Performance Work Statement - Updated.pdf

DHA PWS Template V13 November 16, 2021

Department of War United States Army

Performance Work Statement

(PWS)

Genomics Analysis Services

U.S. Army Research Institute of Environmental Medicine

(USARIEM)

Military Nutrition Program

Solicitation Number:

Version:

Date: 7/8/2026

PART 1

1.0 GENERAL INFORMATION

1.1 This is a non-personal services contract to provide Genomics analysis services.

1.2 Description of services/introduction: The contractor shall provide all personnel, equipment, supplies, facilities, transportation, tools, materials, supervision, and other items and non-personal services necessary to perform roles Genomics analysis services as defined in this Performance Work Statement (PWS) except for those items specified as government furnished property and services. The contractor shall perform to the standards in this PWS.

1.3 Background: 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. The research conducted by the Military Nutrition Division requires assessing the genome of Soldiers who volunteer for our research studies.

1.4 Objectives: The objectives of this contract are to provide genomics analysis (i.e., targeted measurement of millions of Single Nucleotide Polymorphisms [SNPs] in the genome and assessment of specific SNPs) to support analyses in ongoing USARIEM research studies.

1.5 Scope: The contractor shall provide analytical services of existing biological samples for genomics analyses as defined in section 3. Samples will be provided by USARIEM. Analyses must utilize the same procedures as the Federal, National Institute of Health sponsored “All of Us” research program.

1.5.1 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 (CO) immediately

1.6 Period of Performance (PoP): The period of performance will include a 12-month base period.

1.7 Administrative specifications:

1.7.1 Place of performance: All work shall be performed at the contractor facilities.

1.8 Contractor travel: Reserved

1.9 Other Direct Costs (ODC): Reserved

1.10 Quality

1.10.1 Quality Assurance (QA): The government will evaluate the contractor’s performance under this task order in accordance with the Quality Assurance Surveillance Plan (QASP). This plan provides a systematic method for the Government to evaluate performance and to ensure that the contractor has performed in accordance with the performance standards. It defines how the performance standards will be applied, the frequency of surveillance, and the minimum acceptable defect rate(s). The QASP and Performance Requirements Summary Matrix associated with the QASP can be found as a separate attachment.

1.10.2 Quality Control (QC): The contractor shall develop and maintain an effective QC program (QCP) to ensure services are performed in accordance with this PWS. The contractor shall develop and implement procedures to identify, prevent, and ensure nonrecurrence of defective services. The contractor’s QC program is how the work complies with stated requirements. The A draft QCP will shall be submitted to the Contracting Officer (CO) and COR with the contractor’s proposal, and a comprehensive finalized QCP shall be submitted within 15 days after contract award within 5 working days when changes are made thereafter.

After acceptance of the Quality Control Plan (QCP), the contractor shall receive the Contracting Officer’s acceptance in writing of any proposed change to the QC system. (See Part 7, Technical Exhibit 1 – Quality Control Plan – Deliverable 3).

1.11 Contractor personnel: Reserved

1.12 Key personnel (Contractor): Reserved

1.13 Data rights: Reserved

1.14 Reporting:

1.14.1 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 (Section 7 Deliverable 1). 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.

1.14.2 The contractor shall provide a report detailing all work related to the analysis (Section 7 Deliverable 1). The report shall include results from the genomics analyses as requested by USARIEM. These reports shall be completed within 90 days of sample receipt.

1.14.3 Government’s Contracting Officer’s Representative (COR): The COR monitors all technical aspects of the contract and assists in contract administration. The COR is authorized to perform the following functions: assure that the contractor performs the technical requirements of the contract; perform inspections necessary in connection with contract performance; maintain written and oral communications with the contractor concerning technical aspects of the contract; issue written interpretations of technical requirements, including Government drawings, designs, specifications; monitor contractor's performance and notifies both the CO and contractor of any deficiencies; coordinate availability of government furnished property; and provide site entry of contractor personnel. A letter of designation issued to the COR, a copy of which is sent to the contractor, states the responsibilities and limitations of the COR, especially with regard to changes in cost or price, estimates or changes in delivery dates. The COR is not authorized to change any of the terms and conditions of the resulting contract.

1.14.4 Post award conference/periodic progress meetings: The contractor agrees to attend any post award conference convened by the contracting activity or contract administration office in accordance with FAR Subpart 42.5. The CO, COR, and other Government personnel, as appropriate, may meet periodically with the contractor to review the contractor's performance.

At these meetings the CO will apprise the contractor of how the government views the contractor's performance and the contractor will apprise the Government of problems, if any, being experienced. Appropriate action shall be taken to resolve outstanding issues. These meetings shall be at no additional cost to the government.

