Article: Optimal selection strategies for QTL mapping using pooled DNA samples

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TitleOptimal selection strategies for QTL mapping using pooled DNA samples
AuthorsJawaid, A1
Bader, JS1
Purcell, S1
Cherny, SS1
Sham, P1
KeywordsDNA pooling
Experimental errors
QTL association analyses
Sample selection
SNPs
Issue Date2002
PublisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhg
CitationEuropean Journal Of Human Genetics, 2002, v. 10 n. 2, p. 125-132 [How to Cite?]
DOI: http://dx.doi.org/10.1038/sj/ejhg/5200771
AbstractThe cost of large-scale association studies may be reduced substantially by analysis of pooled DNA from multiple individuals. Here we examine the optimal symmetric and asymmetric designs for pooling experiments for quantitative traits under a range of assumptions about the underlying genetic model and the sources of experimental errors in allele frequency estimation. The results indicate that, in the absence of experimental errors and for common alleles with additive effects, a symmetric pooling scheme comparing the top 27% with the bottom 27% of the trait distribution is optimal, extracting 80% the total information available. A symmetric design is not optimal for rare or recessive alleles, which require asymmetric (or other) pooling strategies. Allele frequency measurement errors reduce the optimal pooling fraction as well as the overall efficiency of the pooling design. In contrast, random variation in the amount of DNA contributed by individuals to a pool reduces only the overall efficiency of the pooling design. Our results emphasize the importance of minimising experimental errors and suggest a pooling fraction of around 20%.
ISSN1018-4813
2011 Impact Factor: 4.4
2011 SCImago Journal Rankings: 0.459
DOIhttp://dx.doi.org/10.1038/sj/ejhg/5200771
ISI Accession Number IDWOS:000174997000007
ReferencesReferences in Scopus
DC Field
Value
dc.contributor.authorJawaid, A
dc.contributor.authorBader, JS
dc.contributor.authorPurcell, S
dc.contributor.authorCherny, SS
dc.contributor.authorSham, P
dc.date.accessioned2011-12-16T08:09:08Z
dc.date.available2011-12-16T08:09:08Z
dc.date.issued2002
dc.description.abstractThe cost of large-scale association studies may be reduced substantially by analysis of pooled DNA from multiple individuals. Here we examine the optimal symmetric and asymmetric designs for pooling experiments for quantitative traits under a range of assumptions about the underlying genetic model and the sources of experimental errors in allele frequency estimation. The results indicate that, in the absence of experimental errors and for common alleles with additive effects, a symmetric pooling scheme comparing the top 27% with the bottom 27% of the trait distribution is optimal, extracting 80% the total information available. A symmetric design is not optimal for rare or recessive alleles, which require asymmetric (or other) pooling strategies. Allele frequency measurement errors reduce the optimal pooling fraction as well as the overall efficiency of the pooling design. In contrast, random variation in the amount of DNA contributed by individuals to a pool reduces only the overall efficiency of the pooling design. Our results emphasize the importance of minimising experimental errors and suggest a pooling fraction of around 20%.
dc.description.natureLink_to_subscribed_fulltext
dc.identifier.citationEuropean Journal Of Human Genetics, 2002, v. 10 n. 2, p. 125-132 [How to Cite?]
DOI: http://dx.doi.org/10.1038/sj/ejhg/5200771
dc.identifier.doihttp://dx.doi.org/10.1038/sj/ejhg/5200771
dc.identifier.epage132
dc.identifier.isiWOS:000174997000007
dc.identifier.issn1018-4813
2011 Impact Factor: 4.4
2011 SCImago Journal Rankings: 0.459
dc.identifier.issue2
dc.identifier.pmid11938443
dc.identifier.scopuseid_2-s2.0-0036225328
dc.identifier.spage125
dc.identifier.urihttp://hdl.handle.net/10722/143659
dc.identifier.volume10
dc.publisherNature Publishing Group. The Journal's web site is located at http://www.nature.com/ejhg
dc.publisher.placeUnited Kingdom
dc.relation.ispartofEuropean Journal of Human Genetics
dc.relation.referencesReferences in Scopus
dc.subject.meshAnalysis of Variance
dc.subject.meshAnimals
dc.subject.meshCase-Control Studies
dc.subject.meshChromosome Mapping - statistics & numerical data
dc.subject.meshGene Frequency
dc.subject.meshHumans
dc.subject.meshModels, Genetic
dc.subject.meshQuantitative Trait, Heritable
dc.subjectDNA pooling
dc.subjectExperimental errors
dc.subjectQTL association analyses
dc.subjectSample selection
dc.subjectSNPs
dc.titleOptimal selection strategies for QTL mapping using pooled DNA samples
dc.typeArticle
Author Affiliations
  1. King's College London