ArticleNature communications2020
Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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Who cites it
66 citing papers in PubMed, 135 citations in OpenAlex.
- Trial
- LeafRank: A phylodynamic framework for inferring relative fitness from single-cell phylogenies in chromosomally unstable tumors.bioRxiv : the preprint server for biology · 2026Article
- Decoding immunotherapy response through computational modeling.Nature communications · 2026Review
- Novel driver gene MDC1 confers homologous recombination repair deficiency and genomic instability in chemoresistant relapsing ovarian cancer.Journal of translational medicine · 2026Article
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Loss of IDH1 and IDH2 mutations during the evolution of metastatic chondrosarcoma.Genome biology · 2025Article
- Single-cell transcriptomics redefines focal neuroendocrine differentiation as a distinct prostate cancer pathology.Molecular oncology · 2025Article
- A novel DNA repair-independent role for Gen nuclease in promoting unscheduled polyploidy cell proliferation.PLoS genetics · 2025Article
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- Informatics at the Frontier of Cancer Research.Cancer research · 2025Review
- Selective identification of polyploid hepatocellular carcinomas with poor prognosis by artificial intelligence-based pathological image recognition.Communications medicine · 2025Article
- CLONEID: A Framework for Longitudinal Integration of Phenotypic and Genotypic Data to Monitor and Steer Subclonal Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Interactions between Ploidy and Resource Availability Shape Clonal Evolution in Glioblastoma.Cancer research · 2025Article
- CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling.Genome biology · 2025Article
- The Evolutionary Forest of Pancreatic Cancer.Cancer discovery · 2025Article
- Cancer phylogenetic inference using copy number alterations detected from DNA sequencing data.Cancer pathogenesis and therapy · 2025Review
- Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics.Nature methods · 2024Article
- Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome.Genome biology · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- Disentangling oncogenic amplicons in esophageal adenocarcinoma.Nature communications · 2024Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Copy-number aberrations (CNAs) and whole-genome duplications (WGDs) are frequent somatic mutations in cancer but their quantification from DNA sequencing of bulk tumor samples is challenging. Standard methods for CNA inference analyze tumor samples individually; however, DNA sequencing of multiple samples from a cancer patient has recently become more common. We introduce HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity), an algorithm that infers allele- and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient. We show that HATCHet outperforms current state-of-the-art methods on multi-sample DNA sequencing data that we simulate using MASCoTE (Multiple Allele-specific Simulation of Copy-number Tumor Evolution). Applying HATCHet to 84 tumor samples from 14 prostate and pancreas cancer patients, we identify subclonal CNAs and WGDs that are more plausible than previously published analyses and more consistent with somatic single-nucleotide variants (SNVs) and small indels in the same samples.
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Registered trials
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.