ArticleJournal of medical genetics2018
Whole-genome sequencing analysis of CNV using low-coverage and paired-end strategies is efficient and outperforms array-based CNV analysis.
Article in Journal of medical genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers, 1 of them a synthesis that pooled it.
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Who cites it
62 citing papers in PubMed, 1 synthesis or guideline pooled it, 104 citations in OpenAlex.
- CMDB: the comprehensive population genome variation database of China.Nucleic acids research · 2023Pooled it
- Whole-genome sequencing revealed an interstitial deletion encompassing OCRL and SMARCA1 gene in a patient with Lowe syndrome.Molecular genetics & genomic medicine · 2019Trial
- Untangling the Copy Number Variation at the Basis of Belted Phenotypes in Cattle Using Long-Read Sequencing.Animal genetics · 2026Article
- Genome-wide copy number variation drives adaptive evolution inCurrent zoology · 2026Article
- Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism.Cell genomics · 2026Article
- CNValidatron: accurate and efficient validation of PennCNV calls using computer vision.BMC bioinformatics · 2026Article
- <italic>WT1</italic> Deletion in 46,XY DSD: The Importance of Copy Number Variant Analysis.Sexual development : genetics, molecular biology, evolution, endocrinology, embryology, and pathology of sex determination and differentiation · 2026Article
- Feasibility of Low-Pass Whole Genome Sequencing for Detecting Somatic Copy Number Alterations in Formalin-Fixed Uveal Melanoma Specimens.Translational vision science & technology · 2025Article
- A rare HCN4 variant combined with sick sinus syndrome, left ventricular noncompaction, and complex congenital heart disease.Channels (Austin, Tex.) · 2025Article
- Precision Oncology: Current Landscape, Emerging Trends, Challenges, and Future Perspectives.Cells · 2025Review
- CNValidatron: Accurate And Efficient Validation of PennCNV Calls Using Computer Vision.bioRxiv : the preprint server for biology · 2025Article
- Benchmarking copy number variation detection with low-coverage whole-genome sequencing.Briefings in bioinformatics · 2025Article
- Long-read genome sequencing resolves complex genomic rearrangements in rare genetic syndromes.NPJ genomic medicine · 2024Article
- Review
- Article
- Article
- Investigating copy number variants in schizophrenia pedigrees using a new consensus pipeline called PECAN.Scientific reports · 2024Article
- Resolving the 22q11.2 deletion using CTLR-Seq reveals chromosomal rearrangement mechanisms and individual variance in breakpoints.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- The expanding diagnostic toolbox for rare genetic diseases.Nature reviews. Genetics · 2024Review
- Overexpression of SYNGAP1 suppresses the proliferation of rectal adenocarcinoma via Wnt/β-Catenin signaling pathway.Discover oncology · 2024Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundCopy number variation (CNV) analysis is an integral component of the study of human genomes in both research and clinical settings. Array-based CNV analysis is the current first-tier approach in clinical cytogenetics. Decreasing costs in high-throughput sequencing and cloud computing have opened doors for the development of sequencing-based CNV analysis pipelines with fast turnaround times. We carry out a systematic and quantitative comparative analysis for several low-coverage whole-genome sequencing (WGS) strategies to detect CNV in the human genome.
methodsWe compared the CNV detection capabilities of WGS strategies (short insert, 3 kb insert mate pair and 5 kb insert mate pair) each at 1×, 3× and 5× coverages relative to each other and to 17 currently used high-density oligonucleotide arrays. For benchmarking, we used a set of gold standard (GS) CNVs generated for the 1000 Genomes Project CEU subject NA12878.
resultsOverall, low-coverage WGS strategies detect drastically more GS CNVs compared with arrays and are accompanied with smaller percentages of CNV calls without validation. Furthermore, we show that WGS (at ≥1× coverage) is able to detect all seven GS deletion CNVs >100 kb in NA12878, whereas only one is detected by most arrays. Lastly, we show that the much larger 15 Mbp Cri du chat deletion can be readily detected with short-insert paired-end WGS at even just 1× coverage.
conclusionsCNV analysis using low-coverage WGS is efficient and outperforms the array-based analysis that is currently used for clinical cytogenetics.
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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.