The Genotyping Core will provide genetic information on the UM-HET3 female mice used for all aspects of the Program Project. The 600 Population 1 animals produced in Animal ore will be genotyped at 150 loci, with each locus able to distinguish the four grandparental alleles. For each animal the genotype scan will provide approximately 15 to 20 cM coverage across the genome. Genotyping will be performed on additional UM-HET3 females to screen for a small number of candidate lifespan-associated loci. Animals identified as having the desired combination of alleles at the loci will be retained as Population 2 (180 animals final total). The Populations will be examined for phenotypes in the individual Projects and assessed for genotype by-phenotype associations by Data Analysis Core.
The Specific Aims :
Aim 1. Establish a high-throughput genotyping service capable of handling approximately 30,000 PCR-based genotype assays per year.
Aim 2. Prepare and quantify genomic DNA from all project animals.
Aim 3. Identify, develop, and quality assess 150 polymorphic marker reactions. Additional marker reactions will be identified in candidate regions of the gnome in the final two years of the Project.
Aim 4. Generate high-quality genotype data from 150 marker on 600 Population 1 animals. The final dataset will include approximately 90,000 genotypes with less than 3% missing data and less than 1% error. The data will be transferred to Data Animal Core for analysis.
Aim 5. Generate high-quality genotype data at six polymorphic loci on approximately 1500 UM-HET3 candidate animals for Population 2. Genotypes will be determined at 8 weeks of age and 180 animals will be selected based on the genotypes. The loci used for the screen will bracket three quantitative trait loci (QTL) proposed as candidates for lifespan. For this screen, approximately 9000 genotype values will be obtained over two years, with percent error and missing data levels comparable to Population I.
Aim 6. Develop a laboratory information management system (LIMS) for efficient genotype data handling, resource management, and cost control.
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