Table 3 Inference of germline status for pathogenic BRCA1, BRCA2, and TP53 variants in breast and ovarian cancers.
Case | Primary site | Tumor purity | Variant | Allele fraction | Gene copy number | Known status | Inferred status |
|---|---|---|---|---|---|---|---|
1 | Ovary | 46% | BRCA2 c.7068_7069delTC (p.L2357Vfs*2) | 73% | 2 | Germline | Germline |
2 | Ovary | 71% | BRCA1 c.5266dupC (p.Q1756Pfs*74) | 79% | 1 | Germline | Germline |
3 | Ovary | 49% | BRCA1 c.3254_3255dupGA (p.L1086Dfs*2) | 78% | 2 | Germline | Germline |
4 | Ovary | 48% | BRCA1 c.1165delA (p.S389Vfs*5) | 67% | 1 | Germline | Germline |
5 | Ovary | 38% | BRCA1 c.68_69delAG (p.E23Vfs*17) | 62% | 2 | Germline | Germline |
6 | Ovary | 75% | BRCA1 c.3627dupA (p.E1210Rfs*9) | 89% | 2 | Germline | Germline |
7 | Breast | 87% | BRCA2 c.5286_5287delTC (p.S1764Kfs*3) | 76% | 1 | Somatic | Somatic |
8 | Breast | 58% | BRCA2 c.5857 G > T (p.E1953*) | 82% | 2 | Germline | Germline |
9 | Breast | 71% | BRCA1 c.1964delA (p.Y655Sfs*46) | 77% | 1 | Germline | Germline |
10 | Breast | 77% | BRCA1 c.4868 C > G (p.A1623G) | 92% | 2 | Germline | Germline |
11 | Breast | 75% | BRCA1 c.1687C > T (p.Q563*) | 79% | 2 | Somatic | Somatic |
12 | Breast | 36% | BRCA1 c.1214 C > G (p.S405*) | 19% | 2 | Somatic | Somatic |
13 | Breast | 46% | BRCA2 c.8584_8585insT (p.E2863Rfs*6) | 65% | 2 | Germline | Germline |
14 | Breast | 68% | BRCA2 c.572_573delAT (p.M192Vfs*13) | 81% | 2 | Germline | Germline |
15 | Breast | 28% | BRCA1 c.3817 C > T (p.Q1273*) | 63% | 2 | Germline | Germline |
1 | Ovary | 46% | TP53 c.214_216delCCCinsGC (p.P72Afs*51) | 49% | 2 | Somatic | Somatic |
2 | Ovary | 71% | TP53 c.452 C > G (p.P151R) | 65% | 2 | Somatic | Somatic |
3 | Ovary | 49% | TP53 c.536 A > G (p.H179R) | 52% | 2 | Somatic | Somatic |
4 | Ovary | 48% | TP53 c.818 G > A (p.R273H) | 40% | 1 | Somatic | Somatic |
5 | Ovary | 38% | TP53 c.527 G > T (p.C176F) | 24% | 2 | Somatic | Somatic |
6 | Ovary | 75% | TP53 c.724 T > A (p.C242S) | 66% | 1 | Somatic | Somatic |
7 | Breast | 87% | TP53 c.743 G > A (p.R248Q) | 78% | 1 | Somatic | Somatic |
9 | Breast | 71% | TP53 c.701 A > G (p.Y234C) | 77% | 2 | Somatic | Somatic |
10 | Breast | 77% | TP53 c.1024 C > T (p.R342*) | 82% | 2 | Somatic | Somatic |
12 | Breast | 36% | TP53 c.527 G > T (p.C176F) | 49% | 2 | Somatic | Somatic |
15 | Breast | 28% | TP53 c.1009 C > T (p.R337C) | 19% | 1 | Somatic | Somatic |
