NHLBI-CSB-HV-2016-36-JS_Amendment_1.pdf

PDF 2 MB Posted May 3, 2016

Attached to: Centralized Omic REsource (CORE) for TOPMed Federal contract opportunity
Solicitation number: NHLBI-CSB-HV-2016-36-JS
Issued by: Department of Health and Human Services National Institutes of Health

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Amendment 1 - FINAL Solicitation

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NHLBI-CSB-HV-2016-36-JS

x x

4 copies of the amendment; (b) By acknowledging receipt of this amendment on each copy of the offer submitted ; or (c) By separate letter or telegram which includes a reference to the solicitation and amendment numbers. FAILURE OF YOUR ACKNOWLEDGEMENT TO BE RECEIVED AT

THE PLACE DESIGNATED FOR THE RECEIPT OF OFFERS PRIOR TO THE HOUR AND DATE SPECIFIED MAY RESULT IN REJECTION OF YOUR OFFER. If by virtue of this amendment you desire to change an offer already submitted , such change may be made by telegram or letter, provided each telegram or letter makes reference to the solicitation and this amendment, and is received prior to the opening hour and date specified.

ADM-NHLBI

Bethesda MD 20892-7511 Institute National, Heart, Lung and Blood National Institutes of Health

IO-NHLBI

Bethesda MD 20892-7511 Institutes National Heart, Lung, and Blood National Institutes of Health

04/28/2016000001

13. THIS ITEM ONLY APPLIES TO MODIFICATION OF CONTRACTS/ORDERS. IT MODIFIES THE CONTRACT/ORDER NO. AS DESCRIBED IN ITEM 14.

12. ACCOUNTING AND APPROPRIATION DATA (If required) is not extended.is extended, Items 8 and 15, and returning

Offers must acknowledge receipt of this amendment prior to the hour and date specified in the solicitation or as amended , by one of the following methods: (a) By completing

The above numbered solicitation is amended as set forth in Item 14. The hour and date specified for receipt of Offers

11. THIS ITEM ONLY APPLIES TO AMENDMENTS OF SOLICITATIONS

FACILITY CODE CODE

10B. DATED (SEE ITEM 13)

10A. MODIFICATION OF CONTRACT/ORDER NO.

9B. DATED (SEE ITEM 11)

9A. AMENDMENT OF SOLICITATION NO.

CODE

8. NAME AND ADDRESS OF CONTRACTOR (No., street, county, State and ZIP Code)

7. ADMINISTERED BY (If other than Item 6)CODE 6. ISSUED BY

PAGE OF PAGES

4. REQUISITION/PURCHASE REQ. NO.3. EFFECTIVE DATE2. AMENDMENT/MODIFICATION NO. 5. PROJECT NO. (If applicable)

1. CONTRACT ID CODE

AMENDMENT OF SOLICITATION/MODIFICATION OF CONTRACT

04/28/2016

CHECK ONE A. THIS CHANGE ORDER IS ISSUED PURSUANT TO: (Specify authority) THE CHANGES SET FORTH IN ITEM 14 ARE MADE IN THE CONTRACT

B. THE ABOVE NUMBERED CONTRACT/ORDER IS MODIFIED TO REFLECT THE ADMINISTRATIVE CHANGES (such as changes in paying office, C. THIS SUPPLEMENTAL AGREEMENT IS ENTERED INTO PURSUANT TO AUTHORITY OF:

D. OTHER (Specify type of modification and authority) appropriation date, etc.) SET FORTH IN ITEM 14, PURSUANT TO THE AUTHORITY OF FAR 43.103(b).

E. IMPORTANT: Contractor is not, is required to sign this document and return __________________ copies to the issuing office.

ORDER NO. IN ITEM 10A.

14. DESCRIPTION OF AMENDMENT/MODIFICATION (Organized by UCF section headings, including solicitation/contract subject matter where feasible.)

Solicitation No. NHLBI-CSB-HV-2016-36-JS

Title: Centralized Omics Resource (CORE)

Subject: Note to Offerors (with Attachment A – Sample Proposal Format)

Number (Solicitation Number NHLBI-CSB-HV-2016-36-JS). Potential Offerors do not need to

Continued ...

