Solicitation W81XWH22Q0067-0001 Sample Task Order.pdf

Sample Task Order 0001

PERFORMANCE WORK STATEMENT

Microbiome Sequencing and Analysis Services

US Army Research Institute of Environmental Medicine (USARIEM)

SECTION 1

1.1. Introduction USARIEM's mission is to optimize Warfighter health and performance through medical research. USARIEM is internationally recognized as the premiere DoD laboratory for Warfighter health and performance research and focuses on environmental medicine, physiology, physical and cognitive performance, and nutrition research. USARIEM publishes guidance for DoD operations in hot weather, cold weather, and high-altitude environments, and nutrition for health and performance.

1.2. Mission The Military Nutrition Division is one of four research divisions within USARIEM. The mission of the Military Nutrition Division is to conduct research that provides a biomedical science basis for developing new rations, menus, policies and programs that enable Warfighter health-readiness and optimal performance. Its focus areas include: Recovery Nutrition, Healthy Eating, Dietary Supplements, and Physiological Resilience.

1.3. Background Research conducted by the Military Nutrition Division requires measuring the composition of microorganisms living in the human gastrointestinal tract. The Military Nutrition Division requires DNA extraction, library preparation, high- throughput gene sequencing, and bioinformatics services to support this analysis within a research study.

1.4. Scope The contractor shall provide analytical services of 180 fecal samples for 16S rRNA gene amplicon sequencing and shotgun metagenomics sequencing as defined in section 3. Samples will be provided by USARIEM.

SECTION 2 GENERAL REQUIREMENT

2.1. Performance

2.1.1. Place of Performance: Contractor facility

2.1.1.1. Primary On-Site Government Location: USARIEM

2.1.2. Period of Performance: One (1) year

2.2. Type of Services

2.2.1 Non-Personal Services

This PWS identifies services that are strictly non-personal in nature, as defined by Federal Acquisition Regulation (FAR) Part 37, Service Contracting. To ensure there is no appearance of any personal services, the Government shall neither supervise contractor personnel nor control the method by which the contractor performs the required tasks. Under no circumstances shall the Government assign tasks or prepare work schedules for individual contractor personnel. It shall be the responsibility of the contractor to manage its personnel and to guard against any actions that give the perception of personal services. If the contractor believes that any actions constitute, or are perceived to constitute personal services, it shall be the contractor's responsibility to notify the Contractor Officer (KO) immediately.

2.2.2 Severable / Non-Severable Services

This award identifies services that are severable in nature.

2.2.3 Inherently Governmental Functions

This requirement has been reviewed and contains no services that are inherently governmental functions.

Acquisition Functions Closely Associated with Inherently Governmental Functions: Not applicable for this task.

2.3. Contract Management

2.3.1. Government Management. The Contracting Officer’s Representative (COR) for this contract will be appointed by the Contracting Officer (KO). The COR will serve as the primary point of contact for all activities and issues that occur under this contract.

2.3.2. Contractor Management. The contractor shall designate a single Program Manager (PM) to be the contractor’s authorized point of contact (POC) with the COR. The PM will be responsible for formulating and enforcing performance standards, assigning contractor schedules, reviewing performance quality, communicating policies, purposes, and goals to subordinates. This will include coordination with the KO and the COR to resolve any issues that may arise, trends relating to the contract, or proposed changes or modifications to the contract. The PM shall demonstrate capability in the overall management of complex tasks, and strong team building skills.

2.3.2.1. The contractor shall establish clear organizational lines of authority and responsibility to ensure effective management of the resources assigned to the requirement. The contractor shall ensure that all contractor personnel are advised of their chain of command and who they should contact if they have questions.

2.4. Reports

2.4.1. Reports and documents delivered by the contractor in the performance of this contract shall be considered Technical Data as defined in the applicable FAR clause 52.227-14, Rights in Data. All documentation shall reflect the latest version of the work product or activity, unless specifically directed otherwise by the Government. All documentation shall be prepared in accordance with (IAW) standard industry practices, ensuring electronically produced documents which reflect logical flow of material, tables of contents indexes and page numbering. Where applicable, the contractor’s attention is called to the availability of commercial, industry, federal, and military guides, instructions, and standards for many of the topics addressed in this PWS and under this contract.

