Q517--SOURCES SOUGHT - - Pharmacogenomics (PGx) Testing in the VA

SOURCES SOUGHT - Pharmacogenomics (PGx) Testing in the VA The purpose of this sources sought is to conduct market research to determine if responsible sources exist by determining if this effort can be successfully competed and/or set-aside for Small Businesses. The proposed North American Industry Classification System (NAICS) Code is 541380-Testing Laboratories. The size standard is 16,500,000 or 621511 Medical Laboratories, size standard $35 million. You can still respond to this sources sought if you don t fall under this NAICS code, please provide an alternate relevant NAICS code in your response for consideration. The Department of Veterans Affairs will use this information to determine the best acquisition strategy for this procurement. The NAICS code may change dependent upon market research results. The Government is interested in all large and small businesses to include 8(a), Service-Disabled Veteran-Owned, HubZone and Women-Owned small business concerns. BACKGROUND:

Pharmacogenomics (PGx) Testing in the VA. Every day Veterans are prescribed medication that can be impacted by differences in their genes. Pharmacogenomics (PGx) testing relies on analyzing a patient s DNA to determine how variations in specific genes can impact response to medications used to treat a range of diseases. Depending on the medication of interest, PGx test results along with evidence-based recommendations can optimize prescriptions to help improve efficacy, prevent adverse drug events, or reduce ineffective medication prescriptions VHA is planning to develop a custom VA PGx panel of relevant Pharmacogenomic genes for the clinical test to be performed internally at the VA Pathology & Laboratory Medicine Service (PALMS) laboratories. VA is currently in need of in-house bioinformatics pipeline(s) services to manage and process the raw data generated at its clinical PGx testing being conducted at its various PALMS labs using either the Illumina or Thermofisher Genexus PGx platforms/machines. SCOPE: The objective of this sources sought is to identify potential vendors for building and maintaining a clinical pharmacogenomics bioinformatics platform and services for the VA custom Laboratory developed test (LDT) for clinical PGx testing. The platform aims to enhance patient care by providing a seamless and integrated solution for pharmacogenomics testing and result reporting. The goal is a fully functional and secure pharmacogenomics bioinformatics platform centralized within the VA network in Genomic Information System for Integrative Sciences (Genisis) with all features specified. REQUIREMENTS: all vendors must have the ability to meet the following: Headquarters is located within the Continental United States. No work is performed outside of the United States or in any locality outside of the jurisdiction of the laws of the United States. Ability to transfer to VA all required pipelines and its components to be independently installed, used and managed within the VA firewall without the requirement for any permanent connection to outside the VA firewall. The contractor may be required to work with other partners besides the VA to accomplish the goals of VA Precision Pharmacogenomics Program. Contractors shall be required to submit for a NACI level background investigation and security clearance in accordance with the VA IT Security Clause and complete the required training and procedures to comply with these requirements. TASKS/MODULES: Vendors do NOT need to meet all modules to respond to this notice. Please respond indicating which modules you can meet and which ones you cannot. This will help the VA determine if multiple contracts should be pursued. Module 1: Tracking Clinical Test Order: The primary task in this module will be to enable tracking of test ordering from the VA EHR system and test status at the participating PALMS through the life cycle of a Pharmacogenomic (PGx) test including sample tracking to test data generation and quality validation. The main components will be - -Development of a module for tracking pharmacogenomics tests orders from the VA Vista system, tracking the sample and status for each test that are completed by the each of the testing labs in the VA. Proper accounting of all tests ordered, test assignment to specific testing labs and stages of completion of the tests needs to be recorded and made available in a dashboard format for each testing lab as well as for the national PGx office. -Implementation of financial tracking mechanisms to monitor costs and billing associated with pharmacogenomic testing for each VA PALMS laboratory involved in the PGx testing. Module 2: Develop VA Custom Pharmacogenomics Testing Platform & Perform Bioinformatics Validation. The primary task in this module will be for the vendor to work with the VA PM/POC to develop, test and implement a custom VA Pharmacogenomics panel for clinical testing. The main task associated with this module will be - -Collaborate to develop VA custom pharmacogenomics testing panel for validated PGx biomarkers for clinical testing as Lab developed test (LDT) in collaboration with the VA National Pharmacogenomics Office and the PGx testing platforms from Illumina and Thermofisher. -Develop bioinformatics pipelines to include information including but not limited to primer selection, custom test panels selection with validated clinical results and customized for pharmacogenomic testing and data management . -Collaboration with the testing laboratories for the development and validation of the customized testing kits. -Must have demonstratable experience in operational use of their proposed PGx pipelines for clinical Pharmacogenomic testing in the United States -The contractor shall demonstrate any certification they possess for using their products in clinical practice in the United States. Module 3: Development of Haplotype/Diplotype Genotype and Structural Variant Calling for VA Specific Pharmacogenomics Markers. -The primary task in this module will be the development of VA custom pipelines to call the genotypes (haploid and diploid) reliably and consistently for each of the custom markers that VA will plan to report for clinical use. Tasks in this module will include - -Development of a customized pipeline for diplotype and haplotype calling using various input file formats including but not limited to VCFs, FASTQs, and Json files from both the Thermofisher and Illumina PGx platforms with high reliability (>99.9%)and reproducibility (>99.9%). -Loose Integration of the pipelines with the Illumina and Thermofisher PGx testing platforms data and other modules in this program and validation