ArticleBioinformatics (Oxford, England)2014
Deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity.
Article in Bioinformatics (Oxford, England), 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Benchmarking Ploidy Estimation Methods for Bulk and Single-Cell Whole Genome Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The dual role of whole-genome duplication: biological mechanisms, functional consequences, and detection advances.Acta biochimica et biophysica Sinica · 2025Review
- Comparative study of tools for copy number variation detection using next-generation sequencing data.Scientific reports · 2025Article
- Tumor ploidy determination in low-pass whole genome sequencing and allelic copy number visualization using the Constellation Plot.Genome biology · 2025Article
- Tracing cancer evolution and heterogeneity using Hi-C.Nature communications · 2023Article
- Areas of Crush Nuclear Streaming Should Be Included as Tumor Content in the Era of Molecular Diagnostics.Cancers · 2023Article
- Integrative Genomic Profiling Uncovers Therapeutic Targets of Acral Melanoma in Asian Populations.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022Article
- RAD51B Harbors Germline Mutations Associated With Pancreatic Ductal Adenocarcinoma.JCO precision oncology · 2022Article
- A hidden Markov modeling approach for identifying tumor subclones in next-generation sequencing studies.Biostatistics (Oxford, England) · 2022Article
- Integrative genomic analysis of salivary duct carcinoma.Scientific reports · 2020Article
- Putative biomarkers for predicting tumor sample purity based on gene expression data.BMC genomics · 2019Article
- A systematic evaluation of copy number alterations detection methods on real SNP array and deep sequencing data.BMC bioinformatics · 2019Article
- Ploidy- and Purity-Adjusted Allele-Specific DNA Analysis Using CLONETv2.Current protocols in bioinformatics · 2019Article
- Paired whole exome and transcriptome analyses for the Immunogenomic changes during concurrent chemoradiotherapy in esophageal squamous cell carcinoma.Journal for immunotherapy of cancer · 2019Article
- A detrimental mutation on USP40 unlocks the tumorigenesis in a rare case of lung cancer.International journal of clinical and experimental pathology · 2019Article
- 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.Bioinformatics (Oxford, England) · 2018Article
- A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal.PLoS computational biology · 2018Article
- Low tumor purity is associated with poor prognosis, heavy mutation burden, and intense immune phenotype in colon cancer.Cancer management and research · 2018Article
- Decomposing the subclonal structure of tumors with two-way mixture models on copy number aberrations.PloS one · 2018Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
motivationNext-generation sequencing (NGS) has revolutionized the study of cancer genomes. However, the reads obtained from NGS of tumor samples often consist of a mixture of normal and tumor cells, which themselves can be of multiple clonal types. A prominent problem in the analysis of cancer genome sequencing data is deconvolving the mixture to identify the reads associated with tumor cells or a particular subclone of tumor cells. Solving the problem is, however, challenging because of the so-called 'identifiability problem', where different combinations of tumor purity and ploidy often explain the sequencing data equally well.
resultsWe propose a new model to resolve the identifiability problem by integrating two types of sequencing information-somatic copy number alterations and loss of heterozygosity-within a unified probabilistic framework. We derive algorithms to solve our model, and implement them in a software package called PyLOH. We benchmark the performance of PyLOH using both simulated data and 12 breast cancer sequencing datasets and show that PyLOH outperforms existing methods in disambiguating the identifiability problem and estimating tumor purity. AVAILABILITY AND IMPLEMENTATION: The PyLOH package is written in Python and is publicly available at https://github.com/uci-cbcl/PyLOH. CONTACT: xhx@ics.uci.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.