Attachment_6_Rev.pdf

ATTACHMENT 6: ADDITIONAL TECHNICAL PROPOSAL INSTRUCTIONS,

FORMAT FOR TECHNICAL PROPOSAL, and TABLE OF CONTENTS

Nonhuman Primate Major Histocompatibility Complex Allele Discovery and Typing Technology Development

BAA NIAID-DAIT-NIHAI2015033

It is strongly recommended that offerors use the following template as the format for the Technical Proposal. All information presented in the Technical Proposal should be presented in the order specified below.

These Additional Technical Proposal Instructions reflect the requirements of the BAA and provide specific instructions and formatting for the Technical Proposal. While Section L. of the BAA provides a generic set of Technical Proposal Instructions applicable to all NIH R&D solicitations, these Additional Technical Proposal Instructions are tailored to the specific requirements of the BAA. The information requested in these instructions should be used along with Section L of the BAA to format and prepare the Technical Proposal, and should be used as a Table of Contents for your Technical Proposal. Offerors should follow the instructions in Section L of the BAA, and include the information requested here.

Offerors are advised to give careful consideration to the Broad Agency Announcement Description, Background and Introduction, Research and Technical Objectives, all reference materials and attachments, the Technical Evaluation Criteria in Section M, and the BAA as a whole in the development of their Technical Proposals.

Offerors proposing subcontracts and/or consultants to perform portions of the proposed Statement of Work should clearly identify the specific tasks for which they plan to utilize subcontractors and/or consultants, as well as the method and level of integration/coordination between the prime Contractor and all proposed subcontractors and/or consultants, and the expected advantages of such an approach.

Offerors must refer to the BAA Attachment entitled “Packaging and Delivery of the Proposal,” which details strict guidelines, including page limitations, formatting and layout of proposals, and prohibits the offerors use of links to internet web site addresses (URLs) to direct readers to alternate sources of information.

TECHNICAL PROPOSAL – TABLE OF CONTENTS

SECTION 1:

1) PROPOSAL TITLE PAGE. Include BAA title and number, name of organization, DUNS number, and identify if the proposal is an original or a copy. Offerors that include data in their proposals that they do not want disclosed to the public for any purpose, or used by the Government except for evaluation purposes, shall also include the legend regarding Restriction on Disclosure and Use of Data prescribed by FAR 52.215-1(e)]

2) TABLE OF CONTENTS

SECTION 2: TECHNICAL PROPOSAL OVERVIEW (suggested 3-page maximum)

Provide a brief description of the proposed project, including:

1) 1-2 sentence summary describing the concept the offeror is proposing.

2) A summary describing the scope of the activities proposed.

3) A brief description of the activities proposed by the offeror and all proposed subcontractors, including identification of all proposed subcontractors and a list of key personnel for the offeror and the proposed subcontractors with degrees, titles and role in the project.

4) By area of expertise, provide the total number of staff, the number available to be assigned to the contract for the offeror and all proposed subcontractors, and total number of additional staff to be hired and trained.

5) A brief description of the facilities and other resources to be made available by the proposed prime contractor (offeror) and any proposed subcontractors.

SECTION 3: STATEMENT OF WORK FORMAT (suggested maximum of 10 pages)

Offeror(s) are required to provide a Statement of Work in their proposal. The Statement of Work shall be developed by each offeror based on the information in the Attachment entitled “Research and Technical Objectives,” and shall consist of two parts: (1) Scope, and

(2) Technical Requirements. Provided below is an outline of the Statement of Work format that should be used by all offeror(s) in the preparation of their Technical Proposals. The headers and subheaders may be adjusted to match the requirements as proposed in each offeror’s individual technical proposal.

Contracts awarded as a result of this BAA will include the Statement of Work proposed by the offeror, as negotiated and accepted by the Government. Offeror(s) will be required to perform the activities and provide the resources appropriate to the scope of their specific negotiated Statement of Work.

The opening paragraph under the Technical Requirements section of the Statement of Work shall be followed by a description of all activities that the Contractor shall perform after the award of the contract. The Technical Requirements shall include all activities required to effectively implement the project and shall include a description of all items to be delivered to the Government during performance of the contract, such as progress reports, financial reports, end products, and other deliverables, along with a timetable for their delivery.

