Association Mapping of Disease Loci, by Use of a Pooled DNA Genomic Screen

Abstract

Genomic screening to map disease loci by association requires automation, pooling of DNA samples, and 3,000-6,000 highly polymorphic, evenly spaced microsatellite markers. Case-control samples can be used in an initial screen, followed by family-based data to confirm marker associations. Association mapping is relevant to genetic studies of complex diseases in which linkage analysis may be less effective and to cases in which multigenerational data are difficult to obtain, including rare or late-onset conditions and infectious diseases. The method can also be used effectively to follow up and confirm regions identified in linkage studies or to investigate candidate disease loci. Study designs can incorporate disease heterogeneity and interaction effects by appropriate subdivision of samples before screening. Here we report use of pooled DNA amplifications-the accurate determination of marker-disease associations for both case-control and nuclear family-based data-including application of correction methods for stutter artifact and preferential amplification. These issues, combined with a discussion of both statistical power and experimental design to define the necessary requirements for detecting of disease loci while virtually eliminating false positives, suggest the feasibility and efficiency of association mapping using pooled DNA screening.

Association tests with systemic lupus erythematosus (SLE) of IL10 markers indicate a direct involvement of a CA repeat in the 5′ regulatory region

“…This method, introduced by Barcellos et al, 29 allows testing of a large number of individuals, thus increasing the chance of detecting susceptibility loci with small effect, a typical aspect of complex diseases as SLE. This counterbalances the disadvantages of losing information about genotype frequencies and haplotypes.…”

“…19,[26][27][28] The markers covered the 5' flanking and the transcribed region of the gene. Basically, the study was performed by the DNA pool method [29][30][31][32] on an extended panel of patients and controls. Haplotypic associations were studied by individual typing of selected markers.…”

Reporting, Appraising, and Integrating Data on Genotype Prevalence and Gene-Disease Associations

“…We make this recommendation because it is the genotype that determines risk and because allele frequencies can be calculated from genotype data (e.g., to determine Hardy-Weinberg equilib rium), whereas if only allele frequencies are presented, geno type frequencies cannot be calculated. Clearly, this recommendation would not be appropriate for studies based on DNA pooling, which may be a valuable approach in esti mating allele frequency distributions in many loci in multiple populations (58), for initial investigation of disease loci, or for follow-up to confirm regions identified in linkage studies (59). In studies in which pooling is used, the strategy for pooling specimens from cases and controls should be specified.…”

Haplotypic relationship between SNP and microsatellite markers at the NOS2A locus in two populations

“…20,21 Various disease loci have been successfully mapped employing microsatellites, either alone [21][22][23] or in combination with other markers, 24 and their use in association studies is increasing. 25 There is a growing argument for using haplotypes, or SNPs that identify common haplotypes, as the basis for association mapping of disease loci. 17,26 Thus the haplotypic relationship between microsatellite markers and other genetic variants is of considerable importance, as microsatellites can potentially be incorporated into haplotypes containing SNPs or other stable variants to increase marker density across a region of interest.…”