title: Concordance between direct and imputed APOE genotypes using 1000 Genomes data.
abstract: 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.
authors.affiliation: University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.
authors.forename: Christopher
authors.initials: C
authors.lastname: Oldmeadow
authors.affiliation: University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.
authors.forename: Elizabeth G
authors.initials: EG
authors.lastname: Holliday
authors.affiliation: University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.
authors.forename: Mark
authors.initials: M
authors.lastname: McEvoy
authors.affiliation: University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.
authors.forename: Rodney
authors.initials: R
authors.lastname: Scott
authors.affiliation: Prince of Wales Research Institute and Centre for Healthy Brain Aging, University of New South Wales, Sydney, Australia.
authors.forename: John B J
authors.initials: JB
authors.lastname: Kwok
authors.affiliation: Prince of Wales Research Institute and Centre for Healthy Brain Aging, University of New South Wales, Sydney, Australia.
authors.forename: Karen
authors.initials: K
authors.lastname: Mather
authors.affiliation: Prince of Wales Research Institute and Centre for Healthy Brain Aging, University of New South Wales, Sydney, Australia.
authors.forename: Perminder
authors.initials: P
authors.lastname: Sachdev
authors.affiliation: University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.
authors.forename: Peter
authors.initials: P
authors.lastname: Schofield
authors.affiliation: University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.
authors.forename: John
authors.initials: J
authors.lastname: Attia
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D001057:Apolipoproteins E / Q000235:genetics*; D005260:Female; D020022:Genetic Predisposition to Disease; D016678:Genome / Q000235:genetics*; D005838:Genotype; D006801:Humans; D008297:Male; D008875:Middle Aged
chemical_list: D001057:Apolipoproteins E
keywords: APOE; Agreement; concordance; dementia; genotyping