Table S3. All Somatic Cnvs

Table S3. All somatic CNVs.

NimbleGen Genes Median Subject Tissue ChrStart End Size (bp) Probe Ratio NanoString Validation

1 1 Kidney 1 45,440,708 45,447,562 6,854 0.73 no ZSWIM5

2 1 Kidney 1 241,754,215241,757,6853,470 1.33 yes AKT3

FAM110C(dist=158857),SH 3 1 Kidney 2 195,445 198,701 3,256 1.34 yes 3YL1(dist=9435)

RBMS1(dist=96060),TANK( 4 1 Kidney 2 161,154,624161,159,1664,542 1.31 no dist=542546)

5 1 Kidney 3 65,814,757 65,818,257 3,500 1.49 yes MAGI1

6 1 Kidney 6 163,755,222163,765,79910,577 0.77 no QKI

7 1 Kidney 7 72,481,781 72,485,430 3,649 1.40 yes FZD9

8 1 Kidney 7 101,239,471101,250,53911,068 1.32 yes CUX1

9 1 Kidney 8 613,481 617,206 3,725 1.33 yes ERICH1 10 1 Kidney 8 96,672,562 96,679,885 7,323 0.72 no LOC100616530 23 1 Kidney 9 3,864,751 3,868,364 3,613 1.34 yes GLIS3

11 1 Kidney 9 127,690,680127,694,0143,334 0.75 no PBX3

12 1 Kidney 11 99,193,236 99,196,882 3,646 1.47 yes CNTN5

13 1 Kidney 12 44,403,980 44,419,704 15,724 1.30 no ARID2

RIC8B(dist=5209),C12orf23 14 1 Kidney 12 105,812,433105,816,2393,806 1.34 yes (dist=57435)

15 1 Kidney 12 128,877,358128,882,7995,441 1.34 yes TMEM132D

16 1 Kidney 13 109,227,714109,243,62715,913 1.30 yes IRS2

PKD1P1(dist=717970),XYL 17 1 Kidney 16 17,069,936 17,075,101 5,165 1.34 yes T1(dist=28581)

MMD(dist=8322),TMEM10 18 1 Kidney 17 50,862,662 50,866,937 4,275 1.33 yes 0(dist=285050) 19 1 Kidney 18 65,710,228 65,714,553 4,325 1.33 no CD226 NONE(dist=NONE),NONE( 20 1 Kidney 24 18,944,673 18,970,548 25,875 1.39 yes dist=NONE)

21 1 Liver 2 111,586,916111,600,60913,693 1.30 yes ACOXL,BCL2L11

22 1 Liver 8 12,649,633 12,661,093 11,460 1.38 yes LONRF1

24 1 Liver 12 10,254,489 10,267,488 12,999 1.30 yes GABARAPL1

25 1 Liver 14 20,214,196 20,232,695 18,499 1.31 yes ANG

26 1 Liver 16 78,184,067 78,196,131 12,064 1.39 yes MAF

NONE(dist=NONE),NONE( 27 1 Liver 23 53,306,456 53,317,478 11,022 1.31 yes dist=NONE)

28 1 LM 6 12,114,444 12,120,064 5,620 0.73 no HIVEP1

29 1 LM 11 133,705,007133,708,4493,442 0.74 no GLB1L2

30 1 Pancreas 1 37,270,433 37,273,808 3,375 0.76 no GRIK3 31 1 Pancreas 14 95,276,796 95,283,854 7,058 1.34 no TCL1A(dist=26510),C14orf1 32(dist=291561) 32 1 Pancreas 17 56,824,252 56,833,886 9,634 0.76 no BCAS3,TBX2

NONE(dist=NONE),NONE( 33 1 Pancreas 23 154,830,150154,837,6117,461 1.35 no dist=NONE)

RNF144A(dist=82297),LOC 38 1 Small Intestine 2 7,184,057 7,188,677 4,620 1.33 yes 339788(dist=791330)

