Article

Kosoy, R., Nassir, R., Tian, C., White, P. A., Butler, L. M., Silva, G. et al. Ancestry informative marker sets for determining continental origin and admixture proportions in common populations in America. Hum. Mutat. 30, 69-78

Rowe Program in Human Genetics, Department of Biochemistry, University of California Davis, Davis, California 95616, USA.
Human Mutation (Impact Factor: 5.14). 01/2009; 30(1):69-78. DOI: 10.1002/humu.20822
Source: PubMed

ABSTRACT

To provide a resource for assessing continental ancestry in a wide variety of genetic studies, we identified, validated, and characterized a set of 128 ancestry informative markers (AIMs). The markers were chosen for informativeness, genome-wide distribution, and genotype reproducibility on two platforms (TaqMan assays and Illumina arrays). We analyzed genotyping data from 825 subjects with diverse ancestry, including European, East Asian, Amerindian, African, South Asian, Mexican, and Puerto Rican. A comprehensive set of 128 AIMs and subsets as small as 24 AIMs are shown to be useful tools for ascertaining the origin of subjects from particular continents, and to correct for population stratification in admixed population sample sets. Our findings provide general guidelines for the application of specific AIM subsets as a resource for wide application. We conclude that investigators can use TaqMan assays for the selected AIMs as a simple and cost efficient tool to control for differences in continental ancestry when conducting association studies in ethnically diverse populations.

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    • "We first chose 18 SNPs that are informative in East Asia using F st values (F st > 0.15) and linkage disequilibrium (LD, r 2 < 0.2) across East Asian populations from the SNPs of Brissenden et al. [33]. Then we combined these SNPs with the other two panels [10,13] and generated a panel of 178 SNPs (Supplemental Table 1). "
    [Show abstract] [Hide abstract] ABSTRACT: Many ancestry informative SNP (AISNP) panels have been published. Ancestry resolution in them varies from three to eight continental clusters of populations depending on the panel used. However, none of these panels differentiates well among East Asian populations. To meet this need, we have developed a 74 AISNP panel after analyzing a much larger number of SNPs for Fst and allele frequency differences between two geographically close population groups within East Asia. The 74 AISNP panel can now distinguish at least 10 biogeographic groups of populations globally: Sub-Saharan Africa, North Africa, Europe, Southwest Asia, South Asia, North Asia, East Asia, Southeast Asia, Pacific and Americas. Compared with our previous 55-AISNP panel, Southeast Asia and North Asia are two newly assignable clusters. For individual ancestry assignment, the likelihood ratio and ancestry components were analyzed on a different set of 500 test individuals from 11 populations. All individuals from five of the test populations–Yoruba (YRI), European (CEU), Han Chinese in Henan (CHNH), Rondonian Surui (SUR) and Ticuna (TIC)–were assigned to their appropriate geographical regions unambiguously. For the other test populations, most of the individuals were assigned to their self-identified geographical regions with a certain degree of overlap with adjacent populations. These alternative ancestry components for each individual thus help give a clearer picture of the possible group origins of the individual. We have demonstrated that the new AISNP panel can achieve a deeper resolution of global ancestry.
    Full-text · Article · Apr 2016 · Forensic Science International: Genetics
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    • "Inference of individual and population ancestry is a useful tool in diverse applications, such as association gene mapping [1], the study of evolutionary history [2, 3], and forensic prediction of unknown DNA contributors [4, 5] . Numerous sets of ancestryinformative single nucleotide polymorphisms (AISNPs) have been identified to resolve different levels of population stratifications , including differentiations of intercontinental ancestries6789,intracontinental subpopulations101112,andsubstructures of a unique population [13, 14]. For forensic usage, small-scale multiplex assays have been developed to estimate individuals' continental ancestries and admixture proportions, with special designs to cope with low-amount DNA templates or degraded DNAs15161718. "
    [Show abstract] [Hide abstract] ABSTRACT: Previously, we developed and validated a multiplex assay of 27 ancestry-informative markers (AIMs) for analyzing African (AFR), European (EUR), and East Asian (EAS) ancestry components. In this study, we typed and collectively analyzed a large Uyghur sample of 979 individuals to estimate the genetic coefficients of the 27 AIMs and investigate differentiation parameters between Uyghur and Han. The Uyghur allele frequencies ranged from 0.243 to 0.952, and heterozygosities ranged from 0.091 to 0.500. Values of F st 3 and I n 3 for EUR, Uyghur, and EAS ranged from 0.028 to 0.550 and 0.0002 to 0.345, respectively. The Uyghur population displays a substantial ancestry contribution of 50.3:49.7 (EUR:EAS) and was efficiently discriminated from Han Chinese with an accuracy of 99.285 %. All populations were clustered into AFR, EUR, EAS, and admixture groups of these three ancestries. Central Asian was obviously stratified from the other admixture populations of South Asians, North Asians, and the Americans. The 27 SNPs yield a circle with an average distance of 0.936 from the center (0, 0) in PCA analysis. Using this set, Chinese Uyghur and Han populations achieved accurate differentiation, and our updated genotype database (by citing 1000 Genomes data) of 43 worldwide populations is a useful resource for forensic applications and disease association studies.
    Full-text · Article · Mar 2016 · Deutsche Zeitschrift für die Gesamte Gerichtliche Medizin
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    • "Indeed, Phillips [7] has discussed overlap of some SNPs among some published panels and the seven SNPs of value noted are all among the 46 we have listed, including four of the top six. We feel the optimal panel should distinguish at least a dozen distinct biogeographic regions based on existing results with our panel of 55 SNPs [13,14] and the Seldin Lab panel of 128 [15,16] the two panels studied on the largest number of different populations. Those SNPs and selected SNPs from several of the other published panels should be studied on a large common panel of individuals from many populations around the world. "
    [Show abstract] [Hide abstract] ABSTRACT: The century-old use of genetic markers to determine population relationships has morphed in modern forensics into use of markers to determine the ancestry of an individual from a DNA sample. Researchers have identified sets of SNPs that have frequency differences among populations and many sets of SNPs have been published for the purpose of inferring ancestry. Such inference also requires reference datasets for the particular set of SNPs selected. We have identified 21 largely independent published panels of ancestry informative SNPs (AISNPs) and examined their union of 1397 SNPs. No SNP occurs in more than 6 panels. The 1397 SNPs in 21 panels yield a largely empty matrix that is inhibiting progress on more refined ability to infer ancestry for a forensic sample. The most common set of reference populations is the HGDP set of 52 small population samples totaling a thousand individuals. Only 46 (3%) of the 1397 SNPs occur in three or more panels. We assembled a new dataset for 44 of those SNPs involving 4,559 individuals from 73 populations. Analyses of this dataset provided clear differentiation of only five biogeographic regions: sub-Saharan Africa, Europe and SW Asia, South Asia, East Asia, and the Americas. This is an inadequate level of biogeographic resolution already exceeded by other panels. We conclude that more such AISNP panels are not needed and that the forensic community must collaborate to develop a common set of highly differentiating AISNPs typed on a very large number of population samples. How that can be accomplished will be the subject of future discussion.
    Full-text · Article · Jan 2016 · Forensic Science International: Genetics
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