One of the pivotal MolDX guidance documents, M00130 V2, February 2016, appears to be no longer active on the MolDX website, although some other MolDX documents still refer to it. Some of the same information is now in M00127, V3 which was updated on June 21, 2017.
M00127 V3 is online at Palmetto here. I've also cut-pasted below the break. A cloud archive of M00127 V3 is online here.
The instructions carve out NGS use of sequencing towards unlisted code billing (81479), although some AMA instructions in the CPT handbook state that genomic sequencing procedures are agnostic to method unless otherwise stated. According to 2015 CMS data, about 99% of the use of 81479 in Medicare Part B was via the several MolDX policy MACs.
Next Generation Sequencing Coding and Billing Guidelines (M00127, V3)
June 21, 2017