NIH-NIMH-75N95022R00031.pdf

DEPARTMENT OF HEALTH & HUMAN SERVICES Public Health Service

National Institutes of Health National Institute on Drug Abuse Bethesda, Maryland 20892

NATIONAL INSTITUTE OF MENTAL HEALTH

REQUEST FOR PROPOSAL (RFP) NUMBER: NIH-NIMH-75N95022R00031

PROJECT TITLE: NIMH BRAIN Initiative Cell Atlas Network (BICAN) Sequencing

Core

ISSUED BY:

Michael Horn Contract Specialist NIMH Section Contracts Management Branch, Red Office of Acquisitions, NIDA Email: michael.horn@nih.gov

Christine Frate Supervisory Contracting Officer NIMH Section, Section Head Contracts Management Branch, Red Office of Acquisitions, NIDA Email: christine.frate@nih.gov

DATE ISSUED: July 13, 2022

The National Institute of Mental Health (NIMH) invites you to submit a proposal responding to the requirements of this RFP No. NIH-NIMH-75N95022R00031 for the NIMH BRAIN Initiative Cell Atlas Network (BICAN) requirement.

This Request for Proposal is released under FULL AND OPEN Competition Procedures.

NIMH prepared this Request for Proposal (RFP) in accordance with the Uniform Contract Format prescribed for Government Wide application by the Federal Acquisition Regulation (FAR). The Uniform Contract Format is both a Request for Proposal and a contract award document. The resulting contract will consist of Parts I, II, and III of the Uniform Contract Format.

All offerors must be REGISTERED and have an ACTIVE System for Award Management (www.sam.gov) account at the time an offer/proposal is submitted to the Government. All offerors registered in the System for Award Management (www.sam.gov) must be in full compliance with FAR 52.204-13 System for Award Management Maintenance to be eligible to submit a proposal. The Government will not accept proposals from offerors who do not meet the SAM requirement.

mailto:michael.horn@nih.gov mailto:christine.frate@nih.gov http://www.sam.gov/

General

NIMH anticipates that multiple-award (MAC) indefinite-delivery, indefinite-quantity (IDIQ) contracts with cost reimbursement or fixed price task order type, will be awarded.

Part IV of the RFP contains instructions, provisions, and evaluation factors for the submission and review of proposals. The balance of Parts I, II, and III contain provisions, clauses, and special requirements which will be made a part of any resultant award. Please review these sections and consider their impact on performance, capability, technical, and cost factors as you develop your proposal. Do not fill in blanks or otherwise complete portions of Parts I, II, and III which appear to require additional information. The Government will complete these items prior to contract award and, if negotiations are conducted, will tailor those items through final negotiations.

Offeror Questions

Requests for clarification, additional information, or correction must be made in writing to the Contracting Officer. Offeror questions must be submitted on or before 12:00 P.M., on July 27 2022. Offeror questions may be submitted by e-mail to michael.horn@nih.gov and christine.frate@nih.gov with the subject line:

“NIH-NIMH-75N95022R00031”

NOTE: Site visits will not be provided.

PROPOSAL DUE: August 21, 2022 at 5:00 P.M. (Eastern Standard Time)

Proposals must be submitted via the electronic Contract Proposal Submission (eCPS) website (https://ecps.nih.gov). Proposals submitted by facsimile, e-mail, or hard copy will not be accepted. An official authorized to bind your organization must sign the proposal.

Offerors are solely responsible for submitting proposals in a timely manner. Please note that creating an account to submit may take up to three (3) business days. Please plan accordingly.

Additional instructions on submitting a proposal via eCPS can be found at https://ecps.nih.gov/home/howto and in Attachment 1.

PROPOSAL SET-UP:

When submitting a proposal, the Offerors proposal must include a technical proposal in response to General Task Area 1 of the Statement of Work and any and all other General Task Areas in which they wish to propose. In addition to General Task Areas, Offerors must also include, in a clearly labeled separate section of their proposal, a separate response for each Sample Task Order for the respective General Task Areas in which they proposed. Sample Task Orders are included in this Solicitation as Attachments 8 and 9.

mailto:michael.horn@nih.gov mailto:christine.frate@nih.gov https://ecps.nih.gov/

Additional Technical Proposal Instructions and Business Proposal Instructions specific to this requirement are included in Attachments 6 and 7.

SUMMARY OF SOLICITATON SECTIONS:

SECTIONS A THROUGH I

The information provided in Sections A through I represents what may be in the resulting contract. It is not an exact replica because some of the information will need to be tailored to your organization and your proposal. It is provided for your information, so you will understand the type of terms and conditions that will be in any resulting contract.

SECTION J

This section contains a listing of all the attachments to the solicitation.

SECTION K

This section contains Representations and Certifications that must be completed online and submitted with your proposal.

SECTION L

This section contains instructions to assist you in the preparation of your proposal. It contains general information and instructions, as well as specific preparation instructions for both the technical and business proposals. The technical and business proposals should follow the format outlined in these sections. Page limits apply to the proposal for General Tasks as a whole and each Sample Task Order proposal (ex. Proposal for General Tasks Areas, 1, 2, and 3 must be no more than 25 pages EACH and the technical proposal section for Sample Task Orders 1, 2 and 3 must be no more than 20 pages EACH). Sample Task Orders need only respond to the information included in the specified Sample Task Order Proposal and does not need to include the System Security Plan, Resumes, Past Performance, etc. already included in the Proposal submitted for General Tasks included in the Statement of Work.

