Labs doing more than $12,500 in Medicare revenue in 1H2016 must report all payments by private payers for all lab tests on a list. That list includes the regular CLFS prices, as well as those codes that are under contractor pricing (and possibly gapfilling) during 1H2016. Details after the break.
The inclusion of the latter codes is a correct decision by CMS. PAMA price reporting is about the collection of private payer payments, for codes that are not unlisted codes, in 1H2016. Whether CMS had its own price at the time or not is irrelevant to the nationwide collection of private payer prices.
CMS lists the Tier 2 molecular codes (81401 forward) as well as codes like Administrative MAAA codes, as long as they were active codes in 1H2016.
Some MACs like MolDX have a lengthy, gene by gene spreadsheet of how they price genes one by one inside of Tier 2 codes. It sounds like big labs will report their Tier 2 average pricing under PAMA and CMS will take the median, and as of 1/1/2018, that median will become the single fixed CMS price for each of the nine levels of Tier 2 codes.Note that CMS has also posted a deck and transcript for its PAMA town hall call on July 6.
Toward the bottom of the CMS page, see various zip files for operational guidance.