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


BACKGROUND
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.
Hayes
Ben J
BJ
Animal Genetics and Genomics, Primary Industries Research Victoria, 475 Mickleham Rd, Attwood, Victoria, Australia 3049. ben.hayes@dpi.vic.gov.au
Nilsen
Kjetil
K
Berg
Paul R
PR
Grindflek
Eli
E
Lien
Sigbjørn
S
D000818:Animals; D016477:Artifacts; D001267:Atlantic Ocean; D001483:Base Sequence; D004252:DNA Mutational Analysis / Q000379:methods*; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*; D013552:Swine; D014157:Transcription Factors / Q000235:genetics*
D014157:Transcription Factors