GMFilter and SXTestPlate: software tools for improving the SNPlex genotyping system.

Abstract

Genotyping of single-nucleotide polymorphisms (SNPs) is a fundamental technology in modern genetics. The SNPlex mid-throughput genotyping system (Applied Biosystems, Foster City, CA, USA) enables the multiplexed genotyping of up to 48 SNPs simultaneously in a single DNA sample. The high level of automation and the large amount of data produced in a high-throughput laboratory require advanced software tools for quality control and workflow management.We have developed two programs, which address two main aspects of quality control in a SNPlex genotyping environment: GMFilter improves the analysis of SNPlex plates by removing wells with a low overall signal intensity. It enables scientists to automatically process the raw data in a standardized way before analyzing a plate with the proprietary GeneMapper software from Applied Biosystems. SXTestPlate examines the genotype concordance of a SNPlex test plate, which was typed with a control SNP set. This program allows for regular quality control checks of a SNPlex genotyping platform. It is compatible to other genotyping methods as well.GMFilter and SXTestPlate provide a valuable tool set for laboratories engaged in genotyping based on the SNPlex system. The programs enhance the analysis of SNPlex plates with the GeneMapper software and enable scientists to evaluate the performance of their genotyping platform.