34 1 Small Intestine 2 182,176,215182,181,2575,042 1.33 no CERKL

35 1 Small Intestine 5 172,041,831172,045,0003,169 1.34 no NEURL1B

36 1 Small Intestine 6 106,803,929106,808,0134,084 1.45 no ATG5

PSD3(dist=155922),SH2D4 39 1 Small Intestine 8 19,071,398 19,077,397 5,999 1.32 yes A(dist=137964)

KRAS(dist=93858),IFLTD1( 40 1 Small Intestine 12 25,388,979 25,392,207 3,228 1.37 yes dist=128076) 37 1 Small Intestine 14 19,544,554 19,548,482 3,928 1.34 no OR4K15(dist=29990),OR4K 14(dist=3778) 41 2 Lung 1 230,000,372230,004,5284,156 1.33 no DISC1

42 2 Lung 2 55,022,825 55,030,249 7,424 1.32 no EML6

H19(dist=43821),INS- 43 2 Lung 11 2,019,462 2,049,162 29,700 1.36 yes IGF2(dist=57756)

44 2 Lung 20 54,011,019 54,013,964 2,945 0.77 no CBLN4

45 3 Ovary 2 112,953,098112,961,2398,141 0.76 no TTL

46 3 Ovary 5 130,639,834130,646,8387,004 0.75 yes CDC42SE2

MSX2(dist=9273),DRD1(dis 47 3 Ovary 5 174,099,781174,106,3776,596 0.72 yes t=693904)

48 3 Ovary 5 175,595,003175,601,5966,593 0.77 yes C5orf25

49 3 Ovary 7 24,576,860 24,583,048 6,188 0.73 no MPP6 50 3 Ovary 8 1,032,473 1,041,190 8,717 0.77 no ERICH1(dist=361247),LOC 286083(dist=190511) 51 3 Ovary 10 93,757,255 93,764,113 6,858 0.77 no NEURL

52 3 Ovary 12 128,876,071128,882,7996,728 0.76 no TMEM132D

53 3 Ovary 15 32,113,199 32,122,141 8,942 0.77 no AVEN

54 3 Ovary 16 87,376,434 87,385,405 8,971 0.77 no FAM38A

55 3 Pancreas 1 53,695,072 53,702,040 6,968 0.77 no DMRTB1

56 3 Pancreas 2 10,956,170 10,969,300 13,130 0.73 no KCNF1

KLHL23,PHOSPHO2- 57 3 Pancreas 2 170,295,154170,306,63511,481 0.73 no KLHL23

58 3 Pancreas 2 236,782,454236,790,5828,128 0.72 no ASB18

59 3 Pancreas 3 71,853,510 71,861,093 7,583 0.74 no EIF4E3

NONE(dist=NONE),NCRN 60 3 Pancreas 4 182,098,963182,105,4546,491 0.72 no A00290(dist=116783) 61 3 Pancreas 5 167,215,459167,224,0178,558 0.77 no ODZ2 RFPL4B(dist=850197),MAR 62 3 Pancreas 6 113,629,388113,635,8966,508 0.76 no CKS(dist=649324)

C6orf208(dist=261912),LOC 63 3 Pancreas 6 170,206,806170,212,8606,054 0.74 no 154449(dist=192487)

64 3 Pancreas 7 3,304,102 3,309,710 5,608 0.74 no SDK1

65 3 Pancreas 7 55,997,218 56,002,950 5,732 0.71 no GBAS

66 3 Pancreas 8 31,005,969 31,011,551 5,582 0.76 no PURG

67 3 Pancreas 8 31,612,550 31,620,931 8,381 0.76 no NRG1

68 3 Pancreas 9 2,031,149 2,042,021 10,872 0.76 no SMARCA2

69 3 Pancreas 10 118,881,755118,888,3346,579 0.77 no VAX1

70 3 Pancreas 11 8,057,235 8,066,291 9,056 0.75 no TUB

71 3 Pancreas 11 132,313,412132,321,0467,634 0.77 no OPCML 72 3 Pancreas 12 95,108,475 95,114,126 5,651 0.74 no ELK3 ALOX5AP(dist=70226),LO 73 3 Pancreas 13 30,306,791 30,315,302 8,511 0.71 no C100507064(dist=39670)

