ArticleGenome biology2024
Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 11 citations in OpenAlex.
- A guide to understanding tumour evolution through the lens of population genetics.Nature reviews. Cancer · 2026Review
- An alignment-free strategy for circulating tumor DNA detection and tumor fraction estimation from whole-genome sequencing data.PLoS computational biology · 2026Article
- Gene mutant dosage is associated with prognosis and metastatic tropism in 60,000 clinical cancer samples.Nature genetics · 2026Article
- Exploring copy number alterations (CNAs) to gain new insight into SCLC heterogeneity.Molecular biology reports · 2026Review
- Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally Diverse Cohort.bioRxiv : the preprint server for biology · 2026Article
- Bridging phenotype and function in bladder cancer using immuno-competent organoids and ex vivo drug screening.Journal of experimental & clinical cancer research : CR · 2026Article
- Comprehensive repertoire of the chromosomal alteration and mutational signatures across 16 cancer types.Nature genetics · 2026Article
- Full spatio-temporal analyses of migration and colonization in evolution-dense 3D mapping of cancer metastases provides new insights.Molecular biology and evolution · 2026Article
- BayesCNV: A Bayesian Hierarchical Model for Sensitive and Specific Copy Number Estimation in Cell Free DNA.Diagnostics (Basel, Switzerland) · 2026Article
- Unmasking the "targetless" illusion: branched clonal evolution ofFrontiers in immunology · 2026Article
- CNRein: an evolution-aware deep reinforcement learning algorithm for single-cell DNA copy number calling.Genome biology · 2025Article
- The complexity of tobacco smoke-induced mutagenesis in head and neck cancer.Nature genetics · 2025Article
- The genomic landscape of 2,023 colorectal cancers.Nature · 2024Article
- Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc.Genome biology · 2024Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 3 countries.
Funding
Abstract
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
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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.