T-Cell_ Amendment 1 4_27 Final.pdf

Amendment #1 to BAA-NIAID-DAIT-75N93022R00023

LARGE-SCALE T CELL IMMUNE EPITOPE DISCOVERY AND MECHANISMS OF T CELL

PROTECTION

Amendment to Solicitation No.:

BAA-NIAID-DAIT-75N93022R00023

Amendment No.: 1

Issue Date: April 27, 2023

Effective Date:

Proposal Due Date:

April 27, 2023

July 19, 2023, until 3:00 pm EST (UNCHANGED)

Issued By: Anuj Patel Contracting Officer

NIH/NIAID

Office of Acquisitions 5601 Fishers Lane Room 3B66 MSC 9821 Rockville, MD 20852

Point of Contact: Anuj Patel, Contracting Officer Anuj.patel@nih.gov

Name and Address of Offeror: To All Potential Offerors

The above numbered solicitation is amended as set forth below. The hour and date specified for receipt of proposals has NOT changed. Offerors must acknowledge receipt of this amendment. Failure to receive your acknowledgement of this amendment may result in the rejection of your offer.

NOTE: As part of this Amendment, we request that all questions pertaining to the BAA be submitted to the Government no later than June 19, 2023, 3:00pm EST.

The purpose of this amendment is to update SECTION H of the solicitation document and to provide responses to questions which may be useful to all potential offerors.

SECTION 1- ADMINISTRATIVE

SECTION H - SPECIAL CONTRACT REQUIREMENTS, is hereby modified to include the following:

ARTICLE H.36. RESEARCH AND DEVELOPMENT DATA IN ELECTRONIC RESEARCH

ADMINISTRATION (eRA) COMMONS, is hereby added as follows:

The Contractor shall enter and/or update research and development data fields at the contract project level in Electronic Research Administration (eRA) Commons within fifteen (15) calendar days of being notified by the eRA Commons system. The notification will come in the form of an eRA Commons system-generated email, sent to the Contractor’s registered user(s) under the contract. The eRA Commons website may be accessed at: https://public.era.nih.gov/commonsplus/public/login.era?TARGET=https%3A%2F%2Fpublic.era.nih.gov %3A443%2Fcommonsplus. Please note that if your organization does not currently have an account in eRA Commons, you will first need to register your organization https://public.era.nih.gov/commonsplus/public/login.era?TARGET=https%3A%2F%2Fpublic.era.nih.gov%3A443%2Fcommonsplus https://public.era.nih.gov/commonsplus/public/login.era?TARGET=https%3A%2F%2Fpublic.era.nih.gov%3A443%2Fcommonsplus at https://public.era.nih.gov/commonsplus/public/registration/initRegistration.era. Once your organization is registered, your signing official is then able to create new Commons user accounts (such as for a Project Director/Principal Investigator). For information on how to create/manage accounts, using the Account Management System (AMS) in eRA Commons, please refer to: https://www.era.nih.gov/register-accounts/create-and-edit-an-account.htm. [Note: You must be logged into eRA Commons with appropriate role(s), in order to complete these activities.]

SECTION 2- QUESTIONS AND RESPONSES

This section of the amendment provides questions submitted by potential applicants/offerors and the responses provided by NIAID. The responses are offered for information only and do not modify or become part of this solicitation. This Amendment will be updated as needed to add further questions and their related responses. All potential offerors are advised to refer to the original solicitation document for additional clarification.

Question 1: Can you confirm the application due date?

Response to Question 1: The application due date is 3:00 PM ET local time on 07/19/2023. Please refer to SECTION A - SOLICITATION/CONTRACT FORM, item 8 on page 1 of the solicitation document.

Question 2: The anticipated budget is ~$850,000 per year for the proposal—is that within the limits allowed?

Response to Question 2: Please refer to Attachment 3 - BROAD AGENCY ANNOUNCEMENT DESCRIPTION, on Page 112 of the Solicitation document regarding funding. Budgets should meet the needs to accomplish the goals of the Offeror(s). All budgets are subject to negotiation.

Question 3: Our team has the ability to submit for identifying epitopes in either autoimmune/transplant or infectious disease settings. Is there a way to get feedback on priority areas?

Response to Question 3: Please refer to Attachment 5 - RESEARCH AND TECHNICAL OBJECTIVES, on page 117 of the Solicitation document. Projects within the NIAID mission as detailed in the BAA Attachment 5 are allowed. Applicants should be aware of the areas that the solicitation will not support, also found in Attachment 5. NIAID has not designated priority areas and leaves the section of the proposed area of research to the Offeror within the three categories described in Attachment 5.

Question 4: Is this a grant format and other requirements with page limit?

Response to Question 4: This is not a grant; it is a contract. Please refer to Attachment 1 - Packaging and Delivery of Proposals for Use with the NIH electronic Contract Proposal Submission (eCPS) Website, Section II- FORMATTING AND PAGE LIMITATIONS Formatting for proposals, Paragraph B – Page limitations on page 110 of the solicitation document for more information.

Question 5: What does NIAID have in mind for scope or source of epitopes - viruses, cancer, autoimmunity, transplantation, etc.? Is the scope undefined or does it include all the aforementioned epitopes?

Response to Question 5: The focus of each proposal must be in one of the three research areas listed below. Offerors can only submit one proposal per research area but may submit separate proposals to different research areas.

1. Infectious disease/vaccine responses, including pathogens with pandemic potential.

2. Autoimmune disease: this research area also could include the identification of pathogen specific epitopes that are implicated in induction of autoimmune disease.

https://public.era.nih.gov/commonsplus/public/registration/initRegistration.era https://www.era.nih.gov/register-accounts/create-and-edit-an-account.htm https://www.era.nih.gov/register-accounts/create-and-edit-an-account.htm

3. Transplantation of cells, tissues, or organs (alloantigens and autoantigens involved in transplantation rejection, tolerance, and/or graft versus host disease). – Please refer to ATTACHMENT 5: RESEARCH AND TECHNICAL OBJECTIVES, on page 117 of the solicitation document.

Question 6: Would NIAID consider linking to TCR sequence to epitopes a strength, or necessity?

Response to Question 6: Offerors shall propose a milestone driven research program that must include each of the following activities (1, 2, 3, and 4. Sections 5, and/or 6 can be added if the offeror opts to include: TCR Repertoire Analysis; Epitope Prediction Tools) – Please refer to ATTACHMENT 5:

RESEARCH AND TECHNICAL OBJECTIVES, on page 117 of the solicitation document.

Question 7: How does NIAID envision involving NIH staff?

Response to Question 7: The contractor will work with the following NIH Staff: Please refer to SECTION G - CONTRACT ADMINISTRATION DATA, on page 14 of the solicitation document.

Contracting Officer’s Representative (COR) Contracting Specialist/Officer (CS/CO) The COR will be designated after contract award (see section G - Contract Administration Data). Duties of the COR, CS, and CO are outlined in the BAA.

Question 8: What is the scope of the budget for this solicitation? We have established collaborations with 5 PIs at separate institutions who have substantial expertise in Immunology, Transplantation, T cell epitope discovery, TCR/MHC peptide structure. With this level of involvement, I am envisioning a budget of millions of dollars per year – knowing what the budget limitations are would help planning the scope of the work.

Response to Question 8: NIAID estimates that the average annual total cost (direct and indirect costs combined) is 1.25 million dollars per award. However, it is anticipated that the total cost for the award(s) may vary depending upon the scope of the project and the technical objectives of the award(s). – Please refer to ATTACHMENT 3: BROAD AGENCY ANNOUNCEMENT DESCRIPTION, on page 112 of the solicitation document.

Question 9: As this appears to be a contract rather than a grant, how does the contract work? Are there milestone/timeline reviews?

Response to Question 9: Please refer to SECTION M - EVALUATION FACTORS FOR AWARD on page 101, ATTACHMENT 6: REPORTING REQUIREMENTS AND DELIVERABLES- REPORTING REQUIREMENTS AND DELIVERABLES, on page 121 and Attachment 10 - eRDS Vendor Quick Reference Guide- eRDS Vendor Guide on page 137 of the solicitation document.

Question 10: Do we need to have an industry partner?

