Building a Laboratory Information Management System for FP-TDI Genotyping Research

Our laboratory uses a genotyping method for SNPs that combines the specificity of nucleotide incorporation by DNA polymerase and the sensitivity of fluorescence polarization, known as Template-directed Dye Terminator Incorporation assay with Fluorescent Polarization detection (FP-TDI). Following PCR amplification of the target region, a SNP -specific primer anneals immediately upstream of the polymorphic site in the target DNA. Appropriate dye-labeled terminators extend the SNP-specific primer by one base; by determining which terminator is incorporated, the allele present in the target DNA can be inferred. The highly specific and sensitive nature of FP-TDI allows us to perform high-throughput SNP genotyping in a 384-well plate format, generating about 10,000 genotypes per day.3 The development of a laboratory information system became especially critical with our participation in the International HapMap Project, the goal of which is to develop a haplotype map of the human genome. The freely-available information produced by the Project is expected to be an important resource for researchers who want to find genes related to health, drug response, and disease. As a genotyping center for the HapMap project, our laboratory must have the capability to receive large incremental SNP allocations from a data control center (DCC) over a thousand miles away. Our FP-TDI machines output data in a raw format which has to be processed, organized, put through quality control, and then submitted back to the center.