@article{8812d506af9b41c7b271dd7614b48557,
title = "Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips",
abstract = "Background: Illumina's Infinium SNP BeadChips are extensively used in both small and large-scale genetic studies. A fundamental step in any analysis is the processing of raw allele A and allele B intensities from each SNP into genotype calls (AA, AB, BB). Various algorithms which make use of different statistical models are available for this task. We compare four methods (GenCall, Illuminus, GenoSNP and CRLMM) on data where the true genotypes are known in advance and data from a recently published genome-wide association study.Results: In general, differences in accuracy are relatively small between the methods evaluated, although CRLMM and GenoSNP were found to consistently outperform GenCall. The performance of Illuminus is heavily dependent on sample size, with lower no call rates and improved accuracy as the number of samples available increases. For X chromosome SNPs, methods with sex-dependent models (Illuminus, CRLMM) perform better than methods which ignore gender information (GenCall, GenoSNP). We observe that CRLMM and GenoSNP are more accurate at calling SNPs with low minor allele frequency than GenCall or Illuminus. The sample quality metrics from each of the four methods were found to have a high level of agreement at flagging samples with unusual signal characteristics.Conclusions: CRLMM, GenoSNP and GenCall can be applied with confidence in studies of any size, as their performance was shown to be invariant to the number of samples available. Illuminus on the other hand requires a larger number of samples to achieve comparable levels of accuracy and its use in smaller studies (50 or fewer individuals) is not recommended.",
author = "Ritchie, {Matthew E.} and Ruijie Liu and Carvalho, {Benilton S.} and Irizarry, {Rafael A.} and {Australian and New Zealand Multiple Sclerosis Genetics Consortium (ANZgene)} and Melanie Bahlo and Booth, {David R.} and Broadley, {Simon A.} and Brown, {Matthew A.} and Foote, {Simon J.} and Griffiths, {Lyn R.} and Kilpatrick, {Trevor J.} and Jeanette Lechner-Scott and Pablo Moscato and Perreau, {Victoria M.} and Rubio, {Justin P.} and Scott, {Rodney J.} and Jim Stankovich and Stewart, {Graeme J.} and Taylor, {Bruce V.} and James Wiley and Glynnis Clarke and Cox, {Mathew B.} and Csurhes, {Peter A.} and Patrick Danoy and Dickinson, {Joanne L.} and Karen Drysdale and Judith Field and Greer, {Judith M.} and Preethi Guru and Johanna Hadler and Ella Hoban and McMorran, {Brendan J.} and Jensen, {Cathy J.} and Johnson, {Laura J.} and Ruth McCallum and Marilyn Merriman and Tony Merriman and Andrea Polanowski and Karena Pryce and Lotfi Tajouri and Lucy Whittock and Wilkins, {Ella J.} and Browning, {Brian L.} and Browning, {Sharon R.} and Devindri Perera and Simon Broadley and Helmut Butzkueven and Carroll, {William M.} and Caron Chapman and Kermode, {Allan G.} and Mark Marriott and Deborah Mason and Heard, {Robert N.} and Pender, {Michael P.} and Mark Slee and Niall Tubridy and Ernest Willoughby",
note = "This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.",
year = "2011",
month = mar,
day = "8",
doi = "10.1186/1471-2105-12-68",
language = "English",
volume = "12",
journal = "BMC Bioinformatics",
issn = "1471-2105",
publisher = "BioMed Central",
}