SECTION M

This section contains the evaluation criteria on which your proposal will be evaluated.

All notices related to this solicitation will be posted on the System for Award Management (www.sam.gov). If you would like to receive e-mail notifications of updates to this solicitation, please register with the System for Award Management.

Proposals received in response to this solicitation will be evaluated in accordance with Section M of the solicitation. Awards will be made to the responsible offerors whose offer conforms to the solicitation requirements and provides the best value to the Government.

In accordance with FAR 15.306(a)(3) and FAR 52.215-1, the Government intends to evaluate proposals and award a contract without discussions. Therefore, your initial proposal should contain the best terms from cost or price and technical standpoints. The Government does, however, reserve the right to conduct discussions if the Contracting Officer determines them to be necessary.

Disclaimers

This RFP does not commit the Government to pay the costs for the preparation and submission of a proposal. The Contracting Officer is the only individual who legally can commit the Government to the expenditure of public funds in connection with this acquisition.

Any contract award for this requirement is contingent on the availability of funds (see FAR 52.232-18, Availability of Funds – April 1984).

The RFP shall take precedence if any of the content in this letter is contradictory.

The NIMH appreciates your interest in this RFP and looks forward to the receipt of your proposal. Requests for any information concerning this RFP should be directed to Michael Horn at michael.horn@nih.gov. Discussions with any other individuals should not occur.

mailto:michael.horn@nih.gov

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SOLICITATION

SECTION A - SOLICITATION/CONTRACT FORM

1. Requisition or other Purchase Authority: Public Law 102-321

2. Request for Proposal (RFP) Number:

NIH-NIMH-75N95022R00031

3. Issue Date:

July 13, 2022

4. Set Aside:

[X] No

[ ] Yes See Part IV Section L

5. Title : BRAIN Initiative Cell Atlas Network (BICAN) Sequencing Core

6. ISSUED BY:

Office of Acquisitions National Institute of Mental Health Office of Acquisitions, NIDA National Institutes of Health

7. SUBMIT OFFERS TO:

See Part III, Section J, "Packaging and Delivery of the Proposal," ATTACHMENT 1 of this Solicitation.

8. Proposals for furnishing the supplies and/or services in THE SCHEDULE will be received at the place specified in, and in the number of copies specified in Attachment 1, "Packaging and Delivery of the Proposal," until August 21, 2022 local time on 5:00 P.M., Eastern Time. Offers will be valid for 120 days unless a different period is specified by the offeror on the Attachment entitled, "Proposal Summary and Data Record, NIH 2043.

9. This solicitation requires delivery of proposals as stated in ATTACHMENT 1, "PACKAGING AND DELIVERY OF THE PROPOSAL." If proposals are required to be delivered to two different locations, the OFFICIAL POINT OF RECEIPT for determining TIMELY DELIVERY is the address provided for the OFFICE OF ACQUISITIONS.

IF YOUR PROPOSAL IS NOT RECEIVED BY THE CONTRACTING OFFICER OR HIS DESIGNEE AT THE PLACE AND TIME SPECIFIED FOR THE OFFICE OF ACQUISITIONS, THEN IT WILL BE CONSIDERED LATE AND HANDLED IN ACCORDANCE WITH subparagraph (c)(3) of FAR Clause 52.215-1, Instructions to Offerors--Competitive Acquisition," LOCATED IN SECTION L.1. OF THIS SOLICITATION.

10. Offeror must be registered in the System for Award Management (SAM) prior to award of a contract. Offerors must access the CCR through The System for Award Management (SAM) at https://www.sam.gov/SAM/.

11. FOR INFORMATION CALL: Michael Horn, Contract Specialist

PHONE: (301) 402-7720

e-MAIL: michael.horn@nih.gov

COLLECT CALLS WILL NOT BE ACCEPTED.

Please submit your proposal intent response or any requests for clarification, additional information, or correction to the Contracting Officer on or before 12:00 P.M., EST, on 07/27/2022.

Offeror questions

Christine Frate Contracting Officer, NIMH Section NIDA Office of Acquisitions, NIDA https://www.sam.gov/SAM/

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1. Requisition or other Purchase Authority: Public Law 102-321 must be submitted by e-mail to michael.horn@nih.gov with the subject line: "NIH-NIMH-75N95022R00031"

