AN12--Genomic Analysis System

Active

Contract Opportunity

The Department of Veterans Affairs (VA) Technology Acquisition Center (TAC) is seeking information concerning the availability of capable contractors to provide the Genomic Analysis System identified in the Product Description (PD).
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This is a Request for Information (RFI) only and is limited to ten pages. Do not submit a proposal or quote. There is no obligation on the part of the Government to acquire any products or services described in this RFI. Your response to this RFI will be treated only as information for the Government to consider. You will not be entitled to payment for direct or indirect costs that you incur in responding to this RFI. This request does not constitute a solicitation for proposals or the authority to enter into negotiations to award a contract. No funds have been authorized, appropriated or received for this effort. Interested parties are responsible for adequately marking proprietary, restricted or competition sensitive information contained in their response. The Government does not intend to pay for the information submitted in response to this RFI. Page limit (excluding PD feedback) is 10 pages.

Responses are due by 06/06/2025 via email to Michael Gruen, michael.gruen@va.gov and Debra Clayton, debra.clayton2@va.gov. The file name of your response must be CompanyName.GenomicAnalysisSytem

If interested, please respond to the following:Â

 A capabilities statement that addresses the questions below and draft PD. If additional information is required by VA to determine a contractor s capability to provide the full requirement and the economic feasibility of the information provided, additional information may be requested at a later date. Technical questions may be submitted as part of your response. A draft version of the requirement is below. Please direct all responses to Michael Gruen, michael.gruen@va.gov and Debra Clayton, debra.clayton2@va.gov

Has the draft PD provided sufficient detail to describe the technical requirements?
 ______ YES _______ NO (if No, answer question below)Â
If NO , please provide your technical comments/recommendations on elements of the draft PWS that may contribute to a more accurate proposal submission and efficient, cost effective effort.Â

Any Contract Vehicle of which you are a part that can be used to acquire your solution as well as the company business size and status for each vehicle as designated by the NAICS 541990, All Other Professional, Scientific, And Technical Services, and the associated U.S. Small Business Administration size status (i.e., Large Business, Small Business, Service-Disabled Veteran Owned Small Business, Small Disadvantaged Business, Women-Owned Small Business, Hub Zone Small Business, etc.)Â
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If your company is a small business, please confirm that in the solution provided, your company will be performing at least 50% of the work in accordance with the set aside regulations.Â
Describe your capability to meet the requirements set forth in the PD, entitled Genomic Analysis System section 1.0 Product Requirements.

For your proposed product, please describe the services that would be required to install at VA site.

How large of an infrastructure footprint would be required if VA were to implement your solution? Please ensure that your response takes into consideration the hardware needed to meet VA s computing/processing requirements described in the product description.

What services, including but not limited to networking, setup and configuration be
required to implement your solution?

Would the solution you offer fit in the space VA has available?

How long would it take to set up and install your proposed solution? What duration of consulting services would be required if VA were to implement your proposed solution?

What type of hardware would be needed to process 175,000 whole genome sequences samples per year scaling up to 1,000,000 whole genome sequences samples?






PRODUCT DESCRIPTION (PD)
DEPARTMENT OF VETERANS AFFAIRS
Office of Information & Technology
Development Security & Operations
Infrastructure Operations

Genomic Analysis System

Date: May 28, 2025
PD Version Number: 1.0





Contents
1.0 PRODUCT REQUIREMENTS 5
2.0 NOTICE OF THE FEDERAL ACCESSIBILITY LAW AFFECTING ALL INFORMATION AND COMMUNICATION TECHNOLOGY (ICT) PROCUREMENTSÂ (SECTION 508) 7
2.1 SECTION 508 INFORMATION AND COMMUNICATION TECHNOLOGY (ICT) STANDARDS 7
2.2 COMPATABILITY WITH ASSISTIVE TECHNOLOGY 7
2.3 ACCEPTANCE AND ACCEPTANCE TESTING 8
3.0 INFORMATION TECHNOLOGY USING SUSTAINABLE PRODUCTS AND SERVICES 8
4.0 SHIPMENT OF HARDWARE OR EQUIPMENT 8
4.1 SPECIAL SHIPPING INSTRUCTIONS 9
5.0 GENERAL REQUIREMENTS 9
5.1 VA TECHNICAL REFERENCE MODEL 9
5.2 ZERO TRUST VA CRITICAL SECURITY CONTROLS 9
5.3 SOCIAL SECURITY NUMBER (SSN) REDUCTION 10
5.4 INTERNET PROTOCOL VERSION 6 (IPV6) 10
5.5 SOFTWARE AND LICENSING REQUIREMENTS 11
5.6 TRUSTED INTERNET CONNECTION (TIC) 11

