Clinician treatment preferences affect the ability to perform randomiz
ed clinical trials and the ability to analyze observational data for t
reatment effects. In clinical trials, clinician preferences that are b
ased on a subjective analysis of the patient can make it difficult to
define eligibility criteria for which clinicians would agree to random
ize all patients who satisfy the criteria. In addition, since each cli
nician typically has some preference for the choice of treatment for a
given patient, there are concerns about how strong that preference ne
eds to be before it is inappropriate for him to randomize the choice o
f treatment. In observational studies, the fact that clinician prefere
nces affect the choice of treatment is a major source of selection bia
s when estimating treatment effects. In this paper we review alternati
ve designs that have been proposed in the literature for randomized cl
inical trials that utilize clinician preferences differently than the
standard randomized trial design. We also examine the effects of clini
cian preferences on the ability to estimate causal treatment differenc
es from observational data, and propose an alternative method of analy
sis for observational data that uses clinician preferences explicitly.
We report on our experience to date in using our alternative randomiz
ed clinical trial design and our new method of observational analysis
to compare two treatments at the orthodontic clinics at the University
of California San Francisco and the University of the Pacific, San Fr
ancisco.