Standards for molecular testing in clinical genetics have largely evolved around testing an affected individual or suspected carrier for a mutation or testing an unaffected relative of a patient with a known mutation. In these situations, extensive pre-test counseling can ascertain with confidence the preference of the individual to be tested in terms of choosing whether or not to obtain a specific genetic test for a specific hereditary condition. By contrast, after clinical sequencing for a specific indication, the patient has already undergone an assay of all other disease-associated genes. In order to respect preferences in the same manner as with targeted testing, the patient whose exome or genome is sequenced would have to undergo an extensive, and possibly overwhelming, amount of genetic counseling for numerous conditions unrelated to the primary indication for sequencing. This will become impractical as clinical sequencing becomes more common and both its lack of standardization and its application to patients of all circumstance might result in deeply varying levels of truly informed preference setting.
