<p>Table S3. All somatic CNVs. </p><p>NimbleGen Genes Median Subject Tissue ChrStart End Size (bp) Probe Ratio NanoString Validation</p><p>1 1 Kidney 1 45,440,708 45,447,562 6,854 0.73 no ZSWIM5</p><p>2 1 Kidney 1 241,754,215241,757,6853,470 1.33 yes AKT3</p><p>FAM110C(dist=158857),SH 3 1 Kidney 2 195,445 198,701 3,256 1.34 yes 3YL1(dist=9435)</p><p>RBMS1(dist=96060),TANK( 4 1 Kidney 2 161,154,624161,159,1664,542 1.31 no dist=542546)</p><p>5 1 Kidney 3 65,814,757 65,818,257 3,500 1.49 yes MAGI1</p><p>6 1 Kidney 6 163,755,222163,765,79910,577 0.77 no QKI</p><p>7 1 Kidney 7 72,481,781 72,485,430 3,649 1.40 yes FZD9</p><p>8 1 Kidney 7 101,239,471101,250,53911,068 1.32 yes CUX1</p><p>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</p><p>11 1 Kidney 9 127,690,680127,694,0143,334 0.75 no PBX3</p><p>12 1 Kidney 11 99,193,236 99,196,882 3,646 1.47 yes CNTN5</p><p>13 1 Kidney 12 44,403,980 44,419,704 15,724 1.30 no ARID2</p><p>RIC8B(dist=5209),C12orf23 14 1 Kidney 12 105,812,433105,816,2393,806 1.34 yes (dist=57435)</p><p>15 1 Kidney 12 128,877,358128,882,7995,441 1.34 yes TMEM132D</p><p>16 1 Kidney 13 109,227,714109,243,62715,913 1.30 yes IRS2</p><p>PKD1P1(dist=717970),XYL 17 1 Kidney 16 17,069,936 17,075,101 5,165 1.34 yes T1(dist=28581)</p><p>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)</p><p>21 1 Liver 2 111,586,916111,600,60913,693 1.30 yes ACOXL,BCL2L11</p><p>22 1 Liver 8 12,649,633 12,661,093 11,460 1.38 yes LONRF1</p><p>24 1 Liver 12 10,254,489 10,267,488 12,999 1.30 yes GABARAPL1</p><p>25 1 Liver 14 20,214,196 20,232,695 18,499 1.31 yes ANG</p><p>26 1 Liver 16 78,184,067 78,196,131 12,064 1.39 yes MAF</p><p>NONE(dist=NONE),NONE( 27 1 Liver 23 53,306,456 53,317,478 11,022 1.31 yes dist=NONE)</p><p>28 1 LM 6 12,114,444 12,120,064 5,620 0.73 no HIVEP1</p><p>29 1 LM 11 133,705,007133,708,4493,442 0.74 no GLB1L2</p><p>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</p><p>NONE(dist=NONE),NONE( 33 1 Pancreas 23 154,830,150154,837,6117,461 1.35 no dist=NONE)</p><p>RNF144A(dist=82297),LOC 38 1 Small Intestine 2 7,184,057 7,188,677 4,620 1.33 yes 339788(dist=791330)</p><p>34 1 Small Intestine 2 182,176,215182,181,2575,042 1.33 no CERKL</p><p>35 1 Small Intestine 5 172,041,831172,045,0003,169 1.34 no NEURL1B</p><p>36 1 Small Intestine 6 106,803,929106,808,0134,084 1.45 no ATG5</p><p>PSD3(dist=155922),SH2D4 39 1 Small Intestine 8 19,071,398 19,077,397 5,999 1.32 yes A(dist=137964)</p><p>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</p><p>42 2 Lung 2 55,022,825 55,030,249 7,424 1.32 no EML6</p><p>H19(dist=43821),INS- 43 2 Lung 11 2,019,462 2,049,162 29,700 1.36 yes IGF2(dist=57756)</p><p>44 2 Lung 20 54,011,019 