Best Practices for Managing Billing Related to Inpatient Stays for Clinical Research

The final episode of our three-part Compliance Conversations series on clinical research and billing is here!

In this episode, CJ Wolf, MD, and Mary Veazie, a CPA specializing in clinical research finance, share some common pitfalls and real-world situations related to billing management for clinical studies that require inpatient stays.

Tune in to this episode to hear CJ and Mary’s conversation on:

    • What can happen when clinical communication breaks down – and how to prevent that from happening
    • How to optimize your electronic health records with research-specific fields and designations
    • Keeping sponsors, doctors, and patients in the loop on treatment during inpatient stays
    • Planning for unforeseen financial and coverage issues

CJ and Mary also discuss how to navigate the nuances of billing related clinical trial management. When an inpatient stay is required as part of a study, who is on the hook for the financial part of the patient’s stay – the sponsor? The payer? The patient? CJ and Mary discuss all the implications and considerations that are critical to making sure the study is compliant.

If you missed Part 1 and Part 2 of this series, check them out here:

Interested in being a guest on the show? Email CJ directly at

Listen Now >>


Episode Transcript

CJ: Welcome everybody to another episode of Compliance Conversations. I am CJ Wolf with Healthicity. Today’s guest is Mary Veazie. Welcome Mary.

Mary: Thank you, CJ. I appreciate you having me today.

CJ: Absolutely. Now everyone, if you haven’t listened, this is our third podcast in this three-part series. Mary and I have been talking about, in the first two, about clinical research billing. Mary’s given us a nice overview in that first episode on clinical research billing, why it’s important for compliance professionals to understand, revenue cycle professionals, finance professionals and the second podcast we drilled down a little bit more into a very important portion of these activities, which is a Medicare coverage analysis. Mary shared all sorts of great details from how you do it, where you get resources, how you train staff, timeline, all those important things. And in this third podcast, we’re going to be specifically talking about leveraging the electronic health record, we’ll call that the EHR, to bill for clinical trials with inpatient stays. So keep in mind that work can be done in clinical trials, some of them could be outpatient, some of them could be inpatient, so we’re going to focus on that inpatient stay. And just a little bit of background, Mary and I know each other from our years of work at MD Anderson Cancer Center. I was there for a relatively short time. Mary was there for a very long time in charge of clinical research billing, and Mary I believe you recently retired and you’re teaching and consulting and all those great things, right?

Mary: Yes CJ, I retired in March of 2022 after 22 years of service and really enjoyed my time there but realized that I wanted to venture onto the consulting side and the education side.

CJ: Excellent. Well we’re so grateful that you’re doing that and you’re sticking with this important topic. We’ll mention a little bit later a camp that Mary’s doing on this topic, and we’ve mentioned it in the first two podcasts as well. But Mary let’s jump into this topic about the inpatient stay and leveraging the EHR. Before we get too detailed in the billing piece, can you just talk about how clinical research is incorporated into an EHR?

Mary: Yes, absolutely. So the actual electronic health record is really for patient management research, just almost an afterthought, if you will, by many of the programmers associated with the electronic health record, and so I’ll talk about the billing aspects of it and the treatment pieces of it, because your treatment plan for a clinical research study has to get incorporated into, or should get incorporated into, your electronic health record as well. So that way the clinicians, the clinical ops teams and the nurses really understand, “Here is what the study requirements are, here’s the orders that need to occur for this particular patient at this particular time,” because for a clinical research study it is very regimented as it relates to the treatment for that patient.

CJ: Right, and it’s important to recognize, and I think this is partly what you’re saying, that when you’re doing research, you’re trying to confirm things like safety and efficacy, so you may be doing tests and services that are a little bit more rigorous or a little bit greater than what you would normally do to just treat that disease, so I think that’s part of what you’re probably talking about there.

Mary: That is correct. So you’re doing things to really monitor the safety of the patient, so you may know that a certain class of drugs causes cardiac problems for some of the patients, and you see that as predominantly happening in, say, a certain age range of patients. You want to make sure that you are actually performing certain safety tests and making sure everybody knows that particular patient is on a particular trial. So oftentimes your electronic health record will have a pink banner or a banner to associate that patient with a particular trial.

CJ: Yeah I think that’s probably important, because you want whoever is utilizing the medical record to be alerted relatively soon as they access that patient record, that, “Oh there’s something unique about this patient. They’re on a trial of some sort.” And I guess at some institutions, like Anderson, that pops up a lot, because a lot of patients are involved in trials, right?

