Though they may offer valuable patient and disease information that is impossible to study in a randomized trial, clinical disease registries also require special care and attention in causal inference. Registry data may be incomplete, inconsistent, and subject to confounding. In this paper we aim to address several analytical issues in estimating treatment effects that plague clinical registries such as the Emory amyotrophic lateral sclerosis (ALS) Clinic Registry. When attempting to assess the effect of a surgical insertion of a percutaneous endoscopic gastrostomy (PEG) tube on body mass index (BMI) using the data from the ALS Clinic Registry, one must combat issues of confounding, censoring by death, and missing outcome data that have not been addressed in previous studies of PEG. We propose a causal inference framework for estimating the survivor average causal effect (SACE) of PEG, which incorporates a model for generalized propensity scores to correct for confounding by pre-treatment variables, a model for principal stratification to account for censoring by death, and a model for the missing data mechanism. Applying the proposed framework to the ALS Clinic Registry Data, our analysis shows that PEG has a positive SACE on BMI at month 18 post-baseline; our results likely offer more definitive answers regarding the effect of PEG than previous studies of PEG.
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