ArticleCommunications biology2024
Population-specific reference panel improves imputation quality for genome-wide association studies conducted on the Japanese population.
Article in Communications biology, 2024. 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.
- A population-specific genomic reference panel for Taiwan: NHRI-RP-1.Journal of biomedical science · 2026Article
- gAIRR-wgs: high-resolution T cell receptor allele typing in biobank-scale whole-genome sequencing data.Briefings in bioinformatics · 2026Article
- Imputation in the Wild: Genome-Wide Robustness and Fine-Scale Limitations of Low-Coverage Genomes in Endangered Species.Molecular ecology resources · 2026Article
- National genomic projects in Asia and Africa: a review.Human genomics · 2026Review
- Cardiovascular Genetic Epidemiology in the Genome-Wide Era: From Association Discovery to Mechanistic Dissection and Clinical Translation.Cardiovascular drugs and therapy · 2026Review
- Selphi, a tool for improving genotype imputation accuracy.Scientific reports · 2026Article
- A reanalysis of a genome-wide association study on breast cancer in Asian populations using the SG10K_Health reference panel for imputation: a multi-Centre case-control analysis.Human molecular genetics · 2026Article
- Proteogenomics in cerebrospinal fluid and plasma reveals new biological fingerprint of cerebral small vessel disease.Nature aging · 2025Article
- Benchmarking Imputed Low Coverage Genomes in a Human Population Genetics Context.Molecular ecology resources · 2025Article
- Unraveling time-dependent genetic components underlying alcohol response.Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2025Article
- Establishing Best Practices for Clinical GWAS: Tackling Imputation and Data Quality Challenges.International journal of molecular sciences · 2025Review
- A variant in HMMR/HMMR-AS1 is associated with serum alanine aminotransferase levels in the Ryukyu population.Scientific reports · 2025Article
- Development and application of an updated haplotype reference panel for association analysis of spontaneous sex reversal in XX rainbow trout.Frontiers in genetics · 2025Article
- Machine learning models for pharmacogenomic variant effect predictions - recent developments and future frontiers.PharmacogenomicsReview
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Authors and funding
21 authors.
Funding
Abstract
To improve imputation quality for genome-wide association studies (GWAS) conducted on the Japanese population, we developed and evaluated four Japanese population-specific reference panels. These panels were constructed through the augmentation of the 1000 Genomes Project (1KG) panel using Japanese whole genome sequencing (WGS) data, with sample sizes ranging from 1 K to 7 K individuals enrolled through the Biobank Japan (BBJ) project, and sequencing depths ranging from 3× to 30×. Among these panels, an augmented reference panel comprising 7472 WGS samples of mixed depth (1KG+7K) exhibit the greatest improvement in imputation quality relative to the Trans-Omics for Precision Medicine (TOPMed) reference panel. Notably, we observe these improvements primarily for rare variants with a minor allele frequency (MAF) <5%. To demonstrate the benefits of improved imputation quality in association analyses of complex traits, we conducted GWAS for serum uric acid and total cholesterol levels following imputation up to the 1KG+7K panel. The analysis reveals several loci reaching genome-wide significance (P < 5 × 10
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