Performance Work Statement PWS Strand-Specific RNA-Sequencing Services.docx

Department of Veterans Affairs – Performance Work Statement

PERFORMANCE WORK STATEMENT

Strand-Specific RNA-Sequencing Services for Transcriptomic Characterization of Choroid Plexus Dysfunction in Chronic Traumatic Encephalopathy and Alzheimer’s Disease

1. BACKGROUND

The Department of Veterans Affairs (VA), Bedford VA Medical Center (VAMC), requires strand-specific RNA-sequencing (RNA-seq) services in support of neurodegenerative disease research focused on characterizing gene expression in the human choroid plexus.

The research involves human choroid plexus tissue associated with Chronic Traumatic Encephalopathy (CTE), Alzheimer’s Disease (AD), TDP-43 proteinopathy, and neurologically normal controls. The resulting transcriptomic dataset will support differential gene-expression and related downstream analyses performed by the Government.

The Government requires sequencing of 269 human choroid plexus total RNA samples using strand-specific library preparation with ribosomal RNA (rRNA) depletion and Illumina paired-end sequencing.

2. OBJECTIVE

The objective of this requirement is to obtain high-quality, strand-specific RNA-sequencing data from 269 Government-furnished human choroid plexus RNA samples suitable for subsequent transcriptomic analysis by the Government.

The Contractor shall provide the laboratory services, personnel, equipment, supplies, quality-control activities, sequencing, and data deliverables necessary to accomplish this requirement.

3. SCOPE

The Contractor shall provide strand-specific RNA-sequencing services for 269 human choroid plexus total RNA samples. Services shall include:

1. Receipt, handling, and quality-control (QC) assessment of Government-furnished RNA samples;

2. Ribosomal RNA (rRNA) depletion-based, strand-specific library preparation;

3. Library quality-control assessment;

4. Illumina paired-end sequencing in a 2x150bp configuration, generating approximately 60 million read pairs per sample (~120 million total reads per sample);

5. Sequencing quality-control assessment and reporting; and

6. Generation and delivery of FASTQ data files and associated quality-control reports.

The Government will perform downstream bioinformatics and transcriptomic analyses in-house. Bioinformatics analysis beyond that specifically identified in this PWS is not required.

4. TECHNICAL REQUIREMENTS

4.1 Sample Quantity

The Contractor shall provide the required services for 269 human choroid plexus total RNA samples. Samples are de-identified post-mortem research specimens.

4.2 Sample Quality Control

The Contractor shall perform quality-control assessment of submitted RNA samples prior to library preparation. The following sample acceptance criteria shall apply:

RNA Integrity Number (RIN): >6.0 (≥7.0 preferred) A260/A280 ratio: 1.8–2.2 DNA-free Minimum RNA input: ≥150 ng Minimum concentration: ≥6 ng/µL The Contractor shall notify the designated Government point of contact of any sample that does not meet the applicable acceptance criteria before proceeding with that sample.

4.3 Library Preparation

The Contractor shall perform strand-specific (directional) RNA library preparation using rRNA depletion. The Contractor shall perform appropriate library quality-control procedures prior to sequencing.

4.4 Sequencing

The Contractor shall perform sequencing using an Illumina sequencing platform meeting the following minimum requirements:

The Contractor shall have sufficient sequencing and laboratory capacity to perform the requirement within the required turnaround time.

4.5 Quality Standard

The Contractor shall provide sequencing results meeting a quality standard of at least 85 percent of bases with a Phred quality score of Q30 or greater.

The Contractor shall provide QC documentation sufficient for the Government to verify compliance with the required sequencing specifications. The Contractor shall identify and report any samples or sequencing results that fail to meet applicable quality requirements.

5. DELIVERABLES

Deliverable 1 – Sample QC Results Quality-control results for Government-furnished RNA samples.

Deliverable 2 – Library and Sequencing QC Reports Quality-control documentation associated with library preparation and sequencing sufficient to demonstrate compliance with the technical requirements of this PWS.

