RFPN02CO0700965.pdf

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SOLICITATION

SECTION A - SOLICITATION/CONTRACT FORM

1. Purchase Authority: Public Law 92-218 as amended

2. Request for Proposal (RFP) Number:

N02CO07009-65

3. Issue Date:

March 15, 2010

4. Set Aside:

[X] No

[ ] Yes Part IV Section L

5. Title : RECOVERY - Networks of Tissue Source Site (TSS) in support of The Cancer Genome Atlas (TCGA) Program

6. ISSUED BY:

Office of Acquisitions National Cancer Institute National Institutes of Health Treatment and Support Branch P.O. Box B, 244 Miller Drive, Room 112 Fort Detrick Frederick, Maryland 21702-1201

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 2:00 p.m. local time on April 15, 2010. 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 TO THE OFFICIAL POINT OF RECEIPT FOR

THE PURPOSE OF DETERMINING TIMELY DELIVERY AS STATED IN ATTACHMENT 1, "PACKAGING

AND DELIVERY OF THE PROPOSAL." IF YOUR PROPOSAL IS NOT RECEIVED BY THE CONTRACTING OFFICER OR HIS DESIGNEE AT THE PLACE AND TIME SPECIFIED, THEN IT WILL BE CONSIDERED LATE AND HANDLED IN ACCORDANCE WITH SUBPARAGRAPH (c)(3) OF FAR CLAUSE 52.215-1, ENTITLED, "INSTRUCTIONS TO OFFERORS--COMPETITIVE ACQUISITION" LOCATED IN SECTION L.1.

OF THIS SOLICITATION.

10. Offeror must be registered in the Central Contractor Registry (CCR) prior to award of a contract. http:// www.ccr.gov

11. FOR INFORMATION CALL: C. Timothy Crilley

PHONE: 301-228-4224

e-MAIL: tcrilley@mail.nih.gov

COLLECT CALLS WILL NOT BE ACCEPTED.

Please refer to Section L.1., (General Information) regarding questions pertaining to this Request for Proposal. C. Timothy Crilley

Contracting Officer Office of Acquisitions National Cancer Institute http://www.ccr.gov http://www.ccr.gov

RFP Number : N02CO07009-65

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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. COMMITMENT OF PUBLIC FUNDS

e. COMMUNICATIONS PRIOR TO CONTRACT AWARD

f. RELEASE OF INFORMATION

g. REFERENCE MATERIALS

h. PREPARATION COSTS

i. SERVICE OF PROTEST

j. AVAILABILITY OF THE "FEDERAL ADP AND TELECOMMUNICATIONS STANDARDS INDEX."

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. Standards for Privacy of Individually Identifiable Health Information

10. Privacy Act - Treatment of Proposal Information

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11. Selection of Offerors

12. ROTC Access and Federal Military Recruiting on Campus

13. Past Performance Information

14. Solicitation Provisions Incorporated by Reference

b. TECHNICAL PROPOSAL INSTRUCTIONS

1. Technical Discussions

2. Other Considerations

3. Technical Evaluation

4. Human Subjects

5. Instructions to Offerors Regarding Protection of Human Subjects

6. Required Education in the Protection of Human Research Participants

7. Inclusion of Women and Minorities in Research Involving Human Subjects

8. Inclusion of Children in Research Involving Human Subjects

9. Research Involving Prisoners as Subjects

10. Research Involving Recombinant DNA Molecules (including Human Gene Transfer Research)

11. Obtaining and Disseminating Biomedical Research Resources

12. Information Security

c. BUSINESS PROPOSAL INSTRUCTIONS

1. Basic Cost/Price Information

2. Cost and Pricing Data

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

4. Small Business Subcontracting Plan

5. HUBZone Small Business Concerns

6. Extent of Small Disadvantaged Business Participation

7. Total Compensation Plan

8. Other Administrative Data

9. Qualifications of the Offeror

10. Subcontractors

11. Proposer's Annual Financial Report

12. Travel Costs/Travel Policy

SECTION M - EVALUATION FACTORS FOR AWARD

1. GENERAL

2. EVALUATION OF OPTIONS

3. EVALUATION OF DATA SHARING PLAN

4. TECHNICAL EVALUATION CRITERIA

5. PAST PERFORMANCE FACTOR

6. EXTENT OF SMALL DISADVANTAGED BUSINESS PARTICIPATION

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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 purpose of this project is to establish Tissue Source Site (TSS) Networks capable of delivering clinically annotated biospecimens through either/both retrospective and prospective collections. The tissues and clinical data will be delivered to one of the TCGA's Biospecimen Core Resources(s) (BCRs) for storage, quality control, processing into molecular analyses, and other research efforts. Ultimately, the samples will be characterized for copy number variation, single nucleotide polymorphisms, epigenomic profiles, gene and miRNA expression and mulation analysis.