16A. NAME AND TITLE OF CONTRACTING OFFICER (Type or print)15A. NAME AND TITLE OF SIGNER (Type or print)

15C. DATE SIGNED 16B. UNITED STATES OF AMERICA 15B. CONTRACTOR/OFFEROR 16C. DATE SIGNED

(Signature of person authorized to sign) (Signature of Contracting Officer)

Jennifer E. Swift

STANDARD FORM 30 (REV. 10-83)

Prescribed by GSA

FAR (48 CFR) 53.243

NSN 7540-01-152-8070

Previous edition unusable

Except as provided herein, all terms and conditions of the document referenced in Item 9 A or 10A, as heretofore changed, remains unchanged and in full force and effect .

ITEM NO. SUPPLIES/SERVICES QUANTITY UNIT UNIT PRICE AMOUNT

NAME OF OFFEROR OR CONTRACTOR

2 169

CONTINUATION SHEET

REFERENCE NO. OF DOCUMENT BEING CONTINUED PAGE OF

(A) (B) (C) (D) (E) (F)

NHLBI-CSB-HV-2016-36-JS/000001

Changes to the solicitation:

SECTION M - EVALUATION FACTORS FOR AWARD was revised to add Item 7. Subcontracting Program

Evaluation Criteria.

NSN 7540-01-152-8067 OPTIONAL FORM 336 (4-86)

Sponsored by GSA

FAR (48 CFR) 53.110

Solicitation No. NHLBI-CSB-HV-2016-36-JS

Title: Centralized Omics Resource (CORE)

Subject: Note to Offerors (with Attachment A – Sample Proposal Format)

This is the FINAL Solicitation and is published on FedBizOpps and FedConnect. All future amendments to this solicitation will be published on FedConnect. To find the solicitation in FedConnect, all potential offerors may select the link provided within FedBizOpps and search FedConnect by the Solicitation Title (Centralized Omic REsources) or Reference Number (Solicitation Number NHLBI-CSB-HV-2016-36-JS). Potential Offerors do not need to register to see the solicitation; however, in order to have full access, an account will need to be established.

Proposals will be accepted by the National Heart, Lung, and Blood Institute (NHLBI) in accordance with the requirements of Solicitation No. NHLBI-CSB-HV-2016-36-JS. Multiple Indefinite-Delivery-Indefinite-Quantity (IDIQ) contracts award(s) will be made.

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.

The Government reserves the right to make an award without discussions based solely upon initial proposals. Should the Government hold discussions, you will be notified if your proposal has been selected for discussions. During discussions, offerors will have an opportunity to revise their proposals in response to questions and comments provided by the Government. Please note that if your proposal is selected for negotiations, it does not guarantee that it will be selected for contract award. After receipt of the Final Proposal Revisions (FPR), offerors will be notified if their proposal is selected for award. The Government intends to award multiple IDIQ contracts.

The award is expected to be made on or about September 2016.

Offerors must submit all questions in writing to the Contracting Officer by May 16, 2016, as discussed in the Questions section below. It is important to read this solicitation in its entirety.

The following points are highlighted for your convenience:

1. QUESTIONS: No additional questions will be accepted after May 16, 2016 at 2:30 PM EST. All Questions and Answers will be posted by May 23, 2016.

2. PROPOSAL DUE DATE: Proposals must be received by 12:00 PM (Noon) EST on June 3, 2016 at the address specified, and the number of copies specified, in Attachment 1, Packaging and Delivery of Proposal.

3. 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 8-13.

The business proposal does not need to include a price proposal for the General Task Areas of the Statement of Work; however, a general price/cost list is required as well as a price proposal for each Sample Task Order for which the offeror submits a proposal. In addition, the task order business proposal must follow the requirements of Section L of the Solicitation. All Sample Task Orders are to be proposed as Firm-Fixed-Price Task Orders.

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

4. PROPOSAL REVIEW: While Offerors are to submit one proposal (one Technical Proposal and one Business Proposal) in response to this solicitation, each Sample Task Area will be reviewed as a stand-alone proposal.

A sample proposal format is attached.

5. TYPE OF AWARD: It is anticipated that the majority of task orders will be firm fixed price. However, it is possible that some task orders may be awarded as cost reimbursement.

6. IDIQ AWARDS: NHLBI reserves the right to issue one or more awards in Task Areas based on best value to the Government (ex. Offeror submitted a proposal in response to Task Areas 1, 2, and 3, however, an award is made for Task Areas 1 and 2 only).

