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Assessing a multiple QTL search using the variance component model
Dalarna University, School of Technology and Business Studies, Statistics.ORCID iD: 0000-0002-1057-5401
2010 (English)In: Computational biology and chemistry (Print), ISSN 1476-9271, E-ISSN 1476-928X, Vol. 34, no 1, 34-41 p.Article in journal (Refereed) Published
Abstract [en]

Development of variance component algorithms in genetics has previously mainly focused on animal breeding models or problems in human genetics with a simple data structure. We study alternative methods for constrained likelihood maximization in quantitative trait loci (QTL) analysis for large complex pedigrees. We apply a forward selection scheme to include several QTL and interaction effects, as well as polygenic effects, with up to five variance components in the model. We show that the implemented active set and primal-dual schemes result in accurate solutions and that they are robust. In terms of computational speed, a comparison of two approaches for approximating the Hessian of the log-likelihood shows that the method using an average information matrix is the method of choice for the five-dimensional problem. The active set method, with the average information method for Hessian computation, exhibits the fastest convergence with an average of 20 iterations per tested position, where the change in variance components <0.0001 was used as convergence criterion.

Place, publisher, year, edition, pages
Elseiver , 2010. Vol. 34, no 1, 34-41 p.
National Category
Probability Theory and Statistics
Research subject
Komplexa system - mikrodataanalys, Statistisk modellering är grunden till en ökad förståelse inom genetik!
Identifiers
URN: urn:nbn:se:du-4846DOI: 10.1016/j.compbiolchem.2009.12.001ISI: 000275587800004OAI: oai:dalea.du.se:4846DiVA: diva2:520215
Available from: 2010-06-18 Created: 2010-06-18 Last updated: 2015-09-14Bibliographically approved

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CiteExportLink to record
Permanent link

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Citation style
  • apa
  • ieee
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  • vancouver
  • chicago-author-date
  • chicago-note-bibliography
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
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  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf