Marker selection for genetic case-control association studies.

Journal article

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: Pettersson, F; Anderson, C; Clarke, G; Barrett, J; Cardon, L

• Publication status: Published
• Journal: Nature protocols
• Volume: 4
• Issue: 5
• Pages: 743-752
• Publication date: 2009-01-01
• DOI: 10.1038/nprot.2009.38
• EISSN: 1750-2799
• ISSN: 1754-2189
• Language: English
• Keywords: Linkage Disequilibrium; Case-Control Studies; Humans; Genetic Markers; Software; Genotype; Polymorphism, Single Nucleotide; Genomics; Genome, Human; Genome-Wide Association Study