ArticleNucleic acids research2013
Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- A Novel Technique for Validating Copy Number Variants and Its Application in Familial Exudative Vitreoretinopathy.Human mutation · 2026Article
- Reproductive outcomes of mosaic embryo transfers in preimplantation genetic testing for structural rearrangement cycles: a retrospective cohort study.Journal of assisted reproduction and genetics · 2026Article
- Re-biopsy and modified biopsy in mosaic human embryos with simple segmental chromosomal deletion.Reproductive biology and endocrinology : RB&E · 2025Article
- Copy Number Alteration Profiling from Plasma cfDNA WES in Advanced NSCLC.International journal of molecular sciences · 2025Article
- Comparative study of tools for copy number variation detection using next-generation sequencing data.Scientific reports · 2025Article
- On the core segmentation algorithms of copy number variation detection tools.Briefings in bioinformatics · 2024Article
- Copy number variant detection using next-generation sequencing in EYS-associated retinitis pigmentosa.PloS one · 2024Article
- ARFID Genes and Environment (ARFID-GEN): study protocol.BMC psychiatry · 2023Article
- Novel deleterious splicing variant in HFM1 causes gametogenesis defect and recurrent implantation failure: concerning the risk of chromosomal abnormalities in embryos.Journal of assisted reproduction and genetics · 2023Article
- Comparison of day 5 blastocyst with day 6 blastocyst: Evidence from NGS-based PGT-A results.Journal of assisted reproduction and genetics · 2022Article
- Correspondence of aCGH and long-read genome assembly for detection of copy number differences: A proof-of-concept with cichlid genomes.PloS one · 2021Article
- Detection of chromosomal abnormalities in spontaneous miscarriage by low‑coverage next‑generation sequencing.Molecular medicine reports · 2020Article
- CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing.Scientific reports · 2019Article
- A randomized approach to speed up the analysis of large-scale read-count data in the application of CNV detection.BMC bioinformatics · 2018Article
- iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.PloS one · 2018Article
- CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations.GigaScience · 2017Article
- Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach.Genetics in medicine : official journal of the American College of Medical Genetics · 2016Article
- Copy number analysis of whole-genome data using BIC-seq2 and its application to detection of cancer susceptibility variants.Nucleic acids research · 2016Article
- Joint detection of copy number variations in parent-offspring trios.Bioinformatics (Oxford, England) · 2016Article
- Clinical sequencing: is WGS the better WES?Human genetics · 2016Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Structural variation is an important class of genetic variation in mammals. High-throughput sequencing (HTS) technologies promise to revolutionize copy-number variation (CNV) detection but present substantial analytic challenges. Converging evidence suggests that multiple types of CNV-informative data (e.g. read-depth, read-pair, split-read) need be considered, and that sophisticated methods are needed for more accurate CNV detection. We observed that various sources of experimental biases in HTS confound read-depth estimation, and note that bias correction has not been adequately addressed by existing methods. We present a novel read-depth-based method, GENSENG, which uses a hidden Markov model and negative binomial regression framework to identify regions of discrete copy-number changes while simultaneously accounting for the effects of multiple confounders. Based on extensive calibration using multiple HTS data sets, we conclude that our method outperforms existing read-depth-based CNV detection algorithms. The concept of simultaneous bias correction and CNV detection can serve as a basis for combining read-depth with other types of information such as read-pair or split-read in a single analysis. A user-friendly and computationally efficient implementation of our method is freely available.
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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.