ArticleFrontiers in genetics2014
The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.
Article in Frontiers in genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 25 citations in OpenAlex.
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- On the core segmentation algorithms of copy number variation detection tools.Briefings in bioinformatics · 2024Article
- Human β-Defensin 2 Mutations Are Associated With Asthma and Atopy in Children and Its Application Prevents Atopic Asthma in a Mouse Model.Frontiers in immunology · 2021Article
- Statistical Considerations on NGS Data for Inferring Copy Number Variations.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Sequencing XMET genes to promote genotype-guided risk assessment and precision medicine.Science China. Life sciences · 2019Review
- Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.BMC biotechnology · 2019Article
- SM-RCNV: a statistical method to detect recurrent copy number variations in sequenced samples.Genes & genomics · 2019Article
- Comprehensively benchmarking applications for detecting copy number variation.PLoS computational biology · 2019Article
- iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.PloS one · 2018Article
- HumanWellcome open research · 2018Article
- Copy number variation and disease resistance in plants.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Review
- SRBreak: A Read-Depth and Split-Read Framework to Identify Breakpoints of Different Events Inside Simple Copy-Number Variable Regions.Frontiers in genetics · 2016Article
- The distribution and impact of common copy-number variation in the genome of the domesticated apple, Malus x domestica Borkh.BMC genomics · 2015Article
- Whole-genome CNV analysis: advances in computational approaches.Frontiers in genetics · 2015Review
- Identification of copy number variants in whole-genome data using Reference Coverage Profiles.Frontiers in genetics · 2015Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent advances in high-throughout sequencing technologies have made it possible to accurately assign copy number (CN) at CN variable loci. However, current analytic methods often perform poorly in regions in which complex CN variation is observed. Here we report the development of a read depth-based approach, CNVrd2, for investigation of CN variation using high-throughput sequencing data. This methodology was developed using data from the 1000 Genomes Project from the CCL3L1 locus, and tested using data from the DEFB103A locus. In both cases, samples were selected for which paralog ratio test data were also available for comparison. The CNVrd2 method first uses observed read-count ratios to refine segmentation results in one population. Then a linear regression model is applied to adjust the results across multiple populations, in combination with a Bayesian normal mixture model to cluster segmentation scores into groups for individual CN counts. The performance of CNVrd2 was compared to that of two other read depth-based methods (CNVnator, cn.mops) at the CCL3L1 and DEFB103A loci. The highest concordance with the paralog ratio test method was observed for CNVrd2 (77.8/90.4% for CNVrd2, 36.7/4.8% for cn.mops and 7.2/1% for CNVnator at CCL3L1 and DEF103A). CNVrd2 is available as an R package as part of the Bioconductor project: http://www.bioconductor.org/packages/release/bioc/html/CNVrd2.html.
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