ARTICLE B.2. ESTIMATED COST AND FIXED FEE

a. The estimated cost of the Base Period of this contract is $ .

b. The fixed fee for the Base Period of this contract is $ . The fixed fee shall be paid in installments based on the percentage of completion of work, as determined by the Contracting Officer. Payment shall be subject to the withholding provisions of the clauses ALLOWABLE COST AND PAYMENT and FIXED FEE referenced in the General Clause Listing in Part II, ARTICLE I.1. of this contract. Payment of fixed fee shall not be made in less than monthly increments.

c. The total estimated amount of the contract, represented by the sum of the estimated cost plus the fixed fee for the Base Period is $ .

d. If the Government exercises its option pursuant to the OPTION PROVISION Article in SECTION H of this contract, the Government's total estimated contract amount represented by the sum of the estimated cost plus the fixed fee will be increased as follows:

Estimated Cost

Fixed Fee

Estimated Cost Plus Fixed Fee

Base Period (17 months)

Base Period - Optional Quantities (Not To Exceed)

Option Period One (1) - (12 months)

Option Period One (1) - optional quantities

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Estimated Cost

Fixed Fee

Estimated Cost Plus Fixed Fee

Option Period Two (2) - (12 months)

Option Period Two (2) - optional quantities

Option Period Three (3) - (12 months)

Option Period Three (3) - optional quantities

Option Period Four (4) - (7 months)

Option Period Four optional quantities

Total Estimated Contract Including Option Period(s) and Optional Quantities(s)

e. Total funds currently available for payment and allotted to this contract are $ of which $ represents the estimated costs, and of which $ represents the fixed fee. For further provisions on funding, see the LIMITATION OF COST clause referenced in Part II, ARTICLE I.2. Authorized Substitutions of Clauses.

f. It is estimated that the amount currently allotted will cover performance of the contract through .

g. The Contracting Officer may allot additional funds to the contract without the concurrence of the Contractor.

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) Acquisition, by purchase or lease, of any interest in real property; 2) Special rearrangement or alteration of facilities; 3) Purchase or lease of any item of general purpose office furniture or office equipment regardless of dollar value; 4) Travel Costs; 5) Consultant Costs; 6) Subcontract Costs; 7) Patient Care Costs; 8) Accountable Government Property; and 9) 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. In addition, the following Advance Understandings will be incorporated into the resulting contracts:

1. Disposition of Data

The Cancer Genome Atlas (TCGA) has been identified by NCI and NHGRI as a "community resource project," meaning that its primary goal is to produce a set of resources that will be widely valuable to the broad scientific community. TCGA is also fully committed to the long-standing National Institutes of Health policy on the importance of data sharing as an essential component to the rapid translation of research results into improvements in public health.

Therefore, TCGA has established a policy of data release and data sharing that supports these overall goals while maintaining the rights and privacy of people who participate in TCGA as tissue donors.

Data Release: All data sets from TCGA are managed through a central Data Coordination Center (DCC) that uses caBIGTM infrastructure. Genome characterization data are released by data producers into open- and controlled-access databases as soon as the data are verified, with the recognition that different experimental platforms may have different sets of standards for verification. Clinical data associated with samples are collected by the Biospecimen Core Resource (BCR) and tracked by the DCC. Large-scale sequencing data are submitted to the National Center for Biotechnology Information Short Read Archive.

