ArticleNucleic acids research2016
Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 98 papers.
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98 citing papers in PubMed.
- FFPE-CUTAC: A Single Assay, Multiple Layers.bioRxiv : the preprint server for biology · 2026Article
- Integrated Multiomic Profiling Enhances Risk Stratification and Prognostication in Canine Osteosarcoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- A High-Fidelity and Ancestrally Inclusive Patient-Derived Organoid Platform Resolves Cancer Cell Plasticity in Uterine Carcinosarcoma.bioRxiv : the preprint server for biology · 2026Article
- Comprehensive Molecular Characterization of High-Grade Endometrial Cancer in an Ancestrally Diverse Cohort.bioRxiv : the preprint server for biology · 2026Article
- A Single-Cell Atlas of Uterine Carcinosarcoma from Diverse Ancestries.bioRxiv : the preprint server for biology · 2026Article
- Multimodal antigenic escape to GPRC5D-targeted T cell engagers in multiple myeloma.Nature medicine · 2026Article
- Copy Number Alteration Profiling from Plasma cfDNA WES in Advanced NSCLC.International journal of molecular sciences · 2025Article
- araCNA: somatic copy number profiling using long-range sequence models.NAR genomics and bioinformatics · 2025Article
- High-resolution detection of copy number alterations in single cells with HiScanner.Nature communications · 2025Article
- Multi-omics analysis reveals immunosuppression in oesophageal squamous cell carcinoma induced by creatine accumulation and HK3 deficiency.Genome medicine · 2025Article
- High-resolution detection of copy number alterations in single cells with HiScanner.bioRxiv : the preprint server for biology · 2025Article
- A complex phylogeny of lineage plasticity in metastatic castration resistant prostate cancer.NPJ precision oncology · 2025Article
- Detecting copy-number alterations from single-cell chromatin sequencing data by AtaCNA.Cell reports methods · 2025Article
- Prediction of the 3D cancer genome from whole-genome sequencing using InfoHiC.Molecular systems biology · 2024Article
- Somatic mutation phasing and haplotype extension using linked-reads in multiple myeloma.bioRxiv : the preprint server for biology · 2024Article
- Genome-wide analysis and visualization of copy number with CNVpytor in igv.js.Bioinformatics (Oxford, England) · 2024Article
- Multi-scale signaling and tumor evolution in high-grade gliomas.Cancer cell · 2024Article
- HATCHet2: clone- and haplotype-specific copy number inference from bulk tumor sequencing data.Genome biology · 2024Article
- Comprehensive proteogenomic characterization of rare kidney tumors.Cell reports. Medicine · 2024Article
38 more citing papers are in PubMed but not listed here.
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Authors and funding
5 authors.
Funding
Abstract
Whole-genome sequencing data allow detection of copy number variation (CNV) at high resolution. However, estimation based on read coverage along the genome suffers from bias due to GC content and other factors. Here, we develop an algorithm called BIC-seq2 that combines normalization of the data at the nucleotide level and Bayesian information criterion-based segmentation to detect both somatic and germline CNVs accurately. Analysis of simulation data showed that this method outperforms existing methods. We apply this algorithm to low coverage whole-genome sequencing data from peripheral blood of nearly a thousand patients across eleven cancer types in The Cancer Genome Atlas (TCGA) to identify cancer-predisposing CNV regions. We confirm known regions and discover new ones including those covering KMT2C, GOLPH3, ERBB2 and PLAG1 Analysis of colorectal cancer genomes in particular reveals novel recurrent CNVs including deletions at two chromatin-remodeling genes RERE and NPM2 This method will be useful to many researchers interested in profiling CNVs from whole-genome sequencing data.
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