TPES: tumor purity estimation from SNVs.
Level V
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- Record sourced from PubMed, PMID 31099386.
- Also identified by DOI 10.1093/bioinformatics/btz406 and PMC identifier 6821153.
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Abstract
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. We introduce a computational method, tumor purity estimation from single-nucleotide variants (SNVs), which derives TP from the allelic fraction distribution of SNVs. On more than 7800 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. TPES is available as an R package on CRAN and at https://bitbucket.org/l0ka/tpes.git. Supplementary data are available at Bioinformatics online.
Medical subject headings
- Neoplasms