Pathology Services Packaged With Primary OPPS Procedure

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I am a fairly new coder and I work at an Independent Laboratory and we receive specimens from hospitals, physician offices, and other laboratories. Humana has recently requested payments back from us due to "services are included in the APC reimbursement." I have reviewed the information from the CMS website and the listed CPT codes and most of our services have a status indicator of "N -Items and services are packaged into APC rates" or one of the 4 "Q" indicators which state that they would be packaged with certain other procedures. I am not sure why our MAC has not followed the CMS rule and we are not having this issue with any other payers. The testing that we perform varies from Women's health (STD) to Oncology testing (FISH, BMPE, CYTO and FLOW). Our STD testing is not included in the packaged services but most of our other testing is.

Does anyone have any insight that may help me?

I am not completely sure that I understand how to decipher what we can bill and what is included in the packaged services. From what I was able to gather from CMS we are allowed to bill for the PC portions of pathology services, and laboratory tests when the test is the only service provided on the date for hospital or hospital outpatient facilities. How do you determine if it is the only service provided? We never actually see the patient so the only information we get is from our clients (hospitals, physician offices, and other laboratories.)

Some scenarios that we have are:
1) Our referring provider orders a bone marrow biopsy and sends the patient to a hospital or hospital outpatient facility for the actual biopsy. We perform a BMPE (88305/88311/88313/88342/88341) from the specimen that was obtained from that biopsy. Are services are going to be packaged into the APC rate for the bone marrow biopsy (38221). Correct?
2) Same testing as above but this time, the biopsy is performed in the physicians office by an employee of the office. Since the biopsy was not performed in a hospital or hospital outpatient facility, our BMPE would not be packaged. Correct?
3) The patient is seen in the ED but the ED sends the patient (on the same DOS) to a Urology specialist for testing on a urine sample. The Urologist is our client and so we receive the urine. Our DOS is the collection date so would our testing be included in the ED APC rate?

Any help or direction would be greatly appreciated.