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The resolution of many contractual issues requires coordination between the external funding source, Investigator, Clinical Trials Office, Compliance Office, Intellectual Property Partners (IPP), Office of Grants Management (OGM) and Office of Sponsored Programs (OSP); the involvement of each party is essential to a successful contractual arrangement with mutually acceptable terms.

 Who are the parties to a Clinical Trial Agreement?

All Clinical Trial Agreements should be only between The Research Foundation for The State University of New York and the Sponsor. The Investigator is an employee of Stony Brook University and is never a named party to any Clinical Trial Agreements.

What documents are needed in order to negotiate and execute a Clinical Trial Agreement?

Investigators should provide OSP with a copy of the proposed agreement, if they receive it directly from the sponsor, myResearch application, copy of the Protocol, approved Budget and a company contact person as early in the process as possible. IRB approval is required in order for OSP to execute a Clinical Trial Agreement. To expedite the process even before submitting a COP or protocol, please have the company contact send the agreement electronically to

What involves the negotiation of a Clinical Trial Agreement (CTA)?

SBU faculty and staff participate in numerous clinical trial projects to study investigational drugs or devices. These studies are usually funded by pharmaceutical companies and are an important part of the process to assure the safety and efficacy of the drug or device, obtain Food and Drug Administration (FDA) approval and bring a product to market.

Although each document is reviewed on a case-by-case basis, there are a number of key issues that are common to most clinical trial agreements. These following key items will be negotiated by the OSP with the Sponsor:


The sponsoring company, and the actual owner of the study drug or device if an intermediary is involved, must agree to indemnify and hold harmless the Foundation, Investigator, officers, agents and employees from any and all liabilities, claims, actions or suits for personal injury or death arising from the administration of the study drug or procedures done according to the protocol, including but not limited to the use of the study results by the sponsoring company. The Foundation will only indemnify the sponsor for negligent activities.


It is often necessary for the sponsoring company to provide information of a proprietary nature to the Investigator or his/her staff and it is important to the company's business interests that the confidentiality of this information be protected. It is encouraged that a Non-Disclosure Agreement gets in place prior to executing a CTA. Written confidential information should be stamped as such and oral communication should be reduced to writing and stamped "confidential". Access to confidential information (including the protocol) must be strictly controlled and each Investigator should have a plan for assuring control. All agreements must have a time limit for information to be kept confidential by the Foundation. Our standard language is only to allow information received from the sponsor to be kept confidential for a period of three (3) years after the termination of an Agreement.


Agreements must allow the Investigator the freely to publish results of the study. However, the sponsoring company may have the right of prior review to identify proprietary or confidential information. Approval rights on publications are not granted to sponsors.


Investigator-Initiated Clinical Trials:  Since the protocol is conceived and designed by the SBU investigator, the investigator is likely to be identified as an inventor.  The Foundation retains ownership rights to inventions that result from the study. The company is offered a time-limited first right to negotiate for an exclusive, worldwide, royalty-bearing license to any invention that results from the study.

Industry-Initiated Clinical Trials: Since the study design (protocol) is conceived and designed, or owned by the company, the company retains rights to all inventions developed in the direct performance of the protocol. The Foundation retains the right to use the invention for internal research and educational purposes. The drug or device being tested in the clinical trial is normally owned by the sponsoring company and already covered by patent protection.


Investigator-Initiated Clinical Trials: The University retains ownership rights to data developed under a Clinical Trial conducted using University resources.  The company funding the Clinical Trial may receive copies of de-identified data, case report forms (if applicable), and a report of the results of the study.

Industry-Initiated Clinical Trials: The University retains ownership rights to source data developed under a Clinical Trial conducted using University resources. The company may have access to data and information developed under the study, and receive copies of de-identified data. The company owns the compilation of data in the case report forms.


To support the indemnification the sponsoring company must maintain a sufficient level of insurance. The Foundation has and will maintain in force during the term of its agreements with third parties adequate insurance to cover its indemnification obligations.


Agreements must either be governed by the laws of the State of New York or this provision must be absent from the agreement.


