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Bioinformatics Advance Access originally published online on April 26, 2007
Bioinformatics 2007 23(13):1692-1693; doi:10.1093/bioinformatics/btm154
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates

Ben J. Hayes 1,3,*, Kjetil Nilsen 3, Paul R. Berg 3, Eli Grindflek 4 and Sigbjørn Lien 2,3

1Animal Genetics and Genomics, Primary Industries Research Victoria, 475 Mickleham Rd, Attwood, Victoria, Australia 3049, 2Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, Box 5003, N-1432 Aas, Norway, 3Centre for Integrative Genetics, Norwegian University of Life Sciences, Box 5003, N-1432 Aas, Norway and 4The Norwegian Pig Breeders Association (NORSVIN), Hamar, Norway

*To whom correspondence should be addressed.


  Abstract

Motivation: Single nucleotide polymorphism (SNP) detection exploiting redundancy in expressed sequence tag (EST) collections that arises from the presence of transcripts of the same gene from different individuals has been used to generate large collections of SNPs for many species. A second source of redundancy, namely that EST collections can contain multiple transcripts of the same gene from the same individual, can be exploited to distinguish true SNPs from sequencing error. In this article, we demonstrate with Atlantic salmon and pig EST collections that splitting the EST collection in two, detecting SNPs in both subsets, then accepting only cross-validated SNPs increases validation rates.

Results: In the pig data set, 676 cross-validated putative SNPs were detected in a collection of 160 689 ESTs. When validating a subset of these by genotyping on MassARRAY 85.1% of SNPs were polymorphic in successful assays. In the salmon data set, 856 cross-validated putative SNPs were detected in a collection of 243 674 ESTs. Validation by genotyping showed that 81.0% of the cross-validated putative SNPs were polymorphic in successful assays.

Availability: Cross-validated SNPs are available at dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/), ss69371838-ss69372575 for the salmon SNPs and ss69372587-ss69373226 for the pig SNPs.

Contact: ben.hayes{at}dpi.vic.gov.au

Associate Editor: Burkhard Rost

Received on February 11, 2007; revised on April 10, 2007; accepted on April 16, 2007

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