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Billing Compliance: Step-by-Step


Initial OnCore Set Up
In order to ensure the consistency of information and ease of tracking and monitoring research study services, the Clinical Research Billing Policy stipulates that all new studies with billable services utilize Yale’s Clinical Trial Management System (OnCore). To setup a research study in OnCore and ensure the informational feed to Epic is accurate, the following OnCore set up steps must occur:
  1. The Principal Investigator must complete and submit an OnCore Study Start up Form.
  2. YCCI will input all information received from the PI and Study Team into OnCore and will create the PC Console shell.
Questions regarding the OnCore set up process can be addressed by the OnCore Support at or call 203.737.7039.

Questions regarding registering research studies in can be addressed by the Yale Team at

Questions regarding IND/IDEs can be addressed by Amy Hummel at or call (203) 737-7139.
Calendar Build
After the OnCore study start up form is submitted, YCCI’s OnCore team builds a calendar in OnCore. It is the responsibility of the PI and study team to ensure the OnCore team has all the necessary information to complete the OnCore Calendar. The information the PI must provide includes:
  • The protocol, sponsor informed consent form, sponsor proposed budget, and lab manual if available;
  • Clarifications regarding questions related to the protocol.
Once the OnCore Calendar Build is complete, the PI and study team is required to sign off indicating her/his approval.

Initial OnCore Calendar Builds and subsequent revisions to the Calendar e.g., due to a protocol amendment(s) can only be released after IRB approval.

Medicare Qualifying Trial Determination and Billing Risk Assessment
YCCI is responsible for:
  1. determining whether a study is deemed to be a Medicare Qualifying Trial (MQT); and
  2. assessing the billing risk associated with a designated MQT study. Note that studies deemed not to be a MQT will not have any procedures billed to insurance.
Before billing 'routine costs' associated with a clinical trial to Medicare or other insurance carriers, YCCI determines if the trial meets the CMS qualifying criteria. For information regarding qualifying/non- qualifying clinical trials under the Clinical Trial Policy (CTP) National Coverage Determination (NCD), please click here for more information. Once a research study is identified as a MQT, the Billing Compliance Quality Assurance Team completes a risk assessment determination as to whether a clinical trial is high, moderate, or low risk for research billing compliance purposes.
Conduct Coverage Analysis
Medicare Coverage Analysis (MCA)
MCA is an independent review of a research study to determine which clinical procedures and services are billable to the research subject, third-party payer or sponsored award. The MCA includes a review of the clinical trial documents, published practice guidelines, and Local Coverage Determinations (LCD) and National Coverage Determinations (NCD) to determine the billing status of items and services that are documented in the research protocol and/or research plan. Yale requires that all research studies involving the provision of billable clinical procedures and services must undergo a Medicare Coverage Analysis. Yale School of Medicine's Policy, Research Studies with Billable Clinical Services, dated April 1, 2019, is requiring The Yale Center for Clinical Investigation’s Central Medicare Coverage Analysis Unit to complete a coverage analysis on all qualifying trials. Furthermore, all finalized budgets will be reviewed and signed off by this unit to ensure that the MCA is accurately represented within the clinical trial budget.
Complete Billing Grid in OnCore
YCCI’s coverage analyst(s) will apply the billing determinations to the OnCore Coverage Analysis console which will auto-populate onto the OnCore study calendar/billing grid to accurately represent the billing designations into the OnCore Financial Console. The final billing grid can be utilized as the study budget template once exported into Excel format.
Develop Budget
YCCI’s Research Budget team develops and negotiates budgets for industry sponsored and investigator initiated studies. The budget team uses the OnCore Calendar and the coverage analysis determinations to build a budget, ensuring that Yale recovers all the anticipated costs of a study. Further, any Yale clinical research budget must utilize the YM and YNHH clinical research fee schedules and are expected to have a fully executed budget that will cover the costs of services rendered for research purposes only.

Questions regarding the budget process and/or research fee schedules can be directed to Pat Fontaine, YCCI Manager of Budget Development & Negotiations: or 203-785-3660.

To request the development and negotiation of a budget, please complete a Yale Center for Clinical Investigation Intake Form.
Release OnCore Calendar and Send to Epic
After all approvals are received, the OnCore Calendar is released and is electronically sent to Epic, via the RPE interface, and serves as the study billing grid.

Note: you must be on the Yale University or Yale-New Haven Hospital network to view the document below. If you are off-site, please connect through the VPN.

Related documents:
Subject Management

PIs and their study staff are responsible for managing the study subjects in OnCore, which includes registering subjects, checking in visits, adding any additional visits and managing the subjects’ statuses.

To ensure proper billing compliance:

  • In order to ensure the consistency of information and ease of tracking and monitoring research study services, the Clinical Research Billing Policy stipulates that all new studies with billable services utilize Yale’s Clinical Trial Management System (OnCore).
  • Subjects must be Consented in OnCore on the day of signing consent, close of business day.
  • Subsequent visits must be occurred in OnCore within 24 hours after visit completion.

Note: you must be on the Yale University or Yale-New Haven Hospital network to view the documents below. If you are off-site, please connect through the VPN.

The following documents are available to assist in the proper management of subject information:

Centralized Research Charge Review
All charges incurred for subjects who are enrolled in a study are reviewed by the charge matching teams for Hospital Billing (HB) or Professional Billing (PB) before bills/invoices are sent to either the sponsor, patient, or the appropriate insurer/third-party payor.

Questions regarding HB billing can be directed to Amanda Mincey at

Questions regarding PB billing can be directed to Linda O'Connor at

If a study participant has a question(s) related to a bill that s/he has received, please advise the participant to contact YCCI’s research billing team 1-877-TRIALS0 (1-877-874-2560)
Sponsor Invoicing and Interdepartmental Invoicing

YCCI’s Financial Management team is responsible for invoicing clinical study sponsors on behalf of most clinical departments in accordance with the study fully executed contract. YCCI also provides interdepartmental invoicing services to ensure that departments are reimbursed for research services they have provided in support of another department’s clinical trial.

For information on centralized sponsor invoicing and/or intradepartmental invoicing, please contact Juliann Murphy at

Research Billing Compliance QA
The Research Billing Compliance team is responsible for conducting:
  1. An initial protocol billing compliance assessment; and
  2. A proactive risk-based bill review of randomly selected Medicare Qualifying Trials.
The protocol for conducting a research billing compliance assessment is based on specific clinical trial criteria, scored, and evaluated for one of three levels of risk: high, moderate, and low.

Based on the billing compliance risk determination, studies are randomly selected, and a predetermined number of subjects are reviewed both initially and as part of an ongoing maintenance review plan. The purpose of these reviews is to ensure proper billing early in the study thereby avoiding any negative downstream effects.

For questions, please contact Nancy Shelton at
    Research Billing Compliance QA Training

    In order to comply with federal, state and institutional regulations and standards for clinical trial billing, the Yale Center for Clinical Investigation (YCCI) is responsible for establishing effective processes to ensure that all services for a study are billed properly. The purpose of this training is to inform both faculty and staff about the complexities surrounding clinical trial billing and to ensure that billing of these trials are appropriately directed to either the research sponsor or the designated insurer/third-party payer. This course is offered in two formats to better serve you. Please click on the course title below to register for the instructor led course or complete the online requirement.

    Completion of either the Online Module or Instructor-Led Course will satisfy the requirement for Research Billing Compliance (2019).