Genetic Epidemiology, Translational Neurogenomics, Psychiatric 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.
QIMR Home Page
GenEpi Home Page
About GenEpi
Publications
Contacts
Research
Staff Index
Collaborators
Software Tools
Computing Resources
Studies
Search
GenEpi Intranet
PMID
22950900
TITLE
Comparing linkage and association analyses in sheep points to a better way of doing GWAS.
ABSTRACT
Genome wide association studies (GWAS) have largely succeeded family-based linkage studies in livestock and human populations as the preferred method to map loci for complex or quantitative traits. However, the type of results produced by the two analyses contrast sharply due to differences in linkage disequilibrium (LD) imposed by the design of studies. In this paper, we demonstrate that association and linkage studies are in agreement provided that (i) the effects from both studies are estimated appropriately as random effects, (ii) all markers are fitted simultaneously and (iii) appropriate adjustments are made for the differences in LD between the study designs. We demonstrate with real data that linkage results can be predicted by the sum of association effects. Our association study captured most of the linkage information because we could predict the linkage results with moderate accuracy. We suggest that the ability of common single nucleotide polymorphism (SNP) to capture the genetic variance in a population will depend on the effective population size of the study organism. The results provide further evidence for many loci of small effect underlying complex traits. The analysis suggests a more informed method for GWAS is to fit statistical models where all SNPs are analysed simultaneously and as random effects.
DATE PUBLISHED
2012 Aug
HISTORY
PUBSTATUS PUBSTATUSDATE
entrez 2012/09/07 06:00
pubmed 2012/09/07 06:00
medline 2013/01/18 06:00
AUTHORS
NAME COLLECTIVENAME LASTNAME FORENAME INITIALS AFFILIATION AFFILIATIONINFO
Kemper KE Kemper Kathryn E KE Department of Agriculture and Food, University of Melbourne, Parkville, Victoria 3010, Australia. kathryn.kemper@dpi.vic.giv.au
Daetwyler HD Daetwyler Hans D HD
Visscher PM Visscher Peter M PM
Goddard ME Goddard Michael E ME
INVESTIGATORS
JOURNAL
VOLUME: 94
ISSUE: 4
TITLE: Genetics research
ISOABBREVIATION: Genet Res (Camb)
YEAR: 2012
MONTH: Aug
DAY:
MEDLINEDATE:
SEASON:
CITEDMEDIUM: Internet
ISSN:
ISSNTYPE:
MEDLINE JOURNAL
MEDLINETA: Genet Res (Camb)
COUNTRY: England
ISSNLINKING: 0960-8931
NLMUNIQUEID: 101550220
PUBLICATION TYPE
PUBLICATIONTYPE TEXT
Comparative Study
Evaluation Studies
Journal Article
Research Support, Non-U.S. Gov't
COMMENTS AND CORRECTIONS
GRANTS
GENERAL NOTE
KEYWORDS
MESH HEADINGS
DESCRIPTORNAME QUALIFIERNAME
Animals
Genetic Linkage
Genome-Wide Association Study methods
Linkage Disequilibrium methods
Models, Statistical methods
Polymorphism, Single Nucleotide genetics
Quantitative Trait Loci genetics
Sheep genetics
SUPPLEMENTARY MESH
GENE SYMBOLS
CHEMICALS
OTHER ID's