A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data
Open accessAbstract
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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- Authors
- Trost, B., Walker, S., Wang, Z., Thiruvahindrapuram, B., MacDonald, J. R., Sung, W. W. L., Pereira, S. L., Whitney, J., Chan, A. J. S., Pellecchia, G., Reuter, M. S., Lok, S., Yuen, R. K. C., Marshall, C. R., Merico, D., & Scherer, S. W.
- Affiliations
- Hospital for Sick Children (CA)
- University of Toronto (CA)
- Corresponding author
- Scherer, Stephen W.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2018-01
- Volume
- 102
- Issue
- 1
- Pages
- 142-155
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC5777982
- OpenAlex
- W2782424591
- Cited by
- 191
- References
- 64
- Citations by year
- 2026: 8 · 2025: 8 · 2024: 19 · 2023: 21 · 2022: 28 · 2021: 36 · 2020: 29 · 2019: 34 · 2018: 7
- FWCI
- 16.25
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Government of Ontario
- Autism Speaks
- Canadian Institute for Advanced Research
- Hospital for Sick Children
- Ontario Brain Institute
- Canada Foundation for Innovation
- Canadian Institutes of Health Research (FDN-143295)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- copy number variation, sequencing depth, whole genome sequencing, autism spectrum disorder, de novo CNVs, microarray comparison, genetic testing
- MeSH terms
- Whole Genome Sequencing, Algorithms, Child, Female, Haplotypes, Humans, Male, Reproducibility of Results, Sequence Analysis, DNA, DNA Copy Number Variations, Workflow
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