBL2 13q12.12 23.35-23.89 0,54 3 (3) SPATA13 ADPRTL1 SPATA13 13q12.13-q12.2 26.54-26.73 0,19 3 (3) USP12 RPL21 RPL21 13q12.2 26.91-27.09 0,18 2 (3) MTIF3 MGC9850 MTIF3 27.65-27.7 0,05 3 (3) 13q12.3 29.93-30.21 0,28 3 (3) HMGB1 C13orf22 ALOX5AP HMGB1 13q12.3-q13.1 30.38-31.5 1,13 3 (3) FLJ14834 HSPH1 B3GTL 13CDNA73 HSPH1 13q13.1-q13.3 32.75-35.49 2,74 3 (3) RFC3 13q13.3 35.75-35.77 0,02 2 (3) 36.31-36.95 0,65 3 (3) EXOSC8 P38IP EXOSC8 37.82-38.82 0,99 3 (3) Ufm1 LHFP Ufm1 LHFP 39.13-39.2 0,08 2 (3) COG6 13q13.3-q14.11 39.23-41.71 2,48 4 (4) FOXO1A MRPS31 ELF1 KBTBD6 KIAA0564 MRPS31 ELF1 KIAA0564 13q14.11 41.74-42.5 0,75 3 (3) AKAP11 DNAJD1 AKAP11 42.58-43.36 0,78 3 (3) FLJ38725 FLJ38725 13q14.11-q14.12 43.5-44.86 1,36 3 (3) TGFB1I4 GTF2F2 KCTD4 13q14.12 45.43-45.86 0,42 3 (3) KIAA0853 CPB2 LCP1 C13orf18 LCP1 13q14.13-q14.2 46.03-46.31 0,28 3 (3) LRCH1 NULL HTR2A 13q14.2 47.55-47.96 0,41 4 (4) VDRIP P2RY5 CHC1L VDRIP P2RY5 48.45-48.68 0,24 4 (4) KIAA0970 KIAA0970 13q14.2-q14.3 48.72-48.92 0,2 4 (4) CDADC1 SETDB2 13q14.3 49-49.13 0,13 3 (3) RCBTB1 RCBTB1 EBPL 49.17-49.38 0,21 3 (3) KPNA3 C13orf1 KPNA3 49.87-50.41 0,54 2 (3) FLJ11712 51.02-51.24 0,22 2 (3) 51.25-51.5 0,24 2 (3) ATP7B KIAA0266 ATP7B KIAA0266 51.64-51.93 0,29 3 (3) 13q21.32-q21.33 65.77-70.91 5,14 3 (3) PCDH9 DACH1 DACH1 13q22.1-q22.2 72.18-75 2,82 3 (3) FLJ22624 KIAA1008 KLF12 KIAA1008 COMMD6 13q22.3 76.47-76.48 0,01 3 (3) FBXL3A FBXL3A 77.03-77.21 0,19 3 (3) SCEL FLJ30046 13q22.3-q31.1 77.37-78.79 1,42 3 (3) EDNRB POU4F1 C13orf7 C13orf10 EDNRB C13orf10 13q31.1 78.95-79.81 0,85 3 (3) NDFIP2 NDFIP2 13q31.1-q31.2 85.26-86.89 1,63 3 (3) SLITRK6 18q21.1 42.64-42.94 0,3 2 (3) NULL PIAS2 DKFZP564D1378 HSPC039 DKFZP564D1378 HSPC039 43.62-44.03 0,41 3 (3) SMAD2 44.82-45.56 0,75 3 (3) RPL17 LIPG ACAA2 RPL17 45.6-46.34 0,74 2 (3) MYO5B MAPK4 18q21.2 46.75-49.93 3,19 4 (4) ELAC1 SMAD4 MBD2 ELAC1 SMAD4 MBD2 50-50.72 0,72 3 (4) RAB27B SE57-1 RAB27B 18q21.2-q21.31 51.04-53.18 2,14 4 (4) TCF4 TXNL1 WDR7 TCF4 WDR7 18q21.31 53.37-54.17 0,8 5 (5) FECH NEDD4L NEDD4L 54.27-54.27 0 4 (5) 18q21.31-q21.32 54.3-54.57 0,27 4 (4) HAK 18q21.32 54.68-55.25 0,57 5 (5) ZNF532 LOC90701 LMAN1 ZNF532 LOC90701 LMAN1 18q21.32-q21.33 55.72-58.36 2,64 4 (4) PMAIP1 PIGN ZCCHC2 PIGN ZCCHC2 18q21.33-q22.1 58.38-62.32 3,94 4 (4) ZCCHC2 PLEKHE1 BCL2 FVT1 SERPINB3 CDH19 PLEKHE1 CDH19 18q22.1 63.32-64.54 1,21 5 (5) NCAG1 18q22.2-q22.3 