RFP Number : 75N95022R00031 BICAN

- 3 -

RFP TABLE OF CONTENTS

PART I - THE SCHEDULE

SECTION A - SOLICITATION/CONTRACT FORM

SECTION B - SUPPLIES OR SERVICES AND PRICES/COSTS

SECTION C - DESCRIPTION/SPECIFICATIONS/WORK STATEMENT

SECTION D - PACKAGING, MARKING AND SHIPPING

SECTION E - INSPECTION AND ACCEPTANCE

SECTION F - DELIVERIES OR PERFORMANCE

SECTION G - CONTRACT ADMINISTRATION DATA

SECTION H - SPECIAL CONTRACT REQUIREMENTS

PART II - CONTRACT CLAUSES

PART III - LIST OF DOCUMENTS, EXHIBITS AND OTHER ATTACHMENTS

SECTION J - LIST OF ATTACHMENTS

SOLICITATION ATTACHMENTS

TECHNICAL PROPOSAL ATTACHMENTS

BUSINESS PROPOSAL ATTACHMENTS

INFORMATIONAL ATTACHMENTS

PART IV - REPRESENTATIONS AND INSTRUCTIONS

SECTION K - REPRESENTATIONS, CERTIFICATIONS AND OTHER STATEMENTS OF OFFERORS

SECTION L - INSTRUCTIONS, CONDITIONS, AND NOTICES TO OFFERORS

1. GENERAL INFORMATION

a. INSTRUCTIONS TO OFFERORS--COMPETITIVE ACQUISITION

b. NAICS CODE AND SIZE STANDARD

c. TYPE OF CONTRACT AND NUMBER OF AWARDS

d. TASK ORDERS UNDER MULTIPLE AWARD INDEFINITE DELIVERY CONTRACTS

e. COMMITMENT OF PUBLIC FUNDS

f. PROMOTING EFFICIENT SPENDING

g. COMMUNICATIONS PRIOR TO CONTRACT AWARD

h. RELEASE OF INFORMATION

i. PREPARATION COSTS

j. SERVICE OF PROTEST

2. INSTRUCTIONS TO OFFERORS

a. GENERAL INSTRUCTIONS

1. Contract Type and General Clauses

2. Authorized Official and Submission of Proposal

3. Proposal Summary and Data Record (NIH-2043)

4. Separation of Technical and Business Proposals

5. Alternate Proposals

6. Evaluation of Proposals

7. Potential Award Without Discussions

8. Use of the Metric System of Measurement

9. Privacy Act - Treatment of Proposal Information

10. Selection of Offerors

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11. Institutional Responsibility Regarding Investigator Conflicts of Interest

12. ROTC Access and Federal Military Recruiting on Campus

13. CERTIFICATION REGARDING TAX MATTERS (OCT 2020)

14. Past Performance Information

15. Electronic Information Technology Accessibility Notice, HHSAR 352.239-73 (December 2015)

16. Solicitation Provisions Incorporated by Reference

b. TECHNICAL PROPOSAL INSTRUCTIONS

1. TECHNICAL PROPOSAL INSTRUCTIONS

2. Other Considerations

3. Technical Evaluation

4. Obtaining and Disseminating Biomedical Research Resources

c. BUSINESS PROPOSAL INSTRUCTIONS

1. Basic Cost/Price Information

2. Proposal Cover Sheet

3. Information Other than Cost or Pricing Data

4. Cost and Pricing Data

5. Requirements for Cost or Pricing Data or Information Other than Cost and Pricing Data

6. Salary Rate Limitation

7. Small Business Subcontracting Plan

8. Mentor Protege Program, HHSAR 352.219-70

9. HUBZone Small Business Concerns

10. Total Compensation Plan

11. Other Administrative Data

12. Qualifications of the Offeror

13. Subcontractors

14. Proposer's Annual Financial Report

15. Travel Costs/Travel Policy

SECTION M - EVALUATION FACTORS FOR AWARD

1. GENERAL

2. COST/PRICE EVALUATION

3. MANDATORY QUALIFICATION CRITERIA

4. EVALUATION OF OPTIONS

5. EVALUATION OF DATA SHARING PLAN

6. TECHNICAL EVALUATION FACTORS

7. EVALUATION OF ELECTRONIC AND INFORMATION TECHNOLOGY ACCESSIBILITY- SECTION

8. PAST PERFORMANCE FACTOR

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PART I - THE SCHEDULE

THE INFORMATION SET FORTH IN SECTION A - SOLICITATION/CONTRACT FORM, HEREIN CONTAINS IMPORTANT INFORMATION FOR ANY OFFEROR INTERESTED IN RESPONDING TO THIS SOLICITATION.

ANY CONTRACT RESULTING FROM THIS SOLICITATION WILL INCLUDE IN ITS SECTION A - SOLICITATION/ CONTRACT FORM, ACCOUNTING, APPROPRIATION AND GENERAL INFORMATION APPLICABLE TO THE

CONTRACT AWARD.

THE CONTRACT SCHEDULE SET FORTH IN SECTIONS B THROUGH H, HEREIN, CONTAINS CONTRACTUAL INFORMATION PERTINENT TO THIS SOLICITATION. IT IS NOT AN EXACT REPRESENTATION OF THE CONTRACT DOCUMENT THAT WILL BE AWARDED AS A RESULT OF THIS SOLICITATION. THE CONTRACT COST OR PRICE AND OTHER CONTRACTUAL PROVISIONS PERTINENT TO THE OFFEROR (i.e., those relating to the organizational structure [e.g., Non-Profit, Commercial] and specific cost authorizations unique to the Offeror's proposal and requiring Contracting Officer Prior Approval) WILL BE DISCUSSED IN THE NEGOTIATION PROCESS AND WILL BE INCLUDED IN THE RESULTANT CONTRACT. THE ENCLOSED CONTRACT SCHEDULE IS

INTENDED TO PROVIDE THE OFFEROR WITH THE NECESSARY INFORMATION TO UNDERSTAND THE

TERMS AND CONDITIONS OF THE RESULTANT CONTRACT.

SECTION B - SUPPLIES OR SERVICES AND PRICES/COSTS

ARTICLE B.1. BRIEF DESCRIPTION OF SUPPLIES OR SERVICES

The BRAIN Initiative is creating the BRAIN Initiative Cell Atlas Network (BICAN) to broaden and deepen the systematic cell census and atlas efforts with a new emphasis on the human brain. The objective of BICAN Sequencing Core is to perform large-scale DNA and RNA sequencing of the libraries. The BICAN Sequencing Core contract program will coordinate and collaborate with researchers funded by BICAN and NIH BRAIN Initiative staff to establish and meet sequencing quality control (QC) metrics, perform requested sequencing tasks, streamline the workflow and process, track sample information, operate in a cost effective and time efficient manner, and ensure data integrity and rapid turnaround. An Indefinite Delivery, Indefinite Quantity (IDIQ) contract mechanism will be utilized to support the BICAN Sequencing Core.