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Data Sharing: TCGA data are made available through a Data Portal hosted on the TCGA website (http:// tcga.cancer.gov/dataportal/data/about/) and managed by the DCC. TCGA recognizes the responsibilities involved in undertaking human subjects research, including respect for participant privacy and bioethics concerns associated with genomic studies. With the exception of the original sample providers, no TCGA investigator has access to the identity of research participants. All data in the public database derived from a single participant are linked by a sample identifier. However, TCGA does capture extensive amounts of genomic and clinical data that could theoretically be matched to data in a second database and thereby reveal a participant's identity. To address this possibility, a two-tiered data access system has been established. The Open-access tier contains only data that cannot be assembled in a manner that could allow identification of an individual participant. A second, controlled-access, tier of information includes information that is unique to an individual participant, including both clinical and genomic elements. Access to the second data tier is limited to qualified researchers who agree, along with their institution, to safeguard the data and to respect the privacy of participants; see the TCGA Participants Protections Policies (http://tcga.cancer.gov/ objects/pdfs/TCGA_Human_Subjects_prot_%20policy.pdf) for more information on the procedures implemented by TCGA to ensure protect participant privacy and for the specific data types available in each tier (open- and controlled-access). Failure of a User to follow the requirements of the Data Access Agreement will result in loss of access to the controlled-access data.

2. Required Education in the Protection of Human Research Participants

NIH policy requires education on the protection of human subject participants for all investigators receiving NIH contract awards for research involving human subjects. For a complete description of the NIH Policy announcement on required education in the protection of human subject participants, the Contractor should access the NIH Guide for Grants and Contracts Announcement dated June 5, 2000 at the following website:

http://grants.nih.gov/grants/guide/notice-files/NOT-OD-00-039.html .

The information below is a summary of the NIH Policy Announcement:

The Contractor shall maintain the following information: (1) a list of the names and titles of the principal investigator and any other individuals working under the contract who are responsible for the design and/or conduct of the research; (2) the title of the education program(s) in the protection of human subjects that has been completed for each named personnel and; (3) a one sentence description of the educational program(s) listed in (2) above. This requirement extends to investigators and all individuals responsible for the design and/or conduct of the research who are working as subcontractors or consultants under the contract.

Prior to any substitution of the Principal Investigator or any other individuals responsible for the design and/or conduct of the research under the contract, the Contractor shall provide the following written information to the Contracting Officer: the title of the education program and a one sentence description of the program that has been completed by the replacement.

3. Obtaining and Disseminating biomedical Research Resources

Unique research resources arising from NIH-funded research are to be shared with the scientific research community.

NIH provides guidance, entitled, "Principles and Guidelines for Recipients of NIH Research Grants and Contracts on Obtaining and Disseminating Biomedical Research Resources: Final Notice," (Federal Register Notice, December 23, 1999 [64 FR 72090]), concerning the appropriate terms for disseminating and acquiring these research resources.

This guidance, found at : http://ott.od.nih.gov/pdfs/64FR72090.pdf is intended to help contractors ensure that the conditions they impose and accept on the transfer of research tools will facilitate further biomedical research, consistent with the requirements of the Bayh-Dole Act and NIH funding policy.

Note: For the purposes of this Article, the terms, "research tools", "research materials", and "research resources" are used interchangeably and have the same meaning.

4. Compatibility

All work performed under this project must be compatible with the Biospecimen Core Resource (BCR) contracts and TCGA Data Coordinating Center (DCC) tools and those developed during the course of the project by Genome Data Analysis Centers, including but not limited to the format of the files/information submitted to the Government BCR.

5. Shipping Costs

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Costs for packaging and shipping of tissue shall be paid by the Biospecimen Core Resource (BCR) and shall not be paid under this contract.

6. American Recovery and Reinvestment Act (ARRA) Funds

The base period of this contract will be funded by American Recovery and Reinvestment Act (ARRA) funds. The Government's obligation under this contract is for the initial base period. Funding for the option years and/or optional quantities is subject to the availability of appropriated funds and programmatic relevance/balance/need.

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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 February 3, 2010, attached hereto and made a part of this Solicitation (See SECTION J - List of Attachments).

b. The applicable Privacy Act System of Records Number will be specified and shall be used in any design, development, or operation work to be performed under the resultant contract. Disposition of records shall be in accordance with SECTION C of the contract, and by direction of the Contracting Officer's Technical Representative (COTR).

ARTICLE C.2. REPORTING REQUIREMENTS

All reports required herein shall be submitted in electronic format. In addition, one (1) hardcopy of each report shall be submitted to the Contracting Officer, unless otherwise specified.

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.]

