Towards eliminating bias in cluster analysis of TB genotyped data

dc.contributor.authorVan Schalkwyk, Carien_ZA
dc.contributor.authorCule, Madeleineen_ZA
dc.contributor.authorWelte, Alexen_ZA
dc.contributor.authorVan Helden, Paulen_ZA
dc.contributor.authorVan Der Spuy, Gianen_ZA
dc.contributor.authorUys, Pieteren_ZA
dc.date.accessioned2013-02-25T12:50:58Z
dc.date.available2013-02-25T12:50:58Z
dc.date.issued2012-03
dc.descriptionThe original publication is available at www.plosone.orgen_ZA
dc.description.abstractThe relative contributions of transmission and reactivation of latent infection to TB cases observed clinically has been reported in many situations, but always with some uncertainty. Genotyped data from TB organisms obtained from patients have been used as the basis for heuristic distinctions between circulating (clustered strains) and reactivated infections (unclustered strains). Naıve methods previously applied to the analysis of such data are known to provide biased estimates of the proportion of unclustered cases. The hypergeometric distribution, which generates probabilities of observing clusters of a given size as realized clusters of all possible sizes, is analyzed in this paper to yield a formal estimator for genotype cluster sizes. Subtle aspects of numerical stability, bias, and variance are explored. This formal estimator is seen to be stable with respect to the epidemiologically interesting properties of the cluster size distribution (the number of clusters and the number of singletons) though it does not yield satisfactory estimates of the number of clusters of larger sizes. The problem that even complete coverage of genotyping, in a practical sampling frame, will only provide a partial view of the actual transmission network remains to be explored.en_ZA
dc.description.versionPublishers versionen_ZA
dc.format.extent7 p. : ill.
dc.identifier.citationVan Schalkwyk C, Cule M, Welte A, Van Helden P, van der Spuy G, et al. (2012) Towards Eliminating Bias in Cluster Analysis of TB Genotyped Data. PLoS ONE 7(3): e34109. doi:10.1371/journal.pone.0034109en_ZA
dc.identifier.otherdoi:10.1371/journal.pone.0034109
dc.identifier.urihttp://hdl.handle.net/10019.1/79604
dc.language.isoen_ZAen_ZA
dc.publisherPLOS Oneen_ZA
dc.rights.holderThe author holds the copyrighten_ZA
dc.subjectTuberculosis -- Cluster analysisen_ZA
dc.subjectTuberculosis -- Epidemiologyen_ZA
dc.titleTowards eliminating bias in cluster analysis of TB genotyped dataen_ZA
dc.typeArticleen_ZA
Files
Original bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
vanschalkwyk_towards_2012.pdf
Size:
423.22 KB
Format:
Adobe Portable Document Format
Description:
Publishers' Version
License bundle
Now showing 1 - 1 of 1
Loading...
Thumbnail Image
Name:
license.txt
Size:
1.95 KB
Format:
Item-specific license agreed upon to submission
Description: