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J Alzheimers Dis. 2018;64(1):49-54. doi: 10.3233/JAD-171104.

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

Author information

1
QIMR Berghofer Medical Research Institute, Brisbane, Australia.
2
University of Western Australia Centre for Ophthalmology and Visual Science, Lions Eye Institute, Perth, Australia.
3
Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA.
4
Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.
5
Queensland Brain Institute, University of Queensland, Brisbane, Australia.
6
Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
7
Centre for Advanced Imaging, University of Queensland, Brisbane, Australia.

Abstract

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.

KEYWORDS:

Alzheimer’s disease; ApoE receptor; cohort studies; computational biology; genetic association studies

PMID:
29865051
DOI:
10.3233/JAD-171104

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