Investigator-Initiated Clinical Trials: The University is responsible for providing medical treatment to patients who are injured as a direct result of participation in an Investigator-Initiated Clinical Trial.

Industry-Initiated Clinical Trials: The company is responsible for covering the costs of medical treatment for patients who are injured as a direct result of participation in an Industry-Initiated Clinical Trial.

What are Clinical Trial Master Agreements and does the Foundation have any such agreements in place?

Master Agreements are agreements that embody agreed-upon terms and conditions of a basic relationship between RFSUNY and a sponsor. Once a Master Agreement is in place, an "addendum" , “task order” or "study letter" is generated for each new study to be conducted under the Master Agreement. The Addendum sets forth the items particular to a certain study such as dollar amount, protocol name, and principal investigator. These Addenda are "attached" to each Master Agreement. This alleviates the need to "reinvent" in an agreement for each study with that sponsor; the major terms are agreed upon and only the particulars need to be negotiated.

When dealing with the following sponsors, please inform them to use our Master Agreement

Budgets and Funding Helpful Info

Company sponsored clinical studies are usually funded on a per-patient basis with provisions for pro-rated payment for patients who do not complete the study. All costs necessary to conduct the study, including salaries, supplies and indirect costs, should be considered when determining the fixed per-patient amount. Sponsors usually use one of two options when presenting a budget. They may offer a certain amount per patient and ask that you work within that amount or they may ask you to formulate a budget for them. Regardless, it is the principal investigators responsibility to ensure that the amount agreed upon will adequately cover all costs associated with conducting a clinical trial. Negotiation of budget terms for Industry-Initiated Clinical Trials is necessary and is being conducted by the Office of Clinical Trials (OCT). OSP will not review budgets for Industry-Initiated Clinical Trials when negotiating the agreement with the sponsor but will closely coordinate the negotiation and finalization of such budgets with OCT. If requested, OSP will evaluate your budget for Investigator-Initiated Clinical Trials for compliance with indirect cost calculation and advice to ensure your budget meets your needs.

The Office of Clinical Trials can also help you with all budgets; see their web-site at

Indirect Cost

Indirect cost for human clinical studies generally applicable to both Industry-Initiated and Investigator Initiated Clinical Trials as defined above is 25%. To estimate indirect cost when the direct costs are known, add 25% of the direct costs. The sum of these two figures is the per-patient amount.

Example: If $1,000 is needed to cover direct costs, 25% or $250 should be added for indirect, bringing the total to $1,250 per patient.

All clinical trials funded directly of indirectly by the federal government will be charged the Research and Development Rate in effect.

Office of Clinical Trials (OCT) Fee

An additional fee of $1,000 is charged by OCT for all industry initiated and sponsored clinical trial agreements.  The OCT fee should always be added in your budget as a direct cost line item and not as indirect cost.


SBU investigators wishing to conduct industry-funded, industry-initiated biomedical research studies may choose between the IRB services provided locally by SBU's IRB  or those provided by our associate, Advarra.

For industry funded, industry initiated studies, Sponsors must pay:

a.                  if the IRB services of Advarra are used, an institutional fee, in the amount of $1,000.00, This fee is in support of SBU’s continuing responsibility for all administrative and regulatory compliance. This fee is separate from any IRB fee directly charged to the sponsor by Advarra.

b.                  if local IRB of SBU are used, a combined IRB/Institutional fee of $3,000.00 for full committee review, OR $950.00 for expedited review, This is a one-time fee which covers service for a time period consisting of initial approval and four (4) continuing review periods. Should the protocol last longer than five (5) years, a 5 year application will be completed for renewal. The then current IRB/Institutional fee will be charged unless a) the human subject aspects of the study are limited to data analysis OR b) enrollment has ended, subjects have completed all research-related intervention, AND the study is now limited to long-term follow-up of subjects.

The sponsor understands that payment of the above applicable fee is not contingent on whether the protocol is approved or whether the protocol is funded. No F&A (indirect) cost will be assessed against this fee.