Mary: That is correct. About 30% of the patient population at Anderson was on a clinical trial during my tenure, and so you really want to make sure that everyone is informed that the patient’s on a trial, especially the clinical operations people who may be ordering testing procedures. You want to ensure that they understand, “Here’s what is already required for the study,” and so if you want to do, say, an EKG but you may already have an EKG for the study, so why order another one? Or the big thing that we had around that, CJ, and I don’t want to get into the weeds about this one, was really the ability to pull blood from a patient and actually do all those blood draws. And so you wanted to minimize the number of sticks you did to a patient, so really having folks understand that, “This patient was coming in for a lab anyway, why don’t we just leverage that lab time to do the other testing we’re looking at?” So that really helps to have more cohesive treatment plans for the treatment, and having everyone be on the same page as it relates to what is needed for that patient.

CJ: Yeah, that’s great insight. I’m kind of curious, you may or may not have insight here so feel free to say either way, but EHRs — there’s varied EHRs, right? And some EHRs are really good for a hospital setting versus long-term care or nursing home, and some may not cater to certain aspects of health care. Have you found that there’s a lot of good EHR options? Do most institutions create their own when it comes to clinical research, or do you find that there’s some good options out there to adopt maybe an off the shelf EHR? What are your thoughts in general?

Mary: I think for a hospital setting there are some really good EHRs out there that actually have a research module or the ability to recognize that this patient’s on a research study, and so those, especially in this day and age with the cutting-edge technology that’s out there. So a lot of the major electronic health records do have that research module, so that’s very helpful for health systems. When it comes to provider settings, I don’t have a lot of relevant experience. I have more anecdotal experience with it, and they do have those particular types of systems, and I am not quite sure how effective they are. I know they can track if this patient’s participating in a clinical trial, but I’m not sure about the effectiveness of that.

CJ: Gotcha. Just something for our listeners to be aware of, because as you’re looking at EHRs you may just want to have as many people involved in the initial process of designing what features you need, because if you work at an institution like Mary had, where a large percentage of patients are on research trials and you’re maybe looking at a new EHR, make sure you’re asking questions about all of these features to find out, “Hey, can you show us what you do for research?” if that’s a piece of your work portfolio. So Mary, maybe we can jump now to some of the challenges with clinical research billing that you might find in an EHR. Any thoughts on that?

Mary: Yes. So, of course communication and ensuring that everyone knows that this patient’s on a trial, so how does that happen? It doesn’t happen automatically. So that clinical trial’s management system, or that CTMS, that manages the study should be integrated with your electronic health record. And when I say integrated, it should be communicating with the electronic health record to provide study demographic information, such as the actual study number. So every study is given a number by your institutional review board, so you want to make sure that that number is coming over into the electronic health record from your CTMS. You want to know the name of the study, the PI, the department. What disease are we studying here? So that basic study demographics, and also the date that the IRB approved it, because you don’t want to be putting a patient on study that the IRB has not approved. So all that pertinent information is really key there. And then once that information’s done and the IRB has approved it, you want to ensure that you have your coverage analysis that has actually been converted to a billing grid within the electronic health record, because that billing grid is going to tell your electronic health record charge router where to route the charge. Is it something that is related to the study billable to my patient or my patient's insurance, or is it related to the study billable to my sponsor, and so I should put that in a side book and then send that over to the study sponsor as opposed to the patient or the patient's insurance? So those types of things is really helpful for the billing department to understand that differentiation. So that Medicare coverage analysis we talked about in our second series is really the foundation of that billing compliance aspect when it comes to the revenue cycle for a clinical research study.

CJ: So Mary, I’ve worked a lot in revenue cycle and billing compliance and those sorts of things and frequently get denials, and payers or auditors might want certain things from the medical record, and I’m just curious, in the prior podcast we talked a little bit about working denials maybe from a commercial payer or Medicare, and with the  electronic health record topic we’re talking about now, are there certain things to include when you’re trying to work through denials or payer requests? Like, is it appropriate to even include the protocol, or is that outside of the scope? What do you include? What don’t you include? Are there tips or things to be aware of?

