Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy.
Genome-wide association studies (GWAS) are routinely conducted for both quantitative and binary (disease) traits. We present two analytical tools for use in the experimental design of GWAS. Firstly, we present power calculations quantifying power in a unified framework for a range of scenarios. In t...
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doaj-649af62a85214786a9f4cf3b9932e9052020-11-25T01:32:07ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0188e7149410.1371/journal.pone.0071494Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy.Sang Hong LeeNaomi R WrayGenome-wide association studies (GWAS) are routinely conducted for both quantitative and binary (disease) traits. We present two analytical tools for use in the experimental design of GWAS. Firstly, we present power calculations quantifying power in a unified framework for a range of scenarios. In this context we consider the utility of quantitative scores (e.g. endophenotypes) that may be available on cases only or both cases and controls. Secondly, we consider, the accuracy of prediction of genetic risk from genome-wide SNPs and derive an expression for genomic prediction accuracy using a liability threshold model for disease traits in a case-control design. The expected values based on our derived equations for both power and prediction accuracy agree well with observed estimates from simulations.http://europepmc.org/articles/PMC3747270?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Sang Hong Lee Naomi R Wray |
spellingShingle |
Sang Hong Lee Naomi R Wray Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. PLoS ONE |
author_facet |
Sang Hong Lee Naomi R Wray |
author_sort |
Sang Hong Lee |
title |
Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. |
title_short |
Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. |
title_full |
Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. |
title_fullStr |
Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. |
title_full_unstemmed |
Novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. |
title_sort |
novel genetic analysis for case-control genome-wide association studies: quantification of power and genomic prediction accuracy. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2013-01-01 |
description |
Genome-wide association studies (GWAS) are routinely conducted for both quantitative and binary (disease) traits. We present two analytical tools for use in the experimental design of GWAS. Firstly, we present power calculations quantifying power in a unified framework for a range of scenarios. In this context we consider the utility of quantitative scores (e.g. endophenotypes) that may be available on cases only or both cases and controls. Secondly, we consider, the accuracy of prediction of genetic risk from genome-wide SNPs and derive an expression for genomic prediction accuracy using a liability threshold model for disease traits in a case-control design. The expected values based on our derived equations for both power and prediction accuracy agree well with observed estimates from simulations. |
url |
http://europepmc.org/articles/PMC3747270?pdf=render |
work_keys_str_mv |
AT sanghonglee novelgeneticanalysisforcasecontrolgenomewideassociationstudiesquantificationofpowerandgenomicpredictionaccuracy AT naomirwray novelgeneticanalysisforcasecontrolgenomewideassociationstudiesquantificationofpowerandgenomicpredictionaccuracy |
_version_ |
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