ARTICLE B.2. PRICES/COSTS

a. This is a Multiple Award Indefinite Quantity contract as contemplated by FAR 16.504. The Contractor shall be reimbursed by the Government in an amount not less than $10,000 (minimum) and not more than a total of $149,000,000 (maximum) for successful performance of this contract.

b. The prices set forth in this ARTICLE will cover the contract period January 2023 through January 2028.

c. The Government will compete and award Task Orders based on the work described in SECTION C of this contract.

d. Ordering procedures are described in The TASK ORDER PROCEDURE Article in SECTION G of this contract.

e. The NIMH intends to issue Task Order #001 concurrent with this award. This task order award will obligate an amount not less than the negotiated firm-fixed-price for Task Area #1 Manual of Operations (minimum).

f. Task Orders for Task Areas 2 through 7 will be competed through a Task Order Request for Proposal (TORFP) process as the need arises. It is anticipated that these Task Orders will be cost-reimbursement (completion and/or level of effort type) or fixed-priced orders and will have variable periods of performance. The number of TORFPs issued will depend upon programmatic needs and funding availability, and it may vary from year to year. Due to changes in priorities within NIMH, the projected workload cannot be precisely described for each year.

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ARTICLE B.3. PROVISIONS APPLICABLE TO DIRECT COSTS

This article will prohibit or restrict the use of contract funds, unless otherwise approved by the Contracting Officer. The following is a list of items that may be included in the resultant contract as applicable. 1) Conferences & Meetings, 2) Food for Meals, Light Refreshments & Beverages, 3) Promotional Items, 4) Acquisition, by purchase or lease, of any interest in real property; 5) Special rearrangement or alteration of facilities; 6) Purchase or lease of any item of general purpose office furniture or office equipment regardless of dollar value; 7) Travel Costs including Foreign Travel; 8) Consultant Costs; 9) Subcontract Costs; 10) Patient Care Costs; 11) Accountable Government Property; 12) Printing costs; and 13) Research Funding.

ARTICLE B.4. ADVANCE UNDERSTANDINGS

Specific elements of cost, which normally require prior written approval of the Contracting Officer before incurrence of the cost (e.g., foreign travel, consultant fees, subcontracts) will be included in this Article if the Contracting Officer has granted his/her approval prior to contract award.

a. Unit Price Decreases The Contractor shall continually look for ways to decrease unit pricing/costs as technology changes and services become less expensive to perform. The Contractor shall modify their price list/costs to decrease their unit prices accordingly. Unit prices/costs shall not be increased without prior approval of the Contracting Officer. New services may be added to the price list/costs. Updates to the Contractor's pricing/costs will be automatically incorporated in the contract.

b. Sample Quantity Increases Due to Unit Price Decreases It is hereby agreed that if the price/cost of a service decreases during the period of performance of a task order, the government reserves the right to increase the number of samples up to the value of the savings achieved through the reduced unit price/cost or deobligate the savings. A task order modification shall be executed to reduce the unit price/ cost and either increase the quantity or deobligate the excess funds.

c. Treatment of Unused Samples The Contractor shall only charge for the samples on which services have been performed. If services are not performed on all samples, the corresponding value of the unused samples will be deobligated upon completion of the task order. However, if the value of the unused samples is less than $1,000, theContractor may invoice for the full value of all samples.

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SECTION C - DESCRIPTION/SPECIFICATIONS/WORK STATEMENT

ARTICLE C.1. STATEMENT OF WORK

a. Independently and not as an agent of the Government, the Contractor shall be required to furnish all the necessary services, qualified personnel, material, equipment, and facilities, not otherwise provided by the Government, as needed to perform the Statement of Work, dated April 15, 2022, attached hereto and made a part of this Solicitation (See SECTION J - List of Attachments).

ARTICLE C.2. REPORTING REQUIREMENTS

All reports required herein shall be submitted in electronic format. In addition, one electronic copy of each report shall be submitted to the Contracting Officer.

All electronic reports submitted shall be compliant with Section 508 of the Rehabilitation Act of 1973. Additional information about testing documents for Section 508 compliance, including guidance and specific checklists, by application, can be found at: http://www.hhs.gov/web/508/index.html and at: https://www.section508.gov/create/ documents, "Create Accessible Documents."

All paper/hardcopy documents/reports submitted under this contract shall be printed or copied, double-sided, on at least 30 percent post-consumer fiber paper, whenever practicable, in accordance with FAR 4.302(b).

a. Technical Progress Reports

In addition to the required reports set forth elsewhere in this Schedule, the preparation and submission of regularly recurring Technical Progress Reports will be required in any contract resulting from this solicitation. These reports will require descriptive information about the activities undertaken during the reporting period and will require information about planned activities for future reporting periods. The frequency and specific content of these reports will be determined prior to contract award. [Note: Beginning May 25, 2008, the Contractor shall include the applicable PubMed Central or NIH Manuscript Submission reference number when citing publications that arise from its NIH funded research.]

