Modeling Secondary Phenotypes Conditional on Genotypes in Case–Control Studies

Traditional case–control genetic association studies examine relationships between status and one or more covariates. It is becoming increasingly common to study secondary phenotypes their with the original The Orofacial Pain: Prospective Evaluation Risk Assessment (OPPERA) project, a of temporomandibular disorders (TMD), motivates this work. Numerous measures interest are collected at enrollment, such as number comorbid pain conditions from which participant suffers. Examining potential basis these interest. Assessing associations statistically challenging, participants do not form random sample population Standard methods may be biased lack coverage power. We propose general method for analysis arbitrary utilizing inverse probability weighting bootstrapping standard error estimation. applied complicated tests used in next-generation sequencing studies, analyses haplotypes ambiguous phase. Simulation show that our performs well competing when they applicable yield promising results outcome types, time-to-event, other apply. OPPERA baseline study.