1.0 PRODUCT REQUIREMENTS
The Department of Veterans Affairs (VA) Center for Data and Computational Sciences (C-DACS) requires a high-throughput genomic analysis system capable of performing whole genome sequencing (WGS) and variant calling at an industrial scale. This system will support the department s mission to advance genomic research, precision medicine, and large-scale population studies by enabling rapid, accurate, and cost-efficient sequencing of complex genomes.
The desired solution should leverage cutting-edge sequencing technology to deliver exceptional accuracy, scalability, and automation while integrating seamlessly with bioinformatics pipelines. It must be capable of handling high sample volumes, ensuring streamlined workflows from sample preparation to data analysis, and providing robust variant detection for clinical and research applications. This system will be a cornerstone for ongoing and future genomic initiatives, driving discoveries in genetic disorders, infectious disease surveillance, and personalized medicine. The solution should have the following salient characteristics

A software integrated system to analyze whole genomes, exomes, targeted panels, transcriptomes, and methylomes in a single system.
Must include dedicated field-programmable gate array (FPGA) hardware to expedite key genomic workflows (mapping, alignment, variant calling). Â
On-Premises Control: All hardware and data remain under organizational jurisdiction, ensuring compliance with privacy regulations (e.g., Health Insurance Portability and Accountability Act, General Data Protection Regulation). Â
Ability to handle workload for over one million Million Veteran Program samples, with options for hardware expansion if needed. Â
10GbE or 25GbE network interfaces for fast data transfer between Centre for Development of Advanced Computing High Performance Computing environment and the genomic system.
Pre-installed genomic analysis pipelines out-of-the-box to avoid time delays associated with building custom pipelines.
Ideal solution utilizes sample data on existing VAST brand storage versus having to migrate the data to another storage solution.
The solution shall allow for removal of data storage upon the need to replace the equipment for warranty. VA maintains the storage device.
Capability to utilize the state-of-the-art knowledge/information to call single-nucleotide variants (SNVs), structural variants (SV), copy number variants (CNVs), repeat expansions, targeted panel callers, and biomarkers. Perform standardized validated Whole Genome Sequence (WGS) short read mapping, alignment, sorting, and variant calling with high accuracy of 98.8% or higher.
Supports Oncology for both tumor-only and tumor-normal paired samples with somatic pipeline capable of identifying somatic variants which exist at low allele frequencies in tumor samples.
Supports Genomics, Transcriptomics, Metagnomics, and Epigenomics analysis.
Fast, scalable, comprehensive, and accurate WGS calling from input file formats of at least binary base cell BCL, FASTQ, binary alignment map, and compressed reference-oriented alignment map.
System that will scale with throughput of at least 175,000 samples per year.
High throughput, at a rate of ~30 min per WGS for the full suite of analysis with minimum 99.84% variant calling and minimum 99.4% short Copy Number Variants CNV and indel accuracy.
Software pipelines allowing the flexibility to process large volumes without limitations and updating the Software system as released, providing Single Nucleotide Variant SNV, insertion-deletion (Indel), CNV, structural variants SV, short tandem repeat STR (Repeat expansions), Paralogs, PGx, analysis.
Lossless compression of FASTQ files of 80% or more reduction in file size. 5X compression in 15 minutes or less is desirable.
Star Allele Callers that identify at the minimum genotypes of the Tier-1 PGx genes: CACNA1S, CFTR, CYP2C19, CYP2C9, CYP3A5, CYP4F2, IFNL3, RYR1, NUDT15, SLCO1B1, TPMT, UGT1A1, VKORC1, DPYD, G6PD, MT-RNR1, BCHE, ABCG2, NAT2, F5, UGT2B17. Additional targeted callers, such as SMA, CYP2D6, CYP2B6, CYP21A2, HLA, GBA, LPA, and RH desirable.
Ribonucleic acid (RNA) analysis with RNA-seq (splice-aware) aligner and optional rRNA filtering during alignment. Gene fusion detection, transcript quantification, and variant calling required.
Methylation detection A Methylation pipeline to rapidly analyze whole genome and targeted bisulfite deoxyribonucleic acid sequence data. Should be capable of performing alignment, methyl calling, and calculates alignment and methylation metrics.
Quality control (QC) Metric reporting At the minimum the following QC metrics should be reported for mapper - Number of samples, Reads Processed, Total Biallelic and Multiallelic Single Nucleotide Polymorphism (SNP)s, INDELs, Multiple nucleotide polymorphisms, SNP Transitions, SNP Transversions, Ti/Tv ratio, Heterozygous, Homozygous, Het/Hom ratio. The variant caller QC metrics should include Total input reads, Total alignments, Number of duplicate reads (marked), Number of duplicate reads (marked not removed), Secondary alignments, Number of unique reads, Number of unique reads, Supplementary (chimeric) alignments, Reads with mate sequenced, Reads with mate sequenced, Estimated read length, Reads without mate sequenced, Reads without mate sequenced, Bases in reference genome, QC-failed reads, QC-failed reads, Bases in target bed [% of genome], Mapped reads, Mapped reads, Average sequenced coverage over genome, Number of unique and mapped reads (excluding duplicates), Number of unique and mapped reads (excluding duplicates), Average alignment coverage over genome and Unmapped reads.