Deliverable 3 – FASTQ Files FASTQ files containing the sequencing data generated for each successfully processed sample. FASTQ data shall be provided in a format compatible with commonly used bioinformatics analysis pipelines.

Deliverable 4 - Data Delivery The Contractor shall provide all final FASTQ files and associated quality-control reports on a physical hard drive. The hard drive shall be shipped or delivered to the VA Principal Investigator or other Government recipient designated by the Contracting Officer. In lieu of physical delivery, the Government may authorize secure electronic/cloud-based delivery when the proposed delivery method has been determined by the Government to satisfy applicable VA information security and information technology requirements, including applicable FedRAMP authorization requirements. Electronic/cloud delivery shall not be used without prior Government approval.

6. TURNAROUND TIME

The Contractor shall complete sample QC, library preparation, sequencing, quality-control reporting, and final data delivery within 23–28 business days following receipt of all 269 Government-furnished samples as one batch.

The Government may coordinate with the Contractor, if mutually agreeable, to submit a limited number of samples in advance of the full batch for preliminary quality-control assessment. Any such preliminary submission shall not commence the required 23–28 business-day turnaround period.

If circumstances outside the Contractor’s reasonable control are expected to affect the required turnaround time, the Contractor shall promptly notify the Government point of contact and Contracting Officer.

7. PLACE OF PERFORMANCE

The primary place of performance shall be the successful Contractor's laboratory facility or facilities identified in its quotation. The Contractor shall identify in its quotation the location(s) where sample quality control, library preparation, sequencing, and related laboratory services will be performed.

If any portion of the requirement will be performed by a subcontractor or third-party laboratory, the Contractor shall identify the subcontractor or third-party facility and the work to be performed at that location in its quotation. Government-furnished samples will be shipped from the VA Bedford Healthcare System, Bedford, Massachusetts, to the Contractor's designated laboratory facility.

8. GOVERNMENT-FURNISHED PROPERTY/MATERIALS

The Government will furnish the 269 de-identified human post-mortem choroid plexus total RNA samples required for performance. The Government will coordinate shipment of the samples to the Contractor.

9. DATA AND INFORMATION SECURITY

Samples furnished under this requirement are de-identified post-mortem research specimens. The deliverables contain no Protected Health Information (PHI) or Personally Identifiable Information (PII), and no access to VA networks or information systems is required for performance.

The Contractor shall appropriately safeguard Government-furnished samples and data generated during contract performance.

10. GOVERNMENT RESPONSIBILITIES

1. Provide the 269 de-identified RNA samples;

2. Coordinate shipment of samples to the Contractor;

3. Provide a Government technical point of contact;

4. Provide reasonable technical clarification concerning Government-furnished samples when necessary; and

5. Review Contractor deliverables for compliance with the PWS.

11. CONTRACTOR RESPONSIBILITIES

The Contractor shall provide all personnel, laboratory facilities, equipment, materials, supplies, technical expertise, sequencing capacity, data storage, and other resources necessary to successfully perform the requirement, except for Government-furnished materials specifically identified in this PWS.

The Contractor shall be responsible for performing required sample QC, library preparation, sequencing, sequencing QC, reporting, and final data delivery.

12. PERFORMANCE STANDARDS

13. ACCEPTANCE

The Government will inspect Contractor deliverables for conformity with the requirements of this PWS. Services will be considered acceptable when the Contractor has provided the required sequencing services and deliverables and the Government has determined that the applicable technical, quality, and delivery requirements have been satisfied.

14. PERIOD OF PERFORMANCE

The contract shall have a one-year period of performance from the date of award. The sequencing services and associated deliverables shall be completed within the turnaround requirements specified in Section 6 following receipt of the Government-furnished samples.

15. CONTRACT TYPE

The Government anticipates award of a Firm-Fixed-Price, non-personal services contract.

Strand-Specific RNA-Sequencing Services