ArticleNucleic acids research2018
Human copy number variants are enriched in regions of low mappability.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- High Rate of Recurrent De Novo Mutations in Developmental and Epileptic Encephalopathies.American journal of human genetics · 2017Pooled it
- SVCROWS: a user-defined tool for interpreting significant structural variants in heterogeneous datasets.Nucleic acids research · 2026Article
- Application of long-read sequencing in the diagnosis of Duchenne/Becker muscular dystrophy: unveiling complex structural variations and deep intronic mutations.Italian journal of pediatrics · 2025Article
- Variation in the Content of Three Tandem Repeats of the Human Genome (Ribosomal, Satellite III, and Telomere) in Peripheral Blood Leukocyte DNA of People of Different Ages (5-101 Years).Journal of aging research · 2025Article
- Novel liquid biopsy CNV biomarkers in malignant melanoma.Scientific reports · 2024Article
- Understanding genetic variability: exploring large-scale copy number variants through non-invasive prenatal testing in European populations.BMC genomics · 2024Article
- Article
- DNA sequence features underlying large-scale duplications and deletions in human.Journal of applied genetics · 2022Article
- Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.iScience · 2022Article
- Article
- SMCKAT, a Sequential Multi-Dimensional CNV Kernel-Based Association Test.Life (Basel, Switzerland) · 2021Article
- Inherited duplications of PPP2R3B predispose to nevi and melanoma via a C21orf91-driven proliferative phenotype.Genetics in medicine : official journal of the American College of Medical Genetics · 2021Article
- Optical genome mapping enables constitutional chromosomal aberration detection.American journal of human genetics · 2021Article
- Genome-wide copy number variations in a large cohort of bantu African children.BMC medical genomics · 2021Article
- Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.American journal of human genetics · 2021Article
- Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements.PLoS computational biology · 2021Article
- Low-coverage whole-genome sequencing of extracellular vesicle-associated DNA in patients with metastatic cancer.Scientific reports · 2021Article
- Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Comparison of Circulating Tumour DNA and Extracellular Vesicle DNA by Low-Pass Whole-Genome Sequencing Reveals Molecular Drivers of Disease in a Breast Cancer Patient.Biomedicines · 2020Article
- Evaluating the probability of CRISPR-based gene drive contaminating another species.Evolutionary applications · 2020Article
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Authors and funding
6 authors.
Funding
Abstract
Copy number variants (CNVs) are known to affect a large portion of the human genome and have been implicated in many diseases. Although whole-genome sequencing (WGS) can help identify CNVs, most analytical methods suffer from limited sensitivity and specificity, especially in regions of low mappability. To address this, we use PopSV, a CNV caller that relies on multiple samples to control for technical variation. We demonstrate that our calls are stable across different types of repeat-rich regions and validate the accuracy of our predictions using orthogonal approaches. Applying PopSV to 640 human genomes, we find that low-mappability regions are approximately 5 times more likely to harbor germline CNVs, in stark contrast to the nearly uniform distribution observed for somatic CNVs in 95 cancer genomes. In addition to known enrichments in segmental duplication and near centromeres and telomeres, we also report that CNVs are enriched in specific types of satellite and in some of the most recent families of transposable elements. Finally, using this comprehensive approach, we identify 3455 regions with recurrent CNVs that were missing from existing catalogs. In particular, we identify 347 genes with a novel exonic CNV in low-mappability regions, including 29 genes previously associated with disease.
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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.