Genetic Epidemiology, Psychiatric Genetics, Asthma Genetics and Statistical Genetics Laboratories investigate the pattern of disease in families, particularly identical and non-identical twins, to assess the relative importance of genes and environment in a variety of important health problems.
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PMID
29865051
TITLE
Accuracy of Inferred APOE Genotypes for a Range of Genotyping Arrays and Imputation Reference Panels.
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.
DATE PUBLISHED
2018
HISTORY
PUBSTATUS PUBSTATUSDATE
pubmed 2018/06/06 06:00
medline 2018/06/06 06:00
entrez 2018/06/06 06:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Lupton MK Lupton Michelle K MK QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Medland SE Medland Sarah E SE QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Gordon SD Gordon Scott D SD QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Goncalves T Goncalves Tabatha T QIMR Berghofer Medical Research Institute, Brisbane, Australia.
MacGregor S MacGregor Stuart S QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Mackey DA Mackey David A DA University of Western Australia Centre for Ophthalmology and Visual Science, Lions Eye Institute, Perth, Australia.
Young TL Young Terri L TL Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA.
Duffy DL Duffy David L DL QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Visscher PM Visscher Peter M PM Queensland Brain Institute, University of Queensland, Brisbane, Australia.
Wray NR Wray Naomi R NR Queensland Brain Institute, University of Queensland, Brisbane, Australia.
Nyholt DR Nyholt Dale R DR Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia.
Bain L Bain Lisa L QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Ferreira MA Ferreira Manuel A MA QIMR Berghofer Medical Research Institute, Brisbane, Australia.
Henders AK Henders Anjali K AK Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.
Wallace L Wallace Leanne L Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia.
Montgomery GW Montgomery Grant W GW Queensland Brain Institute, University of Queensland, Brisbane, Australia.
Wright MJ Wright Margaret J MJ Centre for Advanced Imaging, University of Queensland, Brisbane, Australia.
Martin NG Martin Nicholas G NG QIMR Berghofer Medical Research Institute, Brisbane, Australia.
INVESTIGATORS
JOURNAL
VOLUME: 64
ISSUE: 1
TITLE: Journal of Alzheimer's disease : JAD
ISOABBREVIATION: J. Alzheimers Dis.
YEAR: 2018
MONTH:
DAY:
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN: 1875-8908
ISSNTYPE: Electronic
MEDLINE JOURNAL
MEDLINETA: J Alzheimers Dis
COUNTRY: Netherlands
ISSNLINKING: 1387-2877
NLMUNIQUEID: 9814863
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Journal Article
COMMENTS AND CORRECTIONS
GRANTS
GENERAL NOTE
KEYWORDS
KEYWORD
Alzheimer’s disease
ApoE receptor
cohort studies
computational biology
genetic association studies
MESH HEADINGS
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's