Confidentiality Agreements, Clinical Trial Agreements and Budgets

1. Purpose

This SOP describes how [SITE NAME] reviews, negotiates, approves and signs confidentiality agreements (CDAs) and clinical trial agreements (CTAs), builds and negotiates study budgets, and invoices and reconciles study payments. ICH E6(R3) expects the financial aspects of the trial and the arrangements between parties to be documented in agreements, and lists them among the essential records that should be in place before the trial starts.

2. Scope

This SOP applies to all CDAs, CTAs (including master agreements, work orders and amendments), budgets and payment terms for clinical studies at [SITE NAME], whether the counterparty is a sponsor, a CRO acting for a sponsor, or a sponsor-investigator. It covers agreements with the site's own service providers only where they are study-specific; general vendor oversight is in SOP-105.

Out of scope: the Medicare coverage analysis, which must be finished before the budget is final (SOP-202); participant payment processing (SOP-310). This SOP describes operating steps. It is not legal advice; [SITE NAME] confirms legal and contracting positions with [LEGAL COUNSEL]. Terms flagged in step 5.3.4 go to [LEGAL COUNSEL] when the Site Director decides legal review is needed. Where a sponsor, CRO or IRB requirement is stricter than this SOP, the site follows the stricter requirement.

3. Responsibilities

4. Definitions

5. Procedure

5.1 Logging and tracking

5.2 Confidentiality agreements

• the parties are correct ([SITE LEGAL NAME], not an individual staff member, unless the sponsor requires the PI to sign as well)
• disclosure is permitted to IRBs, regulators and staff who need to know, and as required by law

5.3 Clinical trial agreement review

• Parties and roles. Correct legal entity, investigator named, CRO acting as agent identified, payment entity identified.
• Scope and protocol. Protocol identified by number and version; amendments handled by written amendment.
• Indemnification and insurance. Terms reviewed against [CONTRACT PLAYBOOK]; the sponsor's insurance certificate is received; the site's insurance obligations match what the site carries.
• Subject injury. The language matches the consent form (5.3.6). Under the Medicare Secondary Payer rules, a sponsor that agrees to pay for injury care is a primary payer for that care, so the site bills the sponsor, not Medicare, for it (SOP-202).
• Confidentiality. Carve-outs for IRB, regulators, participant consent and law.
• Publication and intellectual property. Terms reviewed against [CONTRACT PLAYBOOK]. Results posting on ClinicalTrials.gov is the sponsor's obligation.
• Data protection and HIPAA. The sponsor receives participant data under the HIPAA authorization in the consent form (45 CFR 164.508). Coded data only; no direct identifiers unless the authorization allows it. Any state privacy law terms are noted on F-201-01. Whether a Business Associate Agreement is appropriate is decided under SOP-400.
• Monitoring, audit and inspection access. The site permits monitoring, audits and regulatory inspection with direct access to source records; the notice period for an FDA inspection matches SOP-702.
• Record retention. The retention period meets 21 CFR 312.62(c) or 812.140(d) and any longer sponsor period, the CTA states who pays for storage and for how long, and the sponsor must notify the site when records may be destroyed (SOP-402).
• Payment terms, holdback and termination. Stated in the CTA and recorded in [ACCOUNTING SYSTEM] under 5.7.3; positions are in [CONTRACT PLAYBOOK].
• Participant care after termination. The site may give participants appropriate follow-up care for their safety.
• Safety reporting. The site's safety reporting duties match the protocol and the reviewing IRB's reporting policy. The CTA states who submits IND safety reports to the IRB: the sponsor on the investigator's behalf, with written confirmation to the site of each submission, or the site. 21 CFR 312.66 requires the investigator to report unanticipated problems to the IRB; FDA's December 2025 investigator safety reporting guidance (Investigator Responsibilities: Safety Reporting for Investigational Drugs and Devices, section VI) states FDA considers IND safety reports to be unanticipated problems (SOP-501 Serious Adverse Event and Expedited Safety Reporting, 5.10.4; SOP-502).
• Financial disclosure. The investigator and Sub-Is provide financial disclosure information (21 CFR 54) and update it during the study and for one year after completion.
• Debarment. Each party represents it is not debarred; the site screens staff and providers under SOP-704 Research Misconduct and Fraud Reporting.
• Governing law and dispute resolution. Acceptable to the Site Director.
• Anti-bribery and transparency. Standard compliance language; payments to investigators may be reported by the manufacturer under the federal Open Payments program.

5.4 Budget build

• the site cost (internal cost or vendor price) or the site's research rate
• staff time: CRC, PI or Sub-I, and other staff, in minutes, at the site's loaded hourly rates
• whether the item is paid by the sponsor or, if the site bills insurance, billed as routine care per the coverage analysis (SOP-202)

• start-up fee (feasibility, regulatory packet, CTA and budget negotiation, SIV preparation)
• IRB fees: initial, continuing review, amendments, closure, if the site pays them rather than the sponsor
• pharmacy or IP management: set-up fee, per-dispensing fee, IP destruction, temperature monitoring
• screen-fail fee per screen-failed participant
• re-consent fee per participant per new consent version
• unscheduled visit fee
• SAE reporting fee per SAE
• advertising and recruitment costs (per SOP-300, IRB-approved materials only)
• participant stipends and travel reimbursement (SOP-310), as pass-through
• monitoring visit and audit preparation fees beyond a stated number
• specimen processing and shipping, dry ice, courier
• protocol amendment fee (administrative work per amendment)
• record storage and archiving per year, and retrieval fees
• close-out fee
• equipment purchases or rental the protocol requires
• out-of-pocket items at cost plus overhead where the CTA allows

5.5 Amendments

5.6 Who may sign

5.7 Execution and filing

5.8 Invoicing, tracking and reconciliation

• completed visits in the site's visit log and EDC against payments received from the sponsor or payment vendor
• invoices issued against payments received
• holdback withheld against the CTA percentage
• participant payments disbursed (SOP-310) against pass-through reimbursements received

6. Related Forms and SOPs

• F-201-01 Contract and Budget Review Checklist
• F-205-01 Study Activation Checklist
• F-303-01 Screening and Enrollment Log
• F-501-01 SAE Reporting Tracker
• F-601-01 Study Closeout Checklist
• Appendix B Central and Site Responsibility Matrix (Model N only)
• SOP-103 Staff Qualification, Training and Training Records
• SOP-104 Conflict of Interest and Financial Disclosure
• SOP-105 Oversight of Service Providers and Vendors
• SOP-200 Study Feasibility and Selection
• SOP-202 Medicare Coverage Analysis and Research Billing Compliance
• SOP-204 Essential Documents and the Investigator Site File
• SOP-205 Site Qualification, Initiation and Study Activation
• SOP-301 Informed Consent Process and Documentation
• SOP-310 Participant Payments and Reimbursement
• SOP-400 Participant Privacy and HIPAA in Research
• SOP-402 Record Retention, Archiving and Destruction
• SOP-501 Serious Adverse Event and Expedited Safety Reporting
• SOP-502 Unanticipated Problems and Reportable New Information
• SOP-601 Study Closeout
• SOP-702 FDA Inspections and Remote Regulatory Assessments
• SOP-704 Research Misconduct and Fraud Reporting
• SOP-902 Network Study Feasibility, Allocation and Central Contracting (Model N only)

7. References