65.66-70.25 4,59 4 (4) DOK5L RTTN SOCS6 HSPC154 CYB5 SOCS6 HSPC154 CYB5 22q12.2 29.69-30.22 0,53 3 (3) FLJ20618 LIMK2 DRG1 KIAA0542 FLJ20618 LIMK2 22q12.3 31.52-31.99 0,47 3 (3) TIMP3 LARGE TIMP3 32.2-34.15 1,95 2 (3) HMG2L1 MCM5 34.33-34.46 0,13 2 (3) MB RBM9 35-35.24 0,24 2 (3) MYH9 MCR PCA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Amplified Genes in PCA Correlated mRNA expression data in PCA 1p33 46.57-46.75 0,18 2 (2) FAAH 46.81-46.85 0,04 2 (2) ATPAF1 46.98-47.25 0,27 2 (2) CYP4B1 CYP4A11 CYP4X1 48.28-48.4 0,12 2 (2) 48.48-50.29 1,81 2 (2) SPATA6 1p33-p32.3 51.14-51.41 0,28 2 (2) CDKN2C RNF11 1p13.1 116.78-116.79 0,01 2 (2) 1q23.2 157.9-157.95 0,05 2 (2) NIT1 158.36-158.45 0,09 2 (2) FCGR2B FREB DUSP12 FCGR2B

3q13.11-q13.12 107.58-108.31 0,73 2 (2) NULL 3q13.12 108.45-109.04 0,59 2 (2) BBX LOC151658 109.24-109.29 0,05 2 (2) CD47 3q13.12-q13.13 109.36-109.75 0,39 2 (2) ESRRBL1 3q21.2 126.65-127.64 0,99 3 (3) SNX4 SLC41A3 MGC11349 3q21.2-q21.3 127.65-128.89 1,24 2 (2) 3q29 197.68-197.77 0,09 2 (2) MGC64882 5q32 143.52-145.56 2,05 5 (5) SMAP-5 SH3RF2 RBM27 6q27 170.53-170.59 0,06 2 (2) KIAA1838 7p15.1 28.64-28.8 0,17 2 (2) 29.48-29.5 0,02 2 (2) 7p14.1 38.07-38.2 0,13 2 (2) TRGV9 TRGV9 38.54-39.38 0,85 2 (2) VPS41 39.76-41.5 1,74 2 (2) CDC2L5 41.77-42.72 0,95 2 (2) GLI3 C7orf25 GLI3 7p14.1-p13 43.25-43.42 0,16 2 (2) 7q11.23 76.47-76.58 0,11 2 (2) FGL2 76.81-77.11 0,3 2 (2) PTPN12 7q21.12 86.62-86.66 0,05 2 (2) TP53AP1 C7orf23 86.67-87.21 0,54 2 (2) CROT ABCB1 7q34 140.99-141.41 0,42 3 (3) TRY1 142.01-142.09 0,08 3 (3) TRPV6 142.48-142.5 0,02 3 (3) FLJ90586 CASP2 8p23.3 0.18-0.21 0,03 2 (2) 8q12.1 59.88-61.28 1,4 2 (2) TOX CA8 8q22.1 97.73-98.24 0,51 2 (2) PGCP 8q23.1 109.28-110.42 1,13 3 (3) EIF3S6 CML66 e(y)2 8q23.2-q23.3 111.05-113.3 2,26 2 (2) KCNV1 CSMD3 8q23.3-q24.11 114.23-117.72 3,49 2 (2) TRPS1 8q24.11 118.03-118.88 0,85 4 (4) SLC30A8 EXT1 EXT1 8q24.11-q24.12 119.12-120 0,89 3 (3) TNFRSF11B 8q24.12 120.64-120.66 0,02 3 (3) ENPP2 8q24.13 125.72-126.11 0,39 2 (2) KIAA0196 8q24.21 128.13-128.22 0,08 2 (3) 128.91-130.3 1,39 3 (3) PVT1 PVT1 8q24.21-q24.22 131.13-133.08 1,95 3 (3) DDEF1 KIAA0143 8q24.22 133.2-134.12 0,92 3 (3) KCNQ3 CGI-72 SLA KCNQ3 134.27-134.64 0,37 2 (3) WISP1 8q24.23-q24.3 139.22-140.28 1,05 3 (3) LOC51059 8q24.3 141.66-141.78 0,12 2 (2) PTK2 144.17-144.19 0,02 2 (2) LY6E FLJ37131 145.59-145.71 0,12 2 (2) CPSF1 145.97-146 0,03 2 (2) 9p22.3 14.61-14.78 0,17 2 (2) ZDHHC21 9q22.32 96.6-96.73 0,14 2 (2) ZNF510 9q31.2 108.86-109.09 0,23 2 (2) C9orf5 EPB41L4B 9q31.2-q31.3 110.21-110.72 0,51 2 (2) POLYDOM EDG2 9q31.3 111.4-111.4 0,01 2 (2) LTB4DH 112.71-112.95 0,23 2 (2) 9q33.1 119.01-120.44 1,43 2 (2) DBC1 9q33.2 125.28-125.63 0,35 2 (2) MAPKAP1 PBX3 9q33.3 127.54-127.78 0,25 2 (2) 137.28-137.43 0,14 2 (2) DPP7 DPP7 COBRA1 11p15.4 5.22-5.22 0 2 (2) 5.57-6.3 0,72 2 (2) TRIM6 TRIM5 13q33.1 101.16-101.17 0,01 2 (2) Xq11.2-q12 65.02-67.54 2,51 2 (2) Z39IG MGC21416 MCR PCA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Deleted Genes in PCA Correlated mRNA expression data in PCA 1q22-q23.1 154.3-155.07 0,78 2 (2) RAB25 CD5L CD1D RAB25 1q23.1 155.39-155.61 0,22 3 (3) SPTA1 SPTA1 1q23.2 157.95-158 0,04 2 (2) B4GALT3 B4GALT3 1q24.1 164.64-165.13 0,49 2 (2) PC326 GPR161 1q24.1-q24.2 165.4-166.22 0,82 2 (2) DPT BLZF1 F5

1q24.2 167.23-167.43 0,2 2 (2) FLJ11752 NULL FLJ11752 NULL 167.96-168.02 0,06 2 (2) FMO1 1q42.13 227.08-227.28 0,19 2 (2) COG2 AGT FLJ14525 FLJ14525 227.44-227.71 0,27 2 (2) ARV1 GNPAT GNPAT 1q42.13-q42.2 228.03-229.25 1,21 2 (2) KIAA1383 2q22.3-q23.1 144.98-148.52 3,54 2 (2) ZFHX1B ACVR2 ORC4L 2q23.1 148.61-148.71 0,09 2 (2) 2q23.1-q23.2 148.77-149.7 0,93 2 (2) EPC2 NULL KIF5C EPC2 3q26.33 181-181.8 0,81 3 (3) NULL TTC14 5q12.3-q13.2 65.49-68.52 3,03 2 (2) SFRS12 LOC375449 KIAA0303 PIK3R1 KIAA0303 PIK3R1 5q13.2 71.44-71.65 0,21 2 (2) MAP1B 72.24-72.29 0,05 2 (2) TNPO1 LOC115548 72.83-72.83 0,01 2 (2) BTF3 5q13.2-q13.3 72.9-74.02 1,12 2 (2) FLJ12787 RGNEF ENC1 HEXB 5q13.3 74.05-74.1 0,05 2 (4) EFG2 74.11-74.41 0,3 3 (4) KIAA0888 ANKRD31 74.57-74.88 0,31 2 (4) COL4A3BP POLK COL4A3BP 75.66-75.8 0,14 4 (4) 75.95-76.28 0,34 2 (4) F2RL2 F2R CRHBP 5q13.3-q14.1 76.36-76.54 0,18 2 (2) VG5Q PDE8B PDE8B 5q14.1 76.76-76.96 0,2 2 (2) FLJ10904 FLJ10904 6q13 74.03-74.08 0,05 2 (2) C6orf148 6q14.1 75.91-76.41 0,5 2 (3) FILIP1 SENP6 76.52-78.33 1,82 3 (3) MYO6 IMPG1 82.28-83.8 1,52 3 (3) C6orf37 C6orf157 6q14.2 83.93-84.11 0,17 3 (3) PGM3 RWDD2 ME1 PGM3 RWDD2 ME1 84.32-84.63 0,31 3 (3) SNAP91 NCB5OR SNAP91 NCB5OR 6q14.3 84.8-86.27 1,47 4 (4) C6orf117 C6orf84 NT5E SYNCRIP 86.31-86.43 0,12 2 (4) 6q15 87.86-88.14 0,28 4 (4) CGA ZNF292 C6orf162 ZNF292 88.17-88.17 0 2 (4) C6orf165 88.28-88.36 0,08 3 (4) C6orf165 C6orf165 90.09-90.12 0,03 3 (4) UBE2J1 NULL 90.13-90.2 