Sidebar: AMA CPT from Method Stack Coding to Coding by Gene Name

The Transition for Method-Based Stack Codes to Gene-Specific Codes

(This entry is a side-bar to a blog on CMS pricing of BRCA codes, here.)

Between the 1990s and 2013, the AMA provided a "method based" code set for human genetic testing.   This involved a small number of codes that described lab steps, such as DNA extraction and DNA amplication, typically paying about $20 each.   For example, a particular genetic analysis might be billed as "DNA extraction x 1, $20" and "DNA amplification x 10, $200."   During part of this period, I worked as a regional CMS medical director and later, in 2008, HHS asked me to write a white paper on the coding system and suggest pathways for improvement.  This was based on HHS's annoyance that the CPT coding system, through 2008, was inadequate and did not seem to be changing.  As of March 2017, the Quinn 2008 white paper was still online at HHS (here).

Beginning at the AMA CPT editorial panel meeting in Los Angeles in October 2010, AMA began producing the multi-hundred gene code set which we use today.  The code set published for the 2012 AMA CPT, but was not adopted for use by CMS until January 2013, due to disputes about pricing methods.   In CY 2013, the genetic codes were gapfilled by CMS MACs, a cumbersome and slow process.   Commercial claims processing was also delayed in 2013, since the codes were active but there was no reference CMS fee schedule for pricing.  Countless US insurers had to set up de novo prices without the crutch of a public CMS fee schedule.