TASK AREA 2 - Large-Scale Single-cell Transcriptome Sequencing

For proposal preparation purposes only, it is estimated that only the required electronic version(s) of these reports will be required as follows:

[X] Bi-weekly

[ ] Quarterly

[ ] Semi-Annually

[ ] Annually

[ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a bi-weekly report describing the activities during the reporting period, and the activities planned for the ensuing reporting period. The initial reporting period consists of the first full two weeks of performance plus any fractional part of the initial week. As a minimum, this report shall include:

i. A qualitative description of overall progress, including the status of the Large-Scale Single Cell Transcriptome Sequencing, the weekly and monthly Quality Control (QC) data (used here and throughout encompassing quality http://www.hhs.gov/web/508/index.html https://www.section508.gov/create/documents https://www.section508.gov/create/documents

- 8 -assurance and quality control activities), the weekly and monthly production and number of data sequences submitted to the designated data repository, and the quality control metrics established during Phase I of the task order by the contractors, BICAN investigators and NIH BRAIN Initiative staff.

ii. An indication of any current problems that may impede performance, and proposed corrective action iii.A discussion of the work to be performed during the next reporting period; and iv.Recommendations.

For proposal preparation purposes only, it is estimated that electronic version(s) of these reports will be required as follows:

[ ] Final - Upon final completion of the contract

[X] Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

This report is to include a summation of the work performed and results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Contractor shall provide the Contracting Officer with copies of the final report in draft form 30 Calendar days prior to the delivery date for the final version of the final report. The Contracting Officer's Representative (COR) shall review the draft report and provide the Contracting Officer with comments within 15 Calendar days after receipt. The Contractor, if necessary, shall correct the final report.

TASK AREA 3 - Large-Scale Single-cell Epigenome Sequencing

For proposal preparation purposes only, it is estimated that only the required electronic version(s) of these reports will be required as follows:

[X] Bi-weekly

[ ] Quarterly

[ ] Semi-Annually

[ ] Annually

[ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a bi-weekly report describing the activities during the reporting period, and the activities planned for the ensuing reporting period. The initial reporting period consists of the first two full weeks of performance.

As a minimum, this report shall include:

i. A qualitative description of overall progress, including the status of the Large-Scale Single Cell Epigenome Sequencing, the weekly and monthly Quality Control (QC) data (used here and throughout encompassing quality assurance and quality control activities), the weekly and monthly production and number of data sequences submitted to the designated data repository, and the quality control metrics established during Phase I of the task order by the contractors, BICAN investigators and NIH BRAIN Initiative staff.

ii. An indication of any current problems that may impede performance, and proposed corrective action

iii. A discussion of the work to be performed during the next reporting period; and

iv. Recommendations.

For proposal preparation purposes only, it is estimated that electronic version(s) of these reports will be required as follows:

Final - Upon final completion of the contract

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X Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

This report is to include a summation of the work performed and results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Contractor shall provide the Contracting Officer with copies of the final report in draft form 30 Calendar days prior to the delivery date for the final version of the final report. The COR shall review the draft report and provide the Contracting Officer with comments within 15 Calendar days after receipt. The Contractor, if necessary, shall correct the final report.

TASK AREA 4 – Large-Scale Single-Cell Multi-omics Sequencing

For proposal preparation purposes only, it is estimated that only the required electronic version(s) of these reports will be required as follows:

[X] Bi-weekly

[ ] Quarterly

[ ] Semi-Annually

[ ] Annually

[ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a bi-weekly report describing the activities during the reporting period, and the activities planned for the ensuing reporting period. The initial reporting period consists of the first two full weeks of performance.

As a minimum, this report shall include:

i. A qualitative description of overall progress, including the status of the Large-Scale Single Cell Epigenome Sequencing, the weekly and monthly Quality Control (QC) data (used here and throughout encompassing quality assurance and quality control activities), the weekly and monthly production and number of data sequences submitted to the designated data repository, and the quality control metrics established during Phase I of the task order by the contractors, BICAN investigators and NIH BRAIN Initiative staff.

ii. An indication of any current problems that may impede performance, and proposed corrective action

iii. A discussion of the work to be performed during the next reporting period; and

iv. Recommendations.

For proposal preparation purposes only, it is estimated that electronic version(s) of these reports will be required as follows:

Final - Upon final completion of the contract

X Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

This report is to include a summation of the work performed and results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Contractor shall provide the Contracting Officer with copies of the final report in draft form 30 Calendar days prior to the delivery date for the final version of the final report. The COR shall review the draft report and provide the Contracting Officer with comments within 15 Calendar days after receipt. The Contractor, if necessary, shall correct the final report.

TASK AREA 5 - Bulk Tissue Transcriptome and Epigenome Sequencing

For proposal preparation purposes only, it is estimated that only the required electronic version(s) of these reports will be required as follows:

[X] Bi-weekly

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[ ] Quarterly

[ ] Semi-Annually

[ ] Annually

[ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a bi-weekly report describing the activities during the reporting period, and the activities planned for the ensuing reporting period. The initial reporting period consists of the first two full weeks of performance. As a minimum, this report shall include:

i. A qualitative description of overall progress, including the status of Bulk Tissue Transcriptome and Epigenome Sequencing, the weekly and monthly Quality Control (QC) data (used here and throughout encompassing quality assurance and quality control activities), the weekly and monthly production and number of data sequences submitted to the designated data repository, and the quality control metrics established during Phase I of the task order by the contractors, BICAN investigators and NIH BRAIN Initiative staff.

ii. An indication of any current problems that may impede performance, and proposed corrective action

iii. A discussion of the work to be performed during the next reporting period; and

iv. Recommendations.