1.15 Contractor Identification: Reserved

1.16 Contractor Access to Health Affairs (HA)/DHA Network(s): Reserved

1.17 Personnel Security: Reserved

PART 2

2.0 DEFINITIONS, ACRONYMS, AND APPLICABLE

PUBLICATIONS/INSTRUCTIONS

2.1 Definitions:

2.1.1 Category D: Information Technology (IT) and Telecommunications Services (called D- Services)

2.1.2 Category R: Support (Professional/Administrative/Management) Services (called R- Services)

2.1.3 Contracting Officer (CO): A person with the authority to enter into, administer, and/or terminate contracts and make related determinations and findings.

2.1.4 Contracting Officer’s Representative (COR): An individual designated and authorized in writing by the CO to perform specific technical or administrative functions. This individual does NOT have authority to change the terms and conditions of the contract.

2.1.5 Nonpersonal services contract: a contract under which the personnel rendering the services are not subject, either by the contract’s terms or by the manner of its administration, to the supervision and control usually prevailing in relationships between the Government and its employees.

2.1.6 Quality Assurance Surveillance Plan (QASP): An organized written document specifying the surveillance methodology to be used for surveillance of contractor performance. The Government may either prepare the QASP or require the offerors to submit a proposed quality assurance surveillance plan for the Government’s consideration in development of the Government’s plan.

2.2 Acronyms:

AQL Acceptable Quality Level ATO Authority to Operate CO Contracting Officer(s) COR Contracting Officer Representative DHA Defense Health Agency FAR Federal Acquisition Regulation FCI Federal contract information ODC Other Direct Costs PoP Period of Performance PRS Performance Requirements Summary PWS Performance Work Statement QA Quality Assurance

QASP Quality Assurance Surveillance Plan US United States

2.3 Applicable Publications, DHA Administrative Instructions (AI), etc.

PART 3

3.0 GOVERNMENT FURNISHED PROPERTY, EQUIPMENT, AND SERVICES

The Requiring Activity Authority has assessed the need for Government Furnished Property, Equipment, and Services and determined: The Government will NOT provide Government Furnished Property, Equipment or Services in support of this contract.

PART 4

4.0 CONTRACTOR FURNISHED ITEMS AND SERVICES

Services: The Contractor will NOT provide Contractor Furnished Items and Services in support of this contract.

4.1 General: The contractor shall furnish all supplies, equipment, facilities and services required to perform work listed under Section 5 of this PWS.

4.2 Secret Facility Clearance: Reserved

4.3 Materials: Reserved

4.4 Equipment: Reserved

4.5 Facilities: Reserved

PART 5

5.0 SPECIFIC TASKS

5.1 Performance Requirements The contractor shall provide all necessary personnel required to perform services at their designated location. The contractor shall provide genomics analysis support services. The following section specifies the Performance Objectives and Performance Elements for the contract.

5.1.1 Objective 1 Perform Genomics Analysis Services. The contractor shall conduct genomics analysis using contractor hardware and software and provide all equipment and consumables necessary for running those analyses on biological samples (i.e., blood) received from USARIEM in support of research studies. The contractor shall also statistically analyze genomics data and provide results of the analyses in a downloadable Word/pdf format with supporting files (Section 7 Deliverable 1)(e.g., figures and tables) from an electronic portal. In addition, 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. The specific requirements are described below.

5.1.1.1. The contractor shall provide full genomics sample analyses of biological samples using the Illumina Infinium Global Diversity Array on samples provided by USARIEM. Full sample analyses include but is not limited to: (a) all reagents required to conduct the genomics analyses; (b) two HapMap controls and 1 blind duplicate for every sample plate; (c) repeat analysis of any sample which has less than a 96.5% call rate for the Illumina array. Contractor will attempt the genome-wide association study (GWAS) assay twice; (d) data analysis to determine their quality and samples which fail to meet quality control standards will be rerun, data will be cleaned, and problems identified for 648 samples provided to the Contractor within 30 days of contract award.

5.1.1.2. The contractor shall provide a full data release (Section 7, Deliverable 1) including:

HapMap concordance, reproducibility of genotype calculations broken down by MAF bin for each sample pair, contractor-provided complete pipeline outputs sufficient for independent reanalysis, including: all raw and intermediate data files (IDAT, GTC or equivalent), final genotype calls in bgzip-compressed and tabix-indexed VCF format aligned to GRCh38 (both per-sample VCFs and a merged multi-sample VCF), all input product files used (BPM manifest, CSV manifest, EGT cluster file, reference genome FASTA with build version), software identification (name, version), exact pipeline parameters or command invocations, sample sheet, and run logs, full SNP technical filter applied, samples reclustered on study data, final report, and README docs explaining the data in each directory. Reports will be delivered within 90 days of sample receipt.

