Open Access Highly Accessed Research article

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

Paula Kersbergen12, Kate van Duijn3, Ate D Kloosterman1, Johan T den Dunnen2, Manfred Kayser3 and Peter de Knijff2*

Author Affiliations

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

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

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

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

Published: 27 October 2009



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.


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 FST ranking 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)


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