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Copy Number Variants VCF
File name: {Sample_ID}_CopyNumberVariants.vcf
Contains CNV calls for DNA libraries of the amplification genes targeted by theTruSight Tumor 170 v1.0 panel. The CNV call indicates fold change results for each gene classified as reference, deletion, or amplification. The value in the QUAL column of the VCF is a Phred transformation of the p-value where Q=-10xlog10(P-value). The p-value is derived from the t-test between the fold change of the gene against rest of the genome. Higher Q-scores indicate higher confidence in the CNV call.
In the VCF notation, <DUP> indicates the detected fold change (FC) is greater than a predefined amplification cutoff, and <DEL> indicates the detected fold change (FC) is less than a predefined deletion cutoff for that gene. This cutoff can vary from gene to gene.
<DEL> calls have only been validated with in silico data sets. As a result, all <DEL> calls have LowValidation filter in the VCF.
Copy number variant is reported in the form of fold change on normalized read depth in a testing sample relative to the normalized read depth in diploid genomes. Given tumor purity, one can infer the ploidy of a gene in the sample from the reported fold change.
Assume the tumor purity X%, for a reported fold change Y, the copy number n can by calculated by: n=[(200×Y)-2×(100-X)]/X
For example, in a testing sample of tumor purity at 30%, MET with fold change of 2.2x indicates 10 copies of MET DNA is observed in the sample.
For Research Use Only. Not for use in diagnostic procedures.