ALL investigator-initiated studies MUST be reviewed by SBU's IRB and are NOT ELIGIBLE for review by Advarra.

If you wish to use Advarra's IRB Service, you first need to confirm with your sponsor that the sponsor will accept direct invoicing from Advarra and allow direct payments to Advarra.  Once you have confirmed (preferably in writing) that this billing method is acceptable to your sponsor, see the Guides for submission at:

 W-9, IRS Identification and Payment Information FAQ’s

What is our Tax ID#?

The Tax ID # for our Institution is 14-1368361.

Who prepares W-9 forms?

OSP prepares all W-9 forms requested by sponsors. This form requires official institutional signature. A copy can be found under Codes and Numbers page. 

To whose attention should check be made and mailed?

Checks from the sponsoring company should be made payable to The Research Foundation of SUNY and mailed to The Research Foundation of State University of New York

P.O. Box 9

35 State Street

Albany, New York, 12201-0009

For electronic payments:

Key Bank of New York

        66 South Pearl Street

        Albany, New York 12207-1501

        ABA # 0213-00077

        Account # 10970107


Non-profitTax Status


What documentation is needed for a Clinical Trial Project/Award Set-Up?

To obtain a Foundation project/task/award number for a clinical study the following documentation is required: a completed myResearch application, a copy of the study protocol, approved budget, a signed written agreement between the sponsoring company and the Research Foundation for The SUNY, Institutional Review Board (IRB) approval.


What happens at Clinical Trial Project/Award Close-Out?

At the conclusion of any clinical trial study there may be a cash balance remaining. If expenditures incurred to conduct the study are reasonable in relation to the projected cost and when all costs (direct and indirect) have been properly charged and documented, the cash balance will be made available to the Investigator but will be under the ownership of the department by a transfer to the departmental fixed price balance award.


What is needed in the case of a Clinical Trial Amendment?

An amendment changes the terms of a previously executed agreement. If the amendment increases the dollar amount of the contract, you will need to complete a new myResearch Grants proposal. If the amendment deals with other non-monetary issues such as extending the timeline of the study, a myResearch Grants application is not required. Simply fax, email, or send a hard copy of the amendment to for OSP review and processing. Terms of amendments may need to be modified or otherwise negotiated with sponsors to assure they are correct and acceptable to the Foundation.


Helpful Links

Office of Clinical Trials

Office of Research Compliance


Clinical provides regularly updated information about federally and privately supported clinical research in human volunteers. gives you information about a trial's purpose, who may participate, locations, and phone numbers for more details.

Intellectual Property Partners

Faculty interested in exchanging confidential information with outside institutions or industry


Does the Foundation have a Clinical Study Agreement template?

See Standard Agreements Templates for information or access the templates through myResearch Agreements/Help Center.

Our institution follows agreement templates under the Accelerated Research Agreements Initiative (ACTA) that that acceptable to participating institutions and organizations. When used, it has been proven to expedite the study initiation process.

What is the definition of a Clinical Trial?

 A controlled, clinical testing in human subjects of investigational new drugs, devices, treatments, or diagnostics, or comparisons of approved drugs, devices, treatments, or diagnostics, to assess their safety, efficacy, benefits, costs, adverse reactions, and/or outcomes.  Such studies may be conducted under an industry-developed protocol or an investigator-developed protocol.  

1.      The objective of the study is either:

        a. testing of a drug, device, diagnostic, treatment, intervention, or preventive measures  including testing for an unapproved indication or

b. data collection, or review of data generated or acquired in a clinical setting, to increase knowledge that would lead to enhanced safety and efficacy of a drug or device.

  2.   The study must involve contact with human subjects or the review of patient care clinical data

  3.   The study must be performed primarily in patient care or clinical space Financial support for a clinical trial must be provided by a private entity, including pharmaceutical companies, interest groups, or charities.   In all cases, the study must include the prospective enrollment of human subjects and the controlled testing of a drug, device, or diagnostic under an approved protocol.   However, retrospective chart reviews, analysis of existing medical data and records, laboratory research, animal studies, and federally funded projects are not categorized as clinical trials for purposes of applying the approved clinical trial indirect cost rate.


