ArticleNature communications2023
Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation.
Article in Nature communications, 2023. 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.
- Application of whole genome sequencing for carrier and diagnostic assessment of spinal muscular atrophy in Taiwan.NPJ genomic medicine · 2025Article
- Refining the detection of complex rearrangements in 15q15.3 region involving the STRC gene in hereditary hearing loss patients.Journal of human genetics · 2025Article
- Diagnosing missed cases of spinal muscular atrophy in genome, exome, and panel sequencing data sets.Genetics in medicine : official journal of the American College of Medical Genetics · 2025Article
- Genome-wide profiling of highly similar paralogous genes using HiFi sequencing.Nature communications · 2025Article
- Diagnosing missed cases of spinal muscular atrophy in genome, exome, and panel sequencing datasets.medRxiv : the preprint server for health sciences · 2024Article
- Resolving intra-repeat variation in medically relevant VNTRs from short-read sequencing data using the cardiovascular risk gene LPA as a model.Genome biology · 2024Article
- Genome sequencing as a generic diagnostic strategy for rare disease.Genome medicine · 2024Article
- Systematic analysis of paralogous regions in 41,755 exomes uncovers clinically relevant variation.Nature communications · 2023Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The short lengths of short-read sequencing reads challenge the analysis of paralogous genomic regions in exome and genome sequencing data. Most genetic variants within these homologous regions therefore remain unidentified in standard analyses. Here, we present a method (Chameleolyser) that accurately identifies single nucleotide variants and small insertions/deletions (SNVs/Indels), copy number variants and ectopic gene conversion events in duplicated genomic regions using whole-exome sequencing data. Application to a cohort of 41,755 exome samples yields 20,432 rare homozygous deletions and 2,529,791 rare SNVs/Indels, of which we show that 338,084 are due to gene conversion events. None of the SNVs/Indels are detectable using regular analysis techniques. Validation by high-fidelity long-read sequencing in 20 samples confirms >88% of called variants. Focusing on variation in known disease genes leads to a direct molecular diagnosis in 25 previously undiagnosed patients. Our method can readily be applied to existing exome data.
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