GMFilter and SXTestPlate: software tools for improving the SNPlex™ genotyping system
| Autor: | Andre Franke, Stefan Schreiber, Michael H. Wenz, Markus Teuber |
|---|---|
| Rok vydání: | 2009 |
| Předmět: |
Genotype
Concordance Information Storage and Retrieval Biology lcsh:Computer applications to medicine. Medical informatics Polymorphism Single Nucleotide Biochemistry User-Computer Interface Software Structural Biology Databases Genetic Humans lcsh:QH301-705.5 Molecular Biology Genotyping Oligonucleotide Array Sequence Analysis Genetics Genome Human business.industry Applied Mathematics Automation Computer Science Applications ComputingMethodologies_PATTERNRECOGNITION Workflow lcsh:Biology (General) lcsh:R858-859.7 Signal intensity business Software engineering |
| Zdroj: | BMC Bioinformatics, Vol 10, Iss 1, p 81 (2009) BMC Bioinformatics |
| ISSN: | 1471-2105 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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