ArticleNAR genomics and bioinformatics2021
Detection of homozygous and hemizygous complete or partial exon deletions by whole-exome sequencing.
Article in NAR genomics and bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 12 citations in OpenAlex.
- Pediatric DOCK8 Deficiency Beyond Infections and Atopy: An Immunoactinopathy with Immune Dysregulation and Multisystem Involvement.Children (Basel, Switzerland) · 2026Article
- High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.Clinical genetics · 2026Article
- Article
- CopyVAE: a variational autoencoder-based approach for copy number variation inference using single-cell transcriptomics.Bioinformatics (Oxford, England) · 2024Article
- Article
- Incorporating CNV analysis improves the yield of exome sequencing for rare monogenic disorders-an important consideration for resource-constrained settings.Frontiers in genetics · 2023Review
- Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia.The Journal of experimental medicine · 2022Article
- Congenital deficiency reveals critical role of ISG15 in skin homeostasis.The Journal of clinical investigation · 2022Article
Corrections and comments
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Authors and funding
12 authors at 4 institutions in 2 countries.
Funding
Abstract
The detection of copy number variations (CNVs) in whole-exome sequencing (WES) data is important, as CNVs may underlie a number of human genetic disorders. The recently developed HMZDelFinder algorithm can detect rare homozygous and hemizygous (HMZ) deletions in WES data more effectively than other widely used tools. Here, we present HMZDelFinder_opt, an approach that outperforms HMZDelFinder for the detection of HMZ deletions, including partial exon deletions in particular, in WES data from laboratory patient collections that were generated over time in different experimental conditions. We show that using an optimized reference control set of WES data, based on a PCA-derived Euclidean distance for coverage, strongly improves the detection of HMZ complete exon deletions both in real patients carrying validated disease-causing deletions and in simulated data. Furthermore, we develop a sliding window approach enabling HMZDelFinder_opt to identify HMZ partial deletions of exons that are undiscovered by HMZDelFinder. HMZDelFinder_opt is a timely and powerful approach for detecting HMZ deletions, particularly partial exon deletions, in WES data from inherently heterogeneous laboratory patient collections.
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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.