Hypothesis tests for stratified mark‐specific proportional hazards models with missing covariates,with application to HIV vaccine efficacy trials

This article develops hypothesis testing procedures for the stratified mark‐specific proportional hazards model with missing covariates where the baseline functions may vary with strata. The mark‐specific proportional hazards model has been studied to evaluate mark‐specific relative risks where the mark is the genetic distance of an infecting HIV sequence to an HIV sequence represented inside the vaccine. This research is motivated by analyzing the RV144 phase 3 HIV vaccine efficacy trial, to understand associations of immune response biomarkers on the mark‐specific hazard of HIV infection, where the biomarkers are sampled via a two‐phase sampling nested case‐control design. We test whether the mark‐specific relative risks are unity and how they change with the mark. The developed procedures enable assessment of whether risk of HIV infection with HIV variants close or far from the vaccine sequence are modified by immune responses induced by the HIV vaccine; this question is interesting because vaccine protection occurs through immune responses directed at specific HIV sequences. The test statistics are constructed based on augmented inverse probability weighted complete‐case estimators. The asymptotic properties and finite‐sample performances of the testing procedures are investigated, demonstrating double‐robustness and effectiveness of the predictive auxiliaries to recover efficiency. The finite‐sample performance of the proposed tests are examined through a comprehensive simulation study. The methods are applied to the RV144 trial.