A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese

Qin, Pengfei; Li, Zhiqiang; Jin, Wenfei; Lu, Dongsheng; Lou, Haiyi; Shen, Jiawei; Li, Jin; Shi, Yongyong; Xu, Shuhua

doi:10.1038/ejhg.2013.111

Cited by 42 publications

(31 citation statements)

References 26 publications

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“…Unlike other AIMs212202139, we chose InDel as the core unit of the markers. InDel is suitable for population analysis, since the allele distributions show significant differences in different geographic regions4041.…”

Section: Resultsmentioning

confidence: 99%

“…F ST and I n are commonly used to measure the ancestral information of AIMs. However, a high correlation has been found between these two parameters2. In this study, we treated F ST value as the leading factor among the selecting criteria, since it concerns the power of differentiation more directly and typically.…”

Section: Resultsmentioning

confidence: 99%

“…A fair amount of Ancestry Information Markers (AIMs) have been proposed for various purposes including detecting stratification in biomedical studies12 and determining an individual’s ancestry from a forensic context34567891011121314. In the genotype-phenotype studies, such as the popular genome-wide association studies (GWAS), the presence of uncontrolled population structure may lead to false-positive or false-negative results1516171819.…”

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confidence: 99%

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Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Sun

Luò

et al. 2016

Sci Rep

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Ancestry inference is of great interest in diverse areas of scientific researches, including the forensic biology, medical genetics and anthropology. Various methods have been published for distinguishing populations. However, few reports refer to sub-populations (like ethnic groups) within Asian populations for the limitation of markers. Several InDel loci located very tightly in physical positions were treated as one marker by us, which is multi-InDel. The multi-InDel shows potential as Ancestry Inference Marker (AIM). In this study, we performed a genome-wide scan for multi-InDels as AIM. After examining the FST distributions in the 1000 Genomes Database, 12 candidates were selected and validated for eastern Asian populations. A multiplexed assay was developed as a panel to genotype 12 multi-InDel markers simultaneously. Ancestry component analysis with STRUCTURE and principal component analysis (PCA) were employed to estimate its capability for ancestry inference. Furthermore, ancestry assignments of trial individuals were conducted. It proved to be very effective when 210 samples from Han and Tibetan individuals in China were tested. The panel consisting of multi-InDel markers exhibited considerable potency in ancestry inference, and was suggested to be applied in forensic practices and genetic population studies.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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confidence: 99%

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Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Sun

Luò

et al. 2016

Sci Rep

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“…These 28 AIMs were previously reported to have different allele frequencies between northern and southern Chinese, with a population differentiation index ≥0.04 (http://onlinelibrary.wiley.com/doi/10.1002/hep.27608/suppinfo). These 28 AIMs were genotyped in the entire cohort using Sequenom Mass Array for 23 markers and TaqMan assays for another five markers (rs2236797, rs9405015, rs2253907, rs9266629, rs174570). Details and quality controls for Sequenom analysis are reported in the http://onlinelibrary.wiley.com/doi/10.1002/hep.27608/suppinfo and those for the TaqMan assay, in our previous article …”

Section: Methodsmentioning

confidence: 99%

The p.Ser267Phe variant in SLC10A1 is associated with resistance to chronic hepatitis B