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

[ ] Monthly [X] Quarterly [ ] Semi-Annually [ ] Annually [ ] Annually (with a requirement for a Draft Annual Report) [X] Final - Upon final completion of the contract [ ] Final - Upon final completion of the contract (with a requirement for a Draft Final Report)

Quarterly Technical Progress Report

Each quarter, a technical progress report will be required. In this report, the Contractor shall present a summary of all the work performed, including the technical approaches employed, the analysis performed, the results obtained during the reporting period and timeline of data submission. The report shall specifically include numbers of samples and cases sequenced, number of samples and cases failed, number of samples and cases analyzed, number of samples and cases in the pipeline and number of cases for whom the data was submitted in each period. The information shall be updated each quarter and project total included for each category. In addition, the Report shall include a description of any problems encountered in sequencing and analysis performance, the solutions found and applied, as well as any recommendations to the COTR for improved technical procedures and/or protocols. The Progress

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Report shall be written (provided electronically) in the format established by NCI. The Contractor shall participate in a quarterly teleconference with TCGA program officials within one (1) week of report submission at which results, problems etc. are discussed, evaluated and resolved.

Final Report

The Contractor shall submit the Final Report, which shall summarize the results of the entire contract work for the complete performance period. This report shall be in sufficient detail to explain comprehensively the results achieved.

The final report shall contain:

a. Title Page

b. Introduction covering the purpose and scope of the contract effort, including technologies used in some detail

c. Description of the overall process

d. Tabulation of the data output for the entire project.

b. Other Reports/Deliverables

1. American Recovery and Reinvestment Act-Reporting Requirements

This contract requires the Contractor to provide products and/or services that are funded by the American Recovery and Reinvestment Act of 2009 (Recovery Act). Section 1512(c) of the Recovery Act requires the contractor to report on its use of Recovery Act funds under this contract.

The Contractor shall report the information required by FAR 52.204-11(d), which is incorporated into Article I.4. of this contract, using the online reporting tool available at http:// www.FederalReporting.gov.

Reports for effort funded, in whole or in part, by the Recovery Act are due no later than the 10th day after the end of each calendar quarter.

These reports will be made available to the public.

In addition, the Contractor shall submit a courtesy copy of each report to the Contracting Officer and Contracting Officer's Technical Representative (COTR).

2. Information Security Reporting Requirements

The Contractor shall submit the following reports as required by the INFORMATION 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 Technical Representative (COTR), with a copy to the Contracting Officer, within 14 calendar days of the effective date of the contract. Any revisions to the roster as a result of staffing changes shall be submitted within 15 calendar days of the change. Reference subparagraph c.(2) of the INFORMATION SECURITY Article in SECTION H of this contract.

b. Information Security Training Report http://www.FederalReporting.gov http://www.FederalReporting.gov

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The Contractor shall maintain a listing by name and title of each employee (including subcontractors) working under this contract that has completed the NIH required information security training. Any additional security training completed by Contractor/ Subcontractor staff shall be included on this listing. The listing of completed training shall be included in the first technical progress report. (See Article C.2.a. Technical Progress Reports.) Any revisions to this listing as a result of staffing changes shall be submitted with next required technical progress report. Reference subparagraph d. of the INFORMATION SECURITY Article in SECTION H of this contract.

c. Reporting of New and Departing Employees

The Contractor shall notify the Contracting Officer's Technical Representative (COTR) and Contracting Officer within five business days of staffing changes for positions that require suitability determinations as follows Reference subparagraph f. of the INFORMATION SECURITY Article in SECTION H of this contract.:

(1) New Employees: Provide the name, position title, e-mail address, and phone number of the new employee. Provide the name, position title and suitability level held by the former incumbent. If the employee is filling a new position, provide a description of the position and the Government will determine the appropriate security level.

(2) Departing Employees: 1) Provide the name, position title, and security clearance level held by or pending for the individual; and 2) Perform and document the actions identified in the "Employee Separation Checklist", attached in Section J, ATTACHMENTS of this contract, when a Contractor/Subcontractor employee terminates work under this contract.

All documentation shall be made available to the COTR and/or Contracting Officer upon request.

d. Contractor - Employee Non-Disclosure Agreement(s)

The contractor shall complete and submit a signed and witnessed "Commitment to Protect Non-Public Information - Contractor Agreement" form for each contractor and subcontractor employee who may have access to non-public Department information under this contract. This form is located at: http://ocio.nih.gov/security/Nondisclosure.pdf.

Reference subparagraph g.of the INFORMATION SECURITY Article in SECTION H of this contract.

e. Self Assessment & Information Security Plan Reporting

(1) NIST SP 800-53 Self-Assessment (Reference subparagraph h. of the INFORMATION SECURITY Article in SECTION H of this contract.)

