Genetic and phenotypic landscape of the mitochondrial genome in the Japanese population

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 wer...

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Bibliographic Details
Published in:Communications biology 2020-03, Vol.3 (1), p.104-104, Article 104
Main Authors: Yamamoto, Kenichi, Sakaue, Saori, Matsuda, Koichi, Murakami, Yoshinori, Kamatani, Yoichiro, Ozono, Keiichi, Momozawa, Yukihide, Okada, Yukinori
Format: Article
Language:English
Subjects:
45/23
45/43
631/114/1305
631/208/205/2138
631/208/514/2254
Biology
Biomedical and Life Sciences
Copy number
Creatine
Creatine kinase
Deoxyribonucleic acid
DNA
Genetic analysis
Genomes
Genotypes
Haplotypes
Learning algorithms
Life Sciences
Linkage disequilibrium
Mitochondrial DNA
Nucleotide sequence
Phenotypes
Pleiotropy
Population genetics
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Summary: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 × 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.
ISSN:2399-3642
2399-3642
DOI:10.1038/s42003-020-0812-9