Mary: It’s a very good question, because we did run into this challenge when we were working with denials for some of our clinical research participants, and so we consulted  of course with our compliance department when insurance was requesting a copy of, say, the study protocol. And so we determined as an organization that was way too much information, so we could give them — with the patient's consent, of course — the consent form, but we also thought that was probably a little bit more information as well. So we decided that the actual medical documentation was going to be sufficient to send to insurance, and so what we would do is we’d work with those providers to ensure that they were not wording the rationale for the order of the test or procedure to say that it was based on study requirements. We really wanted to focus on that medical necessity and why we were medically treating the patient with these testing procedures and what’s the medical benefit there. So trying to get them to refrain from saying, “Per study number X, we’re going to do this procedure.” No, we were doing this procedure to take care of the patient’s issue, whatever the case was that they presented with, and whatever disease that that patient had, so really focusing on that. To help them really focus on that, sometimes we would get for the ones that were really study requirements and we knew that the sponsor was covering that particular patient’s visit, we gave them actual templates, so that way it was standardized. It said, “This patient’s coming in for cycle one, day five of this particular study. Here’s what they had done.” And we would send that information of course over to the sponsor, because we knew the sponsor was covering that. But when we knew that that particular visitor was for medical necessity purposes, or was a routine care visit, we actually told them, “Just use your standard language as though the patient’s not on study and focus on that medical necessity of why you’re treating the patient with these particular tests or procedures.”

CJ: Makes sense. And you know, when you’re describing that, another thought came to my mind. So a lot of us are used to the regular claims development process and submitting claims to payers, but you just talked about submitting certain things that we already know are covered to a sponsor. How is that done? It’s not done with a claim form, right, like you would submit to CMS. Are you submitting an invoice on a monthly basis when the sponsor has to pay? Do they pay in chunks over the course of the trial, or do you have to get granular and say, “Mrs. Smith had her fourth CT scan, you need to pay us now”?

Mary: Yeah, so that’s a really good question as well, CJ, because when it comes to sponsor billing, there are two types of sponsor billing. There’s milestone pace billing, meaning that the organization, the health system and the sponsor have come to an agreement as to how they’re going to be paid, and so that particular milestone may be, “You’re going to get paid after every 10th patient is enrolled.” You may get actually paid after five treatment visits for this patient. So depending on what that requirement was in that contract that we talked about earlier during this podcast, that is how the crux of the milestone payments for the sponsor works. Or you could have the optional procedure invoice, where the study may have some optional biopsies or some optional CT scans that the sponsors will cover because they want more data from patients. And so in that case, that particular one-off or optional procedure, if the patient agreed to do it and it was performed, is a separate invoice that would need to be sent over to the sponsor so that you can get paid. It just really depends on what type of billing you’re doing for that. Typically, 95% of the time it’s going to be a milestone pace bill, where those charges that we know that the sponsor’s agreed to cover is going to move over to your general ledger and be housed in that general ledger until the actual milestone has been met. Once that milestone has been met, the payment is triggered from there.

CJ: Gotcha. Yeah this whole sponsor billing probably brings its whole own complexities and intricacies and workload that a lot of people might not think of. “Oh, the sponsor’s paying for it.” OK well, there’s a lot of work to get the sponsor to pay. You have to track things and you have to keep records and you have to provide them. They’re not just going to pay you when you call them on the phone.

Mary: Correct, because their ultimate goal is to gather data so that they can prove the safety and effectiveness of whatever they’re studying, and so, “Is it moving the field of science along?” is the other piece that the FDA’s question is. And so with all that, the sponsor is also requiring you to do forms, and so to your point, CJ, there is a lot of aspects that goes into getting paid from the sponsor. Not just the fact that you’ve treated the patient and you’ve met that milestone; there’s also some data gathering and data collection that has to be done in order for the sponsor to remit that payment.

CJ: Yeah, so interesting. Sorry, that was a little side track. I don’t want to get us too far off the EHR, because I want to get back to that a little bit and talk about how can organizations be innovative with studies that require inpatient visits and maintain compliance? Maybe you can just give us a little background on inpatient versus outpatient and that question.