0,07 3 (4) RRAGD ANKRD6 RRAGD 90.33-90.41 0,08 3 (4) MDN1 90.61-91.28 0,68 4 (4) CASP8AP2 MAP3K7 MAP3K7 6q16.1 94.01-96.13 2,12 2 (2) EPHA7 MANEA 97.44-97.48 0,04 2 (2) KIAA1900 6q16.1-q16.3 97.86-100.05 2,19 3 (3) MYST3 FBXL4 C6orf111 C6orf111 6q21 105.28-105.65 0,37 3 (3) HACE1 BVES 105.71-105.91 0,2 2 (3) POPDC3 108.3-108.47 0,17 3 (3) SEC63 109.82-109.89 0,07 3 (3) PPIL6 ZBTB24 PPIL6 110.53-111.04 0,51 3 (3) WASF1 CDK11 111.32-111.91 0,6 3 (3) AMD1 SLC16A10 AMD1 111.96-112.03 0,07 3 (3) C6orf4 C6orf4 112.09-112.5 0,41 2 (3) FYN TUBE1 112.52-113.85 1,34 2 (3) LAMA4 6q22.1 116.7-116.71 0 2 (2) TSPYL1 6q22.31 122.65-123.1 0,45 3 (3) HSF2 TDE2 PKIB 8p23.3 0.39-1.7 1,31 2 (2) 8p23.1 6.46-6.59 0,13 2 (2) 6.82-8.9 2,08 2 (2) SPAG11 3'HEXO 9.95-10.62 0,67 2 (2) KRT6A 8p22 17.45-17.55 0,09 2 (2) SLC7A2 MTUS1 17.55-17.96 0,41 2 (2) PDGFRL FGL1 8p21.3-p21.2 23.1-23.45 0,35 2 (2) LYSAL1 LYSAL1 8p21.2 24.86-25.78 0,92 2 (2) NEFL GNRH1 CDCA2 26.2-26.31 0,1 2 (2) PPP2R2A BNIP3L 26.38-27.2 0,82 2 (2) TRIM35 8p21.1 27.44-27.55 0,11 2 (2) SCARA3 27.69-27.72 0,04 2 (2) LOC157570 28.01-28.26 0,25 2 (2) ELP3 PNOC 28.41-28.68 0,27 2 (2) FZD3 FZD3 8p21.1-p12 28.8-30.13 1,33 2 (2) FLJ21616 KIF13B DCTN6 DCTN6 8p12 30.54-30.72 0,18 2 (2) RBPMS GTF2E2 GSR D8S2298E GSR 37.82-37.84 0,02 2 (2) BRF2 RCP 10q21.2 61.46-62.73 1,27 2 (2) ANK3 CDC2 RHOBTB1 10q23.1-q23.2 86.12-88.51 2,39 2 (2) KIAA1128 10q23.2 88.8-88.84 0,04 2 (2) GLUD1 FAM35A 88.95-89.08 0,13 2 (2) 10q23.2-q23.31 89.5-89.61 0,11 4 (4) ATAD1 PTEN ATAD1 10q23.31 90.74-90.77 0,03 4 (4) TNFRSF6 TNFRSF6 90.96-91.05 0,09 3 (4) LIPA IFIT2 91.15-91.33 0,18 3 (4) IFIT1 IFIT5 91.33-91.9 0,57 2 (4) PANK1 MPHOSPH1 10q23.31-q23.32 92.66-94.2 1,54 3 (3) ANKRD1 RNF159 TNKS2 BTAF1 10q23.33 94.82-95.35 0,52 2 (3) CYP26A1 FER1L3 C10orf3 RBP4 95.74-95.85 0,11 2 (3) PLCE1 96.08-96.3 0,21 3 (3) C10orf117 HELLS 96.69-97.06 0,37 3 (3) CYP2C9 CYP2C8 SORBS1 CYP2C9 97.41-97.62 0,2 2 (3) C10orf61 ENTPD1 10q23.33-q24.1 97.79-98.27 0,48 3 (3) CCNJ ZNF518 SMBP ZNF518 SMBP 10q24.1 98.58-99.11 0,52 3 (4) MLR2 SLIT1 ARHGAP19 KIAA0690 KIAA0690 99.21-99.33 0,13 4 (4) MMS19L 10q24.1-q24.2 99.36-100.13 0,77 2 (2) C10orf83 PI4KII 10q24.2 101.46-101.63 0,16 2 (2) COX15 ABCC2 DNMBP COX15 101.9-101.94 0,04 2 (2) C10orf69 C10orf69 10q24.31 102.1-102.29 0,19 2 (2) SCD SCD 13q13.1 31.5-31.79 0,28 2 (2) 13CDNA73 BRCA2 31.99-32.1 0,11 2 (2) PFAAP5 PFAAP5 