NOTE TO OFFEROR: Each offeror shall provide detailed specifications of the requirement utilizing the following sample outline of tasks and subtasks. Any tasks or subtasks that are not applicable to your proposed effort should be deleted. Any tasks or subtasks specific to your proposed effort not addressed below shall be added.

[See Statement of Work outline on next page]

SAMPLE STATEMENT OF WORK

1. SCOPE

Instruction to offerors: Provide a brief description (one to two paragraphs) of the overall project and objectives in broad terms that indicates the size and magnitude of the proposed effort.

2. TECHNICAL REQUIREMENTS

[NOTE TO OFFEROR: The Technical Requirements shall begin with the following introductory paragraph.]

Independently, and not as an agent of the Government, the Contractor shall furnish all necessary services, qualified professional, technical, and administrative personnel, material, equipment and facilities, not otherwise provided by the Government under the terms of this contract, as needed to perform the tasks set forth below. Specifically, the Contractor shall perform the following:

1) NHP MHC CLASS I, MHC CLASS II AND KIR GENE/LOCUS/ALLELE

DISCOVERY

a) Discovery

b) Frequency Studies

2) NHP MHC AND KIR GENOTYPING AND TECHNOLOGY

DEVELOPMENT

a) Develop and Validate Technology

b) Provide Technologies to the NHP Research Community

3) MHC CLASS I AND CLASS II CELL AND TISSUE EXPRESSION

a) Measure MHC expression levels in peripheral blood cells and additional cells and tissues

4) BIOLOGICAL REAGENT RESOURCES

a) Generate Biological Resources

b) Distribute Biological Resources

5) BIOINFORMATICS AND DATA SHARING

a) Establish and Maintain an Internal Database

b) Provide Data to Public Databases

6) NIAID NIH BREEDING COLONIES GENE DISCOVERY AND

GENOTYPING TECHNOLOGY SERVICES

) SCIENTIFIC AND TECHNICAL PERSONNEL

) PROJECT MANAGEMENT

) FACILITIES, EQUIPMENT AND OTHER RESOURCES

SECTION 4: TECHNICAL DISCUSSIONS

In addition to the guidance in section l of the BAA, this section of your technical proposal should include documentation to demonstrate how you will accomplish the work detailed in your proposed Statement of Work. It is recommended that your proposal be organized in accordance with the order of your Statement of Work and the technical evaluation criteria provided in Section M.

Additionally, please ensure that your Technical Proposal addresses the following:

Organizational Experience:

In addition to the information requested under Section L, Part c. Business Proposal Instructions, paragraph 12, Qualifications of the Offeror, all offerors are requested to include in their technical proposals a description of at least two examples of similar projects performed by your organization that are of comparable size and scope and/or related to the effort proposed in response to this BAA. The projects may be either completed or ongoing.

SCIENTIFIC AND TECHNICAL APPROACHES

Provide a detailed description of the experimental rationale, design, approach, procedures, technologies, logistics and scope for the proposed studies, and the relevant experience to perform the tasks. Describe the potential of this research to advance the state-of-the-art and increase knowledge and understanding of NHP MHC and KIR genetics. Include preliminary data, possible caveats and potential impediments that might be encountered and proposed alternatives as well as timelines and milestones, as appropriate, for each of the following:

1) NHP MHC Class I, Class II and KIR gene/locus/allele discovery.

Describe in detail:

a) The approach, methods, technologies and other procedures that will be used to discover and define new genes, loci, and alleles for each species proposed, where applicable.

b) The approach, methods, technologies and other procedures that will be used to determine frequencies of common MHC alleles discovered, or previously discovered, and represented in the specific populations or colonies selected for gene/locus/allele discovery.

c) The rationales and justifications for the: i) priority of the proposed species and/or subspecies of NHPs proposed for gene discovery and the size of effort,

ii) colonies or sources of NHPs proposed, including a discussion of what pedigree information will be available and whether required to address allele frequencies, and iii) relative focus on MHC Class I versus Class II versus KIR genes.

d) Describe the degree and relevance of innovation of the research and techniques proposed.

2) NHP MHC and KIR Genotyping and Technology Development.