54,013,964 2,945 0.77 no CBLN4</p><p>45 3 Ovary 2 112,953,098112,961,2398,141 0.76 no TTL</p><p>46 3 Ovary 5 130,639,834130,646,8387,004 0.75 yes CDC42SE2</p><p>MSX2(dist=9273),DRD1(dis 47 3 Ovary 5 174,099,781174,106,3776,596 0.72 yes t=693904)</p><p>48 3 Ovary 5 175,595,003175,601,5966,593 0.77 yes C5orf25</p><p>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</p><p>52 3 Ovary 12 128,876,071128,882,7996,728 0.76 no TMEM132D</p><p>53 3 Ovary 15 32,113,199 32,122,141 8,942 0.77 no AVEN</p><p>54 3 Ovary 16 87,376,434 87,385,405 8,971 0.77 no FAM38A</p><p>55 3 Pancreas 1 53,695,072 53,702,040 6,968 0.77 no DMRTB1</p><p>56 3 Pancreas 2 10,956,170 10,969,300 13,130 0.73 no KCNF1</p><p>KLHL23,PHOSPHO2- 57 3 Pancreas 2 170,295,154170,306,63511,481 0.73 no KLHL23</p><p>58 3 Pancreas 2 236,782,454236,790,5828,128 0.72 no ASB18</p><p>59 3 Pancreas 3 71,853,510 71,861,093 7,583 0.74 no EIF4E3</p><p>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)</p><p>C6orf208(dist=261912),LOC 63 3 Pancreas 6 170,206,806170,212,8606,054 0.74 no 154449(dist=192487)</p><p>64 3 Pancreas 7 3,304,102 3,309,710 5,608 0.74 no SDK1</p><p>65 3 Pancreas 7 55,997,218 56,002,950 5,732 0.71 no GBAS</p><p>66 3 Pancreas 8 31,005,969 31,011,551 5,582 0.76 no PURG</p><p>67 3 Pancreas 8 31,612,550 31,620,931 8,381 0.76 no NRG1</p><p>68 3 Pancreas 9 2,031,149 2,042,021 10,872 0.76 no SMARCA2</p><p>69 3 Pancreas 10 118,881,755118,888,3346,579 0.77 no VAX1</p><p>70 3 Pancreas 11 8,057,235 8,066,291 9,056 0.75 no TUB</p><p>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)</p><p>74 3 Pancreas 13 95,538,636 95,542,908 4,272 0.68 no HS6ST3</p><p>75 3 Pancreas 14 55,113,566 55,120,332 6,766 0.76 no KTN1</p><p>DKFZP434L187(dist=3245), 76 3 Pancreas 15 28,297,280 28,308,068 10,788 0.73 no CHRFAM7A(dist=132667)</p><p>MCTP2(dist=594355),LOC4 77 3 Pancreas 15 93,422,540 93,427,386 4,846 0.74 no 00456(dist=196137)</p><p>78 3 Pancreas 15 99,843,944 99,852,646 8,702 0.75 no PCSK6</p><p>79 3 Pancreas 17 24,936,846 24,946,452 9,606 0.74 no ANKRD13B,GIT1</p><p>80 3 Pancreas 18 12,295,508 12,302,462 6,954 0.76 no TUBB6</p><p>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</p><p>84 3 Pancreas 20 33,273,796 33,281,087 7,291 0.76 no MMP24</p><p>C20orf85(dist=61368),PPP4 85 3 Pancreas 20 56,230,957 56,240,180 9,223 0.75 no R1L(dist=1059)</p><p>86 3 Pancreas 21 42,168,493 42,174,466 5,973 0.74 no PRDM15</p><p>87 3 Pancreas 22 17,514,194 17,525,049 10,855 0.76 no PI4KAP2</p><p>NONE(dist=NONE),NONE( 88 3 Pancreas X 2,509,332 2,514,665 5,333 0.75 yes dist=NONE)</p><p>NONE(dist=NONE),NONE( 89 3 Pancreas X 106,577,605106,582,7715,166 0.75 no dist=NONE)</p><p>90 3 Small Intestine 12 