LAUSR

MOTIVATION Tumor purity (TP) is the proportion of cancer cells in a tumor sample. TP impacts on the accurate assessment of molecular and genomics features as assayed with NGS approaches. State-of-the-art tools mainly rely on somatic copy-number alterations (SCNA) to quantify TP and therefore fail when a tumor genome is nearly euploid, i.e. "non-aberrant" in terms of identifiable SCNAs. RESULTS We introduce a computational method, Tumor Purity Estimation from SNVs (TPES), which derives TP from the allelic fraction distribution of SNVs. On more than 7,800 whole-exome sequencing data of TCGA tumor samples, it showed high concordance with a range of TP tools (Spearman's correlation between 0.68 and 0.82; > 9 SNVs) and rescued TP estimates of 1,194 samples (15%) pan-cancer. AVAILABILITY TPES is available as an R package on CRAN and at https://bitbucket.org/l0ka/tpes.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.