Abstract
BackgroundGenotyping 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.ResultsWe 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.ConclusionGMFilter 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.
Highlights
Genotyping of single-nucleotide polymorphisms (SNPs) is a fundamental technology in modern genetics
SNPlexTM is a cost-efficient, highly flexible and scalable technique, which is based on oligonucleotide ligation (OLA), multiplex polymerase chain reaction (PCR) and capillary electrophoresis
GMFilter: a tool for improving GeneMapper analysis Under optimal conditions, when most of the SNPlexTM assays perform well and when the DNA samples are of superior quality, i.e. giving rise to high signal intensities, the clustering algorithm of the GeneMapper software performs adequately
Summary
We have developed two programs, which address two main aspects of quality control in a SNPlexTM genotyping environment: GMFilter improves the analysis of SNPlexTM 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 SNPlexTM test plate, which was typed with a control SNP set. This program allows for regular quality control checks of a SNPlexTM genotyping platform. It is compatible to other genotyping methods as well
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