ArticleJournal of biochemistry2021
Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs.
Article in Journal of biochemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 3 of them syntheses that pooled it.
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Who cites it
26 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Identification of risk loci for postpartum depression in a genome-wide association study.Psychiatry and clinical neurosciences · 2024Pooled it
- Genome-wide association study of nausea and vomiting during pregnancy in Japan: the TMM BirThree Cohort Study.BMC pregnancy and childbirth · 2024Pooled it
- Genetic architecture of alcohol consumption identified by a genotype-stratified GWAS and impact on esophageal cancer risk in Japanese people.Science advances · 2024Pooled it
- Osteoporosis genetic risk prediction using bone mineral density polygenic scores in Japanese: TMM CommCohort study.Journal of human genetics · 2026Article
- Genome-Wide Meta-Analysis for High Myopia Provides Insights into Disease Mechanisms and Reveals a Causal Link to Primary Open-Angle Glaucoma.Ophthalmology science · 2026Article
- Article
- Cohort Profile Update: The Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study (TMM BirThree Cohort Study) 2023 update.International journal of epidemiology · 2025Article
- Genetic predisposition for immunoglobulin E production explains atopic risk in children: Tohoku Medical Megabank cohort study.American journal of human genetics · 2025Article
- Causal relationship between body mass index and insulin resistance: Linear and nonlinear Mendelian randomization study in a Japanese population.Journal of diabetes investigation · 2025Article
- Genetic effects on gestational diabetes mellitus and their interactions with environmental factors among Japanese women.Journal of human genetics · 2025Article
- Genome-wide association study of plasma amino acids and Mendelian randomization for cardiometabolic traits.Scientific reports · 2025Article
- Preeclampsia prediction with maternal and paternal polygenic risk scores: the TMM BirThree Cohort Study.Scientific reports · 2025Article
- Genome-wide association study of common side effects following COVID-19 booster vaccination in a cohort of corporate employees in Japan.Scientific reports · 2025Article
- Metabolomic Profiling of Open-Angle Glaucoma Etiologic Endotypes: Tohoku Multi-Omics Glaucoma Study.Investigative ophthalmology & visual science · 2024Article
- Study Profile of the Tsuruoka Metabolomics Cohort Study (TMCS).Journal of epidemiology · 2024Article
- Whole blood transcriptome analysis for age- and gender-specific gene expression profiling in Japanese individuals.Journal of biochemistry · 2024Article
- jMorp: Japanese Multi-Omics Reference Panel update report 2023.Nucleic acids research · 2024Article
- Risk Factors, Prognosis, Influence on the Offspring, and Genetic Architecture of Perinatal Depression Classified Based on the Depressive Symptom Trajectory.Depression and anxiety · 2024Article
- Establishment of the early prediction models of low-birth-weight reveals influential genetic and environmental factors: a prospective cohort study.BMC pregnancy and childbirth · 2023Article
- A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants.Science advances · 2023Article
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22 authors.
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Abstract
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5-5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.
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