For proposal preparation purposes only, it is estimated that electronic version(s) of these reports will be required as follows:

Final - Upon final completion of the contract

X Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

This report is to include a summation of the work performed and results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Contractor shall provide the Contracting Officer with copies of the final report in draft form 30 Calendar days prior to the delivery date for the final version of the final report. The COR shall review the draft report and provide the Contracting Officer with comments within 15 Calendar days after receipt. The Contractor, if necessary, shall correct the final report.

TASK AREA 6 – Whole Genome and Exome Sequencing

For proposal preparation purposes only, it is estimated that only the required electronic version(s) of these reports will be required as follows:

[X] Bi-weekly

[ ] Quarterly

[ ] Semi-Annually

[ ] Annually

[ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a bi-weekly report describing the activities during the reporting period, and the activities planned for the ensuing reporting period. The initial reporting period consists of the first two full weeks of performance.

As a minimum, this report shall include:

i. A qualitative description of overall progress, including the status of the Whole Genome and Exome Sequencing Sequencing, the weekly and monthly Quality Control (QC) data (used here and throughout encompassing quality assurance and quality control activities), the weekly and monthly production and number of data sequences submitted

- 11 -to the designated data repository, and the quality control metrics established during Phase I of the task order by the contractors, BICAN investigators and NIH BRAIN Initiative staff.

ii. An indication of any current problems that may impede performance, and proposed corrective action

iii. A discussion of the work to be performed during the next reporting period; and

iv. Recommendations.

For proposal preparation purposes only, it is estimated that electronic version(s) of these reports will be required as follows:

Final - Upon final completion of the contract

X Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

This report is to include a summation of the work performed and results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Contractor shall provide the Contracting Officer with copies of the final report in draft form 30 Calendar days prior to the delivery date for the final version of the final report. The COR shall review the draft report and provide the Contracting Officer with comments within 15 Calendar days after receipt. The Contractor, if necessary, shall correct the final report.

TASK AREA 7 - Novel Omics Sequencing

For proposal preparation purposes only, it is estimated that only the required electronic version(s) of these reports will be required as follows:

[X] Bi-weekly

[ ] Quarterly

[ ] Semi-Annually

[ ] Annually

[ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a bi-weekly report describing the activities during the reporting period, and the activities planned for the ensuing reporting period. The initial reporting period consists of the first two full weeks of performance.

As a minimum, this report shall include:

i. A qualitative description of overall progress, including the status of the Novel Omics Sequencing, the weekly and monthly Quality Control (QC) data (used here and throughout encompassing quality assurance and quality control activities), the weekly and monthly production and number of data sequences submitted to the designated data repository, and the quality control metrics established during Phase I of the task order by the contractors, BICAN investigators and NIH BRAIN Initiative staff.

ii. An indication of any current problems that may impede performance, and proposed corrective action

iii. A discussion of the work to be performed during the next reporting period; and

iv. Recommendations.

For proposal preparation purposes only, it is estimated that electronic version(s) of these reports will be required as follows:

Final - Upon final completion of the contract

X Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

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This report is to include a summation of the work performed and results obtained for the entire contract period of performance. This report shall be in sufficient detail to describe comprehensively the results achieved. The Contractor shall provide the Contracting Officer with copies of the final report in draft form 30 Calendar days prior to the delivery date for the final version of the final report. The COR shall review the draft report and provide the Contracting Officer with comments within 15 Calendar days after receipt. The Contractor, if necessary, shall correct the final report.

b. Other Technical Reports

1. TASK AREA 1 - Manual of Operations

a. BICAN Final Manual of Operations for Task Areas 2 - 7 (Large-Scale Single-cell Transcriptome Sequencing, Large-Scale Single-cell Epigenome Sequencing, Large-Scale Single-Cell Multi-omics Sequencing, Bulk Tissue Transcriptome and Epigenome Sequencing, Whole Genome and Exome Sequencing, and Novel Omics Sequencing, as proposed)

Within one (1) month of contract award, the Contractor shall deliver a final copy of the Manual of Operations included in their proposal. The final Manual of Operations will incorporate all changes or modifications agreed upon by the Government and the Contractor during contract negotiations and the first month of contract performance. At a minimum, the final Manual of Operations shall contain the following:

i. Detailed description of sample receipt, storage, and tracking methodology assuring participant confidentiality, including:

1. Procedures for the receipt of samples and metadata, including shipping and packaging of samples and acquisition of metadata and integration into the lab information management system (LIMS), (The contractor is expected to provide packaging materials and coordinate shipping of samples from the BICAN investigators).

2. Required procedures for omics library sample preparation, aliquotting, labeling, and shipping, and minimum acceptable standards for sample quantity and quality for samples submitted for proposed omics.

3. Procedures for tracking data and sample identification information for samples submitted for proposed omics sequencing.

4. Methods for electronic and genetic tracking of library samples including but not limited tosample and sequencing barcodes and gender identification; minimization of sample switches, losses, and cross contamination; tracking of work, and details of the in-house LIMS.

5. Methods for storage of omics library samples and back-up plans.

6. Recommendations for sample preparation and other strategies to assist in minimizing batch effects and other biases.

7. Updates in the above agreed to between the Government, BICAN investigators and the Contractor.

ii. Detailed description of the proposed omics profiling method, including:

1. Methods for optimizing and evaluating the proposed omics sequencing method and platform.

2. Instrumentation and robotics necessary to perform the proposed omics sequencing and procedures for equipment calibration and maintenance.

3. Methods for incorporating technology development to increase efficiency, quality and throughput.

4. Laboratory information management systems to be used, including software, nonproprietary platform, hardware, query system, transmission requirements, backups, and security.