7. SUMMARY OF SOLICITATON SECTIONS:

a. 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.

b. SECTION J

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

Solicitation Attachments 14, 15, and 19 are to be submitted with each specific sample task order proposal (Attachments 8-13). Solicitation Attachment 16 should be submitted with the General Technical Task Area Proposal.

c. SECTION K

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

d. 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 30 pages combined and the technical proposal section for Sample Task Orders 1, 2 and 3 must be no more than 30 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.

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

Attachment:

Attachment A – Sample Proposal Format

Attachment A

Sample Proposal Format

The following sample format is provided as guidance to assist the offeror in the submission of their proposal in response to this solicitation.

As this is a solicitation for an IDIQ contract, offerors will submit a Technical and Business proposal in support of the general tasks (see Attachment 3 - Statement of Work) and a Technical and Business proposal for each specific Sample Task Order (see Attachments 8-13).

Each proposal must include all required content detailed in the solicitation. The below sample format is suggested guidance only. It is the offeror’s responsibility to follow Section L of the solicitation and verify all pertinent information is included in their proposal submission.

NOTE TO OFFERORS: All offerors must submit a task order proposal for task order 1 – Manual of Operations and Sample Task Order 1 – Manual of Operations. Task Order 1 reflects the IDIQ minimum.

Proposal (Cover Page)

A. General Task Area Proposal (See Statement of Work)

a. Technical Proposal (Cover Page) – Not to exceed 30 pages (See Section L)

i. Technical Discussions

1. Statement of Work (Page 79-80)

a. Address general task areas in which offeror is proposing (See Attachment 3 – Statement of Work)

b. Address maximum capacity for each task area in which offeror is proposing

2. Personnel (Page 80-83)

ii. Other Considerations (Page 83)

iii. Electronic and Information Technology Accessibility, Section 508

Compliance (Page 83-84)

b. Business Proposal (Cover Page)

i. General Price/Cost List (Page 84 and 90)

1. Identify max capacity with associated cost/price points up to max capacity (refer to item A.a.i.1.b. above), page 84

2. Note: The government reserves the right to issue cost reimbursement task orders. Requirements included on pages 85- 90 will be required when submitting a proposal in response to future cost reimbursement Request for Task Order Proposals

(RFTOP).

3. Reference Salary Rate Limitation, page 90.

ii. Small Business Subcontracting Plan for max IDIQ cost identified in solicitation (if other than small business) (Page 90-92)

iii. Mentor-Protégé Program, HHSAR 352.219-70 (Page 92-93)

Attachment A – Sample Proposal Format

1. If not applicable, state not applicable

iv. HUBZone Small Business Concerns (Page 93)

v. Total Compensation Plan (Page 93-94)

vi. Other Administrative Data (Page 94)

1. Property (Page 94-95)

2. Submission of Electronic Funds transfer Information with Offer, FAR Clause 52.232-38 (JULY 2013) (Page 95)

3. Financial Capacity (Page 95)

4. Adequate Accounting System (Page 96)

5. Facilities Capital Cost of Money, FAR 52.215-16 (June 2003)

(Page 96-97)

vii. Qualifications of the Offeror (Page 97-98)

viii. Subcontractors (Page 98)

ix. Proposer’s Annual Financial Report (Page 98)

x. Travel Costs/Travel Policy (Page 98)

xi. Past Performance (Page 67-68)

xii. Information Systems Security (Page 68-79)

B. Sample Task Order Proposal – Task Area 1 – Manual of Operations

a. Technical Proposal – Not to exceed 30 pages (See Section L)

i. Statement of Work (Page 79-80)

1. Address specific task areas as identified in the request for task order proposal (RFTOP) (attachments 8)

b. Business Proposal

i. Price Proposal based off minimum identified in the solicitation

C. Sample Task Order Proposal (addresses task areas 2-6 as applicable – one for each task area)

a. Technical Proposal - Not to exceed 30 pages for each sample task area (See Section L)

i. Statement of Work (Page 79-80)

1. Address specific task areas as identified in the request for task order proposal (RFTOP) (attachments 9-13, as applicable)

ii. Personnel (Page 80-83)

iii. Other Considerations (Page 83)

b. Business Proposal (addresses costs for task areas 2-6 as applicable)

i. Firm Fixed-Price breakdown for specific task area

1. Supporting price documentation

Sample Task Order Proposals will be evaluated in accordance with SECTION M of the Solicitation. General Proposals will be reviewed to verify they are in compliance with the Solicitation.

