ArticleBMC genomics2007
Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed, 37 citations in OpenAlex.
- Comparison of the performance of two commercial genome-wide association study genotyping platforms in Han Chinese samples.G3 (Bethesda, Md.) · 2013Article
- Article
- Sickle Cell Disease in the Post Genomic Era: A Monogenic Disease with a Polygenic Phenotype.Genomics insights · 2009Article
- Article
- Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals.BMC genomics · 2008Article
- Investigation into the ability of SNP chipsets and microsatellites to detect association with a disease locus.Annals of human genetics · 2008Article
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Authors and funding
6 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNew 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.
resultsIn 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.
conclusionWe 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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