All equipment shall be delivered within 30 days of award or exercise of any optional task to purchase additional quantities

All hardware shall include a one-year manufacturer warranty with Next Business Day replacement part delivery, from date of Government acceptance of delivery.

2.0 NOTICE OF THE FEDERAL ACCESSIBILITY LAW AFFECTING ALL INFORMATION AND COMMUNICATION TECHNOLOGY (ICT) PROCUREMENTSÂ (SECTION 508)
On January 18, 2017, the Access Board issued a final rule that updated accessibility requirements covered by Section 508 and refreshed guidelines for telecommunications equipment subject to Section 255 of the Communications Act. The final rule went into effect on January 18, 2018. The revisions and updates to the Section 508-based standards and Section 255-based guidelines are intended to ensure that information and communication technology (ICT) covered by the respective statutes is accessible to and usable by individuals with disabilities.

2.1 SECTION 508 INFORMATION AND COMMUNICATION TECHNOLOGY (ICT) STANDARDS
The Section 508 standards established by the Access Board are incorporated into, and made part of all VA orders, solicitations and purchase orders developed to procure ICT. These standards are found in their entirety at: Revised 508 Standards and 255 Guidelines (access-board.gov). A single PDF file version of the Revised Section 508 Standards and 255 Guidelines will be supplied upon request, or can be obtained from the Access Board website. Federal agencies must comply with the Rehabilitation Act of 1973, as amended.

The Contractor shall comply with 508 Chapter 2: Scoping Requirements for all electronic ICT and content delivered under this contract. Specifically, as appropriate for the technology and its functionality, the Contractor shall comply with the technical standards marked here:

E205 Electronic Content (Accessibility Standard -WCAG 2.0 Level A and AA Guidelines)
E204 Functional Performance Criteria
E206 Hardware Requirements
E207 Software Requirements
E208 Support Documentation and Services Requirements

2.2 COMPATABILITY WITH ASSISTIVE TECHNOLOGY
The standards do not require installation of specific accessibility-related software or attachment of an assistive technology device. Section 508 requires that ICT be compatible with such software and devices so that ICT can be accessible to and usable by individuals using assistive technology, including but not limited to screen readers, screen magnifiers, and speech recognition software.

2.3 ACCEPTANCE AND ACCEPTANCE TESTING
Deliverables resulting from this solicitation will be accepted based in part on satisfaction of the Section 508 Chapter 2: Scoping Requirements standards identified above.
The Government reserves the right to test for Section 508 Compliance before delivery. The Contractor shall be able to demonstrate Section 508 Compliance upon delivery.
3.0 INFORMATION TECHNOLOGY USING SUSTAINABLE PRODUCTS AND SERVICES
The Contractor shall comply with Sections 524 and Sections 525 of the Energy Independence and Security Act of 2007; Section 104 of the Energy Policy Act of 2005; Executive Order 13221, Energy-Efficient Standby Power Devices, dated August 2, 2001; and the Federal Acquisition Regulation (FAR) to provide ENERGY STAR®, Federal Energy Management Program (FEMP) designated, and products and services that meet EPA Recommendations of Specifications, Standards, and Ecolabels in effect as of October 2023 (e.g. Electronic Product Environmental Assessment Tool (EPEAT) registered products) in providing information technology products and/or services. The Green Procurement Compilation (GPC) website available at Green Procurement Compilation - GSA Sustainable Facilities Tool (sftool.gov) provides a comprehensive list of sustainable products and services and sustainable acquisition guidance.

