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Article: Testing linkage disequilibrium from pooled DNA: A contingency table perspective

TitleTesting linkage disequilibrium from pooled DNA: A contingency table perspective
Authors
KeywordsContingency Table
Dna Pooling
Haplotype
Hypergeometric Distribution
Linkage Disequilibrium
Issue Date2008
PublisherJohn Wiley & Sons Ltd. The Journal's web site is located at http://www.interscience.wiley.com/jpages/0277-6715/
Citation
Statistics in Medicine, 2008, v. 27, p. 5801-5815 How to Cite?
AbstractPooling DNA samples of multiple individuals has been advocated as a method to reduce genotyping costs. Under such a scheme, only the allele counts at each locus, not the haplotype information, are observed. We develop a systematic way for handling such data by formulating the problem in terms of contingency tables, where pooled allele counts are expressed as the margins and the haplotype counts correspond to the unobserved cell counts. We show that the cell frequencies can be uniquely determined from the marginal frequencies under the usual Hardy–Weinberg equilibrium (HWE) assumption and that the maximum likelihood estimates of haplotype frequencies are consistent and asymptotically normal as the number of pools increases. The limiting covariance matrix is shown to be closely related to the extended hypergeometric distribution. Our results are used to derive Wald‐type tests for linkage disequilibrium (LD) coefficient using pooled data. It is discovered that pooling is not efficient in testing weak LD despite its efficiency in estimating haplotype frequencies. We also show by simulations that the proposed LD tests are robust to slight deviation from HWE and to minor genotype error. Applications to two real angiotensinogen gene data sets are also provided. Copyright © 2008 John Wiley & Sons, Ltd.
Persistent Identifierhttp://hdl.handle.net/10722/221690
ISSN
2015 Impact Factor: 1.533
2015 SCImago Journal Rankings: 1.811
PubMed Central ID
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorXu, J-
dc.contributor.authorYang, Y-
dc.contributor.authorYing, Z-
dc.contributor.authorOtt, J-
dc.date.accessioned2015-12-04T15:29:08Z-
dc.date.available2015-12-04T15:29:08Z-
dc.date.issued2008-
dc.identifier.citationStatistics in Medicine, 2008, v. 27, p. 5801-5815-
dc.identifier.issn0277-6715-
dc.identifier.urihttp://hdl.handle.net/10722/221690-
dc.description.abstractPooling DNA samples of multiple individuals has been advocated as a method to reduce genotyping costs. Under such a scheme, only the allele counts at each locus, not the haplotype information, are observed. We develop a systematic way for handling such data by formulating the problem in terms of contingency tables, where pooled allele counts are expressed as the margins and the haplotype counts correspond to the unobserved cell counts. We show that the cell frequencies can be uniquely determined from the marginal frequencies under the usual Hardy–Weinberg equilibrium (HWE) assumption and that the maximum likelihood estimates of haplotype frequencies are consistent and asymptotically normal as the number of pools increases. The limiting covariance matrix is shown to be closely related to the extended hypergeometric distribution. Our results are used to derive Wald‐type tests for linkage disequilibrium (LD) coefficient using pooled data. It is discovered that pooling is not efficient in testing weak LD despite its efficiency in estimating haplotype frequencies. We also show by simulations that the proposed LD tests are robust to slight deviation from HWE and to minor genotype error. Applications to two real angiotensinogen gene data sets are also provided. Copyright © 2008 John Wiley & Sons, Ltd.-
dc.languageeng-
dc.publisherJohn Wiley & Sons Ltd. The Journal's web site is located at http://www.interscience.wiley.com/jpages/0277-6715/-
dc.relation.ispartofStatistics in Medicine-
dc.subjectContingency Table-
dc.subjectDna Pooling-
dc.subjectHaplotype-
dc.subjectHypergeometric Distribution-
dc.subjectLinkage Disequilibrium-
dc.titleTesting linkage disequilibrium from pooled DNA: A contingency table perspective-
dc.typeArticle-
dc.identifier.emailXu, J: xujf@hku.hk-
dc.identifier.authorityXu, J=rp02086-
dc.identifier.doi10.1002/sim.3407-
dc.identifier.pmid18712782-
dc.identifier.pmcidPMC2597697-
dc.identifier.scopuseid_2-s2.0-60849126458-
dc.identifier.volume27-
dc.identifier.spage5801-
dc.identifier.epage5815-
dc.identifier.isiWOS:000261143200001-

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