ArticleBioinformatics (Oxford, England)2018
Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- nf-core/pacsomatic: a scalable somatic analytic pipeline using PacBio HiFi data.Bioinformatics (Oxford, England) · 2026Article
- Selective identification of polyploid hepatocellular carcinomas with poor prognosis by artificial intelligence-based pathological image recognition.Communications medicine · 2025Article
- Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome.Genome biology · 2024Article
- Impact of Aneuploidy and Chromosome 9p Loss on Tumor Immune Microenvironment and Immune Checkpoint Inhibitor Efficacy in NSCLC.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2023Article
- Optimizing cancer immunotherapy response prediction by tumor aneuploidy score and fraction of copy number alterations.NPJ precision oncology · 2023Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- REIA: A database for cancer A-to-I RNA editing with interactive analysis.International journal of biological sciences · 2022Article
- Structural variant detection in cancer genomes: computational challenges and perspectives for precision oncology.NPJ precision oncology · 2021Review
- Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data.BMC bioinformatics · 2021Article
- Analysis of Aneuploidy Spectrum From Whole-Genome Sequencing Provides Rapid Assessment of Clonal Variation Within Established Cancer Cell Lines.Cancer informatics · 2021Article
- Comparison of Circulating Tumour DNA and Extracellular Vesicle DNA by Low-Pass Whole-Genome Sequencing Reveals Molecular Drivers of Disease in a Breast Cancer Patient.Biomedicines · 2020Article
- Tumor purity as a prognosis and immunotherapy relevant feature in gastric cancer.Cancer medicine · 2020Article
- Intratumor heterogeneity: A new perspective on colorectal cancer research.Cancer medicine · 2020Review
- Hierarchical discovery of large-scale and focal copy number alterations in low-coverage cancer genomes.BMC bioinformatics · 2020Article
- Putative biomarkers for predicting tumor sample purity based on gene expression data.BMC genomics · 2019Article
- Identification and Characterization of MicroRNAs Associated with Somatic Copy Number Alterations in Cancer.Cancers · 2018Article
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4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Motivation: Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. Results: We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. Availability and implementation: Accurity is implemented in C++/Rust, available at http://www.yfish.org/software/. Supplementary information: Supplementary data are available at Bioinformatics online.
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