Table 1.
Comparison of the variants detected by Sanger, by GS-Flx with SeqNext analysis, and by GS-Flx with AGSA analysis.
| Gene | HGVS nomenclature | Sanger | AVA + AgsA | SeqNext |
|---|---|---|---|---|
| BRCA1 | c.19-47del29 | h | h (56%)∗∗ | —∗∗ |
| c.81-12delC | — | — | h (41%)† | |
| c.124delA | h | h (48%) | h (48%) | |
| c.212+1G>A | h | h (72%)∗∗ | —∗∗ | |
| c.342-343delTC | h | h (36%) | h (37%) | |
| c.671-11dup | — | h (45%)† | h (43%)† | |
| c.798-799del | h | h (48%) | h (48%) | |
| c.1116G>A | h | h (43%) | h (43%) | |
| c.1390dupA | h | h (49%) | h (48%) | |
| c.1823-1826del | h | h (46%) | h (46%) | |
| c.1953_1956delGAAA | h | h (35%) | h (34%) | |
| c.2077G>A | h | h (60%) | h (62%) | |
| c.2082C>T | H | H (100%) | H (100%) | |
| c.2269delG | h | h (66%) | h (66%) | |
| c.2612C>T | h | h (42%) | h (42%) | |
| c.3113A>G | h | h (51%) | h (52%) | |
| c.3548A>G | h | h (49%) | h (49%) | |
| 3839-3843del5ins4 | h | h (52%) | h (52%) | |
| c.4127del | h | h (56%) | h (44%) | |
| c.4214-4215delIns5 | — | — | h (23%)† | |
| c.4221delins9 | — | — | h (26%)† | |
| C.4227-4237delins16 | — | — | h (24%)† | |
| c.4243-4244delGA | — | — | h (26%)† | |
| c.4281_4282ins39 | h | h (44%) | — †† | |
| c.4308T>C | h | h (55%) | h (49%) | |
| c.4575-4585del11 | h | h (46%) | h (43%) | |
| c.4810C>T | h | h (58%) | h (53%) | |
| c.5266dupC | h | h (59%) | h (59%) | |
| c.5333-20_5333-19insT | — | — | h (25%)† | |
|
| ||||
| BRCA2 | c.37_44del8 | h | h (25%)∗∗ | h (26%) |
| c.1114A>C | h | h (47%) | h (51%) | |
| c.1246A>G | h | h (47%) | h (49%) | |
| c.1553_1554insT | — | h (31%)∗∗† | —∗∗ | |
| c.1748_1749insA | — | h (47%)∗∗† | h (26%)† | |
| c.1759-1761delinsC | — | — | h (25%)† | |
| c.1774delT | — | — | h (33%)† | |
| c.1804-1806delins3 | — | — | h (21%)† | |
| c.1803dupA | — | — | h (43%)† | |
| c.1815dupA | — | h (68%)† | h (31%)† | |
| c.1823dupA | — | — | h (33%)† | |
| c.1833dupA | — | — | h (21%)† | |
| c.2589T>A | — | — | h (34%)† | |
| c.2803G>A | h | h (39%) | h (40%) | |
| c.3479G>A | — | h (31%)∗∗† | — | |
| c.3807T>C | h | h (44%) | h (42%) | |
| c.4332-4333delTA | — | — | h (66%)† | |
| c.4350dupT | — | — | h (44%)† | |
| c.4781delins3 | — | — | h (22%)† | |
| c.5073dupA | h | h (42%) | h (41%) | |
| c.5385dupA | — | — | h (22%)† | |
| c.5459_5460insA | — | h (32%)∗∗† | — | |
| c.7977-10dup | — | — | h (70%)† | |
| c.8125dupA | — | — | h (23%)† | |
| c.8147-8148insA | — | — | h (29%)† | |
| c.8574dup | — | h (38%)† | h (30%)† | |
| c.8797del | — | H† | — | |
| c.8800del | — | h (80%)∗∗† | — | |
| c.8823dupA | — | — | h (28%)† | |
| c.8946dup | — | h (27%)∗∗† | — | |
| c.10083del | — | — | h (21%)† | |
| c.10115dupC | — | — | h (50%)† | |
| c.10122delC | — | — | h (32%)† | |
|
| ||||
| False negative (out of 64)†† | 0 (reference)†† | 0†† | 1† | |
| False positive (out of 64)† | 0 (reference)† | 10† | 28†† | |
% of reads carrying the variant is given in parentheses.
∗∗Depth of the variant was <40 reads.
†Cells highlight false positives; ††cells highlight false negatives.