Quality assessment parameters for EST-derived SNPs from catfish
Shaolin Wang1, Zhenxia Sha, Tad S Sonstegard
1The Fish Molecular Genetics and Biotechnology Laboratory, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Aquatic Genomics Unit, Auburn University, Auburn, AL 36849, USA. wangsha@auburn.edu
BMC Genomics
|October 2, 2008
Summary
Single nucleotide polymorphisms (SNPs) derived from expressed sequence tags (ESTs) require stringent quality control for reliable use in genetic studies. Key factors for validating EST-derived SNPs include contig size and minor allele frequency, with primers designed to avoid introns.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- Single nucleotide polymorphisms (SNPs) are valuable genetic markers for association studies and comparative genomics.
- Discovering SNPs typically requires extensive genome sequencing, resources unavailable for many species like catfish.
- Expressed sequence tag (EST) resources offer a pathway to identify numerous SNPs, but their reliability is often compromised by sequencing errors.
Purpose of the Study:
- To assess the quality of SNPs derived from expressed sequence tags (ESTs).
- To identify critical factors influencing the validation rate of EST-derived SNPs.
- To establish quality control measures for reliable SNP identification in species lacking full genome sequences.
Main Methods:
- Analysis of factors influencing the validation success of EST-derived SNPs.
- Evaluation of contig size and minor allele sequence frequency as predictors of SNP reliability.
- Investigation of sequence quality and the impact of intronic sequences on genotyping success.
Main Results:
- Contig size and minor allele sequence frequency were the most significant factors for validating EST-derived SNPs.
- Higher validation rates were observed for larger contigs with at least four EST sequences.
- The minor allele needed to be represented at least twice for reliable validation, and introns within primer binding sites hindered genotyping.
Conclusions:
- Stringent quality assessment is crucial for EST-derived SNPs, utilizing contigs with four or more ESTs and minor alleles appearing at least twice.
- Genotyping primers must be designed within single exons, explicitly avoiding introns to ensure successful amplification.
- Implementing these quality measures alongside extensive EST resources enables effective SNP discovery in species with limited genomic data.
