ArticleNature communications2021
Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed.
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- From N-of-1 to versatility in propionic acidemia: Antisense oligonucleotide-mediated skipping of a constitutiveMolecular therapy. Nucleic acids · 2026Article
- Accessing medically relevant complex regions with a pangenome graph of 20 near-complete Japanese haplotypes.Nature communications · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
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- Molecular impact of a novelFrontiers in endocrinology · 2026Article
- Advancements in Whole-Genome Sequencing Protocols: A Decade of In-House Operations and Quality Controls at the Tohoku Medical Megabank.JMA journal · 2025Review
- JG2: an updated version of the Japanese population-specific reference genome.Human genome variation · 2025Article
- The usefulness of comprehensive genome profiling test in screening of Lynch syndrome independent of the conventional clinical screening or microsatellite instability tests.Journal of human genetics · 2025Article
- A Japanese Case of Lenz-Majewski Syndrome With a Novel PTDSS1 Variant.Molecular genetics & genomic medicine · 2025Article
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- Benchmarking of bioinformatics tools for the hybridComputational and structural biotechnology journal · 2025Article
- Leveraging long-read sequencing technologies for pharmacogenomic testing: applications, analytical strategies, challenges, and future perspectives.Frontiers in genetics · 2025Review
- Genetic diversity among the present Japanese population: evidence from genotyping of human cell lines established in Japan.Human cell · 2024Article
- Genetic etiology of truncus arteriosus excluding 22q11.2 deletion syndrome and identification of c.1617del, a prevalent variant in TMEM260, in the Japanese population.Journal of human genetics · 2024Article
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18 authors.
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Abstract
The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using > 100× Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the Japanese major allele at most loci. We adopt JG1 as the reference for confirmatory exome re-analyses of seven rare-disease Japanese families and find that re-analysis using JG1 reduces total candidate variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genomes from a single population can aid genome analyses of that population.
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