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Pragmatic trials lack the relatively tight quality control of traditional efficacy studies and hence may pose added analytic challenges owing to the practical realities faced in carrying them out.STOP CRC is a cluster randomized trial testing the effectiveness of automated, electronic medical record (EMR)-driven strategies to raise colorectal cancer (CRC) screening rates in safety net clinics. Screen-eligible participants were accrued during year 1 and followed for 12 months (measurement window) to assess completion of a fecal screening test. Control clinics implemented the intervention in year 2.Due to limitations on how we could build the intervention tools, the overlap of the year 1 measurement windows with year 2 intervention rollout posed a potential for contamination of the primary outcome for control participants. In addition, a variety of factors led to a lack of synchronization of the measurement windows with actual intervention delivery. In both cases, the net impact of these factors would be to diminish the estimated impact of the intervention.We dealt with the overlap issue by delaying the start of intervention rollout to control clinics in year 2 by 6 months and by truncating the measurement windows for intervention and control participants at this point. In addition we formulated three sensitivity analyses to help address the issue of asynchronization.This case study might help other investigators facing similar challenges think about such issues and the pros and cons of various strategies for dealing with them.

Analytic Challenges Arising from the STOP CRC Trial: Pragmatic Solutions for Pragmatic Problems