2.4.2. Monthly Financial Tracking Report: NA

2.4.3. Monthly Report: NA

2.4.4. Contract Manpower Reporting (Deliverable 1). This is a mandatory requirement IAW Army Federal Acquisition Regulation Supplement (AFARS) 5137.91, Accounting for Contract Services.

The contractor shall report ALL contractor labor hours (including subcontractor labor hours) required for performance of services provided under this contract for the via a secure data collection site. The contractor is required to completely fill in all required data fields using the following web address:

https://www.beta.sam.gov starting at the end of FY20, ECMRA has been decommissioned effective June 19, 2020.

Reporting inputs will be for the labor executed during the period of performance during each Government fiscal year (FY), which runs October 1 through September 30.

While inputs may be reported any time during the FY, all data shall be reported no later than October 31 of each calendar year, beginning with 2013. Contractors may direct questions to the help desk at:

https://www.beta.sam.gov starting at the end of FY20, ECMRA has been decommissioned effective June 19, 2020

The contractor shall register under the "All Other Defense Components" module. The USARIEM Unit Identification Code (UIC) is W03WAA.

https://www.beta.sam.gov/ https://www.beta.sam.gov/

*The Office of the Secretary of Defense has issued a Memorandum dated 16 October 2019 which removes the requirement for contractors to report manpower data into the eCMRA system at https://www.ecmra.mil, beginning 1 Oct 2019. It is anticipated, however, that contractors shall be required to report similar manpower data to https://beta.sam.gov beginning sometime within the next year. Currently, there is no reporting requirement or transition plan but the contractor shall perform the documentation/tracking required demonstrating an understanding that manpower data reporting shall be required for the performance of this contract.*

2.4.5 Contractor Performance Assessment Reporting System (CPARS). The Contractor CPARS is the DoD mandatory system to electronically capture assessment data and manage the evaluation process. CPARS is used to assesses a Contractor’s performance and provide a record, both positive and negative, on a given contract during a specific period of time. The CPARS process is designed with a series of checks and balances to facilitate the objective and consistent evaluation of Contractor performance. Both Government and Contractor program management perspectives are captured on the CPAR form and together make a complete CPAR. Once the Assessing Official completes the proposed assessment for the period of performance, the CPARS is released to the appropriate Government Contractor Representative for their review and comments. User ID and password will be provided to the designated Government Contractor Representative upon issuance of a task order. The Contractor has 30 days after the Government's evaluation is completed to comment on the evaluation. The Government Contractor Representative must either concur or nonconcur to each CPAR. If the Contractor concurs with the proposed assessment and the Reviewing Official does not wish to see the CPAR, the Assessing Official may close out the CPAR. Otherwise, they must forward the CPAR to the Reviewing Official for them to review, enter comments if appropriate, and close out. The Reviewing Official may at their option direct the Assessing Official to forward every CPAR to them for review.

2.5. Training Requirements: NA

2.6. Contractor Personnel, Disciplines, and Specialties

2.6.1. General/Specialized Experience: The contract shall possess specialized experience necessary to conduct DNA extraction, library preparation, high-throughput DNA sequencing (16S rRNA gene amplicon sequencing and shotgun metagenomics sequencing), and bioinformatics Support Services.

2.6.2.2. The Government estimate is only put in place for offerors to ascertain the approximate or estimated level of effort for this procurement. However, this is not to be construed as either mandatory or necessarily the best technical approach. It is only in place as a reference to allow offerors to better understand the general scope of this effort from the Governments perspective. The Government is seeking the best level of effort and labor mix that the contractor has determined is right to accomplish the mission contained in this PWS. The contractor is not bound to propose these labor categories or quantities, rather being expected to provide the best solution citing the labor mix and quantity required to accomplish the general scope of the contract requirements in each support areas. If the contractor has determined either the labor categories or overall level of effort provided are not the best technical solution, the contractor shall submit a level of effort consistent with all of the cost/price and non- cost/price aspects of contractors approach.

SECTION 3 PERFORMANCE REQUIREMENTS

3.1. The contractor shall provide all necessary personnel required to perform services at their designated location. The contractor shall provide DNA extraction, library preparation, high-throughput DNA sequencing (16S rRNA gene amplicon sequencing and shotgun metagenomics sequencing), and bioinformatics Support Services. The following section specifies the Performance Objectives and Performance Elements for the contract.

