The allele frequency of <i>ALDH2*Glu504Lys</i> and <i>ADH1B*Arg47His</i> for the Ryukyu islanders and their history of expansion among East Asians

Koganebuchi, Kae; Haneji, Kuniaki; Toma, Takashi; Joh, Keiichiro; Soejima, Hidenobu; Fujimoto, Kazuma; Ishida, Hajime; Ogawa, Motoyuki; Hanihara, Tsunehiko; Harada, Shoji; Kawamura, Shoji; Oota, Hiroki

doi:10.1002/ajhb.22933

Cited by 16 publications

(18 citation statements)

References 36 publications

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“…The top SNPs from the SDS analysis in ADH cluster and BRAP-ALDH2 are in linkage disequilibrium (LD) with functional missense SNPs of ADH1B (Arg47His, rs1229984) and ALDH2 (Glu504Lys, rs671) ( r 2 = 0.76 and 0.86 in the WGS dataset 1, respectively). These SNPs mediate differences in alcohol metabolism by altering the enzymatic activities of alcohol dehydrogenase and aldehyde dehydrogenase, and have been suggested in evolutional adaptations of global populations including Asians mostly by candidate gene-based approaches 22 . Our genome-wide analysis initially indicates that both of these alcohol metabolism-related SNPs are under the strongest recent natural selection pressure in the Japanese population.…”

Section: Resultsmentioning

confidence: 99%

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

et al. 2018

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Understanding natural selection is crucial to unveiling evolution of modern humans. Here, we report natural selection signatures in the Japanese population using 2234 high-depth whole-genome sequence (WGS) data (25.9×). Using rare singletons, we identify signals of very recent selection for the past 2000–3000 years in multiple loci (ADH cluster, MHC region, BRAP-ALDH2, SERHL2). In large-scale genome-wide association study (GWAS) dataset (n = 171,176), variants with selection signatures show enrichment in heterogeneity of derived allele frequency spectra among the geographic regions of Japan, highlighted by two major regional clusters (Hondo and Ryukyu). While the selection signatures do not show enrichment in archaic hominin-derived genome sequences, they overlap with the SNPs associated with the modern human traits. The strongest overlaps are observed for the alcohol or nutrition metabolism-related traits. Our study illustrates the value of high-depth WGS to understand evolution and their relationship with disease risk.

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Section: Resultsmentioning

confidence: 99%

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

et al. 2018

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“…Other physiological and morphological traits of Jomon people unidentified from skeletal remains, e.g. alcohol tolerance (Koganebuchi et al, 2017), Rh-blood type, and ear wax (Omoto, 1992), have been inferred indirectly from the geographical distribution of variants in the Japanese archipelago. Recent ancient DNA studies also uncovered phenotypic traits of Jomons, such as ear-wax and ABO blood type (Sato et al, 2009b(Sato et al, , 2010.…”

Section: Discussionmentioning

confidence: 99%

Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan

et al. 2019

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The Funadomari Jomon people were hunter-gatherers living on Rebun Island, Hokkaido, Japan c. 3500-3800 years ago. In this study, we determined the high-depth and low-depth nuclear genome sequences from a Funadomari Jomon female (F23) and male (F5), respectively. We genotyped the nuclear DNA of F23 and determined the human leukocyte antigen (HLA) class-I genotypes and the phenotypic traits. Moreover, a pathogenic mutation in the CPT1A gene was identified in both F23 and F5. The mutation provides metabolic advantages for consumption of a high-fat diet, and its allele frequency is more than 70% in Arctic populations, but is absent elsewhere. This variant may be related to the lifestyle of the Funadomari Jomon people, who fished and hunted land and marine animals. We observed high homozygosity by descent (HBD) in F23, but HBD tracts longer than 10 cM were very limited, suggesting that the population size of Northern Jomon populations were small. Our analysis suggested that population size of the Jomon people started to decrease c. 50000 years ago. The phylogenetic relationship among F23, modern/ancient Eurasians, and Native Americans showed a deep divergence of F23 in East Eurasia, probably before the split of the ancestor of Native Americans from East Eurasians, but after the split of 40000-year-old Tianyuan, indicating that the Northern Jomon people were genetically isolated from continental East Eurasians for a long period. Intriguingly, we found that modern Japanese as well as Ulchi, Korean, aboriginal Taiwanese, and Philippine populations were genetically closer to F23 than to Han Chinese. Moreover, the Y chromosome of F5 belonged to haplogroup D1b2b, which is rare in modern Japanese populations. These findings provided insights into the history and reconstructions of the ancient human population structures in East Eurasia, and the F23 genome data can be considered as the Jomon Reference Genome for future studies.

