Fixation on Histology

If I Knew What I Know Now: Onboarding PCR in a Histology Lab

Polymerase Chain Reaction TestingMy histology lab onboarded polymerase chain reaction (PCR) for dermatomycosis a couple of years ago. I was charged with figuring out the ins and outs of onboarding this new test while making sure we could pass an audit by CLIA and CAP. Little by little, the path to PCR was painstakingly teased into place, ripped back up and reconstructed anew. Here is what I would’ve done if I knew what I know now.

Training:  Whichever platform is chosen for PCR, make sure to negotiate training of multiple people into the purchase or lease of equipment. Even if someone in the lab has previously worked with the equipment, it’s nothing but beneficial to be over-trained! Hopefully the company will have handouts with step-by-step instructions as well. These can be re-typed up into an SOP and save a lot of overall time.

Regulatory: Once a platform is decided on, contact CLIA and look into the possibility that a new CLIA number might be necessary. As an exclusively derm histology lab, our lab is considered an anatomical pathology lab; PCR is considered a clinical pathology lab test. We ended up needing a new CLIA number just for this one clinical test. Also be sure at least one pathologist is boarded in clinical pathology to be able to sign the pathology reports generated by PCR.

Validation: Now for the hard part. Validation. CAP and CLIA are notoriously vague about exact test numbers needed to be considered an efficient validation. I would suggest to validate using as many tests as you possibly can. Our lab is running fungal PCR, so luckily, we had many FFPE blocks in our back catalog that were PAS(D) positive for fungus. We cut PCR scrolls off of 25 older known positive cases and 25 known negative cases. We ran all of these for PCR, retaining the pathology reports of both tests in our PCR validation binder. As we began running current patient tissue for PCR, we cut a PAS(D) slide and a PCR scroll for each case for a few months. We compared results and found that the PCR was more sensitive than the PAS(D) slide. All of this information was also retained in our validation paperwork. After proving our PCR was as sensitive or more sensitive than traditional PAS(D) tests we were comfortable to begin testing cases using PCR only.

If you are trying to begin PCR testing for something you cannot do a secondary in-house test for, I would recommend going into your back catalog to gather as many older known positive and negative cases as possible and cutting 2 separate PCR scrolls from each case. One scroll should be tested on the new in-house platform while the other scroll should be sent out to another lab for PCR testing. It is even better if you can send the cases out to a lab that is utilizing the same platform as you (It is important to note that all PCR reaction tubes that store PCR scrolls need to be certified PCR clean and free from any RNases or DNases.) Compare all generated pathology reports for matching results. If results do not match at a high percentage, contact your PCR platform provider so they can help you figure out the reason for the difference in results. Retain all documents in a validation binder or however you store validation paperwork.

Proficiency Testing: Finally, register for proficiency testing. Clinical PCR tests require proficiency testing of 5 unknowns, 3 times per year. You will need to enroll in a program that will automatically send you the correct number of unknown tests at the correct intervals. You are required to report your PCR results back to the proficiency testing agency within a designated time frame. The proficiency testing lab will grade your results, get all of the results information to you and automatically send it to your accrediting agency. If there is an issue with your proficiency test results you are required to also report to your accrediting agency and stop testing until you can figure out the issue. Your accrediting agency will walk you through the requirements needed to resume PCR testing again. Different accreditation agencies accept different proficiency testing lab results, check with your accreditation agency to see which proficiency testing agencies you can choose from. Two commonly accepted proficiency testing programs are CAP proficiency testing and the American Proficiency Institute.

A final note on consumables needed for PCR testing. All PCR rection vessels, all centrifuge tubes and all pipette tips need to be certified PCR clean, RNase and DNase free. Pipette tips also should have an aerosol barrier in them. Not purchasing this grade of consumables can cause contaminated results or stop PCR DNA amplification from ever happening resulting in invalid or incomplete outcomes.

I believe PCR testing will begin playing a larger role within private histology labs that lack a genuine microbiology department. Onboarding PCR can seem like a daunting task to anyone without prior experience but our amazing histotechs seem to be up to the challenge! I hope these insights and tips will help guide you in this task, and will make at least one individual feel more comfortable with the path to PCR testing in a histology lab. 

Written by Ariel Liberda