Open Access Highly Accessed Research article

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

Jennifer B Listman1, Deborah Hasin378, Henry R Kranzler4, Robert T Malison12, Apiwat Mutirangura5, Atapol Sughondhabirom5, Efrat Aharonovich3, Baruch Spivak6 and Joel Gelernter11029*

Author Affiliations

1 Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA

2 VA Connecticut Healthcare System, West Haven Campus, West Haven, CT, USA

3 Department of Psychiatry, Columbia University College of Physicians and Surgeons, NY, USA

4 Departments of Psychiatry and Genetics and Developmental Biology, University of Connecticut School of Medicine, Farmington, CT, USA

5 Chulalongkorn Faculty of Medicine, Bangkok, Thailand

6 Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel

7 New York State Psychiatric Institute, NY, USA

8 Dept Epidemiology, Mailman School of Public Health, Columbia University, NY, USA

9 Department of Genetics, Yale University School of Medicine, New Haven, CT, USA

10 Department of Neurobiology, Yale University School of Medicine, New Haven, CT, USA

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BMC Genetics 2010, 11:48  doi:10.1186/1471-2156-11-48

Published: 14 June 2010



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.