Article

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: 2.36). 06/2010; 11(48):48. DOI: 10.1186/1471-2156-11-48
Source: PubMed

ABSTRACT 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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    • "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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    • "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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