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Cohort studies investigating aging and dementia require APOE genotyping. We compared directly measured APOE genotypes to 'hard-call' genotypes derived from imputing genome-wide genotyping data from a range of platforms using several imputation panels. Older GWAS arrays imputed to 1000 Genomes Project (1KGP) phases and the Haplotype Reference Consortium (HRC) reference panels were able to achieve concordance rates of over 98% with stringent quality control (hard-call-threshold 0.8). However, this resulted in high levels of missingness (>12% with 1KGP and 5% with HRC). With recent GWAS arrays, concordance of 99% could be obtained with relatively lenient QC, resulting in no missingness.

Original publication

DOI

10.3233/jad-171104

Type

Journal article

Journal

Journal of Alzheimer's disease : JAD

Publication Date

01/2018

Volume

64

Pages

49 - 54

Addresses

QIMR Berghofer Medical Research Institute, Brisbane, Australia.

Keywords

Humans, Alzheimer Disease, Apolipoproteins E, Cohort Studies, Gene Frequency, Genotype, Polymorphism, Single Nucleotide, Female, Male, Genome-Wide Association Study