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

Hayes, Ben J., Nilsen, Kjetil, Berg, Paul R., Grindflek, Eli and Lien, Sigbjorn (2007). SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates. In: , , (1692-1693). . doi:10.1093/bioinformatics/btm154


Author Hayes, Ben J.
Nilsen, Kjetil
Berg, Paul R.
Grindflek, Eli
Lien, Sigbjorn
Title of paper SNP detection exploiting multiple sources of redundancy in large EST collections improves validation rates
Journal name Bioinformatics   Check publisher's open access policy
Publication Year 2007
Sub-type Fully published paper
DOI 10.1093/bioinformatics/btm154
ISSN 1367-4803
Volume 23
Issue 13
Start page 1692
End page 1693
Total pages 2
Language eng
Abstract/Summary 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.
Subjects 1308 Clinical Biochemistry
1706 Computer Science Applications
1703 Computational Theory and Mathematics
1303 Specialist Studies in Education
1312 Molecular Biology
2605 Computational Mathematics
2613 Statistics and Probability
Q-Index Code E1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Conference Paper
Collections: ResearcherID Downloads
Scopus Import
 
Versions
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 18 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 23 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 05 Aug 2016, 09:59:54 EST by System User