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Table 5 Published studies using Ion Torrent sequencing on BRCA1 and BRCA2 indels

From: Addressing health disparities in Hispanic breast cancer: accurate and inexpensive sequencing of BRCA1 and BRCA2

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  
  1. All known publications using Ion Torrent sequencing instruments to sequence known BRCA1 and BRCA2 mutations are displayed. The number of insertion/deletion variants (indels), those of 1 base pair (1bp) and those in homopolymer regions (homopol.) are tabulated