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Deep sequencing will soon generate comprehensive sequence information in large disease samples. Although the power to detect association with an individual rare variant is limited, pooling variants by gene or pathway into a composite test provides an alternative strategy for identifying susceptibility genes. We describe a statistical method for detecting(More)
For modern evidence-based medicine, a well thought-out risk scoring system for predicting the occurrence of a clinical event plays an important role in selecting prevention and treatment strategies. Such an index system is often established based on the subject's 'baseline' genetic or clinical markers via a working parametric or semi-parametric model. To(More)
MOTIVATION Oligonucleotide microarrays allow genotyping of thousands of single-nucleotide polymorphisms (SNPs) in parallel. Recently, this technology has been applied to loss-of-heterozygosity (LOH) analysis of paired normal and tumor samples. However, methods and software for analyzing such data are not fully developed. RESULT Here, we report automated(More)
For the past two decades the Cox proportional hazards model has been used extensively to examine the covariate effects on the hazard function for the failure time variable. On the other hand, the accelerated failure time model, which simply regresses the logarithm of the survival time over the covariates, has seldom been utilized in the analysis of censored(More)
In comparing two treatments under a typical sequential clinical trial setting, a 50-50 randomization design generates reliable data for making efficient inferences about the treatment difference for the benefit of patients in the general population. However, if the treatment difference is large and the endpoint of the study is potentially fatal, it does not(More)
OBJECTIVE To compare the safety of nelfinavir and nevirapine-based antiretroviral treatment in HIV-1-infected pregnant women. METHODS In Pediatric AIDS Clinical Trials Group Protocol 1022, 38 antiretroviral-naive pregnant women at 10-30 weeks' gestation were randomized to nelfinavir or nevirapine with zidovudine plus lamivudine. The study was suspended(More)
BACKGROUND & AIMS Liver biopsy is invasive and associated with complications, sampling errors, and observer variability. Vibration-controlled transient elastography (VCTE) with FibroScan can be used to immediately assess liver stiffness. We aimed to define optimal levels of liver stiffness to identify patients with chronic viral hepatitis and significant(More)
In a long term clinical trial to evaluate a new treatment, quite often each study subject may experience a number of 'failures' that correspond to repeated occurrences of the same type of event or events of entirely different natures during his/her follow-up period. To obtain efficient inference procedures for the therapeutic effect over time, it is(More)
Recently, meta-analysis has been widely utilized to combine information across comparative clinical studies for evaluating drug efficacy or safety profile. When dealing with rather rare events, a substantial proportion of studies may not have any events of interest. Conventional methods either exclude such studies or add an arbitrary positive value to each(More)
For modern evidence-based medicine, decisions on disease prevention or management strategies are often guided by a risk index system. For each individual, the system uses his/her baseline information to estimate the risk of experiencing a future disease-related clinical event. Such a risk scoring scheme is usually derived from an overly simplified(More)