Handling reviewer comment challenging the novelty of a used method One of the Reviewer comments for a paper that I sent to a journal is the following:


  The authors claim that they are the first to use subjective
  questionnaires  to develop predictive models. This is not accurate, there
  are many studies on the literature that use questionnaires  and some of
  them even compare PQ to objective data coming from sensors in order to
  find correlations.


Now the problem is that I have done a thorough check and have observed that this paper indeed is first to use questionnaire to develop predicitve models for the particular disorder. Now how do I handle such a comment?
I think there's no contradiction. The reviewer said "...first to use subjective questionnaires to develop predictive models", while you said "...first to use subjective questionnaires to develop predictive models for the particular disorder" (emphasis mine).

I would just write in a response what you said, and ask for clarification - something like "I have done a thorough check ... the particular disorder. If the reviewer is aware of a previous paper has also used subjective questionnaires for this disorder, please point it out".