32.13-32.58 0,44 2 (2) KL KL 13q13.2-q13.3 33.44-35.24 1,81 2 (2) RFC3 13q13.3 35.75-35.77 0,02 2 (2) SPG20 36.47-36.95 0,48 2 (2) EXOSC8 P38IP EXOSC8 13q14.11-q14.12 43.5-44.94 1,44 3 (3) TGFB1I4 GTF2F2 KCTD4 COG3 TGFB1I4 13q14.12 45.43-45.52 0,09 2 (5) KIAA0853 45.53-45.6 0,07 5 (5) CPB2 LCP1 LCP1 45.82-45.86 0,04 4 (5) C13orf18 13q14.13-q14.2 46.03-47.51 1,48 3 (3) LRCH1 NULL HTR2A NUDT15 13q14.2 47.55-47.96 0,41 5 (5) VDRIP P2RY5 CHC1L 48.45-48.68 0,24 4 (5) KIAA0970 KIAA0970 48.72-48.9 0,18 5 (5) CDADC1 13q14.3 48.92-49 0,09 2 (3) SETDB2 RCBTB1 RCBTB1 49.13-49.47 0,34 3 (3) EBPL KPNA3 C13orf1 RFP2 RFP2 EBPL RFP2 49.47-49.87 0,4 2 (3) RFP2 RFP2 DLEU1 RFP2 50.41-50.69 0,28 3 (3) FLJ11712 FLJ30707 51.02-51.24 0,21 2 (3) 13q21.33-q22.2 70.91-75 4,09 2 (2) DACH1 FLJ22624 KIAA1008 KLF12 13q22.2 75.09-75.34 0,25 2 (2) LMO7 16p12.2 21.27-21.57 0,3 4 (4) RABIF KIAA0220 IMAA IMAA 16p12.1 21.71-21.74 0,03 3 (3) 16q22.1 66.12-66.43 0,31 2 (2) FLJ13725 CTCF 24432 PARD6A RANBP10 THAP11 CTCF 66.54-66.68 0,14 2 (2) SLC12A4 DPEP2 FLJ20399 SLC12A4 17p13.1 8.28-8.47 0,19 2 (2) NDEL1 17q12 29.61-30.31 0,71 2 (2) CCL2 CCL7 CCL13 30.35-30.58 0,23 2 (2) LIG3 LOC117584 30.93-31.29 0,36 2 (2) PEX12 GAR17 PEX12 17q21.2 35.8-35.88 0,09 2 (2) TOP2A 37.26-37.28 0,02 2 (2) KLHL11 ACLY ACLY 17q21.31 38.06-38.09 0,02 3 (4) TUBG2 CNTNAP1 38.22-38.24 0,02 4 (4) BECN1 PSME3 PSME3 38.25-38.26 0,01 2 (4) AOC2 18p11.31 3-3.34 0,34 2 (2) MRLC2 18q21.32 54.97-55.15 0,18 2 (2) LOC90701 LMAN1 18q21.33 57.86-59.31 1,45 2 (2) PIGN ZCCHC2 ZCCHC2 PLEKHE1 BCL2 FVT1 18q21.33-q22.1 59.47-63.32 3,85 2 (2) SERPINB3 CDH19 Xp22.11-p21.3 23.93-27.12 3,19 3 (3) ZFX EIF2S3 PDK3 Xp21.2 30.03-30.9 0,86 2 (2) MCR H-PCA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Amplified Genes in H-PCA Correlated mRNA expression data in H-PCA 3q29 197.68-197.77 0,09 2 (2) MGC64882

5q32 143.52-143.84 0,32 2 (4) SMAP-5 145.12-145.81 0,69 4 (4) SH3RF2 RBM27 TCERG1 7p14.1 38.07-38.2 0,13 2 (2) TRGV9 TRGV9 38.54-39.38 0,85 2 (2) VPS41 39.76-41.5 1,74 2 (2) CDC2L5 41.77-42.72 0,95 2 (2) GLI3 C7orf25 GLI3 7p14.1-p13 43.25-43.42 0,16 2 (2) 7q11.23 76.47-76.58 0,11 2 (2) FGL2 76.81-77.11 0,3 2 (2) PTPN12 7q21.12 86.62-86.66 0,05 2 (2) TP53AP1 C7orf23 86.67-87.21 0,54 2 (2) CROT ABCB1 7q34 140.99-141.41 0,42 2 (2) TRY1 142.01-142.09 0,09 2 (2) TRPV6 142.5-142.5 0 2 (2) FLJ90586 CASP2 8q12.1 59.88-61.28 1,4 2 (2) TOX