An expectation-maximization-likelihood-ratio test for handling missing data: application in experimental crosses.
The mapping of quantitative trait loci (QTL) is an important research question in animal and human studies. Missing data are common in such study settings, and ignoring such missing data may result in biased estimates of the genotypic effect and thus may eventually lead to errant results and incorrect inferences. In this article, we developed an expectation-maximization (EM)-likelihood-ratio test (LRT) in QTL mapping. Simulation studies based on two different types of phylogenetic models revealed that the EM-LRT, a statistical technique that uses EM-based parameter estimates in the presence of missing data, offers a greater statistical power compared with the ordinary analysis-of-variance (ANOVA)-based test, which discards incomplete data. We applied both the EM-LRT and the ANOVA-based test in a real data set collected from F2 intercross studies of inbred mouse strains. It was found that the EM-LRT makes an optimal use of the observed data and its advantages over the ANOVA F-test are more pronounced when more missing data are present. The EM-LRT method may have important implications in QTL mapping in experimental crosses.
Niu
Tianhua
T
Division of Preventive Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215, USA. tniu@rics.bwh.harvard.edu
Ding
Adam A
AA
Kreutz
Reinhold
R
Lindpaintner
Klaus
K
D000465:Algorithms; D000704:Analysis of Variance; D000818:Animals; D001921:Brain / Q000033:anatomy & histology*; D002874:Chromosome Mapping; D003198:Computer Simulation; D003433:Crosses, Genetic; D008040:Genetic Linkage; D005819:Genetic Markers; D016013:Likelihood Functions; D051379:Mice; D008815:Mice, Inbred Strains; D008957:Models, Genetic; D015233:Models, Statistical; D009929:Organ Size; D010802:Phylogeny; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D015203:Reproducibility of Results
D005819:Genetic Markers
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