I would contact the lab where this was performed and asked to talk to someone from their coding department that is familiar with this type of pathology coding to review the case with you. Below is from AMA CPT Changes 2015
88341 each additional single antibody stain procedure (List separately in addition to code for primary procedure)
(Use 88341 in conjunction with 88342)
(For multiplex antibody stain procedure, use 88344)
88344 each multiplex antibody stain procedure
(Do not use more than one unit of 88341, 88342, 88344 for each separately identifiable antibody per specimen)
(Do not report 88341, 88342, 88344 in conjunction with 88360, 88361 unless each procedure is for a different antibody)
Rationale
The immunohistochemistry/immunocytochemistry codes have been updated to reflect current methodologies. Code 88342 has been revised to allow multiple antibodies that are not separately identifiable to be reported together with a single code. Previously, code 88342 was structured so that each antibody had to be coded separately.
Code 88343 has been deleted and replaced with two new codes (88341, 88344). Code 88341 allows for each additional single antibody stain procedure to be reported separately and should be used in conjunction with parent code 88342. Code 88344 should be reported when multiple separately identifiable antibodies are applied to the same specimen slide. A combination of staining methodologies may be used, and thus, a series of parenthetical instructions have been added to guide the user in the appropriate number of codes to report per specimen.
The difference in the work and technology required in these two different staining methodologies (multiplex antibody staining vs antibody cocktail staining) are significant enough to require separate codes (88341, 88344). Immunohistochemical studies are typically performed singly (ie, single primary antibody used on a single glass slide). However, on occasion multiple primary antibodies can be used on the same tissue/glass slide. When the different antibodies can be differentiated microscopically (eg, by staining location or separate chromogenic detection), the stain is referred to as ?multiplex.? If the separate antibodies cannot be separately differentiated microscopically, it is referred to as an antibody ?cocktail.? A combination of staining methodologies may be used, and thus, a series of parenthetical instructions have been added to guide the user in the use of this new series of codes to enable reporting codes multiple times per specimen.