Clinical Trial Process Map & Step-by-Step Guide

Clinical Trial Process Map

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Step-by-Step Guide

The steps below will guide you through the clinical trial process. The buttons are actionable, providing you with forms, or quick links for each step. If you have additional questions, please contact our OCR team at


To protect confidential information exchanged between Indiana University or Indiana University Health and third parties, the execution of a Confidential Disclosure Agreement (CDA) is required.

To request the negotiation and signature of a Confidential Disclosure Agreement (CDA) for a clinical trial, please click the Request CDA button and complete the form.

You will be notified when your request is complete.


New studies are initiated by completing the Protocol Submission Form, which should be filled out and submitted as soon as a final protocol is available. The submission form collects the needed information and documents from the study team for entering a new protocol into OnCore (IU’s centralized clinical research management system). This form also initiates the Coverage Analysis Review process. The study initiation can happen simultaneously with IRB submission and contract negotiation, with each process informing the others. Submission of this form also lets the OCR know of other system needs like Participant Payment or eReg.

The same Protocol Submission Form is also used for submitting study amendments. Amendment information should be provided as soon as an amended protocol is available. Only amendments that might affect your OnCore Calendar or Coverage Analysis should be submitted. The goal is to have any necessary changes ready to go before the amendment is approved by the IRB.

Centralized Coverage Analysis is mandated across the institute to ensure compliance with federal regulations and goes hand-in-hand with OnCore’s protocol entry; therefore, entering accurate information is critical to ensuring that a study complies with university policies and federal requirements. IU is cultivating OnCore as a “source of truth” for information about clinical research occurring at IU and IU Health. The Coverage Analysis Team (CAT) uses information collected in this form to

    • develop the OnCore protocol entry,
    • communicate with the study team throughout the Coverage Analysis Review, and
    • identify ancillary services involved in the study.

More information about Coverage Analysis can be found here.

What happens after the initial Protocol Submission Form is submitted?
  • The Study Record is created. The submission is routed to the Calendar Analysts who use the information in the first section of the form to create a study record in OnCore. This record, also referred to as the “OnCore Shell,” may be used for effort tracking, pipeline review, and other initial study management tasks within OnCore.
  • The Study Calendar is created. If coverage analysis is necessary, the Calendar Analysts begin building a study calendar in OnCore.
  • The Billing Grid is used to document coverage analysis. Coverage analysis is completed within the Coverage Analysis Console, which may be found in the “Financial” drop down from the menu in OnCore. Inside the Coverage Analysis Console, the Billing Grid is used to provide the documentation of the Coverage Analysis. The Billing Grid includes a version of the study calendar that designates each procedure as being billed to the study “R,” or billed to the subject “S.” Additionally, the Billing Grid includes a comments section, this is where you will find justifications for the procedures designated to be billed to the patient/patient insurance. These justifications come from Medicare National and/or Local Coverage Determinations, National Guidelines (i.e. NCCN, American Heart Association), and Peer Reviewed Journals.
  • The Study Documents are aligned. Additionally, and of equal importance to the billing grid, is the piece of Coverage Analysis referred to as a Document Alignment. This procedure consists of reviewing the Protocol, Informed Consent, and funding documents (i.e. Sponsor or department Budget, Clinical Trial Agreement, or Grant Approval Document) to ensure consistency of Subject Injury Language and Subject Stipend/Reimbursement. The patient injury language needs to align with Medicare “Payer of Last Resort” rules. Specifically, these documents need to state that either the patient or patient’s insurance is responsible for the cost of the procedures if a patient is injured while on the study, or the Study or Study Sponsor is covering all of those costs. An example of unacceptable language is, “Sponsor will pay for any costs not covered by patient insurance, if injured while on this study.” This language indicates that the sponsor will pay copays and deductibles and this cannot be allowed.
  • The study information is reviewed. After receiving notice of completion of the coverage analysis, PIs, coordinators, and other members of the research unit are responsible for reviewing the Billing Grid and the communication from the Coverage Analysis team. If there are questions, comments or concerns on the part of the Research Unit, it should be discussed with the Coverage Analysis Team for clarification.

**Please note: The study initiation form begins the process of entering a new study into OnCore and also initiates the coverage analysis review; however, this form does not initiate an IRB submission.


All Clinical Trial Agreements for researchers at Indiana University and IU Health should be routed to the Office of Clinical Research. The Clinical Trial Agreement (CTA) is a legally binding contract that defines the scope of work required by the protocol and allocates the risks and responsibilities among the sponsor, site, and researcher. The contracts team at the Office Clinical Research works with investigators and sponsors to develop CTAs acceptable to the investigator and to Indiana University or IU Health.


Before conducting human subjects research, protocol review and approval by an Institutional Review Board (IRB) is required. The IU IRBs are the IRB of record for all IU campuses and medical center affiliates, including IU Health, Eskenazi, and Roudebush VA Hospital. The submission must be initiated by the investigator or his/her study staff. 

Kuali Protocols is an IU-hosted system protected by CAS authentication and can be accessed only by those with an IU computing account (username and passphrase). If you need an IU computing account for purposes of accessing Kuali Protocols, complete the IU Affiliate Account survey to request an account.

IU allows the use of external IRBs, including independent IRBs and other academic medical center IRBs, under certain circumstances. Permission to use an external IRB must be requested from the IU Human Subjects Office via Reliance Request in Kuali Protocols. Additional information about Reliance Requests can be found here.

For help with your IRB submission, please contact the Human Subjects Office.

IU Human Subjects Office
Phone: 317.274.8289


Before access to OnCore is granted, OnCore Protocol and Subject management training is required.
The button on the left will take you to a form where you can request Initial Training & OnCore Account Access. 


The blue button on the left links to a Word document outlining the steps you will need to take to access Cerner. This document also includes a link to the survey that begins the process.

Please note that proof of current IRB approval or exemption will be requested during this process, and non-IU Health employees will be required to complete educational modules on regulatory compliance to obtain access to IU Health systems.

For more information, please see IU Health Access.