| Title | TPES: tumor purity estimation from SNVs. |
| Publication Type | Journal Article |
| Year of Publication | 2019 |
| Authors | Locallo A, Prandi D, Fedrizzi T, Demichelis F |
| Journal | Bioinformatics |
| Volume | 35 |
| Issue | 21 |
| Pagination | 4433-4435 |
| Date Published | 2019 Nov 01 |
| ISSN | 1367-4811 |
| Keywords | DNA Copy Number Variations, High-Throughput Nucleotide Sequencing, Humans, Neoplasms, Nucleotides, Software |
| Abstract | 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 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. AVAILABILITY AND IMPLEMENTATION: 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. |
| DOI | 10.1093/bioinformatics/btz406 |
| Alternate Journal | Bioinformatics |
| PubMed ID | 31099386 |
| PubMed Central ID | PMC6821153 |
| Grant List | P50 CA211024 / CA / NCI NIH HHS / United States |