Table 2.
Significant cancer germline copy number variable regions
| Cancer | Chr | Start | Size | Freq (control) | Freq (case) | Type | OR | P-value a | P-value (PCA) b | Gene(s) c |
|---|---|---|---|---|---|---|---|---|---|---|
| BRCA | 11 | 51185363 | 8472 | 0% | 1.49% | Loss | - | 1.08E-05 | 9.66E-01 | |
| BRCA | 3 | 62936471 | 30079 | 0.07% | 1.79% | Loss | 26.85 | 2.54E-05 | 1.05E-04 | |
| BRCA | 3 | 26586501 | 3489 | 0.17% | 2.08% | Loss | 12.56 | 5.47E-05 | 3.44E-06 | |
| COAD | 3 | 107601890 | 16832 | 0.03% | 2.34% | Loss | 70.78 | 1.02E-07 | 4.90E-05 | |
| COAD | 10 | 101261779 | 22068 | 0% | 1.46% | Loss | - | 1.20E-06 | 9.63E-01 | NKX2-3 |
| COAD | 4 | 156797864 | 71044 | 0.24% | 2.34% | Loss | 10.09 | 4.13E-05 | 9.20E-06 | GUCY1A3 |
| COAD | 7 | 29635116 | 120414 | 0.03% | 1.46% | Gain | 43.84 | 6.41E-05 | 6.13E-04 | DPY19L2P3, LOC100271874, LOC646762 |
| GBM | 14 | 21685305 | 117313 | 0.30% | 5.41% | Loss | 18.74 | 5.54E-13 | 6.54E-12 | TRA@, TRD |
| GBM | 5 | 57361784 | 7507 | 16.50% | 33.00% | Loss | 2.5 | 1.54E-12 | 2.52E-20 | |
| GBM | 22 | 47288391 | 152640 | 0.07% | 2.85% | Loss | 43.31 | 8.76E-09 | 6.97E-06 | FAM19A5 |
| GBM | 7 | 38257218 | 88038 | 0.84% | 5.41% | Loss | 6.71 | 2.25E-08 | 1.24E-09 | TARP |
| GBM | 5 | 10927644 | 15240 | 0% | 1.99% | Loss | - | 1.44E-07 | 9.60E-01 | |
| GBM | 14 | 21804698 | 2132 | 0.10% | 2.28% | Loss | 22.96 | 1.85E-06 | 1.42E-05 | TRA@, TRD |
| GBM | 14 | 21681152 | 2379 | 0.20% | 2.56% | Loss | 12.94 | 4.34E-06 | 6.42E-06 | TRA@, TRD |
| GBM | 10 | 42882051 | 56351 | 0.30% | 2.56% | Loss | 8.62 | 3.15E-05 | 3.75E-06 | RET |
| GBM | 7 | 61793773 | 26492 | 1.56% | 5.13% | Loss | 3.42 | 6.89E-05 | 5.00E-07 | |
| KIRC | 14 | 21681152 | 2379 | 0.20% | 5.41% | Loss | 28.1 | 6.44E-15 | 3.49E-12 | TRA@, TRD |
| KIRC | 10 | 96855083 | 4614 | 0.07% | 3.24% | Loss | 49.51 | 2.26E-10 | 1.23E-07 | |
| KIRC | 3 | 89250592 | 142689 | 0% | 1.62% | Gain | - | 1.83E-06 | 9.63E-01 | EPHA3 |
| KIRC | 2 | 97429511 | 99111 | 2.17% | 7.03% | Loss | 3.42 | 2.33E-06 | 1.26E-08 | ANKRD36B |
| KIRC | 6 | 118470482 | 5095 | 0.24% | 2.43% | Loss | 10.5 | 1.33E-05 | 3.52E-06 | SLC35F1 |
| KIRC | 17 | 34990311 | 173216 | 0.64% | 3.51% | Gain | 5.63 | 1.56E-05 | 1.54E-05 | C17orf37, ERBB2, GRB7, NEUROD2, PGAP3, PNMT, PPP1R1B, STARD3, TCAP |
| KIRC | 4 | 103363913 | 68353 | 0.10% | 1.89% | Loss | 18.99 | 1.78E-05 | 4.83E-05 | SLC39A8 |
| KIRC | 2 | 91049141 | 1293 | 0.58% | 3.24% | Loss | 5.79 | 2.68E-05 | 3.67E-06 | |
| KIRC | 4 | 2281 | 109282 | 3.45% | 8.38% | Gain | 2.56 | 5.16E-05 | 2.94E-06 | ZNF595, ZNF718 |
| KIRC | 7 | 19542080 | 79082 | 0.04% | 1.35% | Loss | 40.48 | 9.06E-05 | 6.47E-04 | |
| KIRC | 12 | 130123182 | 31743 | 0.04% | 1.35% | Loss | 40.48 | 9.06E-05 | 1.11E-03 | GPR133 |
| OV | 13 | 54589383 | 6308 | 0.07% | 2.37% | Loss | 35.83 | 1.32E-07 | 1.13E-05 | |
| OV | 4 | 36584413 | 19612 | 0.03% | 2.11% | Loss | 63.55 | 2.15E-07 | 1.52E-04 | |
| OV | 1 | 244904225 | 32016 | 0% | 1.84% | Gain | - | 2.37E-07 | 9.60E-01 | |
| OV | 10 | 66977929 | 15004 | 4.57% | 11.60% | Gain | 2.74 | 3.29E-07 | 3.64E-11 | |
| OV | 2 | 192993 | 16566 | 0% | 1.58% | Gain | - | 2.11E-06 | 9.63E-01 | SH3YL1 |
| OV | 1 | 229982231 | 47730 | 0% | 1.58% | Gain | - | 2.11E-06 | 9.63E-01 | DISC1, DISC2, TSNAX-DISC1 |
| OV | 2 | 7529134 | 41988 | 0% | 1.58% | Gain | - | 2.11E-06 | 9.63E-01 | |
| OV | 10 | 495985 | 75956 | 0% | 1.32% | Gain | - | 1.87E-05 | 9.47E-01 | DIP2C |
| OV | 5 | 174076632 | 49822 | 0% | 1.32% | Gain | - | 1.87E-05 | 9.47E-01 | MSX2 |
| OV | 18 | 48381779 | 37120 | 0% | 1.32% | Gain | - | 1.87E-05 | 9.48E-01 | DCC |
| OV | 18 | 45329306 | 46009 | 0% | 1.32% | Gain | - | 1.87E-05 | 9.47E-01 | LIPG |
| OV | 4 | 172611459 | 3050 | 4.63% | 10.00% | Loss | 2.29 | 6.75E-05 | 1.95E-09 |
aThe P-value is based on two-tailed Fisher’s exact test comparing gain and loss frequency in cases versus controls using a threshold of 10−4. bThe significance estimated in a regression analysis using the first component of principal component analysis as covariates. cOverlapping genes with CNVRs (in either case or control) were determined using Refseq as the annotation source.