Please use this identifier to cite or link to this item: https://doi.org/10.1002/sim.3407
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dc.titleTesting linkage disequilibrium from pooled dna: A contingency table perspective
dc.contributor.authorYang, Y.
dc.contributor.authorXu, J.
dc.contributor.authorYing, Z.
dc.contributor.authorOtt, J.
dc.date.accessioned2014-10-28T05:15:41Z
dc.date.available2014-10-28T05:15:41Z
dc.date.issued2008-12
dc.identifier.citationYang, Y., Xu, J., Ying, Z., Ott, J. (2008-12). Testing linkage disequilibrium from pooled dna: A contingency table perspective. Statistics in Medicine 27 (28) : 5801-5815. ScholarBank@NUS Repository. https://doi.org/10.1002/sim.3407
dc.identifier.issn02776715
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/105403
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 bserved. We develop a systematic way for handling such data by formulating the problem in terms ofcontingency 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 thatthe 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 despiteits 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. © 2008 John Wiley & Sons, Ltd.
dc.description.urihttp://libproxy1.nus.edu.sg/login?url=http://dx.doi.org/10.1002/sim.3407
dc.sourceScopus
dc.subjectContingency table
dc.subjectDNA pooling
dc.subjectHaplotype
dc.subjectHypergeometric distribution
dc.subjectLinkage disequilibrium
dc.typeArticle
dc.contributor.departmentSTATISTICS & APPLIED PROBABILITY
dc.description.doi10.1002/sim.3407
dc.description.sourcetitleStatistics in Medicine
dc.description.volume27
dc.description.issue28
dc.description.page5801-5815
dc.description.codenSMEDD
dc.identifier.isiut000261143200001
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