ArticleGenome biology2015
PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 247 papers.
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Who cites it
247 citing papers in PubMed.
- Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer.Cell reports. Medicine · 2020Trial
- Inferring gene expression profiles of tumor clones.Bioinformatics (Oxford, England) · 2026Article
- A guide to understanding tumour evolution through the lens of population genetics.Nature reviews. Cancer · 2026Review
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- ITHindex: An integrated web-based platform for intratumor heterogeneity evaluation.PLOS digital health · 2026Article
- Accurate detection of tumor clonality and ongoing expansion mode from genomic data.bioRxiv : the preprint server for biology · 2026Article
- Tumor genome and microenvironment alteration by trastuzumab deruxtecan as neoadjuvant therapy for HER2-mutant NSCLC.Scientific reports · 2026Article
- A network-based deep learning model integrating subclonal architecture for therapy response prediction in cancer.Cell reports methods · 2026Article
- Article
- Single base focal hypermutation cooccurs with structural variation as an early event in advanced prostate tumourigenesis with ancestry specific independence: a multi-ancestral observational study.Genome medicine · 2026Observational
- Metapipeline-DNA: A comprehensive germline and somatic genomics Nextflow pipeline.Cell reports methods · 2026Article
- Inferring and summarizing tumor phylogenies from bulk DNA data.Algorithms for molecular biology : AMB · 2026Article
- Theoretical estimates on the expected number of mutations needed to reconstruct clonal lineage trees.Bioinformatics advances · 2026Article
- Spatial omics and its applications for a tumour microenvironment characterization and precision medicine approach of gastric cancer.Ecancermedicalscience · 2026Review
- QeITH: Quantifies Tumor Ecosystem Heterogeneity to Predict Cancer Progression and Treatment Benefit.Computational and structural biotechnology journal · 2026Article
- General-purpose topology-aware embedding of tumor phylogenetic trees with graph neural networks.Bioinformatics advances · 2026Article
- Quantitative profiling of intratumor immune heterogeneity identifies loss of immune diversity as a hallmark of cancer progression.NPJ precision oncology · 2025Article
- DEPTH2 score was associated with cell proliferation and immune cell infiltrations but not with systemic treatment response in breast cancer.Scientific reports · 2025Article
- Tracing metastatic spread in pediatric solid tumors using copy number and targeted deep sequencing.The Journal of pathology · 2025Article
- MyClone: rapid and precise reconstruction of clonal population structures for tumors.BMC bioinformatics · 2025Article
187 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors.
Funding
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Abstract
Tumors often contain multiple subpopulations of cancerous cells defined by distinct somatic mutations. We describe a new method, PhyloWGS, which can be applied to whole-genome sequencing data from one or more tumor samples to reconstruct complete genotypes of these subpopulations based on variant allele frequencies (VAFs) of point mutations and population frequencies of structural variations. We introduce a principled phylogenic correction for VAFs in loci affected by copy number alterations and we show that this correction greatly improves subclonal reconstruction compared to existing methods. PhyloWGS is free, open-source software, available at https://github.com/morrislab/phylowgs.
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