Identification of population substructure among Jews using STR markers and dependence on reference populations included

Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
BMC Genetics (Impact Factor: 2.4). 06/2010; 11(48):48. DOI: 10.1186/1471-2156-11-48
Source: PubMed


Detecting population substructure is a critical issue for association studies of health behaviors and other traits. Whether inherent in the population or an artifact of marker choice, determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Jewish populations, among which association studies are often conducted, have a known history of migrations. As a necessary step in understanding population structure to conduct valid association studies of health behaviors among Israeli Jews, we investigated genetic signatures of this history and quantified substructure to facilitate future investigations of these phenotypes in this population.
Using 32 autosomal STR markers and the program STRUCTURE, we differentiated between Ashkenazi (AJ, N = 135) and non-Ashkenazi (NAJ, N = 226) Jewish populations in the form of Northern and Southern geographic genetic components (AJ north 73%, south 23%, NAJ north 33%, south 60%). The ability to detect substructure within these closely related populations using a small STR panel was contingent on including additional samples representing major continental populations in the analyses.
Although clustering programs such as STRUCTURE are designed to assign proportions of ancestry to individuals without reference population information, when Jewish samples were analyzed in the absence of proxy parental populations, substructure within Jews was not detected. Generally, for samples with a given grandparental country of birth, STRUCTURE assignment values to Northern, Southern, African and Asian clusters agreed with mitochondrial DNA and Y-chromosomal data from previous studies as well as historical records of migration and intermarriage.

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Available from: Robert T Malison, Oct 05, 2015
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    • "The total number of markers used in this study is quite small in comparison to many other available studies, but due to higher mutation rates and number of alleles per locus STRs provide much more information, on average, than SNPs for population assignment and population stratification (Listman et al., 2010). The fifteen used autosomal markers reveal a high population differentiation; this marker set may be more useful for detecting recent admixture or founding events, such as those which formed the North African populations. "
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    ABSTRACT: Detecting population substructure and ancestry is a critical issue for both association studies of health behaviors and forensic genetics. Determining aspects of a population's genetic history as potential sources of substructure can aid in design of future genetic studies. Within this context, fifteen autosomal short tandem repeat (STR), were used to examine population genetic structure and hypotheses of the origin of the modern Moroccan population from individuals belonging to three different ethnical groups from Morocco (Arab, Berber and Sahrawi), by comparing their autosomal STR variation with that of neighboring and non-neighboring populations in North Africa, Europe and Middle East as well as proposed ancestral populations in Morocco (Berber). We report on the results that the gradient of North African ancestry accounts for previous observations of low levels of sharing with Near East and a substantially increased gene flow especially from Morocco and Spain.
    Meta Gene 12/2014; 2:427–438. DOI:10.1016/j.mgene.2014.04.011
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    • "Subsequent studies of the monoallelic Y chromosomal and mitochondrial DNA haplotypes demonstrated founder effects of both Middle Eastern and local origin, but did not adequately resolve the degree of admixture. To resolve this issue and to improve the understanding about the relatedness of contemporary Jewish groups, our research teams and others have independently performed genome-wide analyses of Diaspora Jewish groups and comparison with neighboring populations (Atzmon et al. 2010; Behar et al. 2010; Campbell et al. 2012; Kopelman et al. 2009; Bray et al. 2010; Listman et al. 2010). These studies varied in the specific populations analyzed and in the number of individuals included from each population. "
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    ABSTRACT: Adherents to the Jewish faith have resided in numerous geographic locations over the course of three millennia. Progressively more detailed population genetic analysis carried out independently by multiple research groups over the past two decades has revealed a pattern for the population genetic architecture of contemporary Jews descendant from globally dispersed Diaspora communities. This pattern is consistent with a major, but variable component of shared Near East ancestry, together with variable degrees of admixture and introgression from the corresponding host Diaspora populations. By combining analysis of monoallelic markers with recent genome-wide variation analysis of simple tandem repeats, copy number variations, and single-nucleotide polymorphisms at high density, it has been possible to determine the relative contribution of sex-specific migration and introgression to map founder events and to suggest demographic histories corresponding to western and eastern Diaspora migrations, as well as subsequent microevolutionary events. These patterns have been congruous with the inferences of many, but not of all historians using more traditional tools such as archeology, archival records, linguistics, comparative analysis of religious narrative, liturgy and practices. Importantly, the population genetic architecture of Jews helps to explain the observed patterns of health and disease-relevant mutations and phenotypes which continue to be carefully studied and catalogued, and represent an important resource for human medical genetics research. The current review attempts to provide a succinct update of the more recent developments in a historical and human health context. Electronic supplementary material The online version of this article (doi:10.1007/s00439-012-1235-6) contains supplementary material, which is available to authorized users.
    Human Genetics 10/2012; 132(2). DOI:10.1007/s00439-012-1235-6 · 4.82 Impact Factor
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    • "Population structure—Since our marker set is a subset of the same markers used to analyze population substructure and evaluate ancestry components in theHUGO Pan-Asian SNP Consortium (2009), Xu et al (2009) and Chen et al (2009) studies and we included JPT, CHB, and CHD, three HapMap populations which were included in those studies, as well, we used these three populations as a reference to infer geographic ancestry components for the Hill Tribe population samples in our study (similar to methods used in our previous study of Jewish populations, (Listman et al. 2010)). Relative to their other population samples, these studies identified JPT as Northern Asian and the HapMap CHB sample had a larger Northern Asian component than that of CHD. "
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    ABSTRACT: In Thailand, the term Hill Tribe is used to describe populations whose members traditionally practice slash and burn agriculture and reside in the mountains. These tribes are thought to have migrated throughout Asia for up to 5,000 years, including migrations through Southern China and/or Southeast Asia. There have been continuous migrations southward from China into Thailand for approximately the past thousand years and the present geographic range of any given tribe straddles multiple political borders. As none of these populations have autochthonous scripts, written histories have until recently, been externally produced. Northern Asian, Tibetan, and Siberian origins of Hill Tribes have been proposed. All purport endogamy and have nonmutually intelligible languages. To test hypotheses regarding the geographic origins of these populations, relatedness and migrations among them and neighboring populations, and whether their genetic relationships correspond with their linguistic relationships, we analyzed 2,445 genome-wide SNP markers in 118 individuals from five Thai Hill Tribe populations (Akha, Hmong, Karen, Lahu, and Lisu), 90 individuals from majority Thai populations, and 826 individuals from Asian and Oceanean HGDP and HapMap populations using a Bayesian clustering method. Considering these results within the context of results ofrecent large-scale studies of Asian geographic genetic variation allows us to infer a shared Southeast Asian origin of these five Hill Tribe populations as well ancestry components that distinguish among them seen in successive levels of clustering. In addition, the inferred level of shared ancestry among the Hill Tribes corresponds well to relationships among their languages.
    American Journal of Physical Anthropology 02/2011; 144(2):300-8. DOI:10.1002/ajpa.21408 · 2.38 Impact Factor
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