ArticleNature communications2022
Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Point mutations and complex variants impact gene expression and addiction-related behaviors in Heterogeneous Stock rats.bioRxiv : the preprint server for biology · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- Likelihood-based optimization enables accurate copy number estimation for paralogous genes using exome data.Bioinformatics (Oxford, England) · 2026Article
- SSLCNV: A Semi-supervised Learning Framework for Accurate Copy Number Variation Detection.Interdisciplinary sciences, computational life sciences · 2025Article
- T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population.Genome research · 2025Article
- Locityper enables targeted genotyping of complex polymorphic genes.Nature genetics · 2025Article
- Article
- Genome-wide profiling of highly similar paralogous genes using HiFi sequencing.Nature communications · 2025Article
- Complex genetic variation in nearly complete human genomes.bioRxiv : the preprint server for biology · 2024Article
- Genome engineering on size reduction and complexity simplification: A review.Journal of advanced research · 2024Review
- Short-read aligner performance in germline variant identification.Bioinformatics (Oxford, England) · 2023Review
- A multilocus approach for accurate variant calling in low-copy repeats using whole-genome sequencing.Bioinformatics (Oxford, England) · 2023Article
- Robust and accurate estimation of paralog-specific copy number for duplicated genes using whole-genome sequencing.Nature communications · 2022Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
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Authors and funding
2 authors.
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Abstract
The human genome contains hundreds of low-copy repeats (LCRs) that are challenging to analyze using short-read sequencing technologies due to extensive copy number variation and ambiguity in read mapping. Copy number and sequence variants in more than 150 duplicated genes that overlap LCRs have been implicated in monogenic and complex human diseases. We describe a computational tool, Parascopy, for estimating the aggregate and paralog-specific copy number of duplicated genes using whole-genome sequencing (WGS). Parascopy is an efficient method that jointly analyzes reads mapped to different repeat copies without the need for global realignment. It leverages multiple samples to mitigate sequencing bias and to identify reliable paralogous sequence variants (PSVs) that differentiate repeat copies. Analysis of WGS data for 2504 individuals from diverse populations showed that Parascopy is robust to sequencing bias, has higher accuracy compared to existing methods and enables prioritization of pathogenic copy number changes in duplicated genes.
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