28,009,155 28,020,495 11,340 0.77 no PTHLH</p><p>91 4 Liver 6 147,565,333147,569,4504,117 0.74 no STXBP5</p><p>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)</p><p>METTL19(dist=25547),GPR 94 4 Pancreas 4 8,554,729 8,560,916 6,187 1.38 no 78(dist=72275)</p><p>C4orf41(dist=82686),STOX2 95 4 Pancreas 4 184,954,425184,958,2293,804 0.76 no (dist=105274)</p><p>96 4 Pancreas 7 56,527,153 56,532,976 5,823 1.33 no DKFZp434L192</p><p>97 4 Pancreas 12 130,251,707130,255,7944,087 1.32 no LOC116437</p><p>98 4 Pancreas 17 15,842,495 15,846,025 3,530 0.72 no TTC19,ZSWIM7</p><p>NONE(dist=NONE),NONE( 99 4 Pancreas X 52,573,484 52,577,913 4,429 1.30 no dist=NONE)</p><p>1004 Uterus 2 21,116,836 21,123,573 6,737 0.77 no APOB</p><p>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</p><p>1044 Uterus 6 135,543,285135,547,8324,547 0.74 no MYB</p><p>1054 Uterus 7 24,576,860 24,583,048 6,188 0.77 no MPP6</p><p>1064 Uterus 7 35,040,519 35,045,668 5,149 0.76 no DPY19L1</p><p>1074 Uterus 18 65,710,228 65,714,553 4,325 0.77 no CD226</p><p>GRIK2(dist=1238414),HAC 1085 Liver 6 103,863,065103,870,8757,810 1.37 no E1(dist=1411786)</p><p>GRIK2(dist=1227342),HAC 1095 Small Intestine 6 103,851,993103,864,42812,435 0.72 no E1(dist=1418233)</p><p>KCP(dist=2264),IRF5(dist=2 1105 Small Intestine 7 128,340,273128,345,0224,749 1.31 no 0208)</p><p>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)</p><p>NONE(dist=NONE),NONE( 1145 Small Intestine 23 154,831,176154,837,6116,435 0.75 no dist=NONE)</p><p>1156 Brain 5 108,698,758108,710,24511,487 0.69 yes PJA2</p><p>1166 Brain 6 31,616,403 31,620,082 3,679 1.46 no DDX39B</p><p>1176 Brain 9 131,680,557131,688,5147,957 1.36 no USP20</p><p>MCTP2(dist=359779),LOC4 1186 Brain 15 93,187,964 93,191,272 3,308 0.70 no 00456(dist=432251)</p><p>1196 Brain 17 27,869,055 27,872,703 3,648 0.71 no MYO1D</p><p>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</p><p>1236 IPL 3 184,897,349184,901,3874,038 0.72 no YEATS2</p><p>1246 IPL 5 121,214,422121,218,0243,602 0.68 no FTMT</p><p>1256 IPL 12 70,430,520 70,437,125 6,605 0.73 no RAB21</p><p>1266 IPL 14 63,999,672 64,002,836 3,164 0.68 no AKAP5</p><p>1276 IPL 16 53,518,176 53,526,748 8,572 0.70 no IRX5</p><p>1286 IPL 20 24,395,505 24,401,190 5,685 0.73 no TMEM90B</p><p>1296 IPL 22 44,272,847 44,279,688 6,841 0.74 no FBLN1</p><p>1306 Liver 4 170,154,184170,175,94321,759 1.36 yes CBR4</p><p>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</p><p>1346 Liver 20 32,754,200 32,772,040 17,840 1.37 yes NCOA6,TP53INP2</p><p>1356 MFG 1 92,266,406 92,269,568 3,162 0.73 no EPHX4</p><p>1366 Pancreas 1 51,198,847 51,218,531 19,684 1.37 yes CDKN2C</p><p>1376 Pancreas 1 87,560,135 87,580,513 