ArticleGenome medicine2019
Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population.
Article in Genome medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed.
- Mucopolysaccharidosis type II in tunisian families: IDS gene variations disrupting substrate binding and a novel deep intronic deletion reducing IDS expression.Molecular biology reports · 2026Article
- KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.Database : the journal of biological databases and curation · 2026Article
- Long-read sequencing reveals novel isoform-specific eQTLs and regulatory mechanisms of isoform expression in human B cells.Genome biology · 2025Article
- Mapping crossover events of mouse meiotic recombination by restriction fragment ligation-based Refresh-seq.Cell discovery · 2024Article
- Long-read-based single sperm genome sequencing for chromosome-wide haplotype phasing of both SNPs and SVs.Nucleic acids research · 2023Article
- Targeted deletion of ecto-5'-nucleotidase results in retention of inosine monophosphate content in postmortem muscle of medaka (Oryzias latipes).Scientific reports · 2022Article
- Compound genetic etiology in a patient with a syndrome including diabetes, intellectual deficiency and distichiasis.Orphanet journal of rare diseases · 2022Article
- Article
- Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression.Human genetics · 2021Article
- Whole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer.Genome medicine · 2021Article
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8 authors.
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Abstract
backgroundNext-generation sequencing has allowed for the identification of different genetic variations, which are known to contribute to diseases. Of these, insertions and deletions are the second most abundant type of variations in the genome, but their biological importance or disease association is not well-studied, especially for deletions of intermediate sizes.
methodsWe identified intermediate-sized deletions from whole-genome sequencing (WGS) data of Japanese samples (n = 174) with a novel deletion calling method which considered multiple samples. These deletions were used to construct a reference panel for use in imputation. Imputation was then conducted using the reference panel and data from 82 publically available Japanese samples with gene expression data. The accuracy of the deletion calling and imputation was examined with Nanopore long-read sequencing technology. We also conducted an expression quantitative trait loci (eQTL) association analysis using the deletions to infer their functional impacts on genes, before characterizing the deletions causal for gene expression level changes.
resultsWe obtained a set of polymorphic 4378 high-confidence deletions and constructed a reference panel. The deletions were successfully imputed into the Japanese samples with high accuracy (97.3%). The eQTL analysis identified 181 deletions (4.1%) suggested as causal for gene expression level changes. The causal deletion candidates were significantly enriched in promoters, super-enhancers, and transcription elongation chromatin states. Generation of deletions in a cell line with the CRISPR-Cas9 system confirmed that they were indeed causative variants for gene expression change. Furthermore, one of the deletions was observed to affect the gene expression levels of a gene it was not located in.
conclusionsThis paper reports an accurate deletion calling method for genotype imputation at the whole genome level and shows the importance of intermediate-sized deletions in the human population.
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