ArticleNucleic acids research2017
Homozygous and hemizygous CNV detection from exome sequencing data in a Mendelian disease cohort.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 92 papers.
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Who cites it
92 citing papers in PubMed.
- Trial
- Ataxia and oculomotor apraxia caused by a large-scale deletion in the senataxin gene.Journal of applied genetics · 2026Article
- Systematic analysis of homozygous autosomal copy number losses in exomes improves diagnostic yield and uncovers ultra-rare recessive disorders.European journal of human genetics : EJHG · 2026Article
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- High Concordance of Copy Number Variants Detected by Chromosomal Microarray and Exome Sequencing in Clinical Diagnostics.Clinical genetics · 2026Article
- BayesCNV: A Bayesian Hierarchical Model for Sensitive and Specific Copy Number Estimation in Cell Free DNA.Diagnostics (Basel, Switzerland) · 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
- An integrated platform for concurrent structural and single-nucleotide variants improves copy-number detection and reveals pathogenic alleles in undiagnosed Mendelian families.Genome medicine · 2025Article
- Expanding the Clinical and Molecular Spectrum ofmedRxiv : the preprint server for health sciences · 2025Article
- Contribution of rare coding variants to microcephaly in individuals with neurodevelopmental disorders.Genome medicine · 2025Article
- A Phenotypic Study of CRB1 Retinopathy Secondary to the Variant p.(Pro836Thr) Prevalent in Those of Black African Ancestry.Investigative ophthalmology & visual science · 2025Article
- Targeted long-read sequencing enables higher diagnostic yield of ADPKD by accurate PKD1 genetic analysis.NPJ genomic medicine · 2025Article
- Genomic Balancing Act: deciphering DNA rearrangements in the complex chromosomal aberration involving 5p15.2, 2q31.1, and 18q21.32.European journal of human genetics : EJHG · 2025Article
- Genetic analysis of patients with low-frequency non-syndromic hearing loss.Molecular genetics and genomics : MGG · 2024Article
- Implementing genomic medicine in clinical practice for adults with undiagnosed rare diseases.NPJ genomic medicine · 2024Article
- VizCNV: An integrated platform for concurrent phased BAF and CNV analysis with trio genome sequencing data.bioRxiv : the preprint server for biology · 2024Article
- Optical genome mapping unveils hidden structural variants in neurodevelopmental disorders.Scientific reports · 2024Article
- A Novel Subtype of Acquired Generalized Lipodystrophy Associated With Subcutaneous Panniculitis-Like T-cell Lymphoma.JCEM case reports · 2024Article
- Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads.American journal of human genetics · 2024Article
- NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy.Genome medicine · 2024Article
32 more citing papers are in PubMed but not listed here.
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21 authors.
Funding
Abstract
We developed an algorithm, HMZDelFinder, that uses whole exome sequencing (WES) data to identify rare and intragenic homozygous and hemizygous (HMZ) deletions that may represent complete loss-of-function of the indicated gene. HMZDelFinder was applied to 4866 samples in the Baylor-Hopkins Center for Mendelian Genomics (BHCMG) cohort and detected 773 HMZ deletion calls (567 homozygous or 206 hemizygous) with an estimated sensitivity of 86.5% (82% for single-exonic and 88% for multi-exonic calls) and precision of 78% (53% single-exonic and 96% for multi-exonic calls). Out of 773 HMZDelFinder-detected deletion calls, 82 were subjected to array comparative genomic hybridization (aCGH) and/or breakpoint PCR and 64 were confirmed. These include 18 single-exon deletions out of which 8 were exclusively detected by HMZDelFinder and not by any of seven other CNV detection tools examined. Further investigation of the 64 validated deletion calls revealed at least 15 pathogenic HMZ deletions. Of those, 7 accounted for 17-50% of pathogenic CNVs in different disease cohorts where 7.1-11% of the molecular diagnosis solved rate was attributed to CNVs. In summary, we present an algorithm to detect rare, intragenic, single-exon deletion CNVs using WES data; this tool can be useful for disease gene discovery efforts and clinical WES analyses.
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