Document Type


Date of Degree

Fall 2017

Access Restrictions


Degree Name

PhD (Doctor of Philosophy)

Degree In


First Advisor

Jones, Michael P.

Second Advisor

Sun, Wanjie

First Committee Member

Wolinsky, Fredric D.

Second Committee Member

Zamba, Gideon K.D.

Third Committee Member

Foster, Eric

Fourth Committee Member

Smith, Brian J.


Randomized clinical trials (RCTs) are considered to be the "gold standard" in order to demonstrate a causal relationship between a treatment and an outcome because complete randomization ensures that the only difference between the two units being compared is the treatment. The intention-to-treat (ITT) comparison has long been regarded as the preferred analytic approach for RCTs. However, if there exists an “intermediate” variable between the treatment and outcome, and the analysis conditions on this intermediate, randomization will break down, and the ITT approach does not account properly for the intermediate. In this dissertation, we explore the principal stratification approach for dealing with intermediate variables, illustrate its applications in two different clinical trial settings, and extend the existing analytic approaches with respect to specific challenges in these settings.

The first part of our work focuses on clinical endpoint bioequivalence (BE) studies with noncompliance and missing data. In clinical endpoint BE studies, the primary analysis for assessing equivalence between a generic and an innovator product is usually based on the observed per-protocol (PP) population (usually completers and compliers). The FDA Missing Data Working Group recently recommended using “causal estimands of primary interest.” This PP analysis, however, is not generally causal because the observed PP is post-treatment, and conditioning on it may introduce selection bias. To date, no causal estimand has been proposed for equivalence assessment. We propose co-primary causal estimands to test equivalence by applying the principal stratification approach. We discuss and verify by simulation the causal assumptions under which the current PP estimator is unbiased for the primary principal stratum causal estimand – the "Survivor Average Causal Effect" (SACE). We also propose tipping point sensitivity analysis methods to assess the robustness of the current PP estimator from the SACE estimand when these causal assumptions are not met. Data from a clinical endpoint BE study is used to illustrate the proposed co-primary causal estimands and sensitivity analysis methods. Our work introduces a causal framework for equivalence assessment in clinical endpoint BE studies with noncompliance and missing data.

The second part of this dissertation targets the use of principal stratification analysis approaches in a pragmatic randomized clinical trial -- the Patient Activation after DXA Result Notification (PAADRN) study. PAADRN is a multi-center, pragmatic randomized clinical trial that was designed to improve bone health. Participants were randomly assigned to either intervention group with usual care augmented by a tailored patient-activation Dual-energy X-ray absorptiometry (DXA) results letter accompanied by an educational brochure, or control group with usual care only. The primary analyses followed the standard ITT principle, which provided a valid estimate for the intervention assignment. However, findings might underestimate the effect of intervention because PAADRN might not have an effect if the patient did not read, remember and act on the letter. We apply principal stratification to evaluate the effectiveness of PAADRN for subgroups, defined by patient's recall of having received a DXA result letter, which is an intermediate outcome that's post-treatment. We perform simulation studies to compare the principal score weighting methods with the instrumental variable (IV) methods. We examine principal strata causal effects on three outcome measures regarding pharmacological treatment and bone health behaviors. Finally, we conduct sensitivity analyses to assess the effect of potential violations of relevant causal assumptions. Our work is an important addition to the primary findings based on ITT. It provides a profound understanding of why the PAADRN intervention does (or does not) work for patients with different letter recall statuses, and sheds light on the improvement of the intervention.


Bioequivalence, Causal Inference, Clinical Trials, Intermediate Variable, Principal Stratification, Sensitivity analysis


xiii, 193 pages


Includes bibliographical references (pages 188-193).


Copyright © 2017 Yiyue Lou

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Biostatistics Commons