Copyright (c) 2008 Berkeley Electronic Press All rights reserved. http://www.bepress.com/ijb Recent documents in The International Journal of Biostatistics en-us Sat, 10 May 2008 02:29:58 PDT 3600 http://www.bepress.com/ijb/vol4/iss1/6 http://www.bepress.com/ijb/vol4/iss1/6 Thu, 08 May 2008 20:36:10 PDT Typically locus specific genotype data do not contain information regarding the gametic phase of haplotypes, especially when an individual is heterozygous at more than one locus among a large number of linked polymorphic loci. Thus, studying disease-haplotype association using unphased genotype data is essentially a problem of handling a missing covariate in a case-control design. There are several methods for estimating a disease-haplotype association parameter in a matched case-control study. Here we propose a conditional likelihood approach for inference regarding the disease-haplotype association using unphased genotype data arising from a matched case-control study design. The proposed method relies on a logistic disease risk model and a Hardy-Weinberg equilibrium (HWE) among the control population only. We develop an expectation and conditional maximization (ECM) algorithm for jointly estimating the haplotype frequency and the disease-haplotype association parameter(s). We apply the proposed method to analyze the data from the Alpha-Tocopherol, Beta-Carotene Cancer prevention study, and a matched case-control study of breast cancer patients conducted in Israel. The performance of the proposed method is evaluated via simulation studies. Samiran Sinha General Biostatistics http://www.bepress.com/ijb/vol4/iss1/5 http://www.bepress.com/ijb/vol4/iss1/5 Sun, 04 May 2008 10:49:18 PDT It has long been recognized that covariate adjustment can increase precision in randomized experiments, even when it is not strictly necessary. Adjustment is often straightforward when a discrete covariate partitions the sample into a handful of strata, but becomes more involved with even a single continuous covariate such as age. As randomized experiments remain a gold standard for scientific inquiry, and the information age facilitates a massive collection of baseline information, the longstanding problem of if and how to adjust for covariates is likely to engage investigators for the foreseeable future. In the locally efficient estimation approach introduced for general coarsened data structures by James Robins and collaborators, one first fits a relatively small working model, often with maximum likelihood, giving a nuisance parameter fit in an estimating equation for the parameter of interest. The usual advertisement is that the estimator will be asymptotically efficient if the working model is correct, but otherwise will still be consistent and asymptotically Gaussian.However, by applying standard likelihood-based fits to misspecified working models in covariate adjustment problems, one can poorly estimate the parameter of interest. We propose a new method, empirical efficiency maximization, to optimize the working model fit for the resulting parameter estimate.In addition to the randomized experiment setting, we show how our covariate adjustment procedure can be used in survival analysis applications. Numerical asymptotic efficiency calculations demonstrate gains relative to standard locally efficient estimators. Daniel B. Rubin Clinical Trials Statistical Theory and Methods Survival Analysis