CA8 8q23.1 110.32-110.42 0,09 2 (2) CML66 e(y)2 8q23.2-q23.3 111.05-113.3 2,26 2 (2) KCNV1 CSMD3 8q23.3-q24.11 114.23-117.72 3,49 2 (2) TRPS1 8q24.11 118.88-118.88 0 3 (3) EXT1 EXT1 8q24.11-q24.12 119.12-120 0,89 2 (2) TNFRSF11B 8q24.12 120.64-120.66 0,02 3 (3) ENPP2 8q24.13 125.72-126.11 0,39 2 (2) KIAA0196 ANXA13 8q24.21 128.13-128.22 0,08 2 (3) 128.91-130.3 1,39 3 (3) PVT1 PVT1 8q24.21-q24.22 131.13-133.08 1,95 3 (3) DDEF1 KIAA0143 8q24.22 133.2-134.12 0,92 3 (3) KCNQ3 CGI-72 SLA KCNQ3 134.27-134.64 0,37 2 (3) WISP1 8q24.23-q24.3 139.22-140.28 1,05 2 (2) LOC51059 8q24.3 141.66-141.78 0,12 2 (2) PTK2 144.17-144.19 0,02 2 (2) LY6E FLJ37131 145.59-145.71 0,12 2 (2) CPSF1 145.97-146 0,03 2 (2) 14.61-14.78 0,17 2 (2) ZDHHC21 9q31.2 108.86-109.09 0,23 2 (2) C9orf5 EPB41L4B 9q31.2-q31.3 110.21-110.72 0,51 2 (2) POLYDOM EDG2 9q31.3 111.4-111.4 0,01 2 (2) LTB4DH 112.71-112.95 0,23 2 (2) 9q33.1 119.01-120.44 1,43 2 (2) DBC1 9q33.2 125.28-125.63 0,35 2 (2) MAPKAP1 PBX3 MCR H-PCA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Deleted Genes in H-PCA Correlated mRNA expression data in H-PCA 3q26.33 181-181.8 0,81 2 (2) NULL 5q12.3-q13.2 66.38-68.52 2,14 2 (2) KIAA0303 PIK3R1 KIAA0303 PIK3R1 5q13.2 72.24-72.29 0,05 2 (2) TNPO1 LOC115548 5q13.3 74.11-74.41 0,3 2 (2) KIAA0888 ANKRD31

74.57-74.7 0,13 2 (2) COL4A3BP 75.66-75.8 0,14 2 (2) 6q14.2 83.96-84.11 0,15 2 (2) RWDD2 ME1 RWDD2 84.32-84.63 0,31 2 (2) SNAP91 NCB5OR SNAP91 NCB5OR 6q14.3 84.8-86.27 1,47 2 (2) C6orf117 C6orf84 NT5E SYNCRIP 6q15 88-88.14 0,14 2 (2) C6orf162 88.28-88.36 0,08 2 (2) C6orf165 C6orf165 6q21 109.82-109.89 0,07 2 (2) PPIL6 ZBTB24 PPIL6 110.53-111.04 0,51 2 (2) WASF1 CDK11 111.61-111.98 0,38 2 (2) SLC16A10 C6orf4 C6orf4 112.52-113.85 1,34 2 (2) LAMA4 6q22.1 116.7-116.71 0 2 (2) TSPYL1 8p21.1-p12 29.25-30.13 0,89 2 (2) DCTN6 10q23.1-q23.2 86.12-88.51 2,39 2 (2) KIAA1128 10q23.2 88.8-88.84 0,04 2 (2) GLUD1 FAM35A 10q23.2-q23.31 89.5-89.61 0,11 3 (3) ATAD1 PTEN ATAD1 10q23.31 90.74-90.77 0,03 3 (3) TNFRSF6 TNFRSF6 90.96-91.05 0,09 3 (3) LIPA IFIT2 91.15-91.33 0,18 2 (3) IFIT1 IFIT5 91.33-91.9 0,57 2 (3) PANK1 MPHOSPH1 10q23.32 92.99-94.2 1,21 2 (2) RNF159 TNKS2 BTAF1 10q23.33 94.82-95.35 0,52 2 (3) CYP26A1 FER1L3 C10orf3 RBP4 96.08-96.3 0,21 3 (3) C10orf117 96.69-97.06 0,37 3 (3) CYP2C9 CYP2C8 SORBS1 CYP2C9 97.41-97.62 0,2 2 (3) C10orf61 ENTPD1 10q23.33-q24.1 97.91-98.27 0,37 3 (3) ZNF518 SMBP SMBP 10q24.1 98.58-99.11 0,52 2 (3) MLR2 SLIT1 ARHGAP19 KIAA0690 KIAA0690 99.21-99.33 0,13 3 (3) MMS19L 10q24.1-q24.2 99.36-100.13 0,77 2 (2) C10orf83 PI4KII 10q24.2 101.46-101.63 0,16 2 (2) COX15 ABCC2 DNMBP COX15 101.9-101.94 0,04 2 (2) C10orf69 C10orf69 10q24.31 102.1-102.29 0,19 2 (2) SCD SCD 13q13.1 31.5-31.79 0,28 2 (2) 13CDNA73 BRCA2 31.99-32.1 0,11 2 (2) PFAAP5 PFAAP5 32.13-32.58 0,44 2 (2) KL KL 13q13.2-q13.3 33.44-35.24 1,81 2 (2) RFC3 13q13.3 35.75-35.77 0,02 2 (2) SPG20 36.47-36.95 0,48 2 (2) EXOSC8 P38IP EXOSC8 13q14.11-q14.12 43.5-44.94 1,44 3 (3) TGFB1I4 GTF2F2 KCTD4 COG3 TGFB1I4 13q14.12 45.43-45.52 0,09 2 (4) KIAA0853 45.53-45.6 0,07 4 (4) CPB2 LCP1 LCP1 45.82-45.86 0,04 4 (4) C13orf18 13q14.13-q14.2 46.03-47.51 1,48 3 (3) LRCH1 NULL HTR2A NUDT15 13q14.2 47.55-47.96 0,41 5 (5) VDRIP P2RY5 CHC1L 48.45-48.68 0,24 4 (5) KIAA0970 KIAA0970 48.72-48.9 0,18 5 (5) CDADC1 13q14.3 48.92-49 0,09 2 (3) SETDB2 RCBTB1 RCBTB1 49.13-49.47 0,34 3 (3) EBPL KPNA3 C13orf1 RFP2 RFP2 EBPL RFP2 49.47-49.87 0,4 2 (3) RFP2 RFP2 DLEU1 RFP2 50.41-50.69 0,28 3 (3) FLJ11712 FLJ30707 51.02-51.24 0,21 2 (3) 13q21.33-q22.2 70.91-75 4,09 2 (2) DACH1 FLJ22624 KIAA1008 KLF12 13q22.2 75.09-75.34 0,25 2 (2) LMO7 16p12.2 21.27-21.57 0,3 2 (2) RABIF KIAA0220 IMAA IMAA 16p12.1 21.71-21.74 0,03 2 (2) 17p13.1 8.28-8.47 0,19 2 (2) NDEL1 17q12 29.61-29.71 0,1 2 (2) CCL2 CCL7 CCL13 30.35-30.58 0,23 2 (2) LIG3 LOC117584 30.93-31.29 0,36 2 (2) PEX12 GAR17 PEX12 17q21.2 35.8-35.88 0,09 2 (2) TOP2A 37.26-37.28 0,02 2 (2) KLHL11 ACLY ACLY 17q21.31 38.06-38.09 0,02 2 (3) TUBG2 CNTNAP1 38.22-38.24 0,02 3 (3) BECN1 PSME3 PSME3 38.25-38.26 0,01 2 (3) AOC2 MCR L-PCA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Amplified Genes in L-PCA Correlated mRNA expression data in L-PCA 3q21.2 126.65-127.64 0,99 3 (3) SNX4 SLC41A3 MGC11349 7p15.1 28.64-28.8 0,17 2 (2) 11p15.4 5.22-5.22 0 2 (2) Xq11.2-q12 65.02-67.54 2,51 2 (2) Z39IG MGC21416 MCR L-PCA MCRs Recurrence

Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Deleted Genes in L-PCA Correlated mRNA expression data in L-PCA 1q23.1 155.39-155.61 0,22 2 (2) SPTA1 SPTA1 1q24.1 164.64-165.13 0,49 2 (2) PC326 GPR161 1q24.1-q24.2 165.4-166.22 0,82 2 (2) DPT BLZF1 F5 5q13.3 74.7-75.8 1,1 2 (2) COL4A3BP POLK COL4A3BP 75.95-76.05 0,1 2 (2) F2RL2 F2R 6q13 74.03-74.08 0,05 2 (2) C6orf148 6q14.1 75.91-76.41 0,5 2 (3) FILIP1 SENP6 