Table 1. Mutations detected by integrative genomics viewer inspection but missed by Torrent Variant Caller (VC).
| Genea | cDNA change | Amino acid change | VAFb | VC versionc |
|---|---|---|---|---|
| EGFR (Re) | c.2573T>G | p.L858R | 8.1 | 3.4.51874 |
| EGFR (Re) | c.2171G>C | p.G724A | 16 | 3.4.51874 |
| PIK3CA (Bx) | c.1634A>C | p.E545A | 10 | 3.4.51874 |
| EGFR (FNA) | c.2237_2255delinsTd | p.E746_S752delinsV | 3.2 | 3.4.51874 |
| EGFR (Bx) | c.2156G>C | p.G719A | 8.9 | 3.4.51874 |
| EGFR (Re) | c.2573T>G | p.L858R | 6.1 | 3.4.51874 |
| EGFR (Re) | c.2573T>G | p.L858R | 12 | 3.4.51874 |
| EGFR (FNA) | c.2236_2250del | p.E746_A750del | 5.5 | 3.6.63335 |
| EGFR (Bx) | c.2300_2308dup | p.A767_V769dup | 9.4 | 3.6.63335 |
| EGFR (Bx) | c.2302_2303insCGCTGGCCA | p.A767_S768insTLA | 5 | 3.6.63335 |
| EGFR (Re) | c.2156G>C | p.G719A | 32 | 3.6.63335 |
| ERBB2 (FNA) | c.2313_2324dup | p.A771_M774dup | 7.6 | 3.6.63335 |
| EGFR (Bx) | c.2311_2312delinsGGGTTe | p.N771delinsGF | 65 | 3.6.63335 |
| PIK3CA (Bx) | c.1193G>T | p.R398L | 5.5 | 3.6.63335 |
| EGFR (Re) | c.2239_2256del | p.L747_S752del | 36 | 3.6.63335 |
aRe: resection specimens, Bx: biopsy specimens; FNA: fine needle aspiration specimens. Two specimens (EGFR p.N771delinsGF mutation and PIK3CA p.R398L mutation) were concentrated by using the Amicon filter.
bVAF: variant allelic frequency. Depth of coverage was more than 1000 reads except the specimen with PIK3CA p.R398 mutation (450 reads).
cThe current VC version (5.0.2.1) did not miss mutations detected by IGV since December 2015.
dThe c.2237_2255delinsT mutation was composed of c.2237_2254del and c.2255C>T. Both were missed by Torrent Variant Caller.
eThe c.2311_2312delinsGGGTT mutation was composed of c.2310-2311insGGG, c.2311A>T and c.2312A>T. The Torrent Variant Caller detected c.2311A>T and c.2312A>T, but not c.2310-2311insGGG.