title: Feature-specific penalized latent class analysis for genomic data.
abstract: Genomic data are often characterized by a moderate to large number of categorical variables observed for relatively few subjects. Some of the variables may be missing or noninformative. An example of such data is loss of heterozygosity (LOH), a dichotomous variable, observed on a moderate number of genetic markers. We first consider a latent class model where, conditional on unobserved membership in one of k classes, the variables are independent with probabilities determined by a regression model of low dimension q. Using a family of penalties including the ridge and LASSO, we extend this model to address higher-dimensional problems. Finally, we present an orthogonal map that transforms marker space to a space of "features" for which the constrained model has better predictive power. We demonstrate these methods on LOH data collected at 19 markers from 93 brain tumor patients. For this data set, the existing unpenalized latent class methodology does not produce estimates. Additionally, we show that posterior classes obtained from this method are associated with survival for these patients.
authors.affiliation: Department of Biostatistics, Harvard School of Public Health, 655 Huntington Avenue, Boston, Massachusetts 02115, USA. ahousema@hsph.harvard.edu
authors.forename: E Andrés
authors.initials: EA
authors.lastname: Houseman
authors.forename: Brent A
authors.initials: BA
authors.lastname: Coull
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Betensky
mesh_terms: D001699:Biometry; D001932:Brain Neoplasms / Q000235:genetics; D003627:Data Interpretation, Statistical; D016147:Genes, Tumor Suppressor; D005819:Genetic Markers; D023281:Genomics / Q000706:statistics & numerical data*; D006801:Humans; D016013:Likelihood Functions; D019656:Loss of Heterozygosity; D015233:Models, Statistical
chemical_list: D005819:Genetic Markers