5. A detailed workflow of the proposed omics analysis and Quality Control (QC) (which may include) quantification, library pool prep, on-instrument sequencing raw data and demultiplexing, preprocessing, mapping, post-alignment processing, variant calling, annotation, and prioritization, including criteria, the tools used and versioning.

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iii. Detailed description of laboratory QC procedures, including:

1. Methods to reduce or eliminate systematic errors.

2. Source and frequency of use of internal standards, repeat samples, and blank samples.

3. Procedures for computational checking and rechecking, assessment of reading errors and data consistency, and calculation of error rate and failure rate of sequencing attempts and for samples.

4. Methods for routine alternate procedures to be used when proposed omics sequencing fails.

5. Methods to reduce or eliminate errors in computational and informatics aspects of the sequencing.

6. Methods for identifying sample mix-ups.

7. Procedures for identifying and implementing corrective actions based on QC.

iv. Detailed description of genetic analysis and bioinformatics for data cleaning including:

1. Procedures for analysis including but not limited to the checks for internal standards and QC/Quality Assurance (QA) used in the workflow of the proposed omics analysis: raw data QC, preprocessing, mapping.

2. Methods for correcting inconsistencies and handling inconsistent data to maximize accuracy.

v. Detailed description of informatics used for sequencing, database management, and data transfer including:

1. Software and hardware system components, including commercial products and custom software developed for support of database, associated informatics functions, and protocols and formats for data transfer, including a description of the rationale for the chosen database information model and past experience with it. Offerors should catalog proprietary and open-source elements, and identify specific license limitations including terms that could potentially affect future resource access and portability. For customized applications, describe the use of industry and informatics best practices in the development of the components. Data information management systems to be used, including software, nonproprietary platform(s), hardware, backups, and security.

vi. Key personnel including their responsibilities and contact information, and a key personnel replacement plan

2. TASK AREAS 2 – 7

a. Phase I (Pilot) Report

Secure delivery of pilot QC of representative cohort(s) omics samples to COR, BICAN investigators, designated contractors, NIH staff, and BRAIN Inititaive designated data archive or data coordinating center.

b. Timeline

Provide timeline for novel omics profiles at 1, 3, and 6 months to Contracting officer, COR, and designated NIH staff.

c. Technology Evaluation Proposals

When promising technologies are identified and when requested by COR, the contractor shall prepare a technology evaluation proposal. The proposal shall include an assessment of the potential scientific impact and the costs associated with adopting the new technology. In addition, the Government may require reports focusing on specific technologies and applications. Follow-up reports may also be required.

Summary of Salient Results

The Contractor will be required to prepare and submit, with the final report, a summary (not to exceed 200 words) of salient results achieved during the performance of the contract. This report will be required on or before the expiration date of the contract.

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b. Other Reports/Deliverables

1. Source Code and Object Code

Unless otherwise specified herein, the Contractor shall deliver to the Government, upon the expiration date of the contract, all source code and object code developed, modified, and/or enhanced under this contract.

2. Section 508 Annual Report

The Contractor must submit an annual Section 508 report in accordance with the schedule set forth by the Contracting Officer (CO)/Contracting Officer's Representative (COR). The Section 508 Report Template and Instructions for completing the report are available at: https://www.hhs.gov/sites/ default/files/web/508/contracting/technology/section_508_annual_report.doc.

3. Multiple Principal Investigators Leadership Plan The Contractor must submit a revised/updated Leadership Plan in the event of a change in any of the Principal Investigators named in the Key Personnel Article in SECTION G of this contract. The revised plan is subject to review and approval by the Contracting Officer.

ARTICLE C.3. INVENTION REPORTING REQUIREMENT

All reports and documentation required by FAR Clause 52.227-11, Patent Rights-Ownership by the Contractor including, but not limited to, the invention disclosure report, the confirmatory license, and the Government support certification, shall be directed to the Division of Extramural Inventions and Technology Resources (DEITR), OPERA, OER, NIH, 6705 Rockledge Drive, Suite 310, MSC 7980, Bethesda, Maryland 20892-7980 (Telephone: 301-435-1986). In addition, one copy of an annual utilization report, and a copy of the final invention statement, shall be submitted to the Contracting Officer. The final invention statement (see FAR 27.303(b)(2)(ii)) shall be submitted to the Contracting Officer on the expiration date of the contract.

The first annual utilization report shall be due on or before the anniversary date of contract award. Thereafter, reports shall be due annually. The final invention statement (see FAR 27.303(b)(2)(ii)) shall be submitted on the expiration date of the contract. All reports shall be sent to the following address:

Contracting Officer

Office of Acquisition

Bethesda, Maryland 20892-

If no invention is disclosed or no activity has occurred on a previously disclosed invention during the applicable reporting period, a negative report shall be submitted to the Contracting Officer at the address listed above.

To assist contractors in complying with invention reporting requirements of the clause, the NIH has developed "Interagency Edison," an electronic invention reporting system. Use of Interagency Edison is required as it streamlines the reporting process and greatly reduces paperwork. Access to the system is through a secure interactive Web site to ensure that all information submitted is protected. Interagency Edison and information relating to the capabilities of the system can be obtained from the Web ( http://www.iedison.gov), or by contacting the Extramural Inventions and Technology Resources Branch, OPERA, NIH.

https://www.hhs.gov/sites/default/files/web/508/contracting/technology/section_508_annual_report.doc https://www.hhs.gov/sites/default/files/web/508/contracting/technology/section_508_annual_report.doc http://www.iedison.gov

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SECTION D - PACKAGING, MARKING AND SHIPPING

All deliverables required under this contract shall be packaged, marked and shipped in accordance with Government specifications. At a minimum, all deliverables shall be marked with the contract number and Contractor name. The Contractor shall guarantee that all required materials shall be delivered in immediate usable and acceptable condition.

