ArticleBioinformatics (Oxford, England)2011
Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.
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 13 papers.
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Who cites it
13 citing papers in PubMed.
- Novel Strategy for Structural Variant Genotyping by Short-Read Genomic Sequencing From Restriction-Circles: Experimental and Bioinformatics Proof-of-Concept.Human mutation · 2026Article
- Potentials and challenges of chromosomal microarray analysis in prenatal diagnosis.Frontiers in genetics · 2022Review
- Computational tools to unmask transposable elements.Nature reviews. Genetics · 2018Review
- Human copy number variants are enriched in regions of low mappability.Nucleic acids research · 2018Article
- A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies.Frontiers in genetics · 2018Article
- CNVcaller: highly efficient and widely applicable software for detecting copy number variations in large populations.GigaScience · 2017Article
- Allele-specific copy-number discovery from whole-genome and whole-exome sequencing.Nucleic acids research · 2015Article
- VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.Nucleic acids research · 2014Article
- CNV-TV: a robust method to discover copy number variation from short sequencing reads.BMC bioinformatics · 2013Article
- The mutation rate of mycobacterial repetitive unit loci in strains of M. tuberculosis from cynomolgus macaque infection.BMC genomics · 2013Article
- CNVeM: copy number variation detection using uncertainty of read mapping.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- Improving detection of copy-number variation by simultaneous bias correction and read-depth segmentation.Nucleic acids research · 2013Article
- Repetitive DNA and next-generation sequencing: computational challenges and solutions.Nature reviews. Genetics · 2011Review
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Authors and funding
4 authors.
Funding
Abstract
motivationStructural variations and in particular copy number variations (CNVs) have dramatic effects of disease and traits. Technologies for identifying CNVs have been an active area of research for over 10 years. The current generation of high-throughput sequencing techniques presents new opportunities for identification of CNVs. Methods that utilize these technologies map sequencing reads to a reference genome and look for signatures which might indicate the presence of a CNV. These methods work well when CNVs lie within unique genomic regions. However, the problem of CNV identification and reconstruction becomes much more challenging when CNVs are in repeat-rich regions, due to the multiple mapping positions of the reads.
resultsIn this study, we propose an efficient algorithm to handle these multi-mapping reads such that the CNVs can be reconstructed with high accuracy even for repeat-rich regions. To our knowledge, this is the first attempt to both identify and reconstruct CNVs in repeat-rich regions. Our experiments show that our method is not only computationally efficient but also accurate.
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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.