Table 2.
Variant characteristics of Sample A compared to other reference material (Sample A results are based on hg19), both Class1 and Class2 variants combined
| Reference material | Total variants identified | Total coding variants identified | Coding variantsin COSMIC genes | Total coding variants < 20% VAF | Total coding variants < 20% VAF in COSMIC genes | #genes with 1 or more variants | #COSMIC genes with 1 or more variants (Tier1/Tier2) |
|---|---|---|---|---|---|---|---|
| Sample A | 42,570 | 42,570 | 2432 | 28,064 | 1653 | 12,238 | 422/102 |
| SNV | 42,021 | 42,021 | 2398 | 27,683 | 1624 | ||
| Indel | 549 | 549 | 34 | 381 | 29 | ||
| Acrometrix | 555 | 555 | 555 | 341a | 341a | 53 | 52/1 |
| SNV | 504 | 504 | 504 | 317 | 317 | ||
| MNV/Indel | 2/49 | 2/49 | 2/49 | 0/24 | 0/24 | ||
| Oncospan | 386 | 386 | 319 | 52 | 46 | 152 | 114/2 |
| SNV | 357 | 357 | 297 | 43 | 38 | ||
| Indel | 30 | 30 | 22 | 9 | 8 | ||
| HCC1395 (somatic) | 41,556 | 487 | 193 | 144 | 14 | 466 | 188 |
| SNV | 39,536 | 460 | 186 | 132 | 13 | ||
| Indel | 2020 | 27 | 7 | 12 | 1 | ||
| HCC1395BL (germline) | 3,577,254 | 21,755 | NA | NA | NA | 9566 | NA |
| SNV | 3,225,512 | 21,381 | |||||
| Indel | 351,742 | 374 |
aMost of the Acrometrix variants are synthetic controls. Thus, it is possible to construct a version of the material where 524 of the 555 variants have a VAF < 20%