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Bioinformatics Advance Access originally published online on July 24, 2008
Bioinformatics 2008 24(19):2209-2214; doi:10.1093/bioinformatics/btn386
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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population

Eleni Giannoulatou 1,2,{dagger}, Christopher Yau 1,2,{dagger}, Stefano Colella 3,{ddagger}, Jiannis Ragoussis 3 and Christopher C. Holmes 1,4,*

1Department of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, 2Life Sciences Interface Doctoral Training Centre, University of Oxford, Wolfson Building, Parks Road, Oxford, OX1 3QD, 3Genomics Group, Wellcome Trust Centre for Human Genetics, Oxford, OX3 7BN and 4MRC Mammalian Genetics Unit, MRC Harwell, Harwell, OX11 0RD, UK

*To whom correspondence should be addressed.


  Abstract

Summary: Current genotyping algorithms typically call genotypes by clustering allele-specific intensity data on a single nucleotide polymorphism (SNP) by SNP basis. This approach assumes the availability of a large number of control samples that have been sampled on the same array and platform. We have developed a SNP genotyping algorithm for the Illumina Infinium SNP genotyping assay that is entirely within-sample and does not require the need for a population of control samples nor parameters derived from such a population. Our algorithm exhibits high concordance with current methods and >99% call accuracy on HapMap samples. The ability to call genotypes using only within-sample information makes the method computationally light and practical for studies involving small sample sizes and provides a valuable independent quality control metric for other population-based approaches.

Availability: http://www.stats.ox.ac.uk/~giannoul/GenoSNP/

Contact: cholmes{at}stats.ox.ac.uk

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

{ddagger}Present address: UMR 203 INRA INSA-Lyon BF2I, Biologie Fonction-nelle, Insectes et Interactions, F-69621 Villeurbanne Cedex, France.

Associate Editor: Martin Bishop

Received on April 28, 2008; revised on July 22, 2008; accepted on July 23, 2008

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