Mary: Absolutely. So when we actually review the Medicare coverage analysis, what you should be doing is looking to see what the study requirements are, and as you read the study requirements you’re realizing, “Oh, I can do most of this in an ambulatory setting.” But because of the complexity of some of these new, novel compounds, especially when we’re talking about, say, CAR T cell infusions and really treating those blood-borne cancers in a very different way, those CAR T cell studies are requiring inpatient study stays, because they know that the treatment is so toxic to the patient, because what they’re really doing in effect is taking the patient almost to a — hollowing them out, so to speak, to a level where the patient cannot go home. They actually have to be monitored in a medical setting in order for them to really be safe, and so that’s that safety aspect of it. And so those, they're requiring a three to four inpatient stay, but we all know that sometimes these patients have adverse events. So they may have some unexpected consequences of their treatment, or just the progression of their disease could impact them in that particular time frame that they’re getting treated on that study, and so those complications is part of our issue, right, because the sponsor is saying, “OK, my study’s going to require two to three days of inpatient stay.” When that’s actually in the study requirements, 90% of the time you’re going to ask the sponsor to cover those inpatient stay requirements, because you probably won’t meet the medical necessity criteria for admitting that patient. And so since we realized that, we’re like, ‘OK, what do we do with these types of studies?” And so we actually began a process of looking at putting these patients in an observation status, because that’s really what you’re doing, is observing the patient to see, “Are they having adverse reactions? Can I complete this treatment within this observation window of two to three days and not have to admit them to a hospital setting?” So we actually piloted that particular process and implemented it right before I retired, and it really helped a lot of our inpatient studies, first of all move past the budgeting and negotiation process, because one of our biggest hangups was the sponsor did not want to be on the hook for the entire inpatient stay. What do I mean by that? Study requirements say two to three days, but the patient was so sick and became so sick in that setting, they were in the hospital for two to three weeks, and we all know we can’t split bill an inpatient stay, so between the sponsor and insurance it’s either one or the other. So we would tell the sponsor, “You’re going to have to be on the hook if the patient actually has complications,” and of course that would halt the negotiations. The sponsor didn’t want to be on the hook, so this was an innovative way of actually helping our negotiations with our sponsors go a lot smoother when it comes to inpatient stay requirements and really allowing the providers to evaluate that patient before they actually fully admitted them into the hospital. So really just giving that control back to the provider to assess the patient at the time, and if medical necessity was met at the time, then inpatient status would happen, but if not, if there wasn’t medical necessity, then we could still put them in an observation status and still treat them on that study.

CJ: Yeah, and you know, you bring up such an interesting point, because technology and science is advancing, and you mentioned the car T. For those that aren’t familiar, it’s capital C, capital A, capital R and then T for T cells. These are, as Mary mentioned, inpatient, and essentially what you’re doing is you’re taking patients’ T cells from their bodies. You’re inserting genes in the lab, and then — I’m simplifying here, science is much more complex — and then you grow more T cells with these inserted genes to do certain things, and then you put those cells back in. And as Mary said, your patient really can’t go home, they have to be inpatient. They have to be protected. And some of these inpatient stays, these are expensive. I mean we’re talking, it can get up to half a million dollars and that sort of thing in some of these cases. Is that the scenario you’re talking about, what I just described?

Mary: Yes, thank you for putting the science piece into it, and that’s exactly what happened. And so one of the cases that comes to mind I had to work on was a particular sponsor had a two- to three-day requirement for an inpatient stay of the CAR T cell drug, and the patient really was very, very sick. They wound up being in the hospital six weeks, and unfortunately this patient passed away because of the complication associated with their disease, not necessarily the complication from the actual infusion. It was more the disease progression for them, but the problem was that now the study sponsor was on the hook for six weeks. The sponsor was refusing to cover and really — that particular sponsor was going to have a breach of contract, and so we had to do some negotiations with them to not bill the patient that information, because at the same time the actual medical documentation spoke about the study drugs, so then if you’re trying to bill it out to the patient, is insurance going to really cover it? And so we didn’t really feel that that was fair to the sponsor to have to cover six weeks. That two- to three-day requirement was sufficient, and so we wound up writing off six weeks’ worth of inpatient stays for that particular patient, simply because we didn’t want to bill it out to the patient’s insurance and take the risk of the dental happening. So the institution decided just to write it off and especially since the patient was diseased and being mindful of that estate that would actually probably get the bills, since the patient was diseased was something that we also considered as well.

CJ: Yeah, and so that drives home this point a little bit more about — you can’t just say, “We’re going to follow the science and break down all these scientific barriers,” because you then get scenarios like this, and somebody gets left holding the bag. So to what we started this whole series with, we were just talking about being thoughtful in your financial preparations, and we commented that we’re not saying what a doctor can and can’t do, but when we’re talking that kind of money for one patient — if you’re not thoughtful in making sure these things are covered for the worse-case scenario, you could have scenarios like that, and that can affect things pretty quickly on what you can and can’t do in the future as an organization.

Mary: Correct. Or you take the risk, because I know some organizations have decided they were just going to take the risk and send it out to the door to the patient’s insurance, which again we decided we weren’t going to do, knowing that some of these treatments really weren’t meeting medical necessity requirements, because they may be first in human studies, so how do you justify the medical necessity if it’s the first time you’re actually infusing this particular drug into a patient?

CJ: Right. And from a societal standpoint, we want advances in medicine. Well the way you get advances in medicine is to do this kind of research, but no one wants to pay for it, so you get into these societal debates about who should be paying for the research, and you get financial interests from for-profit companies doing their best to develop a new drug or device, and they have their reasons for doing what they’re doing. It can become really an interesting intersection of all these different perspectives in the broader society of health care.