Describe in detail:

a) The approaches, methods, technologies and other procedures for development and validation of high resolution (where applicable) for robust genotyping of the MHC Class I and Class II, and KIR genes/alleles. Include rationales, justifications, and differences in approaches for the species proposed, if any.

Include a discussion of the various MHC and KIR genotyping needs of the diverse NHP immunological and infectious disease research community, including the special needs to optimally conduct research for solid organ, tissue, and bone marrow/stem cell transplantation. Discuss which genotyping methods may be optimal for which research application. Discuss all relevant factors, advantages, disadvantages and caveats, including accuracy, reproducibility, ease-of-use, cost-effectiveness and practical turn-around rates for methods proposed.

b) The plan to make all technology, software, and protocols developed accessible to the broader scientific community.

c) Describe the degree and relevance of innovation of the research and techniques proposed.

3) MHC Class I and Class II Cell and Tissue Expression

Describe in Detail:

The approaches, methods, technologies, and other procedures for the measurement of MHC expression. Include rationale for the selection of the cells and tissue(s) to be measured and plans for acquiring the necessary samples.

4) Biological Reagent Resources.

Describe in detail:

The biological resources that will be generated. Include all approaches, methods and other procedures as well as caveats and alternatives. Include the plans, rationale, and methods for sharing with the NHP research community.

5) Bioinformatics and Data Sharing.

Describe in detail:

a) The internal database used to manage and track: (i) genomic data; (ii) animal pedigree, relationship, and source information; (iii) resources and inventories generated, and requests for biological, genotyping, or protocols and to whom provided; (iv) genotyping data; and (v) primer/probe definitions. Include additional data collected, backup system, and security.

b) Plans for submission of data to public databases (e.g. Trace Archive http://www.ncbi.nlm.nih.gov/Traces/home/, Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/sra/, and/or NCBI GenBank http://www.ncbi.nlm.nih.gov/Genbank/), and including IPD-MHC/KIR NHP http://www.ebi.ac.uk/ipd/mhc/nhp/. Provide timelines. Describe plans for coordinating nomenclature and curation of submitted sequences with public databases such as IPD-MHC/KIR NHP. In the event that appropriate databases are not available, provide alternative plans for providing readily accessible information as detailed under Research and Technical Objectives, 4.c.

NOTE: To the extent possible, the Contractor shall provide the software (if developed under the contract) to the research community under a license certified by the Open Source Initiative (http://www.opensource.org/licenses/) to guarantee the right to read, redistribute, modify and freely use the software.

6) NIAID NHP Breeding Colonies Gene Discovery and Typing Services.

Describe in detail:

A plan for provision of limited gene/allele discovery and genotyping for NIAID-owned NHPs. Assume for the technical proposal that this would include two of the Offeror’s proposed species for gene/allele discovery and genotyping technology development.

7) MHC and KIR Gene Sequence Validation and Annotation Tools.

Describe in detail:

Plans and justification for the development of software tools to facilitate the validation and annotation of gene sequences, and/or provide support of validation, annotation, and curation of sequences by the IPD-MHC NHP (http://www.ebi.ac.uk/ipd/mhc/nhp).

SECTION 5: SCIENTIFIC AND TECHNICAL PERSONNEL

Provide information relevant to document individual training, experience, qualifications and expertise necessary for the successful completion of the proposed Statement of Work. Limit CVs to 2-3 pages and provide selected references for publications relevant to the scope of the contract.

1) Principal Investigator (PI): Describe the experience, training, expertise, and qualifications, and level of effort of the proposed Principal Investigator to lead and direct the activities to be carried out under the proposed Statement of Work.

Provide the following documentation:

CV (3 page maximum) Qualifications and relevant training Previous experience with projects of similar size and complexity (limited to the past 5 years) References to relevant publications Summary of related activities, including ability to (i) assess progress in accordance with established tasks and timelines; (ii) recommend modifications to research programs based on new information and/or new and improved approaches and technologies; (iii) keep projects on time and on budget; and (iv) assess performance, identify performance problems, and design and implement remedial actions when necessary.

3) Other Key Scientific and Technical Personnel: Describe the experience, training, expertise and qualifications, as well as the level of effort, for all proposed key scientific and technical personnel.

