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Open Access Highly Accessed Research article

Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation

Reedik Mägi1, Arne Pfeufer2, Mari Nelis13, Alexandre Montpetit4, Andres Metspalu135 and Maido Remm1*

Author Affiliations

1 Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia

2 Institute of Human Genetics, Technical University Munich, Munich, Germany

3 Estonian Biocentre, Tartu, Estonia

4 McGill University and Genome Quebec Innovation Centre, Montreal, Canada

5 The Estonian Genome Project Foundation, Tartu, Estonia

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BMC Genomics 2007, 8:159  doi:10.1186/1471-2164-8-159

Published: 11 June 2007



New technologies have enabled genome-wide association studies to be conducted with hundreds of thousands of genotyped SNPs. Several different first-generation genome-wide panels of SNPs have been commercialized. The total amount of common genetic variation is still unknown; however, the coverage of commercial panels can be evaluated against reference population samples genotyped by the International HapMap project. Less information is available about coverage in samples from other populations.


In this study we compare four commercial panels: the HumanHap 300 and HumanHap 550 Array Sets from the Illumina Infinium series and the Mapping 100 K and Mapping 500 K Array Sets from the Affymetrix GeneChip series. Tagging performance is compared among HapMap CEPH (CEU), Asian (JPT, CHB) and Yoruba (YRI) population samples. It is also evaluated in an Estonian population sample with more than 1000 individuals genotyped in two 500-kbp ENCODE regions of chromosome 2: ENr112 on 2p16.3 and ENr131 on 2p37.1.


We found that in a non-reference Caucasian population, commercial SNP panels provide levels of coverage similar to those in the HapMap CEPH population sample. We present the proportions of universal and population-specific SNPs in all the commercial platforms studied.