Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans

doi:10.1186/1471-2156-10-69

BMC Genetics
Volume 10

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Kersbergen P
van Duijn K
Kloosterman AD
den Dunnen JT
Kayser M
de Knijff P

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van Duijn K
Kloosterman AD
den Dunnen JT
Kayser M
de Knijff P
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Research article

Developing a set of ancestry-sensitive DNA markers reflecting continental origins of humans

Paula Kersbergen¹^,2 , Kate van Duijn³ , Ate D Kloosterman¹ , Johan T den Dunnen² , Manfred Kayser³ and Peter de Knijff²

¹Department of Human Biological Traces (R&D), Netherlands Forensic Institute, PO Box 24044, 2490 AA The Hague, The Netherlands

²Department of Human and Clinical Genetics, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands

³Department of Forensic Molecular Biology, Erasmus University Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands

author email corresponding author email

BMC Genetics 2009, 10:69doi:10.1186/1471-2156-10-69


Published:	27 October 2009

Abstract

Background

The identification and use of Ancestry-Sensitive Markers (ASMs), i.e. genetic polymorphisms facilitating the genetic reconstruction of geographical origins of individuals, is far from straightforward.

Results

Here we describe the ascertainment and application of five different sets of 47 single nucleotide polymorphisms (SNPs) allowing the inference of major human groups of different continental origin. For this, we first used 74 cell lines, representing human males from six different geographical areas and screened them with the Affymetrix Mapping 10K assay. In addition to using summary statistics estimating the genetic diversity among multiple groups of individuals defined by geography or language, we also used the program STRUCTURE to detect genetically distinct subgroups. Subsequently, we used a pairwise F_STranking procedure among all pairs of genetic subgroups in order to identify a single best performing set of ASMs. Our initial results were independently confirmed by genotyping this set of ASMs in 22 individuals from Somalia, Afghanistan and Sudan and in 919 samples from the CEPH Human Genome Diversity Panel (HGDP-CEPH)

Conclusion

By means of our pairwise population F_STranking approach we identified a set of 47 SNPs that could serve as a panel of ASMs at a continental level.