The contractor shall annually update and resubmit its Self-Assessment required by NIST SP 800-53, Recommended Security Controls for Federal Information Systems to the Contracting Officer's Technical Representative (COTR), with a copy to the Contracting Officer no later than the completion date of the period of performance/ for all other contracts: indicate due date as determined by the COTR/Contracting Officer. ( http:// csrc.nist.gov/publications - under Special Publications).

The Contractor's annual update to its Self-Assessment Questionnaire shall include similar information for any subcontractor that performs under the SOW to (1) develop a Federal information system(s) at the Contractor's/Subcontractor's facility, or (2) host and/or maintain a Federal information system(s) at the Contractor's/Subcontractor's facility.

(2) Information System Security Plan Reference subparagraph i. of the INFORMATION SECURITY Article in SECTION H of this contract.

http://ocio.nih.gov/security/Nondisclosure.pdf http://csrc.nist.gov/publications

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The Contractor's draft ISSP submitted with its proposal shall be finalized in coordination with the COTR no later than 90 calendar days after contract award.

Following approval of its draft ISSP, the Contractor shall update and resubmit its ISSP to the COTR every three years or when a major modification has been made to its internal system. The Contractor shall use the current ISSP template in Appendix A of NIST SP 800-18, Guide to Developing Security Plans for Federal Information Systems. ( http:// csrc.nist.gov/publications/nistpubs/800-18-Rev1/sp800-18-Rev1-final.pdf ).

The Contractor shall include similar information for any subcontractor performing under the SOW with the Contractor whenever the submission of an ISSP is required.

3. Accrual Plan

Upon final selection of TSS for tissue collection networks, Contractor shall deliver to NCI an Accrual Plan that includes estimates for retrospective and prospective:

• Number of cases worth of samples deliverable.

• Number of samples, sample types, and sample formats deliverable

• Timing for the completion of administrative documents.

• Timing for the availability of biospecimens.

• Timing for the availability of data.

• Issues that risk deviation from Contractor's pricing proposal.

• Risk assessment of factors that may significantly impact the above estimates, specifically including, but not limited to:

o Risk to timing of sample and data availability o Risk of not meeting the case and sample numbers.

o Risk of not collecting the minimum required clinical data.

o Risk of not completing administrative documents (human subjects approvals, MTA, DUA, etc.)

• Communication Plan that describes the interactions and reporting between TSS, Contractor, and

NCI.

4. Biospecimen collection protocols

All prospective TSS collection protocols shall be governed by SOP, including, but not necessarily limited to:

o Human subjects protocols o Tissue collection protocols o Tissue handling and storage protocols o Data collection protocols

5. Weekly TSS Membership Reports

Contractor shall be responsible for managing candidate TSS lists, and managing administrative data sufficient to report to NCI on status and progress of candidate TSS through this engagement process.

Contractor shall keep this information current and be able to report to NCI in writing.

6. Weekly Specimen Delivery Reports

Contractor shall collect all necessary data to be able to report, at regular weekly intervals to NCI on the planned and actual number and timing of cases, specimens, and data delivery to BCR, and to http://csrc.nist.gov/publications/nistpubs/800-18-Rev1/sp800-18-Rev1-final.pdf

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7. Monthly SOP Usage Report

The Contractor shall perform a monthly review of the status of SOP use throughout the network of TSS. The Contractor shall report on status of SOP usage (compliance or breech) to NCI on regular monthly basis.

8. Deliverables for Samples

The contractor and all TSS networks shall provide per-case biospecimen sets that meet the following criteria:

• Both tumor tissue and a source of germline DNA (blood or component, DNA, and/or adjacent normal tissue) samples shall be available for every case.

• Primary tumor samples:

o Derived from patients with a primary, untreated malignancy.

o Snap-frozen to -86 deg C or colder o Sufficient tissue to yield 10 ug of co-isolated DNA and RNA (this is typically 100 -150 mg of tissue).

o Secondary tumors are excluded.

o Optionally, neoadjuvantly treated recurrent tumors and/or metastases are requested, but only when case-matched with a primary, untreated specimen.

o The time from cutoff of in vivo blood supply (devascularization) to ex vivo stabilization (freezing) shall be within 60 minutes; however 30 minutes or less is preferred.

o A case-matched representative FFPE H&E section, or whole slide H&E stained digital image of section, from the original anatomic pathology diagnostic block of the tumor, confirmatory of the cancer.

o Cellular composition of tumor sample shall be known or can be determined. By default for any cancer, the following tissue cellular composition cutoff values shall be used. Note, however, that cancer-specific values are subject to change at the discretion of the NCI, as dictated by TCGA goals and technological requirements.

o Each tumor sample shall be composed predominantly of histologically viable appearing tumor cells o Of viable cell nuclei present, on average, >= 70% shall be tumor nuclei.

o <= 30% of viable cells present may be normal stromal, inflammatory or immune cells o If necrosis is present, it may comprise no more than 30% of sample volume.