74 3 Pancreas 13 95,538,636 95,542,908 4,272 0.68 no HS6ST3

75 3 Pancreas 14 55,113,566 55,120,332 6,766 0.76 no KTN1

DKFZP434L187(dist=3245), 76 3 Pancreas 15 28,297,280 28,308,068 10,788 0.73 no CHRFAM7A(dist=132667)

MCTP2(dist=594355),LOC4 77 3 Pancreas 15 93,422,540 93,427,386 4,846 0.74 no 00456(dist=196137)

78 3 Pancreas 15 99,843,944 99,852,646 8,702 0.75 no PCSK6

79 3 Pancreas 17 24,936,846 24,946,452 9,606 0.74 no ANKRD13B,GIT1

80 3 Pancreas 18 12,295,508 12,302,462 6,954 0.76 no TUBB6

81 3 Pancreas 18 33,395,955 33,401,725 5,770 0.74 no CELF4 82 3 Pancreas 18 65,709,187 65,714,553 5,366 0.75 no CD226 83 3 Pancreas 20 536,089 542,963 6,874 0.75 no TCF15

84 3 Pancreas 20 33,273,796 33,281,087 7,291 0.76 no MMP24

C20orf85(dist=61368),PPP4 85 3 Pancreas 20 56,230,957 56,240,180 9,223 0.75 no R1L(dist=1059)

86 3 Pancreas 21 42,168,493 42,174,466 5,973 0.74 no PRDM15

87 3 Pancreas 22 17,514,194 17,525,049 10,855 0.76 no PI4KAP2

NONE(dist=NONE),NONE( 88 3 Pancreas X 2,509,332 2,514,665 5,333 0.75 yes dist=NONE)

NONE(dist=NONE),NONE( 89 3 Pancreas X 106,577,605106,582,7715,166 0.75 no dist=NONE)

90 3 Small Intestine 12 28,009,155 28,020,495 11,340 0.77 no PTHLH

91 4 Liver 6 147,565,333147,569,4504,117 0.74 no STXBP5

92 4 Pancreas 1 37,157,522 37,163,060 5,538 1.33 no GRIK3 FAM19A1(dist=146054),FA 93 4 Pancreas 3 68,823,515 68,828,906 5,391 1.31 no M19A4(dist=34701)

METTL19(dist=25547),GPR 94 4 Pancreas 4 8,554,729 8,560,916 6,187 1.38 no 78(dist=72275)

C4orf41(dist=82686),STOX2 95 4 Pancreas 4 184,954,425184,958,2293,804 0.76 no (dist=105274)

96 4 Pancreas 7 56,527,153 56,532,976 5,823 1.33 no DKFZp434L192

97 4 Pancreas 12 130,251,707130,255,7944,087 1.32 no LOC116437

98 4 Pancreas 17 15,842,495 15,846,025 3,530 0.72 no TTC19,ZSWIM7

NONE(dist=NONE),NONE( 99 4 Pancreas X 52,573,484 52,577,913 4,429 1.30 no dist=NONE)

1004 Uterus 2 21,116,836 21,123,573 6,737 0.77 no APOB

1014 Uterus 3 125,084,481125,086,4882,007 0.76 no MYLK 1024 Uterus 4 171,181,666171,185,1783,512 0.71 no MFAP3L 1034 Uterus 6 12,115,576 12,122,259 6,683 0.76 no HIVEP1

