Similar comparisons with newer genotyping platforms, which can provide better coverage of the genome because they include larger numbers of tag SNPs, show that imputed genotypes can achieve even greater accuracy. For example, in the GAIN psoriasis study (69) imputed and experimentally derived genotypes were compared at >660,000 SNPs in 90 individuals with an overall allelic discrepancy rate of <0.90% and an r2 correlation between observed and imputed allele counts that averaged 0.93. The r2 correlation coefficient is a particular useful summary of the impact of genotype imputation on power: in the context of the GAIN psoriasis study we expect that, on average, imputing genotypes for one of the 660,000 evaluated markers in 1,000 individuals would provide a similar amount of information as could be obtained by genotyping the same marker in 930 individuals (69).
