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| Research Services: Taqman® SNP |
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Taqman SNP analysis is appropriate for small to medium studies querying up to 20 SNP loci for hundreds to thousands of samples. Pre-developed assays are available. Design services are also commercially available for custom loci. If you would like to initiate a study utilizing this technology, please contact the GPCL for details of sample preparation and assay availability.
The Taqman® Assay Taqman SNP analysis utilizes the 5' exonuclease activity of Taq DNA polymerase and the quenching effects of specific fluorescent dyes to determine the relative frequency of each allele within an individual genome. Primers are designed against a conserved region of the genome flanking the locus of interest. Two probes are designed across the locus of interest, one for each allele. Each probe is labeled with a different reporter dye as well as a quencher molecule. Proximity to the quencher dye inhibits the fluorescence of the reporter molecule. During thermocycling, the probe anneals to the locus of interest in an allele-specific manner. As the Taq DNA polymerase extends the primers, it also degrades the annealed probe, allowing the fluorescent dye to come out of the sphere of influence of the quencher and thus become detectable. Data capture and Delivery The GPCL utilizes an ABI 7900HT instrument with the capability of running SNPs in either 96 or 384 well format. Following PCR, the fluorescent signal is read for each reporter dye for each well on the plate. A sample yielding signal in only one wavelength is homozygous for the appropriate allele. A sample resulting in equal fluorescence from each reporter is determined to be heterozygous. Results are returned in a text file containing sample ID, (if provided, plate location if not) and SNP genotyping call and are available through a web interface. Study Initiation Please complete a study initiation form listing all assays to be run. Investigators are responsible for assay purchase. Sample Preparation Samples must be submitted in 96 well plates with well H12 empty. Genomic DNA should be at 10ng/ul. If the DNA will be submitted at any other concentration, then this must be noted and discussed with the GPCL (labor charges will apply). Please contact the GPCL for instructions for submission of amplified DNA. Minimum sample volume is 30 µl for up to 8 assays. Submit an additional 2 ul for each additional assay to be included. Sample and Assay Submission Samples and assays can be submitted at any of our drop off locations, S534 Scaife Hall, 3343 Forbes Ave, 3rd floor or Room 2.15 Hillman Cancer Center Research Pavilion. Appropriate sample drop off documentation must be supplied. Turn Around Time Project turn around time will depend on the work queue when samples and assays are delivered as well as size of the project. Please contact GPCL at the time of sample submission for estimated date of data delivery. |