Table 1.
Summary of number of (i) tumour detected and (ii) true germline variants detected with application of (A) serial filters (B) gene/context/age criteria, from data on 65 genes for 16 322 tumours (MSK dataset)
| All tumours |
Associated tumours |
Non-associated tumours |
||||||
|---|---|---|---|---|---|---|---|---|
| Tumour detected | True germline | Tumour detected | True germline | Tumour detected | True germline | |||
| (A) Application of serial filters to MSK data on 65 genes for 16 322 tumours: number of variants | 1 997 499 | 1 959 587 | ||||||
| Retained: MAF ≤0.01 | 79 342 | 53 388 | ||||||
| Retained: LP/P/truncating | 17 075 | 1494 | ||||||
| Retained: VAF ≥0.3 (SNV) or ≥0.2 (insdel) | All | 9222 | 1442 | 2904 | 454 | 6305 | 983 | |
| HA-CSGs (AD) | 6141 | 677 | 2259 | 326 | 3882 | 351 | ||
| SA-CSGs (AD) | 2372 | 213 | 539 | 37 | 1820 | 176 | ||
| Other | 709 | 547 | 106 | 91 | 603 | 456 | ||
| (B) Application of ESMO-PWG recommendations for gene/context/age criteria based on 10% germline conversion: number of variants | HA-CSGs (AD) | all ages (18 genes) | 851 | 615 | 410 | 300 | 441 | 315 |
| age <30 (APC, RB1) | 63 | 10 | 37 | 4 | 26 | 6 | ||
| age <30, on-tumour only (TP53) | 59 | 7 | 59 | 7 | n/a | n/a | ||
| Total | 973 | 632 | 506 | 311 | 467 | 321 | ||
| SA-CSGs (AD) | all ages, on tumour only (BAP1, FH, FLCN, POLE), | 60 | 17 | 60 | 17 | n/a | n/a | |
| age <30, on tumour only (NF1) | 9 | 4 | 9 | 4 | n/a | n/a | ||
| Total | 69 | 21 | 69 | 21 | n/a | n/a | ||
| Grand total | 1042 | 653 | 575 | 332 | 467 | 321 | ||
HA-CSGs, high actionability genes; SA-CSGs, standard actionability CSGs; AD, autosomal dominantly inherited; other, CSGs of recessive inheritance, intermediate penetrance and/or non-clinical grade actionability.