Uniplex Genotyping
Recommended Use
Currently the CGF only supports one type of Uniplex Genotyping Assay: Applied Biosystems TaqMan® SNP Genotyping Assays. Single TaqMan® SNP genotyping should be used for the interrogation of a single SNP that has shown an effect in larger screening efforts, or in the targeted screening of genes using tags. Read more about ABI TaqMan® Custom SNP Genotyping Assays.
Process
The CGF has developed and validated a large collection of TaqMan assays for use in genotyping studies. A full list of available validated assays can be seen on the SNP500 Cancer website.
If a TaqMan® SNP assay is not available for the loci of interest in your genotyping project, TaqMan® assays may be requested for any reported biallelic SNP or insertion/deletion of less than six bases. Requested loci that produce successful assay designs are validated using the 102 SNP500 population panel and the 262 HapMap control panel. Assay validation is based on concordance with reported HapMap genotypes. Frequency information is reported using the 102 and 262 validation sets on the SNP500 website.
Requirements
Samples must pass all Sample Handling and Pre-Genotyping QC criteria before they are considered for genotyping. For each assay genotyped in a given project, 6.5 ng of DNA as determined by PicoGreen® ("QDNA") at the CGF will be required. Samples that do not contain enough DNA to complete all TaqMan assays in the project cannot be included for genotyping. Additional sample qualification based on phenotypic evaluation of the study will be performed and the PI will be informed of the results (see Pre-Genotyping QC section).
Due to DNA plating constraints, TaqMan® projects are limited to a maximum of 36 assays per project. Genotyping requests containing more than 36 assays will be divided into two or more projects prior to genotyping.
Reporting
Genotype reporting will follow the standard reporting scheme as listed in under the Post-Genotyping QC Reporting section.