• Normal tissue:

o Blood or blood component, a frozen sample of normal tissue, or both from the same patient shall be available for each case for purpose of obtaining germline DNA. In order of preference, the following are suitable: whole blood, PBL, purified DNA, other normal solid tissue.

o The sample shall be sufficient to yield at least 10 micrograms of DNA.

o If previously extracted DNA is provided, 10 micrograms shall be prepared. Assuming a normal white blood cell count and optimal cell recovery techniques, one 10-ml tube of blood is sufficient for recovery of 20-µg of DNA, which is more than the optimal amount for TCGA analyses. If the white count is low or the cell recovery techniques sub-optimal, more blood may be required. Collection tube types, in descending order of preference are:

o Yellow-top tube (Becton-Dickinson CPT, sodium citrate) o Blue-top tube (Sodium citrate) o Green-top tube (Heparin based tube) o Purple-top tube (EDTA) or red/black tiger-top tube (EDTA)

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• Tumor biospecimens shall be prescreened by the contractor and all TSS to meet TCGA specifications. Prescreening shall be performed on a single section taken directly adjacent to one surface of the frozen candidate sample that would be sent to BCR. Any samples containing tumor within 10% of the cutoff value shall be submitted, as determined by review of a single section from one surface of the frozen material. Standard Operating Protocols for this process are in Appendix C.

9. Clinical Data Requirement for TCGA Samples

For each TCGA case of biospecimens provided to TCGA, the following data shall be provided:

• Original surgical pathology report, appropriately de-identified, to be submitted with the specimens.

• Biospecimen case control form, to be submitted with the specimens, which includes the documentation of informed consent and/or date of death.

• Tier 1, Tier 2 and Supplemental Case Report Forms (CRF) data, to be submitted once BCR has notified the contractor and the TSS that the specimens have passed relevant Quality Control steps.

o For Tier 1: 100% of elements are required o For Tier 2 and Supplemental forms: >50% of form data elements are required for retrospective cases; 100% of form data elements are required for prospectively obtained cases.

o Data shall be delivered within sixty (60) calendar days of BCR notification

• Follow-up / outcomes CRF at 6 month intervals, until either the patient is deceased or the term of the contract expires.

• Current TCGA generic and cancer specific data collection forms are in Appendix E.

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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.

In addition, the contractor shall:

1. Coordinate with the designated Biospecimen Core Resource (BCR) to ensure that biospecimens are packed appropriately to protect them from loss, damage, and temperature variations during transit. The Contractor shall use vapor phase liquid nitrogen containers to receive frozen biospecimens. The shipping and handling of biospecimens shall meet relevant government regulations for packaging, labeling and shipping of such samples. Air shipments shall conform to the International Air Transport Association (IATA) standards, and ground shipments in the United States shall conform to the Department of Transportation (DOT) standards.

2. Receive both remote and onsite training from a BCR in proper shipping procedures and the SOPs for each step in the shipment process will be provided by the BCR.

3. Not claim reimbursement of shipping costs under this contract; these costs will be covered by the BCR.

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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, Contracting Officer's Technical Representative is the authorized representative of the Contracting Officer.

c. Inspection and acceptance will be performed at:

National Cancer Institute Rockville, Maryland

Acceptance 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 52.246-5, Inspection of Services - Cost-Reimbursement (April 1984).

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SECTION F - DELIVERIES OR PERFORMANCE

ARTICLE F.1. PERIOD OF PERFORMANCE

a. The period of performance of this contract shall be from July 15, 2010 through December 14, 2011.

b. If the Government exercises its option(s) pursuant to the OPTION PROVISION Article in Section H of this contract, the period of performance will be increased as listed below:

Option Option Period *Option Period One (1) December 15, 2011 - December 14, 2012 **Option Period Two (2) December 15, 2012 - December 14, 2013 **Option Period Three (3) December 15, 2013 - December 14, 2014 **Option Period Four (4) December 15, 2014 - July 14, 2015

* The base period will utilize ARRA funding.