1044 Uterus 6 135,543,285135,547,8324,547 0.74 no MYB

1054 Uterus 7 24,576,860 24,583,048 6,188 0.77 no MPP6

1064 Uterus 7 35,040,519 35,045,668 5,149 0.76 no DPY19L1

1074 Uterus 18 65,710,228 65,714,553 4,325 0.77 no CD226

GRIK2(dist=1238414),HAC 1085 Liver 6 103,863,065103,870,8757,810 1.37 no E1(dist=1411786)

GRIK2(dist=1227342),HAC 1095 Small Intestine 6 103,851,993103,864,42812,435 0.72 no E1(dist=1418233)

KCP(dist=2264),IRF5(dist=2 1105 Small Intestine 7 128,340,273128,345,0224,749 1.31 no 0208)

C9orf172,C9orf86,MAMDC 1115 Small Intestine 9 138,847,343138,870,81823,475 1.31 no 4,PHPT1 1125 Small Intestine 15 80,701,647 80,722,679 21,032 1.31 no RPS17(dist=89727),LOC727 849(dist=19169) NONE(dist=NONE),NONE( 1135 Small Intestine 23 63,980,447 63,985,969 5,522 0.74 no dist=NONE)

NONE(dist=NONE),NONE( 1145 Small Intestine 23 154,831,176154,837,6116,435 0.75 no dist=NONE)

1156 Brain 5 108,698,758108,710,24511,487 0.69 yes PJA2

1166 Brain 6 31,616,403 31,620,082 3,679 1.46 no DDX39B

1176 Brain 9 131,680,557131,688,5147,957 1.36 no USP20

MCTP2(dist=359779),LOC4 1186 Brain 15 93,187,964 93,191,272 3,308 0.70 no 00456(dist=432251)

1196 Brain 17 27,869,055 27,872,703 3,648 0.71 no MYO1D

GLIS1(dist=2089),TMEM48 1206 IPL 1 53,974,554 53,979,985 5,431 0.67 no (dist=23737) 1216 IPL 1 57,659,184 57,664,947 5,763 0.73 no DAB1 1226 IPL 1 239,583,115239,589,6876,572 0.73 no RGS7

1236 IPL 3 184,897,349184,901,3874,038 0.72 no YEATS2

1246 IPL 5 121,214,422121,218,0243,602 0.68 no FTMT

1256 IPL 12 70,430,520 70,437,125 6,605 0.73 no RAB21

1266 IPL 14 63,999,672 64,002,836 3,164 0.68 no AKAP5

1276 IPL 16 53,518,176 53,526,748 8,572 0.70 no IRX5

1286 IPL 20 24,395,505 24,401,190 5,685 0.73 no TMEM90B

1296 IPL 22 44,272,847 44,279,688 6,841 0.74 no FBLN1

1306 Liver 4 170,154,184170,175,94321,759 1.36 yes CBR4

1316 Liver 6 91,048,808 91,061,450 12,642 1.35 yes BACH2 1326 Liver 9 93,209,441 93,230,677 21,236 1.40 yes NFIL3 1336 Liver 18 42,164,424 42,172,455 8,031 1.43 no RNF165

