Genotyping in Thousands By Sequencing (GT-seq): A Low Cost, High-Throughput, Targeted SNP Genotyping Method

GT-seq is a genotyping method which leverages large read numbers from Illumina sequencers to genotype hundreds of single nucleotide polymorphisms within pools of multiplex PCR amplicons generated from thousands of individual samples (Campbell et al. 2014).  This method produces genotypes that are 99.9% concordant to those produced using TaqMan™ assays at approximately 1/4^th the cost.  Since its development, GT-seq panels have been created for several species (Chinook salmon, coho salmon, sockeye salmon, rainbow trout, and pacific lamprey) and has become the preferred SNP genotyping method in our laboratory.  New genotyping software allows genotypes and summary figures to be produced from a lane of raw sequencing data in under an hour using a desktop linux computer.