**Option periods, if exercised will utilize appropriated funding.

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]:

Item Description Quantity Delivery Schedule

(1) Quarterly Technical

Progress Report Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due on/or before the 15th of the month following the end of the reporting period.

(2) Final Report Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due on/or before the expiration date of the contract.

(3) American Recovery and Reinvestment Act - Reporting Requirements

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due on/or before the 10th day after the end of each calendar quarter.

(4) Roster of Employees Requiring Suitability Investigation

Electronic copy and one (1) hard copy to the Contracting Officer's

Due within fourteen

(14) calendar days of the effective date of the

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Item Description Quantity Delivery Schedule Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer contract. Any revisions to the roster as a result of staffing changes shall be submitted within fifteen

(15) calendar days of the change.

(5) Information Security Training Report

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due prior to performing work under the contract.

Revisions to the list due to staffing changes shall be submitted at least five

(5) calendar days prior to the change. Within ten

(10) calendar days of the anniversary date of the contract, the report shall be updated to reflect the annual refresher course.

(6) Reporting of New and Departing Employees

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due at least five (5) working days before a new employee assumes a position that requires a suitability determination or where an employee stops working under the contract.

(7) Contractor-Employee Nondisclosure Agreements

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due prior to performing work under the contract.

New staff shall complete prior to performing work under the contract.

(8) NIST SP 800-53 Self Assessment & Information

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due on or before the expiration date of the base period and each option period, if exercised.

(9) Security Plan Reporting Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

Due within 90 calendar days after contract award.

Therefore, due when major modifications to the plan are made.

(10) Accrual Plans Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

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Item Description Quantity Delivery Schedule

(11) Biospecimen Collection

Protocols Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

(12) Weekly TSS Membership Reports

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

(13) Weekly Specimen Delivery Reports

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

(14) Monthly SOP Usage Report

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

(15) Deliverables for Samples Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

(16) Clinical Data Requirement for TCGA Samples

Electronic copy and one (1) hard copy to the Contracting Officer's Technical Representative and an electronic copy and one (1) hard copy to the Contracting Officer

As directed by the Contracting Officer's Technical Representative

b. The above items shall be addressed and delivered to:

Addressee Deliverable Item No Quantity Contracting Officer Technical Representative (COTR)

Items (1) through (16) Electronic copy and one (1) hard copy

Contracting Officer Items (1) through (16) Electronic copy and one (1) hard copy

c. Unless otherwise specified, deliveries shall be made to the Delivery Point specified above Mondays through Fridays (excluding Federal Holidays) between the hours of 8:30 a.m. and 3:30 p.m., EST only. Supplies or services scheduled for delivery on a Federal holiday shall be made the following day.

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ARTICLE F.3. CLAUSES INCORPORATED BY REFERENCE, FAR 52.252-2 (FEBRUARY

1998)

This contract incorporates the following clause(s) 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. Also, the full text of a clause may be accessed electronically at this address: http://www.acquisition.gov/comp/far/index.html

FEDERAL ACQUISITION REGULATION (48 CFR CHAPTER 1) CLAUSE:

52.242-15, Stop Work Order (August 1989) with Alternate I (April 1984).

http://www.acquisition.gov/comp/far/index.html

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SECTION G - CONTRACT ADMINISTRATION DATA

ARTICLE G.1. CONTRACTING OFFICER'S TECHNICAL REPRESENTATIVE (COTR)

The following Contracting Officer's Technical Representative (COTR) will represent the Government for the purpose of this contract:

(To be specified prior to award).

The COTR is responsible for: (1) monitoring the Contractor's technical progress, including the surveillance and assessment of performance and recommending to the Contracting Officer changes in requirements; (2) interpreting the statement of work and any other technical performance requirements; (3) performing technical evaluation as required; (4) performing technical inspections and acceptances required by this contract; and (5) assisting in the resolution of technical problems encountered during performance.

The alternate COTR is responsible for carrying out the duties of the COTR only in the event that the COTR can no longer perform his/her duties as assigned.

The Contracting Officer is the only person with authority to act as agent of the Government under this contract. Only the Contracting Officer has authority to: (1) direct or negotiate any changes in the statement of work; (2) modify or extend the period of performance; (3) change the delivery schedule; (4) authorize reimbursement to the Contractor for any costs incurred during the performance of this contract; or (5) otherwise change any terms and conditions of this contract.

The Government may unilaterally change its COTR designation.

