Accuracy of Inferred APOE Genotypes for a Range of Genotyping Arrays and Imputation Reference Panels.


Journal Article

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.

Full Text

Duke Authors

Cited Authors

  • Lupton, MK; Medland, SE; Gordon, SD; Goncalves, T; MacGregor, S; Mackey, DA; Young, TL; Duffy, DL; Visscher, PM; Wray, NR; Nyholt, DR; Bain, L; Ferreira, MA; Henders, AK; Wallace, L; Montgomery, GW; Wright, MJ; Martin, NG

Published Date

  • 2018

Published In

Volume / Issue

  • 64 / 1

Start / End Page

  • 49 - 54

PubMed ID

  • 29865051

Pubmed Central ID

  • 29865051

Electronic International Standard Serial Number (EISSN)

  • 1875-8908

Digital Object Identifier (DOI)

  • 10.3233/JAD-171104


  • eng

Conference Location

  • Netherlands