Linked Life Data

12396586

Source:http://linkedlifedata.com/resource/pubmed/id/12396586

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
5
pubmed:dateCreated
2002-10-24
pubmed:abstractText
Current methods to identify recombination between subtypes of human immunodeficiency virus 1 (HIV-1) fall into a sequential testing trap, in which significance is assessed conditional on parental representative sequences and crossover points (COPs) that maximize the same test statistic. We overcame this shortfall by testing for recombination while inferring parental heritage and COPs using an extended Bayesian multiple change-point model. The model assumes that aligned molecular sequence data consist of an unknown number of contiguous segments that may support alternative topologies or varying evolutionary pressures. We allowed for heterogeneity in the substitution process and specifically tested for intersubtype recombination using Bayes factors. We also developed a new class of priors to assess significance across a wide range of support for recombination in the data. We applied our method to three putative gag gene recombinants. HIV-1 isolate RW024 decisively supported recombination with an inferred parental heritage of AD and a COP 95% Bayesian credible interval of (1,152, 1,178) using the HXB2 numbering scheme. HIV-1 isolate VI557 barely supported recombination. HIV-1 isolate RF decisively rejected recombination as expected, given that the sequence is commonly used as a reference sequence for subtype B. We employed scaled regeneration quantile plots to assess convergence and found this approach convenient to use even for our variable dimensional model parameter space.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Oct
pubmed:issn
1063-5157
pubmed:author
pubmed:issnType
Print
pubmed:volume
51
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
715-28
pubmed:dateRevised
2007-11-14
pubmed:meshHeading
pubmed:year
2002
pubmed:articleTitle
Oh brother, where art thou? A Bayes factor test for recombination with uncertain heritage.
pubmed:affiliation
Department of Biomathematics, School of Medicine, University of California, Los Angeles, California 90095-1766, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't