ArticleNucleic acids research2015
Allele-specific copy number profiling by next-generation DNA sequencing.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed.
- Haplotype-aware segmentation with HapASeg increases accuracy of detecting homolog-specific somatic copy number alterations.Genome biology · 2026Article
- Inferring tumor purity using multi-omics data based on a uniform machine learning framework MoTP.Briefings in bioinformatics · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- scAbsolute: measuring single-cell ploidy and replication status.Genome biology · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.bioRxiv : the preprint server for biology · 2023Article
- Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.Nature communications · 2023Article
- A comprehensive benchmarking of WGS-based deletion structural variant callers.Briefings in bioinformatics · 2022Article
- CONET: copy number event tree model of evolutionary tumor history for single-cell data.Genome biology · 2022Article
- Obtaining spatially resolved tumor purity maps using deep multiple instance learning in a pan-cancer study.Patterns (New York, N.Y.) · 2022Article
- Identification of Copy Number Alterations from Next-Generation Sequencing Data.Advances in experimental medicine and biology · 2022Article
- Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.Briefings in bioinformatics · 2021Article
- Integrative single-cell analysis of allele-specific copy number alterations and chromatin accessibility in cancer.Nature biotechnology · 2021Article
- Genomic and Transcriptomic Characterization of Relapsed SCLC Through Rapid Research Autopsy.JTO clinical and research reports · 2021Article
- Characterization of Clonal Evolution in Microsatellite Unstable Metastatic Cancers through Multiregional Tumor Sequencing.Molecular cancer research : MCR · 2021Article
- Characterizing allele- and haplotype-specific copy numbers in single cells with CHISEL.Nature biotechnology · 2021Article
- Accucopy: accurate and fast inference of allele-specific copy number alterations from low-coverage low-purity tumor sequencing data.BMC bioinformatics · 2021Article
- Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine.PLoS computational biology · 2021Article
- Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data.Nature communications · 2020Article
- Research Autopsy Demonstrates Polyclonal Acquired Resistance in a Patient With Metastatic GI Stromal Tumor.JCO precision oncology · 2020Article
- RBV: Read balance validator, a tool for prioritising copy number variations in germline conditions.Scientific reports · 2019Article
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5 authors.
Funding
Abstract
The progression and clonal development of tumors often involve amplifications and deletions of genomic DNA. Estimation of allele-specific copy number, which quantifies the number of copies of each allele at each variant loci rather than the total number of chromosome copies, is an important step in the characterization of tumor genomes and the inference of their clonal history. We describe a new method, falcon, for finding somatic allele-specific copy number changes by next generation sequencing of tumors with matched normals. falcon is based on a change-point model on a bivariate mixed Binomial process, which explicitly models the copy numbers of the two chromosome haplotypes and corrects for local allele-specific coverage biases. By using the Binomial distribution rather than a normal approximation, falcon more effectively pools evidence from sites with low coverage. A modified Bayesian information criterion is used to guide model selection for determining the number of copy number events. Falcon is evaluated on in silico spike-in data and applied to the analysis of a pre-malignant colon tumor sample and late-stage colorectal adenocarcinoma from the same individual. The allele-specific copy number estimates obtained by falcon allows us to draw detailed conclusions regarding the clonal history of the individual's colon cancer.
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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.