1.2 Study Designs
and Strategies
for GWAS
There are two major types of GWAS: population-based studies and
family-based studies. Here we will focus on population-based case-
control studies, which have been the method of choice due to the
ease of data collection [3]. Case-control study is one of the strate-
gies when selecting the individuals to perform analysis, meaning
ascertaining cases that are affected with or without disease. The
most obvious advantage of the case-control study design is that
large numbers of case and control participants can be obtained in a
short time. However, this design is prone to biases that are mainly
caused by population stratification. It usually follows a two-stage
study design that is cost-effective since markers unlikely to be
associated with the disease can be eliminated in the first stage
[4]. The two-stage approach for GWAS is a common strategy that
maximizes statistical power while still maintaining reasonable
costs [5].
GWAS have been performed and many loci have been identified
where genetic factors are associated with the trait or disease. The
interactive GWAS diagram [6] (Fig.1) is a visualization cataloged
by the NHGRI. This picture shows the various chromosomes and
with some colored dots representing positions of some of these loci,
and most recently there is at least 100,000 SNPs and published
SNP-trait associations withP-values<1.0 10 ^5 [7].Fig. 1The NHGRI GWAS Catalog, a curated resource of SNP-trait associations [7]
An Overview of Genome-Wide Association Studies 99