SpringerProtocols: Abstract: Estimation of SNP Allele Frequencies by SSCP Analysis of Pooled DNA

12. Estimation of SNP Allele Frequencies by SSCP Analysis of Pooled DNA

By: Tomoko Tahira¹, Yoji Kukita¹, Koichiro Higasa¹, Yuko Okazaki¹, Aki Yoshinaga¹, Kenshi Hayashi¹

Abstract

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The single strand conformation polymorphism (SSCP) method is a sensitive technique used to detect subtle sequence differences in PCR-amplified DNA fragments as separated peaks in electrophoretic analysis. In this chapter, we focus on SSCP analysis for quantifying polymorphic alleles rather than scanning for mutations. Short fragments carrying single nucleotide polymorphisms are amplified from individual and pooled DNA samples, then the products are labeled with fluorescent dyes and analyzed by automated capillary electrophoresis under nondenaturing conditions. Dedicated software, QSNPlite, interprets trace data of the electrophoresis to identify alleles of individuals and quantify these alleles in the pool. The software can also incorporate sequencing data to assign alleles at the nucleotide level. The procedures described here are being used in association studies that compare allele frequencies between cases and controls to identify genes responsible for common diseases.

Affiliation(s): (1) Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Higashi-ku, Japan

Book Title: Single Nucleotide Polymorphisms: Methods and Protocols

Series: Methods in Molecular Biology | Volume: 578 | Pub. Date: Sep-01-2008 | Page Range: 193-207 | DOI: 10.1007/978-1-60327-411-1_12

Subject: Genetics/Genomics

Key Words: Allele frequency - capillary electrophoresis - pooled DNA - single nucleotide polymorphism - single strand conformation polymorphism

References

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