ArticleAmerican journal of human genetics2018
A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data.
Article in American journal of human genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 110 papers.
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Who cites it
110 citing papers in PubMed.
- Characterizing features of the genetic architecture underlying autism from a multi-ancestry perspective.Molecular psychiatry · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Article
- Quality and consistency of genetic newborn screening reports in China: insights from a multi-laboratory analysis using simulated samples.BMC pediatrics · 2026Article
- Genome-wide copy number variation drives adaptive evolution inCurrent zoology · 2026Article
- The Contribution of Massively Parallel Sequencing in Disclosing Unusual Tri- and Tetra-Allelic Type Patterns Detected at the Multicopy Loci DYS385a/b and DYF387S1.International journal of molecular sciences · 2026Article
- Findings from comprehensive genome sequencing in the Canadian population: Results from the GENCOV Study.Genetics in medicine open · 2026Article
- UBR5 loss-of-function variants in autism spectrum disorder and intellectual disability: case series and review of the literature.NPJ genomic medicine · 2025Article
- Copy number loss Of APP cause thoracic aortic dissection.Hypertension research : official journal of the Japanese Society of Hypertension · 2025Article
- Flexible, production-scale, human whole genome sequencing on a benchtop sequencer.BMC genomics · 2025Article
- The known structural variations in hearing loss and their diagnostic approaches: a comprehensive review.Molecular biology reports · 2025Review
- Pre-T cell receptor-α immunodeficiency detected exclusively using whole genome sequencing.NPJ genomic medicine · 2025Article
- Chromosome X-wide common variant association study in autism spectrum disorder.American journal of human genetics · 2025Article
- SurVIndel2: improving copy number variant calling from next-generation sequencing using hidden split reads.Nature communications · 2024Article
- Combining Off-flow, a Nextflow-coded program, and whole genome sequencing reveals unintended genetic variation in CRISPR/Cas-edited iPSCs.Computational and structural biotechnology journal · 2024Article
- A validated heart-specific model for splice-disrupting variants in childhood heart disease.Genome medicine · 2024Article
- Article
- A brief clinical genetics review: stepwise diagnostic processes of a monogenic disorder-hypertriglyceridemia.Translational pediatrics · 2024Review
- A large structural variant collection in Holstein cattle and associated database for variant discovery, characterization, and application.BMC genomics · 2024Article
- Genetic architecture of long-distance migration and population genomics of the endangered Japanese eel.iScience · 2024Article
50 more citing papers are in PubMed but not listed here.
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Authors and funding
16 authors.
Funding
Abstract
A remaining hurdle to whole-genome sequencing (WGS) becoming a first-tier genetic test has been accurate detection of copy-number variations (CNVs). Here, we used several datasets to empirically develop a detailed workflow for identifying germline CNVs >1 kb from short-read WGS data using read depth-based algorithms. Our workflow is comprehensive in that it addresses all stages of the CNV-detection process, including DNA library preparation, sequencing, quality control, reference mapping, and computational CNV identification. We used our workflow to detect rare, genic CNVs in individuals with autism spectrum disorder (ASD), and 120/120 such CNVs tested using orthogonal methods were successfully confirmed. We also identified 71 putative genic de novo CNVs in this cohort, which had a confirmation rate of 70%; the remainder were incorrectly identified as de novo due to false positives in the proband (7%) or parental false negatives (23%). In individuals with an ASD diagnosis in which both microarray and WGS experiments were performed, our workflow detected all clinically relevant CNVs identified by microarrays, as well as additional potentially pathogenic CNVs < 20 kb. Thus, CNVs of clinical relevance can be discovered from WGS with a detection rate exceeding microarrays, positioning WGS as a single assay for genetic variation detection.
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