PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

Zhang, Chao; Gao, Yang; Ning, Zhilin; Lü, Yan; Zhang, Xiaoxi; Liu, Jiaojiao; Xie, Bo; Xue, Zhe; Wang, Xiaoji; Yuan, Kai; Ge, Xueling; Pan, Yuwen; Liu, Chang; Tian, Lei; Wang, Yuchen; Lu, Dongsheng; Hoh, Boon Peng; Xu, Shuhua

doi:10.1186/s13059-019-1838-5

Cited by 35 publications

(35 citation statements)

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“…Network v5 [21] and Network publisher were used to construct the median joining (MJ) networks (Fig 2 and S3 Fig). The spatial map of rs4646120 and rs2285666 were drawn from PGG toolkit (S4 Fig) [22].…”

Section: Methodsmentioning

confidence: 99%

Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations

et al. 2020

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It was shown that the human Angiotensin-converting enzyme 2 (ACE2) is the receptor of recent coronavirus SARS-CoV-2, and variation in this gene may affect the susceptibility of a population. Therefore, we have analysed the sequence data of ACE2 among 393 samples worldwide, focusing on South Asia. Genetically, South Asians are more related to West Eurasian populations rather than to East Eurasians. In the present analyses of ACE2, we observed that the majority of South Asian haplotypes are closer to East Eurasians rather than to West Eurasians. The phylogenetic analysis suggested that the South Asian haplotypes shared with East Eurasians involved two unique event polymorphisms (rs4646120 and rs2285666). In contrast with the European/American populations, both of the SNPs have largely similar frequencies for East Eurasians and South Asians, Therefore, it is likely that among the South Asians, host susceptibility to the novel coronavirus SARS-CoV-2 will be more similar to that of East Eurasians rather than to that of Europeans.

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Section: Methodsmentioning

confidence: 99%

Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations

et al. 2020

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“…Genetic traces extracted from the ancient genomes supported that Han Chinese were formed via admixture of the major ancestry from Neolithic YRB farmer ancestry and geographically different indigenes (20). Xu et al analyzed the genome-wide SNVs of 114,783 Han Chinese (Han100K) individuals and found six population subgroups: Northwest Hans, Northeast Hans, Central Hans, Southwest Hans, Southeast Hans and Lingnan Hans (25). Our recent genetic survey focused on geographically distinct Hans also identified their differentiated demographic history: Northwest Hans from Gansu harboring more western Eurasian ancestry; Southwest Hans from Sichuan possessing more genetic influence from Tibeto-Burman speakers; Southmost Hans from Hainan having more ancestry related to Tai-Kadai people; Southeast Hans from Fujian possessing more Austronesian-related ancestry; Central Hans from Chongqing, Guizhou, Hubei, and Hunan harboring equal ancestry related to Neolithic YRB millet farmers and southern indigenes, and North Hans in Shaanxi and Shanxi possessing dominant local millet farmer ancestry.…”

Section: Genetic History Of Northeast Han Chinese Populationsmentioning

confidence: 99%

Genomic insights into the differentiated population admixture structure and demographic history of North East Asians

Wang

Zou

et al. 2021

Preprint

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North China and South Siberia, mainly populated by Altaic-speaking populations, possess extensive ethnolinguistic diversity and serve as the crossroad for the initial peopling of America and western-eastern trans-continental communication. Yet, the complex scenarios of genetic origin, population structure, and admixture history of North-East Asia remain to be fully characterized, especially for Mongolic people in China with a genome-wide perspective. Thus, we genotyped genome-wide SNPs for 510 individuals from 38 Chinese Mongolic, Tungusic, and Sinitic populations to explore the sharing alleles and haplotypes within the studied groups and following merged it with 3508 modern and ancient Eurasian individuals to reconstruct the deep evolutionary and natural selection history of northern East Asians. We identified significant substructures within Altaic-speaking populations with the primary common ancestry linked to the Neolithic northern East Asians: Western Turkic people harbored more western Eurasian ancestry; Northern Mongolic people in Siberia and eastern Tungusic people in Amur River Basin (ARB) possessed dominant Neolithic Mongolian Plateau (MP) or ARB ancestry; Southern Mongolic people in China owned obvious genetic impact from Neolithic Yellow River Basin (YRB) farmers. Additionally, we found the differentiated admixture history between western and eastern Mongolians and geographically close Northeast Hans: the former received a genetic impact from western Eurasians and the latter retained the dominant YRB and ARB Neolithic ancestry. Moreover, we demonstrated that Kalmyk people from the northern Caucasus Mountain possessed a strong genetic affinity with Neolithic MP people, supporting the hypothesis of their eastern Eurasian origin and long-distance migration history. We also illuminated that historic pastoral empires in the MP contributed considerably to the gene pool of northern Mongolic people but rarely to southern ones. We finally found natural signatures in Mongolians associated with alcohol metabolism. Generally, our results not only illuminated that complex population migration and admixture of Neolithic ancestral sources from the MP or ARB played an important role in the spread of Altaic-speaking populations and Proto-Altaic language, which partly supported the Northeast Asia-origin hypothesis, but also demonstrated that the observed multi-sources of genetic diversity contributed significantly to the modern existing extensive ethnolinguistic diversity in North-East Asia.

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“…Without this representation, the success and benefits of genomic medicine will be disproportionately less. For this reason, efforts are being undertaken around the globe to produce BVDs for previously excluded populations recognizing that both affiliated policies and scientific infrastructure are required (29)(30)(31)(32).…”

Section: Reasons For Health Inequities In Genomic Medicine In Indigenmentioning

confidence: 99%

Indigenous Genomic Databases: Pragmatic Considerations and Cultural Contexts

Caron

Chongo

Hudson

et al. 2020

Front. Public Health

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PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

Cited by 35 publications

References 100 publications

Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations

Most frequent South Asian haplotypes of ACE2 share identity by descent with East Eurasian populations

Genomic insights into the differentiated population admixture structure and demographic history of North East Asians

Indigenous Genomic Databases: Pragmatic Considerations and Cultural Contexts

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