ARTICLE G.2. KEY PERSONNEL, HHSAR 352.270-5 (January 2006)

The key personnel specified in this contract are considered to be essential to work performance. At least 30 days prior to diverting any of the specified individuals to other programs or contracts (or as soon as possible, if an individual must be replaced, for example, as a result of leaving the employ of the Contractor), the Contractor shall notify the Contracting Officer and shall submit comprehensive justification for the diversion or replacement request (including proposed substitutions for key personnel) to permit evaluation by the Government of the impact on performance under this contract. The Contractor shall not divert or otherwise replace any key personnel without the written consent of the Contracting Officer. The Government may modify the contract to add or delete key personnel at the request of the Contractor or Government.

(End of Clause)

The following individual(s) is/are considered to be essential to the work being performed hereunder:

Name Title

ARTICLE G.3. INVOICE SUBMISSION/CONTRACT FINANCING REQUEST AND CONTRACT

FINANCIAL REPORT

a. Invoice/Financing Request Instructions and Contract Financial Reporting for NIH Cost-Reimbursement Type Contracts NIH(RC)-4 are attached and made part of this contract. The Contractor shall follow the attached instructions and submission procedures specified below to meet the requirements of a "proper invoice" pursuant to FAR Subpart 32.9, Prompt Payment.

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1. Payment requests shall be submitted to the offices identified below. Do not submit supporting documentation (e.g., receipts, time sheets, vendor invoices, etc.) with your payment request unless specified elsewhere in the contract or requested by the Contracting Officer.

a. The original invoice shall be submitted to the following designated billing office:

National Institutes of Health Office of Financial Management Commercial Accounts 2115 East Jefferson Street, Room 4B-432, MSC 8500 Bethesda, MD 20892-8500

b. One copy of the invoice shall be submitted to the following approving official:

Contracting Officer Office of Acquisitions National Cancer Institute, NIH PO Box B, 244 Miller Drive Room 112 Fort Detrick MSC 1201 Frederick, Maryland 21702- 1201

E-Mail: tcrilley@mail.nih.gov

The Contractor shall submit an electronic copy of the payment request to the approving official instead of a paper copy. The payment request shall be transmitted as an attachment via e-mail to the address listed above in one of the following formats: MSWord, MS Excel, or Adobe Portable Document Format (PDF). Only one payment request shall be submitted per e-mail and the subject line of the e-mail shall include the Contractor's name, contract number, and unique invoice number.

Note: The original payment request must still be submitted in hard copy and mailed to the designated billing office to meet the requirements of a "proper invoice."

2. In addition to the requirements specified in FAR 32.905 for a proper invoice, the Contractor shall include the following information on the face page of all payment requests:

a. Name of the Office of Acquisitions. The Office of Acquisitions for this contract is National Cancer Institute .

b. Central Point of Distribution. For the purpose of this contract, the Central Point of Distribution is NCI OA Branch C - ncibranchcinvoices@mail.nih.gov .

c. Federal Taxpayer Identification Number (TIN). If the Contractor does not have a valid TIN, it shall identify the Vendor Identification Number (VIN) on the payment request. The VIN is the number that appears after the Contractor's name on the face page of the contract. If the Contractor has neither a TIN, DUNS, or VIN, contact the Contracting Officer.

d. DUNS or DUNS+4 Number. The DUNS number must identify the Contractor's name and address exactly as stated in the contract and as registered in the Central Contractor Registration (CCR) database. If the Contractor does not have a valid DUNS number, it shall identify the Vendor Identification Number (VIN) on the payment request. The VIN is the number that appears after the Contractor's name on the face page of the contract. If the Contractor has neither a TIN, DUNS, or VIN, contact the Contracting Officer.

e. Invoice Matching Option. This contract requires a two-way match.

f. Unique Invoice Number. Each payment request must be identified by a unique invoice number, which can only be used one time regardless of the number of contracts or orders held by an organization.

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b. Inquiries regarding payment of invoices shall be directed to the designated billing office, (301) 496-6452.

ARTICLE G.4. INDIRECT COST RATES

In accordance with Federal Acquisition Regulation (FAR) (48 CFR Chapter 1) Clause 52.216-7 (d)(2), Allowable Cost and Payment incorporated by reference in this contract in PART II, SECTION I, the cognizant Contracting Officer representative responsible for negotiating provisional and/or final indirect cost rates is identified as follows:

Director, Division of Financial…