On December 13, 2015, the Association for Molecular Pathology (AMP) released a 15-age response to the FDA's case. Find it here. Generally, AMP found that the FDA concerns were overstated (or worse). In a few cases, such as the Kif6 case study and the OvaSure case study, AMP notes that a modernized CLIA that includes some clinical validity review would have caught any problems and FDA LDT review was not required.
Edward Ashwood, associate VP for government relations at ARUP, also penned an op-ed (here) on the poor quality of the FDA's white paper. Ashwood writes:
[T]he FDA has raised a number of new red flags on itself casting further doubt on whether it has the expertise to properly assess the validity of current or future LDTs, a development that is very troubling to patient groups, and the medical and laboratory communities....The FDA report on LDTs, perhaps intended to be a bombshell shattering the position of the lab community to maintain the regulatory framework under the CMS, in fact has exposed how unprepared the agency really is to assume oversight of LDT clinical validity.