The Contractor shall provide products that meet the definition of sustainable products and services if the products are delivered to the Government; furnished by the Contractor for use by the Government, incorporated into the construction of a public building or public work, or acquired by the Contractor for use in performing services under a Government contract where the cost of the products is a direct cost to a Government contract (versus costs which are normally applied to a contractor's general and administrative expenses or indirect costs).

Specifically, the Contractor shall provide sustainable products under this contract in accordance with FAR 52.223-23. The applicable products with their associated certification, designation, and/or ecolabel (e.g. Energy Star, FEMP, and/or EPEAT) are identified within the product specifications in this PD. The Contractor shall ensure proposed products meet the certification(s) / designation(s) / ecolabel(s) specified at the time of submission of proposals and at the time of award.
4.0 SHIPMENT OF HARDWARE OR EQUIPMENT

Inspection: Destination
Acceptance: Destination
Free on Board (FOB): Destination

Ship To and Mark For:

Primary

Alternate
Name:

Name:

Address:

Address:

Voice:

Voice:

Email:

Email:

4.1 SPECIAL SHIPPING INSTRUCTIONS
Prior to shipping, Contractor shall notify Site POCs, by phone followed by email, of all incoming deliveries including line-by-line details for review of requirements. The Contractor shall not make any changes to the delivery schedule at the request of Site POC.

Contractors shall coordinate deliveries with Site POCs before shipment of hardware to ensure sites have adequate storage space.

All shipments, either single or multiple container deliveries, shall bear the VA IFCAP Purchase Order number (if applicable) on external shipping labels and associated manifests or packing lists. In the case of multiple container deliveries, a statement readable near the VA IFCAP PO or Contract number shall indicate total number of containers for the complete shipment (e.g. Package 1 of 2 ), clearly readable on manifests and external shipping labels.

Packing Slips/Labels and Lists shall also include the following:

IFCAP PO # or Contract No.: ____________ (e.g., 166-E11234 (the IFCAP PO number is located in block #20 of the SF 1449))
Project Description: (e.g. Tier I Lifecycle Refresh)

Total number of Containers: Package ___ of ___. (e.g., Package 1 of 3)

5.0 GENERAL REQUIREMENTS
5.1 VA TECHNICAL REFERENCE MODEL
The Contractor shall comply with the VA OIT Technical Reference Model (VA TRM). Compliance with the VA TRM is achieved by using only technologies and standards that are listed as approved for use in the VA TRM. The Contractor shall provide all necessary information requested by VA to ensure TRM approval is obtained prior to use on VA s network.
5.2 ZERO TRUST VA CRITICAL SECURITY CONTROLS
VA has established minimum mandatory security requirements and requires that any network connected software system or service must meet the VA Critical Security Controls as outlined in the VA Memorandum, VA Security Controls , https://www.voa.va.gov/DocumentView.aspx?DocumentID=5010. VA Critical Security Controls identify the minimum mandatory requirements that must be implemented across all VA enterprise infrastructure, cloud computing environments, information systems, networks, and specialized devices (medical devices/systems, special-purpose systems, and research scientific computing devices) that process, store, and/or transmit VA data. Effective July 1, 2025, the Contractor shall implement these VA Critical Security Controls, within any network connected software system or service prior to being authorized for use in the VA. This functional requirement is not negotiable, and Plan of Action & Milestones (POAM) will not be accepted in the event these controls cannot be implemented for new systems. Critical Security Controls are intended to increase VA s security posture and provide security and privacy risk visibility into the VA network and is not a new requirement. The Contractor s failure to maintain these VA Critical Controls after implementation will result in VA discontinuing the use of the system.

