Dataset Information

Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System.

ABSTRACT: In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (I n) and pairwise fixation index (F st) values, multidimensional scaling analysis, and success ratio of estimation with cross-validation showed that the novel panel could well reveal the genetic structural differentiations of the East Asian, European, African, and South Asian populations. Besides, the biogeographical ancestry origin inference both at the individual and population levels was conducted on the Chinese Hui group by principal component analysis and STRUCTURE analysis, and the results revealed that the Hui group had the East Asian origin, and the East Asian component ratio of Hui group was approximately 88.87%. Furthermore, the population genetic analyses among the Hui group and reference populations were performed based on the insertion allele frequency heat map, population pairwise F st values and phylogenetic tree, and the results indicated that the Hui group was genetically closer to East Asian populations, especially two Chinese Han populations (CHS and CHB populations).

SUBMITTER: Xie T

PROVIDER: S-EPMC7468629 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System.

Xie Tong T Shen Chunmei C Jin Xiaoye X Lan Qiong Q Fang Yating Y Zhu Bofeng B

BioMed research international 20200825

In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (<i>I</i> <sub> ...[more]

PMID: 32908873

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Project description:BackgroundHispanic/Latino (HL) populations bear a disproportionately high burden of type 2 diabetes (T2D). The ability to predict T2D genetic risk using polygenic risk scores (PRS) offers great promise for improved screening and prevention. However, there are a number of complications related to the accurate inference of genetic risk across HL populations with distinct ancestry profiles. We investigated how ancestry affects the inference of T2D genetic risk using PRS in diverse HL populations from Colombia and the United States (US). In Colombia, we compared T2D genetic risk for the Mestizo population of Antioquia to the Afro-Colombian population of Chocó, and in the US, we compared European-American versus Mexican-American populations.MethodsWhole genome sequences and genotypes from the 1000 Genomes Project and the ChocoGen Research Project were used for genetic ancestry inference and for T2D polygenic risk score (PRS) calculation. Continental ancestry fractions for HL genomes were inferred via comparison with African, European, and Native American reference genomes, and PRS were calculated using T2D risk variants taken from multiple genome-wide association studies (GWAS) conducted on cohorts with diverse ancestries. A correction for ancestry bias in T2D risk inference based on the frequencies of ancestral versus derived alleles was developed and applied to PRS calculations in the HL populations studied here.ResultsT2D genetic risk in Colombian and US HL populations is positively correlated with African and Native American ancestry and negatively correlated with European ancestry. The Afro-Colombian population of Chocó has higher predicted T2D risk than Antioquia, and the Mexican-American population has higher predicted risk than the European-American population. The inferred relative risk of T2D is robust to differences in the ancestry of the GWAS cohorts used for variant discovery. For trans-ethnic GWAS, population-specific variants and variants with same direction effects across populations yield consistent results. Nevertheless, the control for bias in T2D risk prediction confirms that explicit consideration of genetic ancestry can yield more reliable cross-population genetic risk inferences.ConclusionsT2D associations that replicate across populations provide for more reliable risk inference, and modeling population-specific frequencies of ancestral and derived risk alleles can help control for biases in PRS estimation.

Dataset Information

Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System.

Publications

Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System.

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