1346 Liver 20 32,754,200 32,772,040 17,840 1.37 yes NCOA6,TP53INP2

1356 MFG 1 92,266,406 92,269,568 3,162 0.73 no EPHX4

1366 Pancreas 1 51,198,847 51,218,531 19,684 1.37 yes CDKN2C

1376 Pancreas 1 87,560,135 87,580,513 20,378 1.38 yes LMO4

1386 Pancreas 1 145,866,228145,868,3112,083 1.37 no GPR89B

1396 Pancreas 2 156,890,257156,907,17216,915 1.35 yes NR4A2

1406 Pancreas 2 196,229,174196,239,46110,287 1.37 no SLC39A10

1416 Pancreas 3 4,984,941 5,012,135 27,194 1.37 yes BHLHE40

1426 Pancreas 3 158,010,833158,030,97420,141 1.35 yes LEKR1

1436 Pancreas 3 188,925,954188,959,44933,495 1.45 yes BCL6

1446 Pancreas 4 89,415,770 89,433,001 17,231 1.36 yes PPM1K 1456 Pancreas 5 175,888,203175,904,57616,373 1.37 yes RNF44

CBX3,HNRNPA2B1,NFE2L 1466 Pancreas 7 26,191,257 26,214,104 22,847 1.49 yes 3

1476 Pancreas 7 66,091,425 66,107,367 15,942 1.41 no SBDS,TYW1

1486 Pancreas 7 111,869,656111,895,17525,519 1.39 yes IFRD1

1496 Pancreas 8 27,495,161 27,534,390 39,229 1.41 yes CLU

1506 Pancreas 8 110,611,866110,738,283126,417 1.36 yes EBAG9,SYBU

1516 Pancreas 9 92,985,690 93,021,811 36,121 1.35 yes AUH

1526 Pancreas 10 44,784,383 44,814,399 30,016 1.44 yes C10orf10,RASSF4

1536 Pancreas 10 76,823,641 76,853,136 29,495 1.37 yes ZNF503

1546 Pancreas 11 6,580,473 6,599,224 18,751 1.49 yes ILK,RRP8,TAF10,TPP1

1556 Pancreas 11 118,261,700118,310,20448,504 1.38 yes BCL9L,CXCR5

1566 Pancreas 12 10,254,489 10,269,030 14,541 1.47 yes GABARAPL1 1576 Pancreas 12 48,637,502 48,648,586 11,084 1.37 yes AQP5 1586 Pancreas 12 123,956,167123,992,63536,468 1.40 yes UBC

1596 Pancreas 14 20,208,447 20,232,695 24,248 1.40 yes ANG

1606 Pancreas 14 103,060,972103,067,3966,424 1.39 yes TRMT61A

1616 Pancreas 16 20,226,136 20,250,529 24,393 1.39 yes GP2

1626 Pancreas 16 22,102,579 22,127,188 24,609 1.43 yes EEF2K

1636 Pancreas 16 55,511,416 55,536,398 24,982 1.36 yes HERPUD1

1646 Pancreas 17 7,675,763 7,697,250 21,487 1.42 yes DNAH2,KDM6B

1656 Pancreas 17 21,116,426 21,133,749 17,323 1.42 yes MAP2K3

1666 Pancreas 17 23,391,896 23,397,559 5,663 1.41 yes NLK

1676 Pancreas 18 44,713,065 44,742,508 29,443 1.36 yes SMAD7

AKT1S1,PNKP,PTOV1,TB 1686 Pancreas 19 55,054,868 55,073,275 18,407 1.40 yes C1D17

1696 Pancreas 20 22,499,060 22,510,719 11,659 1.36 yes FOXA2 1706 Pancreas 20 23,283,755 23,305,948 22,193 1.37 yes GZF1

1716 Pancreas 20 43,388,697 43,432,265 43,568 1.36 yes SDC4,SYS1

1726 Pancreas 22 40,169,632 40,174,377 4,745 1.47 yes TOB2

C22orf32,FAM109B,NAGA, 1736 Pancreas 22 40,792,846 40,832,863 40,017 1.36 yes NDUFA6

1746 Pancreas 22 44,747,130 44,931,494 184,364 1.38 yes C22orf26,WNT7B

1756 Pancreas 22 48,685,508 48,759,107 73,599 1.38 yes ALG12,CRELD2,PIM3

NONE(dist=NONE),NONE( 1766 Pancreas 23 39,815,040 39,847,432 32,392 1.36 yes dist=NONE)

NONE(dist=NONE),NONE( 1776 Pancreas 23 53,116,022 53,141,249 25,227 1.36 yes dist=NONE)

NONE(dist=NONE),NONE( 1786 Pancreas 23 102,823,065102,835,57612,511 1.37 yes dist=NONE)