Provide the following documentation:

Scientific and Technical Personnel (limit CVs to 3 page maximum per person) Qualifications and relevant training Previous experience with projects of similar size and complexity (limited to the past 5 years) References to relevant publications Summary of related activities

SECTION 6: PROJECT MANAGEMENT

1) Provide a Project Management Plan for the overall organization that addresses the coordination, planning, initiation, implementation, conduct, monitoring and completion of tasks identified in the proposed Statement of Work. If consultants and/or subcontractors are proposed, include a plan to manage, coordinate, and oversee the work performed by consultants and/or subcontractor(s).

2) Provide a Staffing Plan that describes roles and responsibilities, and for all scientific and technical personnel, including the project manager and all proposed subcontractors and consultants. Provide an administrative and technical framework indicating clear lines of authority and responsibility for all proposed personnel. Include a chart of the proposed organizational/management structure for the project, and describe the milestones and timelines for completing the work.

3) Describe the plans for the collection, management, security, and dissemination of data collected.

4) Describe the project management systems that will be used to track activities and to keep multiple activities on time and budget. The plan must include a description of the quality control methods that will be used to ensure the effective and efficient initiation, implementation, management, and oversight of contract requirements.

5) Outline how the PI (or Project Manager) will communicate with the Contracting Officer’s Representative and Contracting Officer and how the PI (or Project Manager) will communicate, monitor, and manage the project both internally and externally (at subcontractor facilities).

6) If the Offeror or a proposed subcontractor is a commercial firm, the Technical Proposal must address how potential conflicts of interest and intellectual property rights issues will be resolved and how the technologies or software developed under the contract will be provided and remain accessible to the NHP research community.

SECTION 7: FACILITIES, EQUIPMENT, AND OTHER RESOURCES

The Technical Proposal should document availability and adequacy of facilities, equipment, space and other resources necessary to carry out the proposed Statement of Work, including:

1) Location and features of facilities including a floor plan and a list of equipment and resources dedicated to the project for the prime contractor and any proposed subcontractors (lease or ownership information should be provided).

2) Identification and description of ALL support resources (including Information Technology systems) that will be required to effectively complete the proposed Statement of Work.

3) Experience and capability of the organization, as well as of the proposed subcontractors and consultants organization, if any, with similar projects of comparable size and scope.

SECTION 8: OTHER CONSIDERATIONS

This section of the Technical Proposal should document other resources not covered in 1 through 4 above necessary to carry out the proposed Statement of Work.

POST-AWARD REQUIREMENTS/ISSUES:

1) MHC and KIR data

Submit all MHC and KIR sequence and expression data, including raw data, into the appropriate public archive [e.g. Trace Archive http://www.ncbi.nlm.nih.gov/Traces/home/ or Sequence Read Archive (SRA) http://www.ncbi.nlm.nih.gov/sra/ ] and the NCBI GenBank (http://www.ncbi.nlm.nih.gov/Genbank/) for download into the IPD- MHC/KIR NHP (http://www.ebi.ac.uk/ipd/mhc/nhp) database and subsequent curation, validation and annotation. The submission timelines shall be as determined by the COR, in consultation with the Contracting Officer and Contractor.

2) Genotyping Technologies

Make all developed genotyping technologies and related software and protocols accessible to the NHP research community on a timeline that shall be set by the COR in consultation with the Contracting Officer and Contractor. See Attachment: “Research and Technical Objectives”, Section 2.

3) Biological Reagent Resources

Provide all cell lines, DNA, and/or vectors generated and all related information to the research community on a schedule to be set by the COR in consultation with the Contracting Officer and Contractor. See Attachment: “Research and Technical Objectives”, Section 4.

4) Contract Initiation Meeting

The Contractor shall participate in a contract initiation meeting within three months after the effective date of the contract to discuss contract initiation. The meeting location will be in or near Bethesda, MD unless otherwise determined by the COR. This meeting will shall be attended by all of the Contractor’s key personnel.

5) Annual Program Meetings.

The Contractor shall participate in 1-2 day Annual Program Meetings organized by NIAID to promote collaborations and the exchange of ideas among the investigators from other Contacts awarded under this program, if requested by the COR. The meeting location will be in or near Bethesda, MD, unless otherwise determined by the COR. Each meeting will be attended by the Principal Investigator (PI) and other Key Personnel (maximum of four individuals in addition to the PI, without prior approval of the COR). The COR, Contracting Officer, and other relevant NIH staff will also attend.

