Linked Life Data

16451686

Source:http://linkedlifedata.com/resource/pubmed/id/16451686

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:dateCreated
2010-1-19
pubmed:abstractText
In genetic association studies, linkage disequilibrium (LD) within a region can be exploited to select a subset of single-nucleotide polymorphisms (SNPs) to genotype with minimal loss of information. A novel entropy-based method for selecting SNPs is proposed and compared to an existing method based on the coefficient of determination (R2) using simulated data from Genetic Analysis Workshop 14. The effect of the size of the sample used to investigate LD (by estimating haplotype frequencies) and hence select the SNPs is also investigated for both measures. It is found that the novel method and the established method select SNP subsets that do not differ greatly. The entropy-based measure may thus have value because it is easier to compute than R2. Increasing the sample size used to estimate haplotype frequencies improves the predictive power of the subset of SNPs selected. A smaller subset of SNPs chosen using a large initial sample to estimate LD can in some instances be more informative than a larger subset chosen based on poor estimates of LD (using a small initial sample). An initial sample size of 50 individuals is sufficient in most situations investigated, which involved selection from a set of 7 SNPs, although to select a larger number of SNPs, a larger initial sample size may be required.
pubmed:grant
pubmed:commentsCorrections
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:issn
1471-2156
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
6 Suppl 1
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
S72
pubmed:dateRevised
2010-9-20
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
Strategies for selecting subsets of single-nucleotide polymorphisms to genotype in association studies.
pubmed:affiliation
Cancer Research UK Genetic Epidemiology Division, University of Leeds, Cancer Genetics Building, St James's University Hospital, Beckett Street, Leeds LS9 7TF, UK. joe.butler@cancer.org.uk
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't