ArticleCell genomics2023
Detection of trait-associated structural variations using short-read sequencing.
Article in Cell genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Comparative genomic analysis of pigs differing in survival following African swine fever virus infection.Veterinary research communications · 2026Article
- Interchromosomal Translocations and Large Deletions Drive the Evolution of the Outlier Chromosome in the Smallest Photosynthetic Eukaryote.Genome biology and evolution · 2026Article
- Genome-wide associations of structural variants with human traits through imputation from long-read assemblies.Nature genetics · 2026Article
- Article
- TRsv: simultaneous detection of tandem repeat variations, structural variations, and short indels using long read sequencing data.Genome biology · 2025Article
- Comparative analysis of hybrid-SNP microarray and nanopore sequencing for detection of large-sized copy number variants in the human genome.Molecular cytogenetics · 2025Article
- Mining for gene-environment and gene-gene interactions: parametric and non-parametric tests for detecting variance quantitative trait loci.Frontiers in genetics · 2025Article
- Detection of Complex Genomic Rearrangements Using Short-Read Whole Genome Sequencing in C. elegans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.Genome biology · 2024Article
- Detecting gene-environment interactions from multiple continuous traits.Bioinformatics (Oxford, England) · 2024Article
- Investigating mobile element variations by statistical genetics.Human genome variation · 2024Review
- MHConstructor: A high-throughput, haplotype-informed solution to the MHC assembly challenge.bioRxiv : the preprint server for biology · 2024Article
- Decoding triancestral origins, archaic introgression, and natural selection in the Japanese population by whole-genome sequencing.Science advances · 2024Article
- Comparative evaluation of SNVs, indels, and structural variations detected with short- and long-read sequencing data.Human genome variation · 2024Article
- Enhancing interpretation of clinical disease-associated copy number variations from multiple sequencing strategies with CNVSeeker.Bioinformatics (Oxford, England) · 2022Article
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8 authors.
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Abstract
Genomic structural variation (SV) affects genetic and phenotypic characteristics in diverse organisms, but the lack of reliable methods to detect SV has hindered genetic analysis. We developed a computational algorithm (MOPline) that includes missing call recovery combined with high-confidence SV call selection and genotyping using short-read whole-genome sequencing (WGS) data. Using 3,672 high-coverage WGS datasets, MOPline stably detected ∼16,000 SVs per individual, which is over ∼1.7-3.3-fold higher than previous large-scale projects while exhibiting a comparable level of statistical quality metrics. We imputed SVs from 181,622 Japanese individuals for 42 diseases and 60 quantitative traits. A genome-wide association study with the imputed SVs revealed 41 top-ranked or nearly top-ranked genome-wide significant SVs, including 8 exonic SVs with 5 novel associations and enriched mobile element insertions. This study demonstrates that short-read WGS data can be used to identify rare and common SVs associated with a variety of traits.
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