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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

From: A verified genomic reference sample for assessing performance of cancer panels detecting small variants of low allele frequency

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    
  1. 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%