Nucleic Acids Research Advance Access originally published online on August 9, 2006
Nucleic Acids Research 2006 34(14):e100; doi:10.1093/nar/gkl475
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Nucleic Acids Research, 2006, Vol. 34, No. 14 e100
© 2006 The Author(s).
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Genotyping and annotation of Affymetrix SNP arrays
1 Bioinformatics Research Center, University of Aarhus Høegh-Guldbergsgade 10, Bldg 1090, 8000 Aarhus C, Denmark 2 Molecular Diagnostic Laboratory, Aarhus University Hospital Skejby, Brendstrupgaardsvej 100, 8200 Aarhus N, Denmark
*To whom correspondence should be addressed. Tel: +45 8942 3155; Fax: +45 8942 3077; Email: wiuf{at}birc.au.dk.
Received February 13, 2006. Revised June 20, 2006. Accepted June 21, 2006.
In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose–response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization it is indicated that our method is likely to be correct in majority of these cases. In addition, we demonstrate that our method produces more SNPs that are in concordance with Hardy–Weinberg equilibrium than the method by Affymetrix. Finally, we have validated our method on HapMap data and shown that the performance of our method is comparable to other methods.
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