Frequently Asked Questions About RFA-HG-06-014

Frequently Asked Questions About RFA-HG-06-014

Genome-wide Association Studies in the Genes and Environment Initiative Genotyping Facilities (U01)

November 15, 2006

Study Investigators may apply for initial genome-wide scanning, replication studies, or both, and may include fine mapping in their research plans. What genotyping costs need to be provided in the application?

As part of your Research Proposal (item D in the application) and the budget, please provide estimates of genotyping costs for high-throughput genotyping that covers at least 80 percent of the genome, as described in the RFA: Genome-wide Association Studies in the Genes and Environment Initiative - Coordinating Center.

In addition, as part of your Research Proposal (item D in the application), please provide estimates for custom SNP panels that may be within the scope of Study Investigator applications. For comparison among applications, provide the costs for genotyping 1,000 SNPs near association peaks for each study. Please make clear where there are breakpoints in costs for a certain number of samples or SNPs.

The RFA states that high-throughput genotyping for 12,000 specimens should be planned over a three-year period: about 60 percent the first year, 20 percent the second year, and 20 percent the third year. What should we include in the budget for the fourth year?

The Genotyping Facilities will work with NCBI and the Study Investigators to resolve any genotyping issues, and will participate in collaborative activities. Please include these activities in your budget, extending into the fourth year.