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SNPflow - A laboratory information system for automated data processing and quality management of SNP genotyping results

High-throughput genotyping projects in large epidemiological study populations require sophisticated laboratory information management systems (LIMS). Small to medium sized genotyping facilities often lack such LIMS and thus have to rely on basic R or VBA scripts for the quality control of their genotyping experiments. Since modern genetic epidemiological studies often comprise >10,000 individuals, automated workflows are, however, required to handle and review the large amount of genotypic data generated by modern multiplex genotyping approaches such as Sequenom iPLEX.
To address this issue, we developed the web application “SNPflow”. This solution provides automated data management and quality control for genotyping experiments employing the ABI 7900 HT-platform (e.g. TaqMan, KASPar Assays) or the Sequenom iPLEX platform. It automatically merges single raw output files of different DNA plates, converts them to ready-to-use genotype lists and stores the quality-controlled genotypes in a dedicated MySQL database. For each SNP assay QC values such as call rates, discordance rates and Hardy Weinberg Equilibrium (HWE) are calculated and a comparison of the observed genotype frequencies with the HapMap data is generated. It even provides a fast overview on these QC values for dozens of SNPs in one list. All data can be finally exported in well-arranged files for further analysis. Our software is, to the best of our knowledge, the first completely freely available, web-based application for an automated quality control of Sequenom iPLEX genotypes and can be accessed at genepi.i-med.ac.at/snpflow. It significantly improved the handling of and the overview on our genotyping projects in various cohorts.