20,378 1.38 yes LMO4</p><p>1386 Pancreas 1 145,866,228145,868,3112,083 1.37 no GPR89B</p><p>1396 Pancreas 2 156,890,257156,907,17216,915 1.35 yes NR4A2</p><p>1406 Pancreas 2 196,229,174196,239,46110,287 1.37 no SLC39A10</p><p>1416 Pancreas 3 4,984,941 5,012,135 27,194 1.37 yes BHLHE40</p><p>1426 Pancreas 3 158,010,833158,030,97420,141 1.35 yes LEKR1</p><p>1436 Pancreas 3 188,925,954188,959,44933,495 1.45 yes BCL6</p><p>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</p><p>CBX3,HNRNPA2B1,NFE2L 1466 Pancreas 7 26,191,257 26,214,104 22,847 1.49 yes 3</p><p>1476 Pancreas 7 66,091,425 66,107,367 15,942 1.41 no SBDS,TYW1</p><p>1486 Pancreas 7 111,869,656111,895,17525,519 1.39 yes IFRD1</p><p>1496 Pancreas 8 27,495,161 27,534,390 39,229 1.41 yes CLU</p><p>1506 Pancreas 8 110,611,866110,738,283126,417 1.36 yes EBAG9,SYBU</p><p>1516 Pancreas 9 92,985,690 93,021,811 36,121 1.35 yes AUH</p><p>1526 Pancreas 10 44,784,383 44,814,399 30,016 1.44 yes C10orf10,RASSF4</p><p>1536 Pancreas 10 76,823,641 76,853,136 29,495 1.37 yes ZNF503</p><p>1546 Pancreas 11 6,580,473 6,599,224 18,751 1.49 yes ILK,RRP8,TAF10,TPP1</p><p>1556 Pancreas 11 118,261,700118,310,20448,504 1.38 yes BCL9L,CXCR5</p><p>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</p><p>1596 Pancreas 14 20,208,447 20,232,695 24,248 1.40 yes ANG</p><p>1606 Pancreas 14 103,060,972103,067,3966,424 1.39 yes TRMT61A</p><p>1616 Pancreas 16 20,226,136 20,250,529 24,393 1.39 yes GP2</p><p>1626 Pancreas 16 22,102,579 22,127,188 24,609 1.43 yes EEF2K</p><p>1636 Pancreas 16 55,511,416 55,536,398 24,982 1.36 yes HERPUD1</p><p>1646 Pancreas 17 7,675,763 7,697,250 21,487 1.42 yes DNAH2,KDM6B</p><p>1656 Pancreas 17 21,116,426 21,133,749 17,323 1.42 yes MAP2K3</p><p>1666 Pancreas 17 23,391,896 23,397,559 5,663 1.41 yes NLK</p><p>1676 Pancreas 18 44,713,065 44,742,508 29,443 1.36 yes SMAD7</p><p>AKT1S1,PNKP,PTOV1,TB 1686 Pancreas 19 55,054,868 55,073,275 18,407 1.40 yes C1D17</p><p>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</p><p>1716 Pancreas 20 43,388,697 43,432,265 43,568 1.36 yes SDC4,SYS1</p><p>1726 Pancreas 22 40,169,632 40,174,377 4,745 1.47 yes TOB2</p><p>C22orf32,FAM109B,NAGA, 1736 Pancreas 22 40,792,846 40,832,863 40,017 1.36 yes NDUFA6</p><p>1746 Pancreas 22 44,747,130 44,931,494 184,364 1.38 yes C22orf26,WNT7B</p><p>1756 Pancreas 22 48,685,508 48,759,107 73,599 1.38 yes ALG12,CRELD2,PIM3</p><p>NONE(dist=NONE),NONE( 1766 Pancreas 23 39,815,040 39,847,432 32,392 1.36 yes dist=NONE)</p><p>NONE(dist=NONE),NONE( 1776 Pancreas 23 53,116,022 53,141,249 25,227 1.36 yes dist=NONE)</p><p>NONE(dist=NONE),NONE( 1786 Pancreas 23 102,823,065102,835,57612,511 1.37 yes dist=NONE)</p>