of calling pipeline for consistent calling results across the PGx testing platforms. --Must have demonstratable experience in operational use of their proposed PGx pipelines for clinical Pharmacogenomic testing in the United States -The contractor shall demonstrate any certification they possess for using their products in clinical practice in the United States. Module 4: Clinical Interpretation and VA Custom Pharmacogenomics Reporting Engine. This task will include the most up to date expert clinical interpretations of the PGx calls from module 3. The primary tasks will include - Pharmacogenomics subject matter expertise to collaborate with the VA PGx National office in implementing the VA custom reporting for the VA PGx panel reporting. --Up-to-date customizable Clinical interpretation knowledgebase to include but limited to relevant PGx knowledge standards CPIC, DPWG, FDA etc. -Creation of a customized reporting pipeline that translates the VA custom PGx genomic data into clinically actionable information. -Development of a reporting interface for SMEs to access and interpret pharmacogenomic results. -Ability for automatic and manual checks and validation of the individual sample results -Development of a VA custom PDF report for each test. --Must have demonstratable experience in operational use of their proposed PGx pipelines for clinical Pharmacogenomic testing in the United States. -The contractor shall demonstrate any certification they possess for using their products in clinical practice in the United States. Module 5: PGx Clinical Testing Pipeline Training and Support Services: -Provide PGx Subject Matter Experts (SMEs) to work with the VA PGx team to provide ongoing support and issue resolution. -Establishment of a dedicated support system to address technical issues, provide troubleshooting assistance, and ensure the seamless integration of the platform into existing workflows. -Provision comprehensive training programs for VA healthcare personnel on the effective use and interpretation of the pharmacogenomics pipelines and interpretations. -The contractor shall demonstrate any certification they possess for using their products in clinical practice in the United States. ***Potential sources who are interested must provide the following in word format, please copy and paste the following format for your response: BUSINESS NAME: SAM UNIQUE ID#: POC EMAIL: RELEVENT NAICS WITH BUSINESS SIZE: SOCIO-ECONOMIC STATUS (LARGE, SMALL, VETERAN OWNED SMALL BUSINESS, ETC): MODULE 1 - Tracking Clinical Test Order: Can you meet the requirements listed under the REQUIREMENTS AND TASKS/MODULES sections for this module? If yes, provide a service capability statement that clearly demonstrates your ability to meet the requirements and address each bullet under the module. Your description should include recent and relevant work within the past five (5) years. If possible, please include specific projects. Vendors do NOT need to meet the requirements for all modules to respond to this notice. The government is using this information to determine if multiple contracts should be awarded. If no, no description is required. MODULE 2 - Develop VA Custom Pharmacogenomics Testing Platform & Perform Bioinformatics Validation: Can you meet the requirements listed under the REQUIREMENTS AND TASKS/MODULES sections for this module? If yes, provide a service capability statement that clearly demonstrates your ability to meet the requirements and address each bullet under the module. Your description should include recent and relevant work within the past five (5) years. If possible, please include specific projects. Vendors do NOT need to meet the requirements for all modules to respond to this notice. The government is using this information to determine if multiple contracts should be awarded. If no, no description is required. MODULE 3 - Development of Haplotype/Diplotype Genotype & Structural Variant Calling for VA Specific Pharmacogenomics Markers: Can you meet the requirements listed under the REQUIREMENTS AND TASKS/MODULES sections for this module? If yes, provide a service capability statement that clearly demonstrates your ability to meet the requirements and address each bullet under the module. Your description should include recent and relevant work within the past five (5) years. If possible, please include specific projects. Vendors do NOT need to meet the requirements for all modules to respond to this notice. The government is using this information to determine if multiple contracts should be awarded. If no, no description is required. MODULE 4 - Clinical Interpretation & VA Custom Pharmacogenomics Reporting Engine: Can you meet the requirements listed under the REQUIREMENTS AND TASKS/MODULES sections for this module? If yes, provide a service capability statement that clearly demonstrates your ability to meet the requirements and address each bullet under the module. Your description should include recent and relevant work within the past five (5) years. If possible, please include specific projects. Vendors do NOT need to meet the requirements for all modules to respond to this notice. The government is using this information to determine if multiple contracts should be awarded. If no, no description is required. MODULE 5 - PGx Clinical Testing Pipeline Training & Support Services: Can you meet the requirements listed under the REQUIREMENTS AND TASKS/MODULES sections for this module? If yes, provide a service capability statement that clearly demonstrates your ability to meet the requirements and address each bullet under the module. Your description should include recent and relevant work within the past five (5) years. If possible, please include specific projects. Vendors do NOT need to meet the requirements for all modules to respond to this notice. The government is using this information to determine if multiple contracts should be awarded. If no, no description is required. Send written responses electronically in Word format to Lynn.Portman@va.gov & saiju.pyarajan@va.gov by 3/29/24. ***You may submit questions or industry insight at the end of your submission. However, the Government is not required to address questions. This notice is to assist in determining sources only--a solicitation is not currently available. This information is for planning purposes only and is not to be construed as a commitment by the Government, implied or otherwise, to issue a solicitation or award a contract. Potential sources responding to this sources sought notice are advised their responses do not ensure participation in future solicitations or contract awards. The Government will not reimburse any company or individual for any expense.