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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    • "STR studies of human differentiation providing an overview of population structure and demographic history of human populations (e.g. Deka et al. 1995, Jorde et al. 1997, Rosenberg et al. 2002, Rosenberg et al. 2005, Rosenberg et al. 2006, Perez-Miranda et al. 2005, Handley et al. 2007, Zhivotovsky et al. 2009, Listman et al. 2010), including admixture analyses (e.g. Halder et al. 2009, Kutanan et al. 2011). "
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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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    • "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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