Concordance between direct and imputed APOE genotypes using 1000 Genomes data.

There are a growing number of large cohorts of older persons with genome-wide genotyping data available, but APOE is not included in any of the common microarray platforms. We compared directly measured APOE genotypes with those imputed using microarray data and the "1000 Genomes" dataset in a sample of 320 Caucasians. We find 90% agreement for ε2/ε3/ε4 genotypes and 93% agreement for predicting ε4 status, yielding kappa values of 0.81 and 0.84, respectively. More stringent thresholds around allele number estimates can increase this agreement to 90-97% and kappas of 0.90-0.93.