- 1 -

SOLICITATION

SECTION A - SOLICITATION/CONTRACT FORM

1. Requisition or other Purchase Authority: Public Health Service Act (42 USC 301 )

2. Request for Proposal (RFP) Number:

NHLBI-CSB-HV-2016-36-JS

3. Issue Date:

April 28, 2016

4. Set Aside:

[X] No

[ ] Yes See Part IV Section L

5. Title : Centralized Omics REsource (CORE)

6. ISSUED BY:

Office of Acquisitions National Heart, Lung, and Blood Institute National Institutes of Health 6701 Rockledge Drive RKL II, Room 6135A Bethesda, MD 20892

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 3:00 PM EST on June 1, 2016. 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. Questions on this solicitation shall be submitted electronically by 2:30 PM EST on May 16, 2016 to Jennifer.Swift@nih.gov. If an offeror intends to submit a proposal, the Proposal Intent Response Sheet, Attachment 2, must be completed and submitted by 3:00 PM EST on May 23, 2016.

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 http://www.sam.gov

11. FOR INFORMATION CALL: Jennifer Swift

PHONE: 301-435-0355

e-MAIL: Jennifer.Swift@nih.gov

COLLECT CALLS WILL NOT BE ACCEPTED.

Jennifer Swift Contracting Officer Office of Acquisitions National Heart, Lung, and Blood Institute http://www.sam.gov

RFP Number : NHLBI-CSB-HV-2016-36-JS

- 2 -

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. NOTICE OF SMALL BUSINESS GOAL

c. NAICS CODE AND SIZE STANDARD

d. TYPE OF CONTRACT AND NUMBER OF AWARDS

e. TASK ORDERS UNDER MULTIPLE AWARD INDEFINITE DELIVERY CONTRACTS

f. COMMITMENT OF PUBLIC FUNDS

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. Uniform Resource Locators (URLs) in Contract Proposals

6. Page and Formatting Limitations

7. Alternate Proposals

8. Evaluation of Proposals

9. Potential Award Without Discussions

10. Use of the Metric System of Measurement

- 3 -

11. Privacy Act - Treatment of Proposal Information

12. Selection of Offerors

13. ROTC Access and Federal Military Recruiting on Campus

14. Certification of Filing and Payment of Taxes

15. Past Performance Information

16. Information and Physical Access Security

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

18. Solicitation Provisions Incorporated by Reference

b. TECHNICAL PROPOSAL INSTRUCTIONS

1. Technical Discussions

2. Other Considerations

3. Technical Evaluation

c. BUSINESS PROPOSAL INSTRUCTIONS

1. Basic Cost/Price Information

2. Proposal Cover Sheet

3. Cost and Pricing Data

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

5. Salary Rate Limitation

6. Small Business Subcontracting Plan

7. Mentor Protege Program, HHSAR 352.219-70

8. HUBZone Small Business Concerns

9. Total Compensation Plan

10. Other Administrative Data

11. Qualifications of the Offeror

12. Subcontractors

13. Proposer's Annual Financial Report

14. Travel Costs/Travel Policy

SECTION M - EVALUATION FACTORS FOR AWARD

1. GENERAL

2. COST/PRICE EVALUATION

3. MANDATORY QUALIFICATION CRITERIA

4. TECHNICAL EVALUATION FACTORS

5. EVALUATION OF ELECTRONIC AND INFORMATION TECHNOLOGY ACCESSIBILITY- SECTION

6. PAST PERFORMANCE FACTOR

7. SUBCONTRACTING PROGRAM EVALUATION CRITERIA

- 4 -

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 objective of the Centralized Omics REsource (CORE) contract program is to acquire services to generate Omics data for studies selected by NHLBI for participation in TOPMed. Omics technologies include Large Scale WGS, DNA Methylation, RNA Sequencing, Metabolic Profiling, and Novel Omics Technologies.

These services will be applied to studies and cohorts selected for the TOPMed program to discover factors that influence disease risk, identify subtypes of disease, and develop more targeted and personalized treatments. In addition to providing a comprehensive view of the genetic architecture, an unprecedented rich and multilayered data resource will be available to the scientific community stimulating innovative approaches to examine novel questions and generate cutting-edge methodologies to address heart, lung, blood, and sleep (HLBS) disorders.

