title: Marker selection for genetic case-control association studies.
abstract: 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.
authors.affiliation: Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. fredrikp@well.ox.ac.uk
authors.forename: Fredrik H
authors.initials: FH
authors.lastname: Pettersson
authors.forename: Carl A
authors.initials: CA
authors.lastname: Anderson
authors.forename: Geraldine M
authors.initials: GM
authors.lastname: Clarke
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Barrett
authors.forename: Lon R
authors.initials: LR
authors.lastname: Cardon
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Morris
authors.forename: Krina T
authors.initials: KT
authors.lastname: Zondervan
mesh_terms: D016022:Case-Control Studies; D005819:Genetic Markers; D015894:Genome, Human; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D005838:Genotype; D006801:Humans; D015810:Linkage Disequilibrium; D020641:Polymorphism, Single Nucleotide; D012984:Software
chemical_list: D005819:Genetic Markers