Table 1.
Pathogenic/likely pathogenic germline variants not detected by tumor-only sequencing by lack of technical detection according to variant type
| CSG | Nonsense or splice site SNV | Missense SNV | Indel <5 bp | Indel >5 bp | Deletion/duplication | Intronic SNV | Alu insertion | High homology | Total | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | Total | Not detected, n (%) | |
| BRCA1 | 45 | 0 (0.0) | 30 | 0 (0.0) | 58 | 0 (0.0) | 10 | 0 (0.0) | 13 | 5 (38.5) | 5 | 5 (100.0) | 0 | NA | 0 | NA | 161 | 10 (6.2) |
| BRCA2 | 74 | 0 (0.0) | 16 | 0 (0.0) | 158 | 0 (0.0) | 26 | 0 (0.0) | 3 | 2 (66.7) | 2 | 2 (100.0) | 2 | 2 (100.0) | 0 | NA | 281 | 6 (2.1) |
| NF1 | 16 | 0 (0.0) | 5 | 0 (0.0) | 18 | 0 (0.0) | 3 | 0 (0.0) | 6 | 1 (16.7) | 0 | NA | 0 | NA | 0 | NA | 48 | 1 (2.1) |
| PALB2 | 21 | 0 (0.0) | 2 | 0 (0.0) | 32 | 0 (0.0) | 5 | 0 (0.0) | 14 | 9 (64.3) | 3 | 3 (100.0) | 1 | 1 (100.0) | 0 | NA | 78 | 13 (16.7) |
| ATM | 83 | 0 (0.0) | 21 | 0 (0.0) | 82 | 0 (0.0) | 15 | 0 (0.0) | 12 | 4 (33.3) | 9 | 9 (100.0) | 0 | NA | 0 | NA | 222 | 13 (5.9) |
| BRIP1 | 26 | 0 (0.0) | 2 | 0 (0.0) | 19 | 0 (0.0) | 1 | 0 (0.0) | 3 | 2 (66.7) | 0 | NA | 0 | NA | 0 | NA | 51 | 2 (3.9) |
| CHEK2 | 24 | 0 (0.0) | 11 | 0 (0.0) | 9 | 0 (0.0) | 1 | 0 (0.0) | 11 | 5 (45.5) | 6 | 6 (100.0) | 1 | 1 (100.0) | 4 | 4 (100.0) | 67 | 16 (23.9) |
| MLH1 | 22 | 0 (0.0) | 13 | 0 (0.0) | 16 | 0 (0.0) | 0 | NA | 5 | 0 (0.0) | 0 | NA | 0 | NA | 0 | NA | 56 | 0 (0.0) |
| MSH2 | 23 | 0 (0.0) | 12 | 0 (0.0) | 10 | 0 (0.0) | 3 | 0 (0.0) | 16 | 7 (43.8) | 16 | 16 (100.0) | 0 | NA | 0 | NA | 80 | 23 (28.8) |
| MSH6 | 10 | 0 (0.0) | 5 | 0 (0.0) | 32 | 0 (0.0) | 3 | 0 (0.0) | 2 | 2 (100.0) | 0 | NA | 0 | NA | 0 | 0 | 52 | 2 (3.8) |
| PMS2 | 14 | 0 (0.0) | 11 | 0 (0.0) | 9 | 0 (0.0) | 1 | 0 (0.0) | 12 | 11 (91.7) | 0 | NA | 0 | NA | 10 | 10 (100.0) | 57 | 21 (36.8) |
| RB1 | 19 | 0 (0.0) | 3 | 0 (0.0) | 13 | 0 (0.0) | 3 | 0 (0.0) | 7 | 1 (14.3) | 2 | 2 (100.0) | 0 | NA | 0 | NA | 47 | 3 (6.4) |
| TP53 | 9 | 0 (0.0) | 29 | 0 (0.0) | 3 | 0 (0.0) | 1 | 0 (0.0) | 2 | 0 (0.0) | 0 | NA | 0 | NA | 0 | NA | 44 | 0 (0.0) |
| BAP1 | 7 | 0 (0.0) | 2 | 0 (0.0) | 3 | 0 (0.0) | 1 | 0 (0.0) | 2 | 1 (50.0) | 2 | 2 (100.0) | 0 | NA | 0 | NA | 17 | 3 (17.6) |
| RAD51C | 8 | 0 (0.0) | 2 | 0 (0.0) | 5 | 0 (0.0) | 1 | 0 (0.0) | 2 | 1 (50.0) | 2 | 2 (100.0) | 0 | NA | 0 | NA | 20 | 3 (15.0) |
| RAD51D | 11 | 0 (0.0) | 1 | 0 (0.0) | 9 | 0 (0.0) | 1 | 0 (0.0) | 3 | 0 (0.0) | 0 | NA | 0 | NA | 0 | NA | 25 | 0 (0.0) |
| Total | 412 | 0 (0.0) | 165 | 0 (0.0) | 476 | 0 (0.0) | 75 | 0 (0.0) | 113 | 51 (45.1) | 47 | 47 (100.0) | 4 | 4 (100) | 14 | 14 (100) | 1306 | 116 (8.9) |
CSG, cancer susceptibility gene; NA, not applicable; SNV, single-nucleotide variant.