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


RESULTS
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.


CONCLUSIONS
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.
Mägi
Reedik
R
Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia. reedik.magi@ut.ee <reedik.magi@ut.ee>
Pfeufer
Arne
A
Nelis
Mari
M
Montpetit
Alexandre
A
Metspalu
Andres
A
Remm
Maido
M
D005819:Genetic Markers; D014644:Genetic Variation; D023281:Genomics / Q000379:methods / Q000592:standards*; D006801:Humans; D020641:Polymorphism, Single Nucleotide; D011933:Reagent Kits, Diagnostic / Q000592:standards*; D012015:Reference Standards
D005819:Genetic Markers; D011933:Reagent Kits, Diagnostic