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

doi:10.1186/1471-2105-10-81

BMC Bioinformatics

Volume 10

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Wenz MH
Schreiber S
Franke A

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

Markus Teuber¹ , Michael H Wenz² , Stefan Schreiber¹^,3 and Andre Franke¹

¹Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel, Arnold-Heller-Str. 3, D-24105 Kiel, Germany

²Applied Biosystems, 850 Lincoln Center Drive, Foster City, California 94404, USA

³Department of General Internal Medicine, University Clinic S-H, Campus Kiel, Arnold-Heller-Str. 3, D-24105 Kiel, Germany

author email corresponding author email

BMC Bioinformatics 2009, 10:81doi:10.1186/1471-2105-10-81


Published:	9 March 2009

Abstract

Background

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.

Results

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.

Conclusion

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.