Table 5 Published studies using Ion Torrent sequencing on BRCA1 and BRCA2 indels
Publication | Ref. | known mutations | indels | 1bp indels | Homopol. indels | Comments/Conclusions |
|---|---|---|---|---|---|---|
Costa et al. | [33] | 9 | 9 | 2 | 1 | Largest indel is a 3bp homopolymer |
Tarabeau et al. | [57] | 48 | 35 | 25 | 22 | 9 in BRCA1, 13 in BRCA2, established 130X as minimum coverage to detect all variants |
Dacheva et al. | [58] | 7 | 10 | 5 | 4 | Established minimum coverage of 70X to detect all variants |
Kluska et al. | [59] | 20 | 15 | 7 | 3 | 8 in BRCA1 (3 1bp) and 7 in BRCA2 (4 1bp) |
Yeo et al. | [60] | 3 | 3 | 2 | 0 | Used multiple mappers and variant callers to show that high sensitivity and specificity can be obtained in BRCA1/2 with Ion Torrent sequencing, but no mutations are in homopolymers |
Trujillano et al. | [47] | 19 | 8 | 6 | 3 | 115 known validation samples and 95 unknown samples |
Chan et al. | [61] | 3 | 2 | 1 | Compares Solid to PGM, estimates reagent cost as $123 (Solid) and $220 (PGM) | |
Bosdet et al. | [62] | 517 | 18 | 5 | 4 | Known variants includes SNPs. Establish 100X minimum coverage to find all variants |
Total | 101 | 54 | 38 | |||