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“…The LDproxy analyses indicated that rs671 in ALDH2 and five SNPs, including three disease‐associated SNPs detected by our longitudinal exome‐wide association studies, were in significant LD ( r 2 > 0.8) in JPT from the 1KGP (Table ). Recent positive selection is likely to have acted on the genomic region containing rs671, and the minor alleles have expanded throughout East Asia in recent evolutionary time (Koganebuchi et al, ; Luo et al, ; Oota et al, ; Yasukochi et al, ).…”

Section: Resultsmentioning

confidence: 99%

“…In fact, the function prediction tools suggest that the missense variant has an effect on the protein function (PolyPhen score = 0.964, SIFT = 0.019, CADD scaled C‐score = 34.0, and PhyloP = 9.71). It is possible that the derived allele of rs671 may have arisen ~8,000 years ago when large‐scale rice cultivation started in southern China (Koganebuchi et al, ). Previous studies suggested that positive selection has acted on ALDH2 in EAS because of acquired resistance against parasite infection related to large‐scale rice cultivation (Koganebuchi et al, ; Luo et al, ; Oota et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…It is possible that the derived allele of rs671 may have arisen ~8,000 years ago when large‐scale rice cultivation started in southern China (Koganebuchi et al, ). Previous studies suggested that positive selection has acted on ALDH2 in EAS because of acquired resistance against parasite infection related to large‐scale rice cultivation (Koganebuchi et al, ; Luo et al, ; Oota et al, ). ALDH2 may be involved in the metabolism of 4‐hydroxy‐2‐nonenal, a byproduct of lipid peroxidation (Breitzig, Bhimineni, Lockey, & Kolliputi, ).…”

Section: Discussionmentioning

confidence: 99%

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Evolutionary history of disease‐susceptibility loci identified in longitudinal exome‐wide association studies

Yasukochi

Sakuma

Takeuchi

et al. 2019

Molec Gen & Gen Med

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Background Our longitudinal exome‐wide association studies previously detected various genetic determinants of complex disorders using ~26,000 single‐nucleotide polymorphisms (SNPs) that passed quality control and longitudinal medical examination data (mean follow‐up period, 5 years) in 4884–6022 Japanese subjects. We found that allele frequencies of several identified SNPs were remarkably different among four ethnic groups. Elucidating the evolutionary history of disease‐susceptibility loci may help us uncover the pathogenesis of the related complex disorders. Methods In the present study, we conducted evolutionary analyses such as extended haplotype homozygosity, focusing on genomic regions containing disease‐susceptibility loci and based on genotyping data of our previous studies and datasets from the 1000 Genomes Project. Results Our evolutionary analyses suggest that derived alleles of rs78338345 of GGA3, rs7656604 at 4q13.3, rs34902660 of SLC17A3, and six SNPs closely located at 12q24.1 associated with type 2 diabetes mellitus, obesity, dyslipidemia, and three complex disorders (hypertension, hyperuricemia, and dyslipidemia), respectively, rapidly expanded after the human dispersion from Africa (Out‐of‐Africa). Allele frequencies of GGA3 and six SNPs at 12q24.1 appeared to have remarkably changed in East Asians, whereas the derived alleles of rs34902660 of SLC17A3 and rs7656604 at 4q13.3 might have spread across Japanese and non‐Africans, respectively, although we cannot completely exclude the possibility that allele frequencies of disease‐associated loci may be affected by demographic events. Conclusion Our findings indicate that derived allele frequencies of nine disease‐associated SNPs (rs78338345 of GGA3, rs7656604 at 4q13.3, rs34902660 of SLC17A3, and six SNPs at 12q24.1) identified in the longitudinal exome‐wide association studies largely increased in non‐Africans after Out‐of‐Africa.

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The allele frequency of ALDH2Glu504Lys* and ADH1BArg47His* for the Ryukyu islanders and their history of expansion among East Asians

Cited by 16 publications

References 36 publications

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan

Evolutionary history of disease‐susceptibility loci identified in longitudinal exome‐wide association studies

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The allele frequency of ALDH2*Glu504Lys and ADH1B*Arg47His for the Ryukyu islanders and their history of expansion among East Asians

Cited by 16 publications

References 36 publications

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Deep whole-genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan

Evolutionary history of disease‐susceptibility loci identified in longitudinal exome‐wide association studies

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The allele frequency of ALDH2Glu504Lys* and ADH1BArg47His* for the Ryukyu islanders and their history of expansion among East Asians