3.1.1. General Requirements.

The contractor shall conduct DNA extraction, library preparation, high-throughput gene sequencing and bioinformatics analysis, and provide all equipment and consumables necessary for running those analyses on 180 fecal samples received from USARIEM in support of USARIEM research studies. The contractor shall also statistically analyze sequencing data and provide results of the analyses in various electronic formats. In addition, http://www.ecmra.mil/ the contractor shall assist USARIEM scientists in study design as needed, in understanding the methods and analyses used, and in interpreting and reporting the results. All procedures will be developed in consultation with USARIEM scientists prior to sample analysis and follow best practice recommendations in place at the time of analysis.

The specific requirements are described below and in Table 1.

3.1.1.1 Specific Requirements:

3.1.1.2 The contractor shall conduct DNA extraction and library preparation from fecal samples provided as individual projects led by individual USARIEM investigators. Any primers used for library preparation will be determined in consultation with USARIEM investigators.

3.1.1.3 The contractor shall conduct amplicon sequencing and shotgun metagenomics sequencing in accordance with standard validated protocols.

3.1.1.4 The contractor shall conduct quality control, taxonomic assignment, and gene annotation of sequencing data using validated protocols and standards.

3.1.1.5 The contractor shall perform bioinformatics analyses in consultation with USARIEM investigators to include computing and analyzing measures of community and genetic diversity (alpha- and beta-diversity), differential abundance analyses, and generating graphical outputs in accord with best practices.

3.1.1.6 The contractor shall provide raw sequencing files, tables of read counts with taxonomy and gene annotations assigned, relative and absolute abundance of taxa and genes, diversity metrics, and results of all analyses as requested by USARIEM investigators. A report describing the results and their biological interpretation, and the methods used to generate results shall also be provided. These reports shall be delivered to the USARIEM investigator leading each individual project, or their designee, within 60 calendar days of sample receipt unless otherwise agreed upon within the individual task order for each project (Deliverable 2).

3.1.1.7 The contractor shall consult on all sample and data analysis protocols, interpretation and reporting with the USARIEM investigator leading each individual project, or their designee. This consulting is intended to facilitate identification of the appropriate sequencing method, bioinformatics pipeline, and data analysis plan based on study goals and funding availability.

3.1.2.7

Table 1. Minimum and advanced requirements for bioinformatics services

Tier 1 (baseline) ≥ 25,000 reads/sample for 16s sequencing ≥ 5 Gb/sample for metagenome sequencing.

Basic bioinformatics analyses using validated procedures and databases and incorporate quality control steps Taxonomy tables at phyla, family, genus, and when possible, species level-resolution that include read counts and relative abundances with assigned taxonomies Tables with identified genes, gene families, gene pathways and functional annotations with associated read counts for metagenomics analyses Rarefaction plots

Alpha diversity metrics (observed ASVs, Shannon, Simpson)

Beta diversity metrics (Bray-Curtis, weighted and unweighted UniFrac)

Tier 2 (includes baseline requirements)

≥ 50,000 reads/sample for 16s sequencing ≥ 10 Gb/sample for metagenome sequencing.

Complex bioinformatics analyses, e.g. metagenome assembled genomes

Statistical techniques handling paired and/or longitudinal 16S and metagenome data based on best practice recommendations at the time of analysis

Tier 3 (includes baseline and Tier 2 requirements)

Multi-omics data integration: Analysis of microbiome sequencing data along with additional metadata to include metabolomics data sets.

3.2. Performance Requirement Summary Matrix

The Government intends to utilize a Quality Assurance Surveillance Plan (QASP) to monitor the quality of the Contractor’s performance in relation to performance objectives. The Government will finalize the QASP immediately following award, and the COR will provide a copy of the final QASP to the contractor. The QASP is a living document and may be updated by the Government as necessary.

The Government will use the following performance requirements to measure the performance of the contractor.

The contractor shall meet the Performance Objective(s) and Acceptable Quality Level(s) within the “Performance Requirements Summary Matrix” (PRS Matrix).

PERFORMANCE REQUIREMENTS

SUMMARY MATRIX

# PWS

Ref.

Performance Objective Acceptable Quality Level

Performance Measurement Incentive

1 3.1.2.1, 3.1.2.7

Obtain sufficient DNA yields for sequencing analysis, and generate high quality amplicon libraries using appropriate primers and methods.

No more than one customer complaint per task order

In accordance with lab standard procedures;

proportion of samples yielding sufficient DNA.

