Genotyping in Thousands by Sequencing (GT-seq): Development to Implementation

GT-seq is a genotyping method which leverages large read numbers from Illumina sequencers to genotype 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 and has become the preferred SNP genotyping method in our laboratory.  This talk will include discussion of the development of primer panels, designing primers for SNPs identified in RAD (restriction site associated DNA) sequencing, and new bioinformatics tools for GT-seq.