5.3 SOCIAL SECURITY NUMBER (SSN) REDUCTION
The Contractor solution shall support the Social Security Number (SSN) Fraud Prevention Act (FPA) of 2017 which prohibits the inclusion of SSNs on any document sent by mail. The Contractor support shall also be performed in accordance with Section 240 of the Consolidated Appropriations Act (CAA) 2018, enacted March 23, 2018, which mandates VA to discontinue using SSNs to identify individuals in all VA information systems as the Primary Identifier. The Contractor shall ensure that any new IT solution discontinues the use of SSN as the Primary Identifier to replace the SSN with the Integrated Control Number (ICN) in all VA information systems for all individuals. The Contractor shall ensure that all Contractor delivered applications and systems integrate with the VA Master Person Index (MPI) for identity traits to include the use of the ICN as the Primary Identifier. The Contractor solution may only use a Social Security Number to identify an individual in an information system if and only if the use of such number is required to obtain information VA requires from an information system that is not under the jurisdiction of VA.

5.4 INTERNET PROTOCOL VERSION 6 (IPV6)
The Contractor solution shall support IPv6-Only based upon the memo issued by the Office of Management and Budget (OMB) on November 19, 2020 (https://www.whitehouse.gov/wp-content/uploads/2020/11/M-21-07.pdf). Which defines IPv6-only as the state of an operational system or service when IPv4 protocol functions (addressing, packet forwarding) are not in use. The NIST USGv6 profile defines technical requirements for a product to be capable of operating in IPv6-Only environments. IPv6-Only technology, in accordance with the USGv6 Program ((https://www.nist.gov/programs-projects/usgv6-program/usgv6-revision-1), NIST Special Publication (SP) 500-267B Revision 1 USGv6 Profile (https://doi.org/10.6028/NIST.SP.500-267Br1), and NIST SP 800-119 Guidelines for the Secure Deployment of IPv6 (https://doi.org/10.6028/NIST.SP.800-119), compliance shall be included in all IT infrastructures, application designs, application development, operational systems and sub-systems, and their integration. In addition to the above requirements, all devices, applications, and systems shall support all applicable functionality on native IPv6-Only as well as dual stack (IPv6 / IPv4) connectivity without additional memory or other resources being provided by the Government, so that they can function in a mixed environment. All public/external facing servers and services (e.g., web, email, DNS, ISP services, etc.) shall support native IPv6-Only and dual stack (IPv6 / IPv4) users and all internal infrastructure and applications shall support using native IPv6-Only and dual stack (IPv6 / IPv4) for all functionality and operations.

5.5 SOFTWARE AND LICENSING REQUIREMENTS
The Contractor shall be responsible for the provision of all software licenses and any associated licensing maintenance required for any development, delivery, integration, operation, and/or maintenance associated with its proposed application(s), software products, software solution, and/or system including, but not limited to, any and all application(s), software and/or software products that comprise, are a part of, or integrate with the Contractor s proposed application(s), software products, software solution, and/or system for the life of any resulting contract.

5.6 TRUSTED INTERNET CONNECTION (TIC)
The Contractor solution shall meet the requirements outlined in Office of Management and Budget Memorandum M-19-26, Update to the Trusted Internet Connections (TIC) Initiative (https://www.whitehouse.gov/wp-content/uploads/2019/09/M-19-26.pdf), VA Directive 6513 Secure External Connections , and shall comply with the TIC 3.0 Core Guidance Documents, including all Volumes and TIC Use Cases, found at the Cybersecurity & Infrastructure Security Agency (CISA)
(https://www.cisa.gov/publication/tic-30-core-guidance-documents.)






POINTS OF CONTACT
VA Program Manager:
Name: Brian Ibbison
Voice: (774) 826-1269
Email: brian.ibbison@va.gov

Contracting Officer s Representative:
Name: L. Jani Shrout
Voice: (512) 981-4555
Email: Lillian.Shrout@va.gov

Contracting Officer:
Name: Debra Clayton
Address: Technology Acquisition Center
23 Christopher Way
Eatontown, NJ 07724
Voice: (848) 377-5174
Email: Debra.clayton2@va.gov

Contract Specialist:
Name: Michael Gruen
Address: Technology Acquisition Center
23 Christopher Way
Eatontown, NJ 07724
Voice: (848)-377-5251
Email: michael.gruen@va.gov
INFORMATION SECURITY CONSIDERATIONS
The C&A requirements do not apply, and that a Security Accreditation Package is not required.

All VA sensitive information shall be protected at all times in accordance with local security field office System Security Plans (SSP s) and Authority to Operate (ATO) s for all systems/LAN s accessed while performing the tasks detailed in this Product Description.

Attachments/Links