Copy Number Variants VCF

File name: {Sample_ID}_CopyNumberVariants.vcf

Contains CNV calls for DNA libraries of the amplification genes targeted by the TruSight Tumor 170 v2.0 panel. Each copy number variant is reported with a corresponding fold change. This value is derived from the normalized read depth of the gene in the sample relative to the normalized read depth of diploid regions from the same sample. The value in the QUAL column of the VCF is a Phred transformation of the 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 for the respective gene. <DEL> indicates the detected fold change is less than a predefined deletion cutoff for the respective gene. This cutoff varies from gene to gene.

<DEL> calls have only been validated with in silico data sets. As a result, all <DEL> calls have the LowValidation filter in the VCF.

Given tumor purity, the copy number of the gene in the tumor can be inferred from the reported fold change of the gene.

Given tumor purity X%, for a reported fold change Y, the copy number n can be calculated using the following equation:

 

For example, in a testing sample of tumor purity at 30%, MET with fold change of 2.2x indicates that 10 copies of MET DNA are observed.