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Association studies can focus on candidate gene(s), a particular genomic region, or adopt a genome-wide association approach, each of which has implications for marker selection. The strategy for marker selection will affect the statistical power of the study to detect a disease association and is a crucial element of study design. The abundant single nucleotide polymorphisms (SNPs) are the markers of choice in genetic case-control association studies. The genotypes of neighboring SNPs are often highly correlated ('in linkage disequilibrium', LD) within a population, which is utilized for selecting specific 'tagSNPs' to serve as proxies for other nearby SNPs in high LD. General guidelines for SNP selection in candidate genes/regions and genome-wide studies are provided in this protocol, along with illustrative examples. Publicly available web-based resources are utilized to browse and retrieve data, and software, such as Haploview and Goldsurfer2, is applied to investigate LD and to select tagSNPs.

Original publication




Journal article


Nat Protoc

Publication Date





743 - 752


Case-Control Studies, Genetic Markers, Genome, Human, Genome-Wide Association Study, Genomics, Genotype, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Software