Tumor Purity and Fold Change

Due to the sparseness of WES and targeted panels, b-allele data are insufficient for an accurate estimate of tumor purity. The Somatic WES CNV Caller only reports copy ratio, also known as fold change. Fold change is encoded in the FORMAT/SM field as a linear copy ratio of the segment mean.

If tumor purity is known, you can infer the ploidy of a gene or segment in the sample from the reported fold change using the following calculation.

For example, if the tumor purity is 30% for MET with a fold change of 2.2x, then there are 10 copies of MET DNA in the sample.