5.1.1.3. The contractor shall consult with USARIEM investigators regarding data analysis, interpretation and reporting.

5.1.1.4. Upon receiving the samples, the contractor will confirm delivery via email to the COR on the day of delivery (Section 7, Deliverable 2) and will place blood samples into a -80°C freezer until analysis. The contractor shall keep all samples until confirmation that all analysis is complete and satisfactory.

5.2 Special Qualifications: The contractor shall possess specialized experience necessary to provide genomic assessment in human biological (i.e. serum) samples and associated analysis. Specialized experience includes:

5.2.1 Use of the Infinium Global Diversity Array, a powerful, cost-effective array with optimized genome-wide content. The Infinium Global Diversity Array provides targeted coverage of more than 4800 key genes across the genome. Approximately 1.8 million markers are included in the BeadChip for high exonic coverage in regions of disease relevance, providing highly accurate copy number variation calls, and an average resolution of 1.5Mb. This array was chosen by the All of Us Research Program, the Federal, NIH-sponsored research program. The markers chosen for the array combine highly optimized, genome-wide content with curated clinical research variants. The array is highly informative, with a backbone optimized for cross-population imputation coverage of the genome. It also enables polygenic risk score development and characterization of genetic architecture in diverse populations.

5.2.2 The array must provide updated broad coverage of clinical research variants for a range of applications with optimized content.

5.2.3 Technology, microarray variant class – SNPs, loss of heterozygosity (LOH), chromosomal abnormalities, structural variants, copy number variants (CNVs).

5.2.4 Maximized variant coverage – a high-density SNP global backbone for cross-population imputation coverage of the genome enables polygenic risk score development and characterization of genetic architecture in diverse populations.

5.2.5 Content – contractor will provide a standardized robust genome-wide scaffold designed to tag common and low-frequency variants in global populations.

5.2.6 Contractor’s laboratory systems must be governed by a set of Standard Operating Procedures (SOP’s) that are documented, periodically reviewed and updated, and must adhere to Clinical Laboratory Improvement Amendments (CLIA) certification and College of American Pathologists (CAP) accreditation standards and practices with quality control in place for all analysis conducted.

5.2.7 Laboratory technicians trained on appropriate measurement procedures and validated equipment.

5.2.8 Contractor must have previous history of providing genomics services to the Federal government in terms of analysis of at least 10,000 samples.

PART 6

6.0 INFORMATION TECHNOLOGY & SECURITY

All work under this contract is UNCLASSIFIED.

PART 7

7.0 ATTACHMENTS/TECHNICAL EXHIBIT LISTING

PART 7, ATTACHMENT 1

PERFORMANCE REQUIREMENTS SUMMARY

The contractor service requirements are summarized into performance objectives that relate directly to mission essential items. The performance threshold briefly describes the minimum acceptable levels of service required for each requirement. These thresholds are critical to mission success.

Performance Objective

(The Service required—usually a shall statement from Part 5)

PWS Reference Acceptable Quality Level (AQL) (This is the maximum error rate. It could possibly be “Zero deviation from standard”)

Method of Surveillance

Performance Requirements Summary

(PRS) # 1.

The contractor shall conduct analysis of biological samples with 100% accuracy.

5.1.1.1 No more than one

customer complaint

Validated Customer Complaint received by

COR.

PRS # 2

The contractor shall enter data, manage large directories and provide full deidentified data release.

5.1.1.2 No more than one

customer complaint

Validated Customer Complaint received by

COR.

PRS # 3

The contractor shall deliver reports within 90 days of sample receipt.

5.1.1.2 No more than one

customer complaint

Validated Customer Complaint received by

COR.

PRS # 4

The contractor shall Consult on data analysis, interpretation and reporting.

5.1.1.3 No more than one

customer complaint

Validated Customer Complaint received by

COR.

PRS # 5

The contractor shall submit draft QCP to the Contracting Officer upon submission of proposal, and finalized QCP within fifteen days of contract award.

1.10.2 100% Validated by Contracting Officer.

PART 7, ATTACHMENT 2

PERFORMANCE REQUIREMENTS SUMMARY

Deliverable Schedule Table

PWS

Ref. Number Title/Description Due

5.1.1.2 Deliverable 1 Technical data including full data

release and report in a downloadable format with all supporting files including figures and tables

Within 90 days of sample receipt.

5.1.1.4 Deliverable 2 Email to COR stating samples

received

Same day as sample delivery.

1.10.2 Deliverable 3 Quality Control Plan Draft due upon proposal submission. Finalized QCP due within fifteen days of contract award.

PART 7, ATTACHMENT 3

ESTIMATED WORKLOAD DATA

ITEM NAME ESTIMATED QUANTITY

1 Individual sample analyses 648

PART 7, ATTACHMENT 3 ESTIMATED WORKLOAD DATA