Peng

Zhao

Li³

et al. 2015

Hepatology

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In the past 50 years there have been considerable efforts to identify the cellular receptor of hepatitis B virus (HBV). Recently, in vitro evidence from several groups has shown that the sodium-taurocholate cotransporting polypeptide (NTCP, which is encoded by SLC10A1 and transports bile acids into hepatic cells in enterohepatic recirculation) is a strong candidate. In particular, in vitro the p.Ser267Phe variation of SLC10A1 results in loss of HBV receptor function. We tested the role of NTCP as a receptor for HBV in chronic hepatitis B patients using a genetic association study. We selected SLC10A1 variants from 189 exomes. We used Sanger sequencing to follow up the association of the various SLC10A1 variants in a Han Chinese cohort of 1899 chronic hepatitis B patients and 1828 healthy controls. We further investigated the potential impact of the p.Ser267-Phe variant on NTCP function using structural analysis. The p.Ser267Phe variant was associated with healthy status (P 5 5.7 3 10 223 , odds ratio 5 0.36) irrespective of hepatitis B virus surface antibody status (P 5 6.2 3 10 221 and 1.5 3 10 210 , respectively, when the cases were compared with hepatitis B virus surface antibody-positive and -negative controls). The variation was also associated with a lower incidence of acute-on-chronic liver failure (P 5 0.007). The estimated heritability explained by this single variation was 3.2%. The population prevented fraction was around 13.0% among the southern Chinese. Our structural modeling showed that the p.Ser267Phe variant might interfere with ligand binding, thereby preventing HBV from cellular entry. Conclusion: The p.Ser267Phe NTCP variant is significantly associated with resistance to chronic hepatitis B and a lower incidence of acute-on-chronic liver failure. Our results support that NTCP is a cellular receptor for HBV in human infection. (HEPATOLOGY 2015;61:1251-1260 C hronic hepatitis B (CHB) affects approximately 240 million people worldwide and is responsible for about 780,000 deaths annually (http://www.who.int/mediacentre/factsheets/fs204/en/).Clinically, CHB holds the most significant medical consequences among hepatitis B virus (HBV)-infected individuals. Acute-on-chronic liver failure (ACLF) is the most urgent and lethal condition related to CHB.Abbreviations: ACLF, acute-on-chronic liver failure; AIM, ancestry-informative marker; ASBT, apical sodium-dependent bile acid transporter; CHB, chronic hepatitis B; HBV, hepatitis B virus; HBsAb, hepatitis B virus surface antibody; HBsAg, hepatitis B virus surface antigen; HDV, hepatitis D virus; NTCP, sodiumtaurocholate cotransporting polypeptide..From the

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“…Using AIMs is an effective and low-cost way to study population genetic structure [3][4][5][6][7]. Identifying population structure allows one to trace the migration and admixture history of populations [8,9], to uncover genetic signatures of natural selection [10][11][12], and to assign unknown individuals to proper populations, which is a useful tool to infer the ancestral origins of unmatched DNA contributors in forensic investigations [3,[13][14][15] and to correct for the effects of population stratification in genome-wide association studies (GWAS) [16].…”

Section: Introductionmentioning

confidence: 99%

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

Wei

Zhao

et al. 2015

Int J Legal Med

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A single-tube multiplex assay of a small set of ancestry-informative markers (AIMs) for effectively estimating individual ancestry and admixture is an ideal forensic tool to trace the population origin of an unknown DNA sample. We present a newly developed 27-plex single nucleotide polymorphism (SNP) panel with highly robust and balanced differential power to perfectly assign individuals to African, European, and East Asian ancestries. Evaluating 968 previously described intercontinental AIMs from three HapMap population genotyping datasets (Yoruban in Ibadan, Nigeria (YRI); Utah residents with Northern and Western European ancestry from the Centre de'Etude du Polymorphism Humain (CEPH) collection (CEU); and Han Chinese in Beijing, China (CHB)), the best set of markers was selected on the basis of Hardy-Weinberg equilibrium (p > 0.00001), population-specific allele frequency (two of three δ values >0.5), according to linkage disequilibrium (r (2) < 0.2), and capable of being multiplexed in one tube and detected by capillary electrophoresis. The 27-SNP panel was first validated by assigning the ancestry of the 11 populations in the HapMap project. Then, we tested the 27-plex SNP assay with 1164 individuals from 17 additional populations. The results demonstrated that the SNP panel was successful for ancestry inference of individuals with African, European, and East Asian ancestry. Furthermore, the system performed well when inferring the admixture of Eurasians (EUR/EAS) after analyzing admixed populations from Xinjiang (Central Asian) as follows: Tajik (68:27), Uyghur (49:46), Kirgiz (40:57), and Kazak (36:60). For individual analyses, we interpreted each sample with a three-ancestry component percentage and a population match probability sequence. This multiplex assay is a convenient and cost-effective tool to assist in criminal investigations, as well as to correct for the effects of population stratification for case-control studies.

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A panel of ancestry informative markers to estimate and correct potential effects of population stratification in Han Chinese

Cited by 42 publications

References 26 publications

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

Multi-InDel Analysis for Ancestry Inference of Sub-Populations in China

The p.Ser267Phe variant in SLC10A1 is associated with resistance to chronic hepatitis B

A single-tube 27-plex SNP assay for estimating individual ancestry and admixture from three continents

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