Work

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

Year: 2018

Type: article

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.

Source: Journal of Alzheimer s Disease

DOI: 10.3233/jad-171104

Authors: Michelle K. Lupton, Sarah E. Medland, Scott D. Gordon, Tabatha Goncalves, Stuart MacGregor, David A. Mackey, Terri L. Young, David L. Duffy, Peter M. Visscher, Naomi R. Wray, Dale R. Nyholt, Lisa Bain, Manuel A. Ferreira, Anjali K. Henders, Leanne Wallace, Grant W. Montgomery, Margaret J. Wright, Nicholas G. Martin

Institutions: QIMR Berghofer Medical Research Institute, Lions Eye Institute, The University of Western Australia, University of Wisconsin–Madison, The University of Queensland, Institute for Molecular Bioscience, Queensland University of Technology

Language: English

Topic: Genetic Associations and Epidemiology

Subfield: Genetics

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: green

Funders: National Institutes of Health, National Health and Medical Research Council

Awards: Prospective Imaging Study of Ageing: Genes, Brain & Behaviour, Validation and Replication of Genes Associated with Common Human Disease Using Australian Twin Families, Genome-wide combined linkage-association scan of multiply phenotyped twin sibships, Pigmentation genes and melanoma risk, Mapping Genes for typical migraine using twin families., Genetics of moliness, Uncoupled Research Fellowship, Genetics of moliness, Statistical Methods and Algorithms for Analysis of High-throughput Genetics and Genomics Platforms

OpenAlex ID: W2805643480

FWCI: 0.613

Cites: 12

Cited by: 10

Related to: 10