Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine

Table 2 Filters applied for TMB calculation with Foundation One ® (FO) algorithm and Institut Curie (IC) algorithm

	FoundationOne® algorithm	Institut Curie algorithm
Metrics
Low-quality variant removal	YES PASS tag from VarScan2	YES Intra-run recurrence
Minimum VAF	5%	5% for frozen tumors 10% for FFPE tumors
Minimum depth of coverage	100X	100X
Germline removal	SGZ algorithm And SNP from 1000 Genomes or Exac with a MAF > 0.1% were filtered	SNP from 1000 Genomes, Gnomad or Exac with a MAF > 0.1% were filtered
Variants types
Drivers	Excluded COSMIC	Included
Synonymous	Included	Excluded
Splicing	Included	Excluded
Indels	Included	Included
Nonsense	Included	Included
Non-coding	Excluded	Excluded

The FO algorithm was applied on FFPE samples only as required by the FoundationOne®CDx test, while the IC algorithm was used on both frozen and FFPE samples
FFPE Formalin-fixed paraffin-embedded, VAF Variant allele frequency, SGZ Somatic-germline-zygosity, COSMIC Catalogue of Somatic Mutations in Cancer, MAF Mutation allele frequency, SNP Single-nucleotide polymorphism

ISSN: 1741-7007