期刊
COMMUNICATIONS BIOLOGY
卷 3, 期 1, 页码 -出版社
NATURE PORTFOLIO
DOI: 10.1038/s42003-020-0812-9
关键词
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资金
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
- Japan Agency for Medical Research and Development (AMED)
- Japan Society for the Promotion of Science (JSPS) KAKENHI [15H05911, 19H01021]
- AMED [JP19gm6010001, JP19ek0410041, JP19ek0109413, JP19km0405211]
- Takeda Science Foundation
- Bioinformatics Initiative of Osaka University Graduate School of Medicine
- Osaka University
The genetic landscape of mitochondrial DNA (mtDNA) has been elusive. By analyzing mtDNA using the whole genome sequence (WGS) of Japanese individuals (n = 1928), we identified 2023 mtDNA variants and high-resolution haplogroups. Frequency spectra of the haplogroups were population-specific and were heterogeneous among geographic regions within Japan. Application of machine learning methods could finely classify the subjects corresponding to the high-digit mtDNA sub-haplogroups. mtDNA had distinct genetic structures from that of nuclear DNA (nDNA), characterized by no distance-dependent linkage disequilibrium decay, sparse tagging of common variants, and the existence of common haplotypes spanning the entire mtDNA. We did not detect any evidence of mtDNA-nDNA (or mtDNA copy number-nDNA) genotype associations. Together with WGS-based mtDNA variant imputation, we conducted a phenome-wide association study of 147,437 Japanese individuals with 99 clinical phenotypes. We observed pleiotropy of mtDNA genetic risk on the five late-onset human complex traits including creatine kinase (P = 1.7 x 10(-12)). Kenichi Yamamoto et al. report a genetic analysis of mitochondrial DNA (mtDNA) and a phenome-wide association study in Japanese individuals from the BioBank Japan Project. They describe the genetic landscape of the mitochondria and identify pleiotropic mtDNA variants associated with 5 late-onset complex traits.
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