Table 2. Comparison of genotypes for amino acid changing variants in paired panel and sample series.
| sample ID (1) | TCC | panel | variant coverage | VF | gene | protein | sample ID (2) | TCC | panel | variant coverage | VF | gene | protein | tumor heterogeneity |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| BR8-262 | 70 | T | 136 | 0,28 | TP53 | p.Arg273Cys | TN158 | 50 | T | 1372 | 0,29 | TP53 | p.Arg273Cys | potentially |
| BR8-262 | T | amplicon failure (16 reads) | TN158 | T | 1192 | 0,92 | TP53 | p.Pro72Arg | heterogeneous | |||||
| BR8-262 | T | AR 416, no variant | TN158 | T | 794 | 0,38 | TP53 | p.Arg175Gly* | (TP53) | |||||
| BR8-439 | 55 | T | 728 | 0,14 | PIK3CA | p.His1047Arg | TN167 | 60 | T | 1996 | 0,47 | PIK3CA | p.His1047Arg | inconclusive |
| BR8-439 | T | amplicon failure (16 reads) | TN167 | T | 796 | 0,26 | TP53 | p.Pro72Arg | ||||||
| BR8-439 | T | amplicon failure (45 reads) | TN167 | T | 1239 | 0,46 | TP53 | p.Tyr163Cys | ||||||
| BR8-590 | 65 | T | 1992 | 0,31 | TP53 | p.Tyr107* | TN149 | 85 | T | 1996 | 0,24 | TP53 | p.Tyr107* | heterogeneous |
| BR8-590 | T | AR 659, no variant | TN149 | T | 1986 | 0,29 | TP53 | p.Pro72Arg | (TP53, PIK3CA) | |||||
| BR8-590 | T | AR 1494, no variant | TN149 | T | 2000 | 0,12 | PIK3CA | p.His1047Arg | ||||||
| BR8-590 | T | AR 666, no variant | TN149 | T | 1966 | 0,17 | TP53 | p.Arg209Lys | ||||||
| BR8-590 | B | 544 | 0,36 | TP53 | p.Tyr107* | TN149 | B | 1996 | 0,75 | TP53 | p.Tyr107* | no heterogeneity | ||
| BR8-590 | B | AR 408, no variant | TN149 | B | AR 798, no variant | TP53 | p.Pro72Arg | (discordant B and T | ||||||
| BR8-590 | B | AR 1754, no variant | TN149 | B | AR >4000, no variant | PIK3CA | p.His1047Arg | panel results for | ||||||
| BR8-590 | B | AR 259, no variant | TN149 | B | AR 940, no variant | TP53 | p.Arg209Lys | TN149) | ||||||
| BR8-601 | 60 | T | 222 | 0,84 | TP53 | p.Pro72Arg | TN011 | 90 | T | 65** | 0,92 | TP53 | p.Pro72Arg | no heterogeneity |
| BR8-601 | T | 1994 | 0,26 | PIK3CA | p.His1047Arg | TN011 | T | 1550 | 0,47 | PIK3CA | p.His1047Arg | (TP53, PIK3CA) | ||
| BR8-601 | B | 364 | 0,23 | PIK3CA | p.His1047Arg | TN011 | B | 1994 | 0,49 | PIK3CA | p.His1047Arg | no heterogeneity | ||
| BR8-601 | B | 72** | 0,72 | TP53 | p.Pro72Arg | TN011 | B | 153 | 0,76 | TP53 | p.Pro72Arg | (TP53, PIK3CA) | ||
| BR8-628 | 65 | T | 1999 | 0,15 | PTEN | p.Asp24Gly | TN131 | 75 | T | AR 1697, no variant | heterogeneous | |||
| BR8-628 | T | 455 | 0,44 | TP53 | p.Pro72Arg | TN131 | T | 1391 | 0,10 | TP53 | p.Pro72Arg | (PTEN, TP53) | ||
| BR8-628 | T | AR 1047, no variant | TN131 | T | 1666 | 0,79 | TP53 | p.Thr155Pro | ||||||
| BR8-628 | B | AR 1912, no variant | TN131 | B | AR 892, no variant | no heterogeneity | ||||||||
| BR8-628 | B | 403 | 0,18 | TP53 | p.Pro72Arg | TN131 | B | 898 | 0,09 | TP53 | p.Pro72Arg | (discordant B and T | ||
| BR8-628 | B | 1101 | 0,67 | TP53 | p.Thr155Pro | TN131 | B | 1947 | 0,82 | TP53 | p.Thr155Pro | panel results for | ||
| BR8-628) | ||||||||||||||
TCC = tumor cell content (%); VF = variant frequency; AR = amplicon reads
*: variant observed with the old library with the same panel for the same DNA sample
**: low coverage / high frequency variants that were initially missed with the 125 coverage cut-off.