Marker selection for genetic case-control association studies.
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.
Pettersson
Fredrik H
FH
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. fredrikp@well.ox.ac.uk
Anderson
Carl A
CA
Clarke
Geraldine M
GM
Barrett
Jeffrey C
JC
Cardon
Lon R
LR
Morris
Andrew P
AP
Zondervan
Krina T
KT
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
D005819:Genetic Markers