ArticleBioinformatics (Oxford, England)2011
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV.
Article in Bioinformatics (Oxford, England), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 223 papers, 1 of them a synthesis that pooled it.
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Who cites it
223 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application.Molecular neurodegeneration · 2022Pooled it
- Dynamic epigenetic changes to VHL occur with sunitinib in metastatic clear cell renal cancer.Oncotarget · 2016Trial
- Targeted next generation sequencing identifies clinically actionable mutations in patients with melanoma.Pigment cell & melanoma research · 2014Trial
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.Bioinformatics (Oxford, England) · 2026Article
- Distinct mutational signature and clonal evolution in constitutional mismatch repair deficiency-associated high-grade gliomas.iScience · 2026Article
- Genomic landscape and molecular subtypes of primary central nervous system lymphoma.Blood cancer journal · 2025Article
- Diagnostic Utility of Trio-Exome Sequencing for Children With Neurodevelopmental Disorders.JAMA network open · 2025Article
- Review
- Copy number variation analysis in 138 families with steroid-resistant nephrotic syndrome identifies causal homozygous deletions in PLCE1 and NPHS2 in two families.Pediatric nephrology (Berlin, Germany) · 2024Article
- OTSUCNV: an adaptive segmentation and OTSU-based anomaly classification method for CNV detection using NGS data.BMC genomics · 2024Article
- Non-Invasive Prenatal Diagnosis of Chromosomal and Monogenic Disease by a Novel Bioinspired Micro-Nanochip for Isolating Fetal Nucleated Red Blood Cells.International journal of nanomedicine · 2024Article
- Genetic landscape and PD-L1 expression in Epstein-Barr virus-associated gastric cancer according to the histological pattern.Scientific reports · 2023Article
- Super-enhancer hijacking drives ectopic expression of hedgehog pathway ligands in meningiomas.Nature communications · 2023Article
- Longitudinal multi-omics study of palbociclib resistance in HR-positive/HER2-negative metastatic breast cancer.Genome medicine · 2023Article
- Whole-exome sequencing identifies a set of genes as markers of hepatocellular carcinoma early recurrence.Hepatology international · 2023Article
- A Clinician's Guide to Bioinformatics for Next-Generation Sequencing.Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer · 2023Review
- JLOH: Inferring loss of heterozygosity blocks from sequencing data.Computational and structural biotechnology journal · 2023Article
- Efficacy and safety of a triple combination of atezolizumab, bevacizumab plus GEMOX for advanced biliary tract cancer: a multicenter, single-arm, retrospective study.Therapeutic advances in gastroenterology · 2023Article
- Read Count Patterns and Detection of Cancerous Copy Number Alterations in Plasma Cell-Free DNA Whole Exome Sequencing Data for Advanced Non-Small Cell Lung Cancer.International journal of molecular sciences · 2022Article
163 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
motivationThe ability to detect copy-number variation (CNV) and loss of heterozygosity (LOH) from exome sequencing data extends the utility of this powerful approach that has mainly been used for point or small insertion/deletion detection.
resultsWe present ExomeCNV, a statistical method to detect CNV and LOH using depth-of-coverage and B-allele frequencies, from mapped short sequence reads, and we assess both the method's power and the effects of confounding variables. We apply our method to a cancer exome resequencing dataset. As expected, accuracy and resolution are dependent on depth-of-coverage and capture probe design. AVAILABILITY: CRAN package 'ExomeCNV'. CONTACT: fsathira@fas.harvard.edu; snelson@ucla.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.