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 a total of $1,000 (minimum) nor more than a total of approximately $505,000,000 (maximum) for successful performance of this contract.

b. The prices set forth in this ARTICLE will cover the contract period September 2016 through September 2021.

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

Task Area Description Cost Type

1 Generate a Manual of Operations

Firm Fixed Price

2 Whole Genome Sequencing Firm Fixed Price / Cost

3 DNA Methylation Profiles Firm Fixed Price / Cost

4 RNA Transcriptome Sequence Profiles

Firm Fixed Price / Cost

5 Metabolite Profiles Firm Fixed Price / Cost

- 5 -

Task Area Description Cost Type

6 Novel Omics Profiles Firm Fixed Price / Cost

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

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, the Contractor may invoice for the full value of all samples.

- 6 -

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 January 20, 2016, 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 hardcopy of each final 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 under "Making Files Accessible."

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

1. 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 - Whole Genome 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] Weekly [ ] Quarterly [ ] Semi-Annually [ ] Annually [ ] Annually (with a requirement for a Draft Annual Report)

The Contractor shall submit a 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 week 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 Whole Genome Sequencing (WGS), the weekly and monthly Quality Control (QC) data (used here and http://www.hhs.gov/web/508/index.html

- 7 -throughout encompassing quality assurance and quality control activities), the weekly and monthly production, completeness, mean coverage, heterozygosity, fraction of coverage at 2/3 of the mean, median library insert size, % of bases above Q10, Q20, and Q30 for the given read size, known (filtered) SNV Ti/Tv Ratio, and novel (filtered) SNV Ti/Tv Ratio. Status data should include: initial QC data parsed into "not yet processed," "failed," and passed; number of samples attempted sequencing parsed into "in progress," "failed sequencing, "and "passed sequencing (and passed all QC)"; and "number of samples submitted to Informatics Resource Center (IRC)."

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 in addition to the required electronic version(s) 1 hard copy to the COR 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 - Genome-Wide Methylation Profiles

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 genome-wide DNA methylation profiling, the bi-weekly and monthly QC data, the bi-weekly and monthly profiling completeness. Status data should include: number of samples attempted profiling parsed into "in progress," "failed profiling, "and "passed profiling (and passed all QC)"; and "number of samples submitted to IRC."

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

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iv. Recommendations.

For proposal preparation purposes only, it is estimated that in addition to the required electronic version(s) 1 hard copy to the COR 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)

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 - RNA Transcriptome Sequencing Profiles

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)

i. A qualitative description of overall progress, including the status of the RNA transcriptome sequence profiling, the bi-weekly and monthly QC data, the bi-weekly and monthly profiling completeness. Status data should include: number of samples attempted profiling parsed into "in progress," "failed profiling, "and "passed profiling (and passed all QC)"; and "number of samples submitted to IRC."

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

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

- 9 -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 - Metabolite Profiles

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

i. A qualitative description of overall progress, including the status of the targeted and non-targeted metabolite profiling, the bi-weekly and monthly QC data, the bi-weekly and monthly profiling completeness. Status data should include: number of samples attempted profiling parsed into "in progress," "failed profiling, "and "passed profiling (and passed all QC)"; and "number of samples submitted to IRC."

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

Final - Upon final completion of the contract X Final - Upon final completion of the contract (with a requirement for a Draft 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 - Novel Omics Profiles

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

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i. A qualitative description of overall progress, including the status of the novel omics profiling, the bi-weekly and monthly QC data, the bi-weekly and monthly profiling completeness. Status data should include: number of samples attempted profiling parsed into "in progress," "failed profiling, "and "passed profiling (and passed all QC)"; and "number of samples submitted to IRC."

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 in addition to the required electronic version(s) 1 hard copy to the COR 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)

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. WGS Final Manual of Operations for Task Area 2

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 data, including, if necessary, completion of distribution agreements with participating studies and providing evidence of the Contractor's Institutional Review Board approval.

2. Required procedures for DNA preparation, aliquotting, labeling, and shipping, and minimum acceptable standards for DNA quantity and quality for samples submitted for sequencing.