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SECTION E - INSPECTION AND ACCEPTANCE

a. The Contracting Officer or the duly authorized representative will perform inspection and acceptance of materials and services to be provided.

b. For the purpose of this SECTION, NIMH COR is the authorized representative of the Contracting Officer.

c. Inspection and acceptance will be performed at either the Contractor's facility or at the NIMH

Acceptance of work, materials, services, and reports may be presumed unless otherwise indicated in writing by the Contracting Officer or the duly authorized representative within 30 days of receipt.

d. This contract incorporates the following clause by reference, with the same force and effect as if it were given in full text. Upon request, the Contracting Officer will make its full text available.

FAR Clause 52.246-7, Inspection of Research and Development - Fixed Price (August 1996).

FAR Clause 52.246-8, Inspection of Research and Development - Cost-Reimbursement (May 2001).

Alternate I (April 1984) is not applicable to this contract.

FAR Clause 52.246-9, Inspection of Research and Development (Short Form) (April 1984).

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SECTION F - DELIVERIES OR PERFORMANCE

ARTICLE F.1. PERIOD OF PERFORMANCE

The total ordering period of this contract shall be from January 2023 through January 2028.

It is anticipated that the period of performance, including options, for some task orders may extend multiple years past the end of the IDIQ ordering period. However, under FAR Clause 52.216-22, Contractors shall not be required to make any deliveries under this contract for more than two years past the end of the IDIQ ordering period unless mutually agreed to in writing.

All terms and conditions of the parent IDIQ contract will be incorporated by reference and remain in full force and effect throughout the period of performance of the TO, including during and after the end of the IDIQ ordering period.

ARTICLE F.2. DELIVERIES

Satisfactory performance of the final contract shall be deemed to occur upon performance of the work described in the Statement of Work Article in SECTION C of this contract and upon delivery and acceptance by the Contracting Officer, or the duly authorized representative, of the following items in accordance with the stated delivery schedule:

a. The items specified below as described in the REPORTING REQUIREMENTS Article in SECTION C of this contract will be required to be delivered F.o.b. Destination as set forth in FAR 52.247-35, F.o.b. DESTINATION, WITHIN CONSIGNEES PREMISES (APRIL 1984), and in accordance with and by the date(s) specified below and any specifications stated in SECTION D, PACKAGING, MARKING AND SHIPPING, of this contract:

Description Quantity Delivery Schedule

TECHNICAL REPORTS –

TASK AREA 1

Manual of operations 1 e-copy to the CO and COR Within 1 month of issuance of the task order

TECHNICAL REPORTS –

TASK AREAS 2-7

Phase I (Pilot study) report - biweekly 1 e-copy to the CO and COR Will be determined by the terms of each individual Task Order Phase I, Pilot QC report 1 e-copy to the CO and COR Will be determined by the terms of each individual Task Order Sequencing Data Sets – Submit data & meta-data to NIH-Designated Data Archive (CUBIE – Coordinating Unit for Biostatistics, Informatics and Engagement), notify NIH COR & Coordinating Center.

As determined in Task Order Within 14 days of receipt of the sequencing samples (libraries)

Phase II (Production) – biweekly summary report

1 e-copy to the CO and COR Within 14 days of the start of Phase II of the task order

Final Invention Statement 1 e-copy to the CO and COR Within 30 days Task order expiration Draft final report 1 e-copy to the CO and COR Within 30 days Task order expiration Final report 1 e-copy to the CO and COR At Task order expiration All stored data - Within 30 days Task order expiration

OTHER REPORT REQUIREMENTS –

TASK AREAS 2-7

Roster of Employees Requiring Suitable Investigations

1 e-copy to the CO and COR Within 14 days of the issuance of the task order

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Description Quantity Delivery Schedule IT Security Plan 1 e-copy to the CO and COR Within 30 days of the issuance of the task order IT Risk Assessment 1 e-copy to the CO and COR Within 30 days of the issuance of the task order FIPS 199 Assessment 1 e-copy to the CO and COR Within 30 days of the issuance of the task order IT Security Certification and Accreditation (IT- SC&A)

1 e-copy to the CO and COR Within 30 days of the issuance of the task order

Reporting of New and Departing Employees

1 e-copy to the CO and COR Within 30 days of the issuance of the task order

Contractor – Employee Non-Disclosure Agreement(s)

1 e-copy to the CO and COR Within 30 days of the issuance of the task order

Vulnerability Scanning Reports 1 e-copy to the CO and COR Monthly Incident Report 1 e-copy to the CO and COR As soon as possible, but no later than 1 hour of discovery Protection of Information in a Cloud Environment

1 e-copy to the CO and COR Within 14 days of the issuance of the task order

For system or cloud service, such as the Disposition/Decommission Plan

1 e-copy to the CO and COR Task order expiration

FedRamp Authorization 1 e-copy to the CO and COR Prior to use Financial Conflict of Interest (FCOI) 1 e-copy to the CO and COR Task order start and ongoing

Contract Closeout:

Contract Closeout:

In accordance with FAR 4.804, following contract expiration/completion, the Contractor shall be responsible for and provide the following items:

i. Indirect cost rate proposals for all years (in which a proposal was not…