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DOI: 10.1186/1471-2164-8-159
¤ OpenAccess: Gold
This work has “Gold” OA status. This means it is published in an Open Access journal that is indexed by the DOAJ.

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

Reedik Mägi,Arne Pfeufer,Mari Nelis,Alexandre Montpetit,Andres Metspalu,Maido Remm

International HapMap Project
Biology
Single-nucleotide polymorphism
2007
Abstract 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. Conclusion 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.
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    Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation” is a paper by Reedik Mägi Arne Pfeufer Mari Nelis Alexandre Montpetit Andres Metspalu Maido Remm published in 2007. It has an Open Access status of “gold”. You can read and download a PDF Full Text of this paper here.