high-throughput genotyping (from life science news 4)

I N N O V A T I O N S F O R U M Life Science News 4, 2000 Amersham Biosciences 1 MegaBACE ™ 1000 Genotyping System is a high- throughput, fluorescence-bas ed DNA genotyping system utilizing capillary electrophoresis with 96 capillaries operating in parallel. The system automates sample injection, gel matrix replacement , DNA separation, detection, and data analysis. Introduction Genotyping is used to help determine which genes are responsible for specific inherited traits. Identifying these genetic markers can help researchers understand the mechanisms behind certain, inherited medical disorders. The knowledge gained through genotyping can then be used to improve early detection and treatment of disease. MegaBACE 1000 Genotyping System The current method for production-scale genotyping is a time-consuming process because researchers must manually analyse data in order to loca te the informa- tion of interest. MegaBACE 1000 Genotyping System streamlines this process by automating all aspects of genotyping. Combined with MegaBACE Genetic Profiler analysis software, MegaBACE 1000 Geno- typing System automatically processes 96 samples per run. The total turnaround time per run is less than two hours from injection to injection, corresponding to more than 20 000 genotypes per system in 24 hours of operation. MegaBACE Genetic Profiler MegaBACE Genetic Profiler analysis software is the first genotyping program to fully integrate fragment sizing with allele calling in a Windows NT ™ format. MegaBACE Genetic Profiler greatly reduces manual review of data by assigning quality scores to every marker and sorting the samples based on how well a marker fits within a specified pattern. Genotypes with high quality scores do not require further review, enabling researchers to focus on genotypes with lower quality markers. The software further streamlines data management by enabling multiple runs to be viewed and assembled together in one display as an entire project. The runs added to a project share the same analysis parameters, such as sizing, dye set and marker panel set. High-throughput genotyping N. Stover Amersham Biosciences Inc., Sunnyvale, CA G E N O T Y P I N G Fig 1. MegaBACE Genetic Profiler workflow. s Dye set s Marker panels s Sizing parameters MegaBACE Genetic Profiler Project Setup MegaBACE Genetic Profiler Automated Genotyping MegaBACE Genetic Profiler Manual Review and Editing s Allele calls of all runs or selected runs for each marker s Run-by-run comparisons for each marker s Allele tables MegaBACE Genetic Profiler Project Summary Reports s Background subtraction s Spectral separation s Peak smoothing Trace Processing s Size standard peak finding s Label all marker peaks Fragment Sizing s Peak selection s Allele histogram Allele Calling s Genotype quality scores Genotype Calling Run n Run ... Run 2 Run 1 Instrument Control Manager MegaBACE Data Collection

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