GENOTYPING

Cleveland Clinic Lerner Com-Cwru, Cleveland OH

Investigators

Linked publications & trials

Abstract

The purpose of Core D is act as a centralized facility to perform large scale and high throughput genotyping[unreadable] of genetic polymorphisms as well as routine DNA sequencing. The advantages for such a centralized facility[unreadable] include: 1) Conservation of resources; the core is more time and cost efficient than individual labs; 2) Avoid[unreadable] unnecessary duplication of effort: 3) Standardization of quality control; and 4) Facilitation of data sharing. In[unreadable] addition, the Core will also function as an educational resource to train members of the Program Project[unreadable] laboratories in proper genotyping methodologies and to provide advice for Project Leaders in the design and[unreadable] implementation of relevant experiments. The training will be valuable for Postdoctoral Fellows and Graduate[unreadable] Students and useful if the demands on the Core exceed its capacity at a particular time. The Genotyping[unreadable] Core will provide one ABI Prism 7900HT Genetic Analyzer with SDS 384-well Block, and a semi-automatic[unreadable] robotic system, Hydra II for high throughput SNP genotyping. We will use the 5' nuclease allelic[unreadable] discrimination assay for large-scale, high throughput genotyping of SNPs. All SNP assays will be tested for[unreadable] their accuracy and reproducibility. We have developed a strict protocol for evaluation of each SNP assay[unreadable] where the SNP of interest is identified by the Wave system or direct sequencing. SNPs chosen from[unreadable] published databases will be first confirmed by direct sequencing, followed by testing for the robustness and[unreadable] reproducibility of the assay. If the SNP passes these tests, it will be genotyoed in the rest of study samples.[unreadable] For further quality control, we include two negative controls (no DNA), two wells of allele 1 standard, and two[unreadable] wells of allele 2 standard. The Genotyping Core represents an integral part of the Program Project. Projects[unreadable] 1 and 2 will use the SNP detection service extensively. The other projects will make use of the DNA[unreadable] sequencing facility for analysis of plasmid probes and cDNA cloning (Project 3).