Mary: That is absolutely correct, and that’s — I felt like a traffic cop sometimes trying to direct the traffic with all those intersections happening and colliding at one time, so to speak. And so part of that aspect that you spoke about earlier, CJ, about really beginning that financial process and really being thoughtful and fiscally responsible all the way through is something that I would strongly recommend any organization who’s participating in clinical research billing.

CJ: Yeah, because it’s kind of a sexy idea to think, “Oh, we’re doing research, clinical trials,” and it sounds awesome, and it is awesome, but there’s a lot of stuff that might not be so sexy about it when it comes to bills and those sorts of things. But fortunately there are people like you that are teaching others about those important office procedures that need to be done and not just the headlines of, “We’re doing research and X, Y and Z,” which brings great acclaim to your institution and your reputation, so those are important things for sure. Mary, tell us a little bit about — we’re getting a little bit close to our time on this last podcast — I know you’re doing some boot camps to further your efforts to educate people. Tell us a little bit about those.

Mary: Yes, it’s a three-day boot camp sponsored through the University of Houston’s executive development department. It’s really a branch of their master’s degree programs, and it’s a certificate-bearing course, but these camps are designed to really focus on the financial management of clinical research. They’re virtual, and so that way we can get to the masses of individuals that really need this type of training, or you can be an individual who just really wants to have a career in clinical research finance and you don't know where to start. These boot camps are really helpful and designed for that particular purpose. They are going to be offered beginning in September of 2022. We have mapped out a time frame for each of these classes to occur at least once or twice a month over the next year.

CJ: That’s exciting.

Mary: Yeah, it’s going to — I’m really excited about the opportunity and looking forward to helping train individuals in the financial management realm.

CJ: Well excellent, Mary, this has been wonderful. Any last-minute thoughts? We’re wrapping up our third podcast episode and talked about — just to kind of summarize a little bit — clinical research billing, an overview. In the second podcast we talked about Medicare coverage analysis, and on this one we talked about electronic health records, inpatient considerations. Anything else that we didn’t cover? I know we could probably do a 20-part series if we wanted, but what other big topics or last-minute thoughts that you might have for this series?

Mary: So last-minute thoughts I would share with the audience is it’s not a one size fits all. Every study is different, so really dive into your study requirements, understand those study requirements and then begin to put them into financial management tools and translate them into financial management is really the key there. But really understanding your study requirements and not assuming simply because, “This is the same class of drugs. I can treat this study the exact same.” That’s not the case, because it could be a different disease you’re looking at, but it also could be different frequencies that you’re performing testing procedures, so you really want to hone in on those study requirements, and treat all studies are the same is one of the big recommendations I would provide to this audience. And then the other one is communication. I know I’ve said it at the end of podcast one and two, and I’m going to say it again: communication is so key here. Making sure that your PI, your principal investigator, and your study team, as well as the finance team that’s going to be working with you, the clinical ops team and the revenue cycle team understand that the patient’s on a clinical trial and understand the requirements that are there. So that communication is really key to make sure that you have a compliant billing program.

CJ: Yeah, and you’ve made that point in each podcast, as you just mentioned, and you can’t overemphasize it, because miscommunication leads to bad stuff happening, ruined relationships that you worked so hard to try to develop. You work for years to make the process smooth, and a few miscommunications can erode trust, and so you can’t overemphasize that, so I appreciate you making that point.

Mary: Agreed, and when you said “erode trust,” you have to also think about the patient’s trust in your organization as well as your investigative organization as well, so you want to make sure that you’re not only communicating effectively with these guys but the patient as well, because at the end of the day you can’t do clinical research without the patient, so you really want to make sure that that patient satisfaction remains high and that patient quality is also high.

CJ: That’s right, and it’s not always easy to recruit patients into studies. They’re dealing with a potentially life-threatening disease, and, “Now you want me to be a guinea pig in your trial?” That’s what they think. I know that’s not what it is, but a lay person hears research, “What do you mean you want to put me in a trial? I don’t want to be” — you know, so that trust for the patient is so important that you just said.

Mary: Yes, absolutely.

CJ: Well Mary, thank you so much for sharing your time and your expertise over the course of this three-podcast series. Look forward to your exciting work and your boot camps, and maybe we’ll find some opportunities to have you back at some point.

Mary: Thank you so much, CJ. I appreciate the opportunity to share a part of my knowledge with this audience and look forward to any other opportunities that may come.

CJ: Excellent. Thanks everybody for listening. This concludes our three-part series on clinical research and clinical research billing. Thanks everyone.

Mary: Thank you.

Questions or Comments?