3. Provision for whole genome amplification if submitted DNA samples are not sufficient for proposed analyses.

4. Procedures for tracking data and sample identification information for samples submitted for whole genome sequencing.

5. Methods for electronic and genetic tracking of samples including but not limited to genetic barcodes and gender identification; minimization of sample switches, losses, and

- 11 -cross contamination; tracking of work, and details of the in-house Laboratory Information Management System (LIMS).

6. Methods for storage of DNA samples and back-up plans.

7. Recommendations for sample platting and other strategies to assist in minimizing batch effects and other biases.

8. Updates in the above agreed to between the Government and the Contractor.

ii. Detailed description of the large-scale WGS method, including:

1. Methods for optimizing and evaluating the WGS method and platform.

2. Instrumentation and robotics necessary to perform whole genome 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 WGS analysis and Quality Control (QC) (which may include):

quantification, post library prep, on-instrument sequencing raw data and post genome build, preprocessing, mapping, post-alignment processing, variant calling, annotation, and prioritization, including criteria, the tools used and versioning.

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 DNA samples or 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 genetic analysis including but not limited to the evaluation of Mendelian inconsistencies and checks for Hardy-Weinberg equilibrium, as well as internal standards and QC/Quality Assurance (QA) used in the workflow of WGS analysis: raw data QC, preprocessing, mapping, post-alignment processing, variant calling, annotation, and prioritization.

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

- 12 -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

b. Final Manual of Operations for Task Areas 3-6 (DNA Methylation Profiles, RNA Transcriptome Sequence Profiles, Metabolite Profiles, Novel Omics Profiles)

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

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

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

4. Methods for electronic tracking of samples including but not limited to barcodes;

minimization of sample switches, losses, and cross contamination; tracking of work, and details of the in-house Laboratory Information Management System (LIMS).

5. Methods for storage of omics 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 and the Contractor.

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

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

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

3. Methods for incorporating approaches 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 QC.

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 the proposed omics profiling 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.

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

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

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

v. Detailed description of informatics used for the proposed omics profiling, 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 AREA 2 - Whole Genome Sequencing

a. Pilot QC Report

Secure delivery of pilot QC of representative cohort(s) DNA samples and TOPMed controls to Contracting Officer's Representative (COR), designated cohort, and NHLBI designated Data Coordinating Center (DCC).

3. TASK AREA 3 - Genome-Wide Methylation

a. Timeline

Provide timeline for generating genome-wide methylation profiles at 90 days, 6 months, 9 months and 1 year to Contracting officer, Contracting Officer Representative

4. TASK AREA 4 - RNA Transcriptome Sequencing

a. Timeline

Provide timeline for generating RNA transcriptome sequencing profiles at 90 days, 6 months, 9 months and 1 year to Contracting officer, Contracting Officer Representative

5. TASK AREA 5 - Targeted and Non-Targeted Metabolite Profiles

a. Timeline

Provide timeline for generating targeted and non-targeted metabolite profiles at 90 days, 6 months, 9 months and 1 year to Contracting officer, Contracting Officer Representative

6. TASK AREA 6 - Novel Omics

a. Timeline

Provide timeline for novel omics profiles at 90 days, 6 months, 9 months and 1 year to Contracting officer, Contracting Officer Representative

7. TASK AREAS 2 - 6 - Technology Evaluation Proposals

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As described in the SOW, 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.

c. Other Reports/Deliverables

1. Information Security and Physical Access Reporting Requirements - TASK 2 ONLY (Whole Genome Sequencing)

The Contractor shall submit the following reports as required by the INFORMATION AND PHYSICAL ACCESS SECURITY Article in SECTION H of this contract. Note: Each report listed below includes a reference to the appropriate subparagraph of this article.

a. Roster of Employees Requiring Suitability Investigations

The Contractor shall submit a roster, by name, position, e-mail address, phone number and responsibility, of all staff (including subcontractor staff) working under the contract who will develop, have the ability to access, or host and/or maintain a Federal information system(s). The roster shall be submitted to the Contracting Officer's Representative (COR), with a copy to the Contracting Officer, within 14 calendar days of the effective date of the contract. (Reference subparagraph A.e. of the INFORMATION AND PHYSICAL ACCESS SECURITY Article in SECTION H of this contract.)

b. IT Security Plan (IT-SP)

The contractor shall submit the IT-SP within thirty (30) days after contract award.

This is the start of the file's text. The full file is on GovTribe.

File details come from the government source that posted it. Updated Nov 14, 2017.