Positive

CPARS

2 3.1.2.2, 3.1.2.7

Generate high quality gene sequences at appropriate read depths and using appropriate methods.

No more than one customer complaint per task order

In accordance with lab standard procedures; read depth sufficient to cover community diversity.

Positive

CPARS

3 3.1.2.3, 3.1.2.7

Quality control and annotation of sequencing data, identify taxa and genes, enter data, manage and provide databases with sequencing results (read counts and relative/ absolute abundances at different levels of taxonomy and gene pathway).

No more than one customer complaint per task order

In accordance with standard analysis pipelines using standard databases.

The contractor-provided services shall be timely, accurate, and conform to established scientific professional standards.

Positive

CPARS

4 3.1.2.4, 3.1.2.7

Perform statistical analysis as required.

No more than one customer

The contractor-provided services shall be timely, Positive

CPARS

complaint per task order accurate, and conform to established scientific professional standards.

Analyses include, but are not limited to, diversity metrics, supervised and unsupervised multivariate analyses, and differential abundance analysis.

5 3.1.2.5 Databases suitable for statistical analyses, interpretable reports describing procedures and results.

No more than one customer complaint per task order

The contractor-provided services shall be timely, accurate, and conform to established scientific professional standards.

6 3.1.2.6 Consult on analytical approach and data analysis, interpretation and reporting

No more than one customer complaint per task order

Consultants are available as need, are expert in the field, and maintain high professional and scientific integrity

Positive

CPARS

SECTION 4 SPECIAL REQUIREMENT

4.1. Government Furnished Equipment:

USARIEM will provide fecal samples to the laboratory for analysis.

SECTION 5 DELIVERABLES

5.1. Deliverables. The contractor shall provide the following deliverable as listed

PWS

Ref.

Number Title/Description Due

2.4.4 Deliverable 1 Contractor Manpower

Reporting

Due no later than 31 October each year of the contract or on the last day of the contract performance, whichever is first

3.1.2.5 Deliverable 2 Data files, analyses and reports as

described in 3.1.2.5. This will include 16S rRNA amplicon and shotgun metagenomics analyses

Due to the USARIEM investigator no later than 60 calendar days of sample receipt unless otherwise agreed upon within the individual task order for each project

3.1.2.6 Deliverable 3 Consultation on sample and data

analysis, and interpretation of methods and results.

Throughout the duration of each project

SECTION 6 APPLICABLE DIRECTIVES, REGULATIONS, AND POLICIES

6.1. Environmental Requirements

6.1.1. Mandatory Compliance. Occupational Safety and Health Act and AR 200-1 Environmental Protection and Enhancement.

6.1.2. Non Mandatory Documents. Additional DoD and Army environmental program and regulations are available on-line at http://aec.army.mil.

6.2. Applicable Directives. The contractor shall comply with all documents listed below as mandatory and referenced under Section 3, Performance Requirements.

6.3. Mandatory Compliance

6.3.1 Dissemination of Information/Publishing

There shall be no dissemination or publication, except within and between the Contractor and any Sub Contractors or specified Integrated Product/Process Team (IPT) members who have a need to know, of information developed under this order or contained in the reports to be furnished pursuant to this order without prior written approval of the COR or the Contracting Officer. Business Program Management Office (PMO) approval for publication will require provisions that protect the intellectual property and patent rights of both Business PMO and the Contractor.

6.3.2 Contractor Identification

The Contractor shall ensure that Contractor personnel identify themselves as Contractors when attending meetings, answering Government telephones, providing any type of written correspondence, or workingin situations where their actions could be construed as official Government acts.

http://aec.army.mil/

6.3.3 Attendance at Meetings

Contractor personnel may be required to attend meetings or otherwise communicate with Government and/or other contract or assistance agreement representatives to meet the requirements of this order. Contractor personnel shall make their contractor status known during introductions.

6.3.4 Use of Military Rank by Contractor Personnel

Contractors may not use or allude to former or current military rank during the performance of this work.

6.3.5 Data Rights

The Government will retain rights to all data produced in the course of developing, deploying, training, using and supporting USARIEM or other federal agencies that utilize this order.

Data in Transit:

The Parties are responsible for ensuring that any data shared is transmitted, protected, and stored in a secured information system network that is fully compliant with all applicable Federal legal authorities and DoD regulations. The data described above may be shared through electronic file transfer via a secure, mutually agreed upon method such as DOD SAFE (https://safe.apps.mil/). Hard copies of such files will be handled per applicable DoD or Service regulations and guidelines.

