Open Access Highly Accessed Research article

An ancestry informative marker set for determining continental origin: validation and extension using human genome diversity panels

Rami Nassir1, Roman Kosoy1, Chao Tian1, Phoebe A White2, Lesley M Butler3, Gabriel Silva4, Rick Kittles5, Marta E Alarcon-Riquelme6, Peter K Gregersen7, John W Belmont8, Francisco M De La Vega2 and Michael F Seldin1*

Author Affiliations

1 Rowe Program in Human Genetics, Departments of Biochemistry and Medicine, University of California Davis, Davis, CA 95616, USA

2 Applied Biosystems, Foster City, CA 94404, USA

3 Department of Public Health Sciences, University of California Davis, Davis, CA 95616, USA

4 Obras Sociales del Hermano Pedro, Antigua, Guatemala

5 Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois 60637, USA

6 Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden

7 The Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institute for Medical Research, North Shore LIJ Health System, Manhasset, NY 11030, USA

8 Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA

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BMC Genetics 2009, 10:39  doi:10.1186/1471-2156-10-39

Published: 24 July 2009



Case-control genetic studies of complex human diseases can be confounded by population stratification. This issue can be addressed using panels of ancestry informative markers (AIMs) that can provide substantial population substructure information. Previously, we described a panel of 128 SNP AIMs that were designed as a tool for ascertaining the origins of subjects from Europe, Sub-Saharan Africa, Americas, and East Asia.


In this study, genotypes from Human Genome Diversity Panel populations were used to further evaluate a 93 SNP AIM panel, a subset of the 128 AIMS set, for distinguishing continental origins. Using both model-based and relatively model-independent methods, we here confirm the ability of this AIM set to distinguish diverse population groups that were not previously evaluated. This study included multiple population groups from Oceana, South Asia, East Asia, Sub-Saharan Africa, North and South America, and Europe. In addition, the 93 AIM set provides population substructure information that can, for example, distinguish Arab and Ashkenazi from Northern European population groups and Pygmy from other Sub-Saharan African population groups.


These data provide additional support for using the 93 AIM set to efficiently identify continental subject groups for genetic studies, to identify study population outliers, and to control for admixture in association studies.