Automated Detection and Sequencing of Single Nucleotide Polymorphisms

Deborah Nickerson, Ph.D.
University of Washington
NIEHS Contract N01ES15478

Background: Identifying and analyzing the particular genetic variations existing in individual DNA samples is fundamental to genetic analysis. Additionally, mapping of disease genes invariably leads to the discovery of genetic variations in candidate genes that have effects on the disease or trait of interest. With the advent of faster and more accurate methods of identifying gene variants, DNA sequencing has emerged as the technique of choice because of its sensitivity and automation. Combining sequence-based approaches to detect variants with computational and statistical methods has greatly aided the identification of single nucleotide polymorphisms (SNPs).

Advance: NIEHS-supported scientists at the University of Washington recently published findings that describe a new sequencing algorithm that accurately detects and sequences SNPs. This algorithm, used in v5.0 of a software package known as PolyPhred, focuses on the accurate identification of heterozygous subjects and statistically measures the evidence for potential genotypes, providing an excellent method for the analysis of diploid samples after DNA amplification. It proved to be substantially more accurate than other tested methods, including an earlier version (PolyPhred v4.29) of the software, and is equipped to provide a confidence estimate for each detected SNP and each genotype. The new algorithm detected 93% of all SNPs and 100% of high-frequency SNPs with 99.9% accuracy in the genotyping.

Implications: The new algorithm presented by these investigators makes considerable advances in methods for SNP identification and genotyping and could greatly ease and enhance automation in these efforts. PolyPhred is available free-of-charge to academic and non-profit institutions and is compatible with a number of computing platforms. To learn more about the software, visit: http://droog.gs.washington.edu/PolyPhred.html (http://droog.gs.washington.edu/PolyPhred.html) .

Citation: Stephens M, Sloan JS, Robertson PD, Scheet P, Nickerson DA. Automating sequence-based detection and genotyping of SNPs from diploid samples. Nat Genet. 2006 Mar;38(3):375-81.