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

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.

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