Response to Question 10: Inclusion of an industry partner is permitted but not required. Please refer to

ATTACHMENT 7: ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS FORMAT FOR

TECHNICAL PROPOSAL, and TABLE OF CONTENTS, SECTION 5 - SCIENTIFIC AND TECHNICAL PERSONNEL, on page 130 of the solicitation document.

Question 11: Do we need to incorporate artificial intelligence approaches to epitope discovery (i.e., sequence to specificity)?

Response to Question 11: Inclusion of artificial intelligence approaches is allowed, but not required.

Please refer to ATTACHMENT 7: ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS FORMAT FOR TECHNICAL PROPOSAL, and TABLE OF CONTENTS, SECTION 4 - TECHNICAL DISCUSSIONS, on page 127 of the solicitation document.

Question 12: Do we need to involve/work with people from the IEDB as part of the application? If so, who do we contact?

Response to Question 12: No, individuals from the IEDB do not need to be involved in the application.

Question 13: Is a foreign component is allowed?

Response to Question 13: Applications from Domestic and Foreign Institutions are allowed. Inclusion of Foreign Components are allowed.

Question 14: Does NIAID have a sense of how competitive/likelihood of funding? The announcement includes the number of contracts awarded in previous years but not how many applications there were.

Response to Question 14: The selection of proposals for award is based upon the evaluation factors, importance to the agency programs (programmatic balance), and fund availability. We cannot anticipate the number of proposals that will be submitted or ultimately awarded.

Question 15: Are there any websites that walk applicants through the basics of contracts?

Response to Question 15: Additional information concerning contracts can be found on websites below:

https://grants.nih.gov/funding/contracts.htm https://oamp.od.nih.gov/content/technical-proposal-instructions

Question 16: Would a proposed approach with V/J gene usage be appropriate for this grant solicitation?

Response to Question 16: This is not a grant solicitation; this is a contract solicitation.

Offerors shall propose a milestone driven research program that must include each of the following activities (1, 2, 3, and 4. Sections 5, and/or 6 can be added if the offeror opts to include: TCR Repertoire Analysis; Epitope Prediction Tools):

1) Epitope Identification (Required)

2) Epitope Validation (Required)

3) T Cell Mechanisms of Protection or Pathogenesis (Required)

4) Epitope Submission (Required)

5) TCR Repertoire Analysis (If applicable)

6) Epitope Prediction Tools (If applicable)

See ATTACHMENT 5: RESEARCH AND TECHNICAL OBJECTIVES

Question 17: The SOW section has a suggested maximum of 10 pages noted. However, within the SOW is the Scientific and Technical Approach has a suggested maximum of 30 pages. Please clarify.

Response to Question 17: The Statement of Work and the Technical Discussion are two different sections of the technical proposal.

The Statement of Work will cover:

What work will be done on the contract (A. SCIENTIFIC AND TECHNICAL APPROACH) Who will perform the work (B. SCIENTIFIC AND TECHNICAL PERSONNEL https://grants.nih.gov/funding/contracts.htm https://oamp.od.nih.gov/content/technical-proposal-instructions

Who will manage the project performance (C. PROJECT MANAGEMENT) Where the project will be performed (D. FACILITIES, EQUIPMENT AND OTHER RESOURCES) What are additional considerations for this project and what post-award activities will be included in what the offeror proposes to do on this contract. (E and F. OTHER CONSIDERATIONS and POST-AWARD ACTIVITIES)

The Section 4 TECHNICAL DISCUSSION and Scientific and Technical Approach tells us in detail how the offeror will perform the work proposed in the Statement of Work for the Scientific and Technical Approach required components (1, 2, 3, and 4). If TCR repertoire analysis (5) and/or Epitope Prediction Tools (6) are proposed, then detailed descriptions of those tasks are also described in this section.

A. SCIENTIFIC AND TECHNICAL APPROACH

1. EPITOPE IDENTIFICATION

2. EPITOPE VALIDATION

3. T CELL MECHANISMS OF PROTECTION OR PATHOGENESIS

4. EPITOPE SUBMISSION

5. TCR REPERTOIRE ANALYSIS, if applicable

6. EPITOPE PREDICTION TOOLS, if applicable