OpenSSL SSL_connect: Connection reset by peer in connection to v2.sherpa.ac.uk:443 PuSH - Publication Server of Helmholtz Zentrum München: Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

PuSH - Publication Server of Helmholtz Zentrum München

Mägi, R.* ; Pfeufer, A. ; Nelis, M.* ; Montpetit, A.* ; Metspalu, A.* ; Remm, M.

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

BMC Genomics 8:159 (2007)
Publ. Version/Full Text Volltext DOI PMC
Open Access Gold
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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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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords SINGLE-NUCLEOTIDE POLYMORPHISMS; LINKAGE DISEQUILIBRIUM; WIDE ASSOCIATION; POPULATIONS; HAPMAP; SELECTION; COVERAGE
ISSN (print) / ISBN 1471-2164
e-ISSN 1471-2164
Journal BMC Genomics
Quellenangaben Volume: 8, Issue: , Pages: , Article Number: 159 Supplement: ,
Publisher BioMed Central
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Human Genetics (IHG)