        1.1 Clinical Trial Phases I - IV Definitions

An Investigational New Drug (IND) may be submitted for one or more phases of an investigation.   The clinical investigation of a previously untested drug, antibiotic drug or biological drug that is used in a clinical investigation is divided into phases that are generally conducted sequentially, but may also overlap (31CFR Part 312, FDA Regulations, Investigational Drugs 312.22, Definitions):

 ·         Phase I - Are typically closely monitored studies of 20 to 80 subjects that are designed to determine the metabolism and pharmacologic actions of the drug in humans, including side effects associated with dose increases,   and if possible, obtain early evidence of effectiveness. During Phase I, sufficient information should be obtained to permit the design of well-controlled, scientifically valid, Phase II studies.   

·         Phase II - Are typically well controlled, closely monitored clinical studies of not more than several hundred subjects that are conducted to evaluate the effectiveness of the drug for a particular indication or indications, and to determine the common short-term side effects and risks associated with the drug.

·         Phase III - Are expanded controlled and uncontrolled trials of several hundred to several thousand subjects conducted to gather additional efficacy and safety information needed to evaluate the overall benefit-risk relationship and to provide adequate basis for physician labeling of the drug.

·         Phase IV - Post-marketing studies to delineate additional information including the drug's risks, benefits, and optimal use.      

How does the Foundation determine if a Clinical Trial is Industry-Initiated or Investigator-Initiated?

 The study is an Industry-Initiated Clinical Trial if:

  • The protocol is conceived and designed:

    1. Solely by an employee of the company funding the study, or

    2. By a researcher from another institution, or

    3. By a SBU researcher under a private consulting agreement without the use of University resources.

  • The study must be funded by a for-profit entity.

The study is Investigator-Initiated Clinical Trial if:

  • The protocol is conceived and designed by a SBU researcher using University facilities, or

  • By a SBU researcher in the scope of their employment jointly with an employee of another entity (e.g. an employee of another non-profit institution or an employee of the for-profit entity funding the clinical trial), and

  • The study is funded by a for-profit entity, foundation, charity or other non-profit organization. 


What is the typical language for Subject Injury in an sponsor-initiated Informed Consent Form that is acceptable to our institution?

If you become ill , have an adverse reaction or become hurt or injured as a direct result of this optional research study that you are part of, get the medical care that you need right away, and please contact the study doctor  right away at the telephone number listed on the first page of this form. The services of SUNY-Stony Brook University Hospital will be open to you in case of such injury, adverse reaction or illness.
If you suffer any research study-related illness, adverse reaction or injury as a result of taking part in the study, including from the study drug or procedures required and performed in accordance with the study protocol, your medical expenses for the medically necessary diagnosis and treatment of such injury, including hospitalization, will be provided at no cost to you by the sponsor of the study.
No other compensation will be offered by Stony Brook University or sponsor for injuries related to this study.
To pay these medical expenses, the sponsor will need to know some information about you like your name, date of birth, and social security number or Medicare Health Insurance Claim Number. This is because the sponsor has to check to see if you receive Medicare and if you do, report the payment it makes to Medicare.
In no way does signing this consent form waive your legal rights nor does it relieve the investigators, Sponsor or involved institutions from their legal and professional responsibilities.


What should be the corresponding Subject Injury language in a sponsor-initiated CTA?

If a Study subject suffers an adverse reaction, illness, or injury which, in the reasonable judgment of Institution, was directly caused by a Study Drug or Study Device or any properly performed procedures required by the Protocol, Sponsor shall reimburse for the reasonable and necessary costs of diagnosis and treatment of any Study subject injury, including hospitalization, but only to the extent such expenses are not attributable to (i) Institution's negligence or willful misconduct or (ii) the natural progression of an underlying or pre-existing condition or events, unless exacerbated by participating in the Study.

 Who in the Office of Sponsored Programs (OSP) administers CTA’s on behalf of the Foundation?

A list of Contracts and Clinical Trials Administrators can be accessed here.