76.52-78.33 1,82 2 (3) MYO6 IMPG1 82.51-83.8 1,29 3 (3) C6orf37 6q14.2 83.98-84.32 0,34 2 (2) ME1 SNAP91 ME1 SNAP91 6q14.2-q14.3 84.63-84.89 0,26 3 (3) NCB5OR C6orf117 C6orf84 NCB5OR 6q14.3-q15 86.22-88 1,79 3 (3) NT5E SYNCRIP CGA ZNF292 ZNF292 6q15 90.09-90.12 0,03 2 (3) UBE2J1 NULL 90.13-90.2 0,07 2 (3) RRAGD ANKRD6 90.33-90.41 0,08 2 (3) 90.61-91.28 0,67 3 (3) CASP8AP2 MAP3K7 MAP3K7 6q16.1-q16.3 94.01-100.05 6,04 2 (2) EPHA7 MANEA KIAA1900 MYST3 FBXL4 C6orf111 C6orf111 6q21 105.28-105.65 0,37 2 (2) HACE1 BVES 105.71-105.91 0,2 2 (2) POPDC3 108.3-108.47 0,17 2 (2) SEC63 110.86-111.91 1,05 2 (2) CDK11 AMD1 SLC16A10 AMD1 111.96-112.03 0,07 2 (2) C6orf4 C6orf4 6q22.31 122.76-123.1 0,34 2 (2) HSF2 TDE2 PKIB 8p21.2 25.33-26.31 0,98 2 (2) GNRH1 CDCA2 PPP2R2A BNIP3L 8p21.1 28.23-28.26 0,03 2 (2) PNOC 16p12.2 21.27-21.57 0,3 2 (2) RABIF KIAA0220 IMAA IMAA 16q22.1 66.12-66.43 0,31 2 (2) FLJ13725 CTCF 24432 PARD6A RANBP10 THAP11 66.54-66.61 0,08 2 (2) SLC12A4 DPEP2 FLJ20399 SLC12A4 18p11.31 3-3.34 0,34 2 (2) MRLC2 Xp22.11-p21.3 24.39-27.12 2,73 2 (2) PDK3 MCR PIN MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Amplified Genes in PIN Correlated mRNA expression data in PIN 3q29 197.18-197.26 0,08 2 (2) TFRC 5q31.3-q32 142.74-145.3 2,56 3 (3) SMAP-5 SH3RF2 5q32 145.56-145.81 0,24 2 (2) RBM27 TCERG1 6q27 169.97-170.78 0,81 2 (2) TCTE3 KIAA1838 TBP 8q24.3 146-146.03 0,03 2 (2) ZNF517 COMMD5 9p11.2-q12 44.43-64.19 19,76 2 (2) 9q12 66.89-66.92 0,02 2 (2) 67.16-67.94 0,78 2 (2) DC36 11q23.1-q23.2 111.46-114.55 3,09 2 (2) SDHD NCAM1 HTR3A ZNF145 FLJ20010 MCR PIN MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Deleted Genes in PIN Correlated mRNA expression data in PIN 6q22.31 122.76-122.81 0,04 2 (2) HSF2 11q13.4 73.18-73.4 0,23 2 (2) MRPL48 E2IG2 UCP2 16p12.2 21.27-21.57 0,3 2 (2) RABIF KIAA0220 IMAA IMAA 17q21.2 37.1-37.28 0,18 2 (2) SUI1 KLHL11 ACLY ACLY ATP6V0A1 HUMGT198A TUBG1 TUBG2 CNTNAP1 17q21.31 37.92-38.26 0,33 2 (2) BECN1 PSME3 AOC2 TUBG1 MCR PIA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Amplified Genes in PIA Correlated mRNA expression data in PIA

6q16.3 100.1-103.73 3,63 3 (3) CCNC GRIK2 11q13.1 65.81-65.99 0,18 2 (2) MGC35521 MCR PIA MCRs Recurrence Within MCR Size (Within Cytogenetic Band Position (Mb) (Mb) Cytoband) Candidate Deleted Genes in PIA Correlated mRNA expression data in PIA 9q34.2 135.19-135.6 0,41 2 (2) OLFM1 SURF1