6.3.6 Section 508 Requirement

The Contractor shall comply with Section 508 of the Rehabilitation Act of 1973 (29 U.S.C. 794d). Specifically, the procurement, development, maintenance, or integration of electronic and information technology (EIT) under this contract must comply with the applicable accessibility standards issued by the Architectural and Transportation Barriers Compliance Board at CFR part 1194.

6.3.7 Protection of Human Subjects and Adherence to Ethical Standards in Department of Defense (DoD)- Supported Research The Contractor shall adhere to all applicable DoD regulations pertaining to Human Subjects Protection and Ethical Standards. Specifically, 32 Code of Federal Regulations (CFR) 219, National Defense, Protection of Human Subjects; Department of Defense (DoD) Instruction 3216.02, Protection of Human Subjects and Adherence to Ethical Standards in DoD-Supported Research, dated November 2011; Army Regulation (AR) 70-25 (under revision): Use of Volunteers as Subjects of Research, Headquarters, Department of the Army, dated 25 January 1990. Applicable US CFR regulations are: Title 21, CFR Part 50 Protection of Human Subjects, Title 21 CFR Part 56, Institutional Review Boards; Title 21 CFR Part 812, Investigational Device Exemptions, April 1, 2014; Title 32 CFR Part 219, Protection of Human Subjects; Title 45 CFR 46, Protection of Human Subjects, April 1, 2014.

6.3.8 Public Key Infrastructure Authentication and Encryption Contractors shall follow the DoD standards, policies, and procedures related to the use of Public Key Infrastructure (PKI) certificates and biometrics for positive authentication including authentication to DoD private web servers or applications. Where interoperable PKI is required for the exchange of unclassified information, including the encryption of e-mail containing sensitive information, between DoD and its Contractors, industry partners shall obtain all necessary certificates if they are not eligible for a DoD Common Access Card. (refer to:

http://iase.disa.mil/pki/eca/ and http://www.cac.mil/)

SECTION 7 DEFINITIONS

7.1. Definitions

7.1.1. CONTRACTOR. A supplier or vendor awarded a contract to provide specific supplies or service to the government. The term used in this contract refers to the prime.

7.1.2. CONTRACTING OFFICER. A person with authority to enter into, administer, and/or terminate contracts, and make related determinations and findings on behalf of the government. The Contracting Officer http://www.access-board.gov/sec508/508standards.htm http://iase.disa.mil/pki/eca/ http://www.cac.mil/) is the only individual who can legally bind the government.

7.1.3. CONTRACTING OFFICER'S REPRESENTATIVE (COR). An employee of the U.S.

Government appointed by the contracting officer to administer the contract. Such appointment shall be in writing and shall state the scope of authority and limitations. This individual has authority to provide technical direction to the contractor as long as that direction is within the scope of the contract, does not constitute a change, and has no funding implications. This individual does NOT have authority to change the terms and conditions of the contract.

7.1.4. DEFECTIVE SERVICE. A service output that does not meet the standard of performance associated with the Performance Work Statement.

7.1.5. DELIVERABLE. Anything that can be physically delivered, but may include non- manufactured things such as meeting minutes or reports.

7.1.6. KEY PERSONNEL. Contractor personnel that are evaluated in a source selection process and that may be required to be used in the performance of a contract by the Key Personnel listed in the PWS. When key personnel are used as an evaluation factor in best value procurement, an offer can be rejected if it does not have a firm commitment from the persons that are listed in the proposal.

7.1.7. PHYSICAL SECURITY. Actions that prevent the loss or damage of Government property.

7.1.8. QUALITY ASSURANCE. The government procedures to verify that services being performed by the contractor are performed according to acceptable standards.

7.1.9. QUALITY ASSURANCE SURVEILLANCE PLAN (QASP). An organized written document specifying the surveillance methodology to be used for surveillance of contractor performance.

7.1.10. QUALITY CONTROL. All necessary measures taken by the contractor to assure that the quality of an end product or service shall meet contract requirements.

7.1.11. SUBCONTRACTOR. One that enters into a contract with a prime contractor. The Government does not have privity of contract with the subcontractor.

7.1.12. WORK DAY. The number of hours per day the contractor provides services IAW the contract.

7.1.13. WORK WEEK. Monday through Friday, unless specified otherwise.