Linked Life Data

18428428

Source:http://linkedlifedata.com/resource/pubmed/id/18428428

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
2008-8-14
pubmed:abstractText
We consider the analysis of multiple single nucleotide polymorphisms (SNPs) within a gene or region. The simplest analysis of such data is based on a series of single SNP hypothesis tests, followed by correction for multiple testing, but it is intuitively plausible that a joint analysis of the SNPs will have higher power, particularly when the causal locus may not have been observed. However, standard tests, such as a likelihood ratio test based on an unrestricted alternative hypothesis, tend to have large numbers of degrees of freedom and hence low power. This has motivated a number of alternative test statistics. Here we compare several of the competing methods, including the multivariate score test (Hotelling's test) of Chapman et al. ([2003] Hum. Hered. 56:18-31), Fisher's method for combining P-values, the minimum P-value approach, a Fourier-transform-based approach recently suggested by Wang and Elston ([2007] Am. J. Human Genet. 80:353-360) and a Bayesian score statistic proposed for microarray data by Goeman et al. ([2005] J. R. Stat. Soc. B 68:477-493). Some relationships between these methods are pointed out, and simulation results given to show that the minimum P-value and the Goeman et al. ([2005] J. R. Stat. Soc. B 68:477-493) approaches work well over a range of scenarios. The Wang and Elston approach often performs poorly; we explain why, and show how its performance can be substantially improved.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:month
Sep
pubmed:issn
1098-2272
pubmed:author
pubmed:copyrightInfo
(c) 2008 Wiley-Liss, Inc.
pubmed:issnType
Electronic
pubmed:volume
32
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
560-6
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2008
pubmed:articleTitle
Analysis of multiple SNPs in a candidate gene or region.
pubmed:affiliation
London School of Hygiene and Tropical Medicine, London, United Kingdom. juliet.chapman@lshtm.ac.uk
pubmed:publicationType
Journal Article, Comparative Study, Research Support, Non-U.S. Gov't