6) Site visits.

The Contractor shall plan, conduct, and be responsible for the logistical arrangements for a 1 day site visit by NIH staff to the Contractor’s or subcontractor’s site, as requested by the COR. The PI, Key Personnel, and any key subcontractor personnel shall be present at the site visit. The COR, Contracting Officer, and other relevant NIH Staff will also attend at Government expense. The purpose of the site visit is to review plans and progress of the proposed work and to coordinate activities and communication between the Contractor, COR, and Contracting Officer. The PI shall provide a copy of all slide presentations to the COR within 5 business days prior to the site visit.

7) Quarterly Teleconferences with the COR.

The Contractor shall arrange and hold teleconferences four times per year (once every three months) with the COR. Additional Contractor staff and the Contracting Officer shall participate as needed. The exact meeting schedule will be established by the Contractor and COR within 15 business days of the effective date of the contract. The main purpose of these meetings is to apprise the COR of technical achievements or hurdles related to the program goals and objectives. Additional topics may include budgetary issues, subcontracting agreements, travel requirements, and planning site visits.

Ten business days prior to each teleconference, the Contractor shall submit to the COR, for review, an electronic version of the proposed meeting agenda, including progress on action items from the previous teleconference. Upon approval of the COR, the Contractor shall distribute the final agenda to all of the teleconference participants. The COR shall provide feedback within five business days of receiving the draft, and the Contractor shall send out the final agenda, call-in information, and updated minutes from the prior teleconference to all participants at least two business days prior to the teleconference.

Within 5 business days following each teleconference, the Contractor shall submit a summary of the meeting discussions and list of action items, including any proposed due dates for the actions, to the COR for review. The COR shall submit any comments or approval for distribution, to the Contractor within five business days of receipt of the summary of the meeting discussions. The Contractor shall distribute the meeting minutes and action items to all the meeting participants within two business days of receiving the COR’s comments.

8) Interactions with Other NIAID NHP Programs

The Contractor may be required to collaborate with investigators from other NIAID NHP programs. These interactions may extend to limited MHC and KIR discovery, genotyping, nomenclature, and curation activities or consultation for such activities or extend to information sharing.

9) Intellectual Property

The Contractor shall be solely responsible for the timely acquisition of all appropriate proprietary rights, including intellectual property rights, and all materials needed to perform the project. Before, during, and subsequent to the award, the U.S. Government is not required to obtain for the Contractor any proprietary rights, including intellectual property rights, or any materials needed by the Contractor to perform the project. The Contractor is required to report to the U.S. Government all inventions made in the performance of the project, as specified at FAR 52.227-11 (Bayh-Dole Act).

10)Throughout the contract period of performance, NIAID may direct changes in the research to better accomplish the goals of the contract.

Other Considerations

2. PACKAGING, MARKING, AND SHIPPING

Offerors are required to discuss and document in their technical proposals their processes for complying with the following packaging, marking and shipping procedures:

Temperature controlled environment Shipments will be time sensitive/time critical International shipping Shipping insurance Hazardous Materials shipping Other (list as necessary) ________________________

Provide, operate and maintain procedures for the receipt and proper storage of specimens for testing and/or repository deposition as designated by the COR in accordance with cGCP regulations and in compliance with domestic and non-domestic laws and regulations. (All shipments shall be made according to Federal regulations and the International Air Transport Association (IATA) requirements for the shipment of dangerous goods, as applicable (http://www.iata.org/whatwedo/cargo/dangerous_goods/Pages/index.aspx). Shipments shall be temperature controlled, as necessary.

3. OTHER CONSIDERATIONS

Section L of the BAA provides minimum documentation requirements for the following items. The required information described in Section L should be assembled together in clearly marked sections of the Technical Proposal. Refer to Section L of the BAA for specific requirements. In some cases, offerors may be asked to provide documentation which is in addition to the minimum requirements identified in Section L.

Human Subjects

Care of Live Vertebrate Animals

Biological Agents or Toxins

Obtaining and Disseminating Biomedical Research Resources

Sharing Research Data (Plan)

Sharing of Model Organisms for Biomedical Research (Plan)

Information Technology (IT) Systems Security