For each SNP, GWAS platforms assess each of the two possible alleles with independent assays which can be viewed as a scatter plot. Figure 3a depicts scatter plots for two SNPs in a GWAS. The scatter plots show the intensity values for one SNP allele plotted by the intensity values for the other SNP allele with each point corresponding to one subject. In the scatter plot on the left, the points fall into three well-defined clusters, and individuals in each cluster are “called” as having the same genotype for that SNP (i.e., GG, AG, or AA). A genotype calling algorithm is used to assign these clusters into genotypes for each subject. The scatter plot on the right shows an example of poor cluster separation, and this SNP should be excluded from analysis.
