ArticleHuman genome variation2019
Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing.
Article in Human genome variation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Article
- Methods for Chromosome-Scale Haplotype Reconstruction.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Benchmarking of bioinformatics tools for the hybridComputational and structural biotechnology journal · 2025Article
- Developing CIRdb as a catalog of natural genetic variation in the Canary Islanders.Scientific reports · 2022Article
- Computational methods for chromosome-scale haplotype reconstruction.Genome biology · 2021Review
- SVA retrotransposon insertion in exon of MMR genes results in aberrant RNA splicing and causes Lynch syndrome.European journal of human genetics : EJHG · 2021Article
- Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.Nature communications · 2021Article
- Review
- Structural variation in the sequencing era.Nature reviews. Genetics · 2020Review
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Authors and funding
24 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented. Here, we assembled a Japanese genome using single-molecule real-time sequencing data and characterized insertions found in the assembled genome. We identified 3691 insertions ranging from 100 bps to ~10,000 bps in the assembled genome relative to the international reference sequence (GRCh38). To validate and characterize these insertions, we mapped short-reads from 1070 Japanese individuals and 728 individuals from eight other populations to insertions integrated into GRCh38. With this result, we constructed JRGv1 (Japanese Reference Genome version 1) by integrating the 903 verified insertions, totaling 1,086,173 bases, shared by at least two Japanese individuals into GRCh38. We also constructed decoyJRGv1 by concatenating 3559 verified insertions, totaling 2,536,870 bases, shared by at least two Japanese individuals or by six other assemblies. This assembly improved the alignment ratio by 0.4% on average. These results demonstrate the importance of refining the reference assembly and creating a population-specific reference genome. JRGv1 and decoyJRGv1 are available at the JRG website.
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