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Linkage disequilibrium in European populations

Livrables

DNAs from 994 individuals in 11 European and 1 African population(s) for studies of European genetic diversity. Knowledge of population genetic diversity is important for designing and interpreting genome wide association studies (GWAS) of complex, common disorders, public health problems in the Community and other developed and developing world regions. At present, only GWAS can systematically provide information about genetic factors underlying these disorders, and in turn, about causative environmental components. Applications of this information are specific treatments and prevention strategies for these disorders. This result, a collection of DNAs from individuals from 11 European populations and an African population, provides a research resource useful for studying and describing genetic diversity of European populations. This is a quasi-unique collection for studying European genetic diversity. Such a resource is the first step for diversity research. Once the DNA is collected from populations, the second step is to genotype the DNAs with thousands to hundreds of thousands of genetic markers (the more the better). The third step is to analyze the data resulting from the genotyping process, comparing the results among the populations. This results in a description of population genetic diversity. The DNAs were produced from blood or other cells, sources provided by all partners, at the Foundation Jean Dausset-CEPH, partner 1. Aliquots of the DNAs were distributed to partners 2, 4, 5, 6, and 7 (and also used at CEPH) for genotyping. Varying amounts of the remaining 670 DNA samples are stored at CEPH at -80C, available to project partners (and potentially to other scientists) for diversity and other population genetic studies. At present, 2-1/2 years after completion of the project, the DNAs have not been further distributed.
DNA genotypes from 994 individuals in 11 European and 1 African population(s) for studies of European genetic diversity. Knowledge of population genetic diversity is important for designing and interpreting genome wide association studies (GWAS) of complex, common disorders, public health problems in the Community and other developed and developing world regions. At present, only GWAS can systematically provide information about genetic factors underlying these disorders, and in turn, about causative environmental components. Applications of this information are specific treatments and prevention strategies for these disorders. This result, almost 1 million SNP genotypes of 994 individuals from 11 European populations and an African population, generated with ~1000 SNP DNA markers, provides the raw data necessary for analyzing European population diversity. These data represent a quasi-unique research tool of interest to the research community. These data were analyzed jointly within this project. Stored in the project database, these genotypes and results of their analyses will be disseminated to the public via the project web site and scientific publications in refereed journals. Two publications are in preparation at this time.
European population genetic diversity. Knowledge of population genetic diversity is important for designing and interpreting genome wide association studies (GWAS) of complex, common disorders, public health problems in the Community and other developed and developing world regions. At present, only GWAS can systematically provide information about genetic factors underlying these disorders, and in turn, about causative environmental components. Applications of this information are specific treatments and prevention strategies for these disorders. The final result of this RTD project consists of the results from analyzing almost 1 million SNP genotypes of 994 individuals from 11 European populations and an African population, generated with ~1000 SNP DNA markers. A standard analysis package, developed by partner 3, was used for the analysis. This provided results for each of 11 genome regions, the most important of which include 1) a comparative study of genetic diversity among populations (allele frequencies, Fst genetic distances, multidimensional Fst scaling), 2) a comparative study of LD patterns among the populations (D', r**2, pair wise SNP and sliding window comparisons), 3) a study of LD blocks and their conservation across European populations, 4) long range SNP haplotype frequencies for each population, and 5) a comparative study of fine-scale recombination rate patterns across populations. These and other results will be disseminated to the public via the project website and scientific publications in refereed journals. Two publications are in preparation at this time.