Monday, February 11, 2008

Collecting 20,000 genomes and phenotypes

The title of this paper is a bit deceiving because it sounds like they're trying to come up with environmental variables to complement genetic information. They're basically planning on getting DNA from 20,000 people and recording associated phenotypic information. I didn't find a description or list of the phenotypes they're looking at. The population is from North Carolina, and seems pretty diverse, although mostly blacks and whites. They stress that they are not just getting a clinical population as several other studies are:
The EPR offers a valuable resource for human genomic studies especially when compared to anonymous DNA registries. It was designed for scientists to screen for functionally significant alleles and to identify subpopulations of individuals with shared genotypes, and then correlate their genotypes with their phenotypes in a process known as “recruit-by-genotype.” A unique feature of the EPR is that two distinct populations are solicited, an apparently healthy population recruited from the general population as well as a clinic population recruited from various clinics and hospitals in the area. Individuals in the clinic population have a wide array of medical conditions, and their inclusion in the EPR increases the likelihood of identifying subjects with both the genotypes and phenotypes of interest. These aspects of the EPR give scientists more flexibility in designing follow-up studies while reducing the ascertainment bias that can occur in genetic epidemiology studies when subjects are recruited based on phenotype. In addition, a comprehensive program has been established to maintain contact with EPR participants, to update their personal information and maximize response rates for follow-up studies.
They discuss the pretty high enrollment and consent rates - about 75% of people are willing to give their DNA linked to their name - the researchers can go back and get follow up phenotypic data - which is pretty cool. They are giving subjects $20 for their time, which seems to be an ethical issue in itself, but they don't really talk about that.
The discussion is pretty interesting since they discuss some of the advantages in having a non-clinic population in examining gene x environment interactions.

The Environmental Polymorphisms Registry: a DNA resource to study genetic susceptibility loci
Patricia C. Chulada, Heather L. Vahdat, Richard R. Sharp, Tracy C. DeLozier, Paul B. Watkins, Susan N. Pusek and Perry J. Blackshear
Human Genetics early online
Abstract The National Institute of Environmental Health Sciences is establishing a DNA repository named the Environmental Polymorphisms Registry (EPR). The goal is to recruit 20,000 subjects from the greater Research Triangle Park region of North Carolina and collect a sample of each subject’s DNA for genetic study. Personal information is obtained from each EPR subject and linked to their sample in coded form. Once individuals with the genotypes of interest are identified, their samples are decoded, and their names and contact information are given to scientists for follow-up studies in which genotype is important. “Recruit-by-genotype” resources such as the EPR require a transparent consent process and rigorous human subjects protection measures. Unlike the EPR, most US DNA resources are anonymous. Once scientists identify potentially significant genetic variants, they must screen new populations to find individuals with the variants of interest to study. The EPR eliminates this time consuming and expensive step. In designing the EPR, consideration was given to achieving high response rates, minimizing attrition and maximizing usefulness for future research studies. Subjects are recruited from outpatient clinics in area medical centers as well as from the general population to ascertain individuals in diverse states of health. Data are collected on race, ethnicity, gender and age, and are monitored for demographic diversity. As of November 2007, 7,788 individuals have been recruited into the EPR and their DNA samples have been used in numerous genetic studies. EPR subjects have also been solicited for several follow-up studies with high response rates (>90%). The success of the EPR based on the number of subjects recruited and genetic studies underway, suggests that it will be a model for future DNA resources.

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