SAM #36C24E26Q0028

Sole Source Prostate Cancer-Specific Sequencing Services for SFVAHCS

This opportunity is a sole source procurement by the Department of Veterans Affairs for specialized prostate cancer sequencing services. - Sole source contract to The Broad Institute, Inc. for prostate cancer-specific sequencing - Supports San Francisco VA Healthcare System (SFVAHCS) and VA Merit award research led by Dr. Franklin W. Huang - Services required: - PCR+ Human Whole Genome Sequencing (WGS) at 30x and 60x coverage - 150 samples for each coverage level (total 300 samples) - FFPE-compatible workflow for challenging clinical biopsy specimens - Tumor-normal matched sequencing - Secure delivery of FASTQ, BAM, and VCF files - Anonymization and secure handling of all samples - Quality metrics reporting - The Broad Institute is the only vendor with a validated protocol for these requirements - Contract period: one-year base with two option years (up to three years total) - Place of performance: San Francisco VA Healthcare System - Contracting office: Veterans Health Administration Regional Procurement Office East, Pittsburgh, PA - No specific part numbers; protocols are uniquely specified - Justified as sole source due to unique technical requirements and risk of data failure with alternatives

Description

Pre-Solicitation Notice for the notice of intent to award a sole source contract. This is not a solicitation. Regional Procurement Office (RPO) - East intends to negotiate a sole source contract for a one (1) year base period to include two (2) option years with The Broad Institute, Inc., located at 415 Main Street, Cambridge, Massachusetts, for the San Francisco VA Healthcare System (SFVAHCS) for its prostate cancer-specific sequencing services. These services are essential to VA Merit award study under Dr. Franklin W. Huang, MD, Ph. D.

Background: Franklin W. Huang, MD PhD VA Merit award has tumor sequencing requirements across Aim 1 and Aim 3. The vendor has a prostate cancer-specific sequencing protocol critical to the success of both aims. Aim 1: Utilizes previously collected tissue samples (N=60) from the SFVAHCS Department of Pathology and prospectively collected samples (n=40) from African American men undergoing radical prostatectomy. All samples are from Veterans and have already been collected at SFVAHCS. Aim 3: Requires prospective enrollment of 20 patients (of the 40 from Aim 2) over 4 years. This aim involves generating prostate epithelial organoid lines for genetic perturbations and single-cell RNA sequencing analysis.

Scope: Vendor shall perform prostate cancer-specific sequencing for the SFVAHCS over a 3-year period. This includes: Minimum 30x and 60x coverage FFPE-compatible workflow Tumor-normal matched sequencing FASTQ, BAM, VCF file delivery Quality metrics (Q30, coverage uniformity, etc.) Secure data transfer method PCR+ Human WGS - 30x v3_FFPE_DRAGEN - 150 Samples PCR+ Human WGS - 60x v3_FFPE_DRAGEN 150 Samples

Specific Tasks: Perform PCR+ Human WGS - 30x v3_FFPE_DRAGEN for 150 samples Perform PCR+ Human WGS - 60x v3_FFPE_DRAGEN for 150 samples Ensure anonymization and secure handling of all samples Provide tumor and normal genome sequencing specific to prostate cancer tissue

The requirement for a prostate cancer-specific sequencing protocol is a unique and corroborated capability that makes this vendor the only one capable of meeting the Government's needs. This protocol is important for the success of Aim 1 and Aim 3 of Dr. Huang s VA Merit award because:

Tissue Specificity: Prostate cancer tissue samples, particularly those from clinical biopsies, often have low tumor content and exhibit high degrees of heterogeneity. The requested vendor's established protocol is uniquely optimized to handle these challenging specimens, ensuring sufficient data yield and quality for both the Whole Genome Sequencing (WGS) runs (30x and 60x) and downstream analysis.

Downstream Research Impact (Aim 3): The WGS data directly informs the generation of prostate epithelial organoid lines and subsequent single-cell RNA sequencing analysis in Aim 3. Using a non-specific or unvalidated protocol would introduce significant data failure risk, rendering the downstream genetic perturbations and analysis unreliable.

Cost and Delay: Mandating the use of an unproven protocol would necessitate re-sequencing samples, leading to a substantial duplication of cost and a significant delay to the 4-year prospective enrollment schedule for the veteran patients in the study. This would jeopardize the success and integrity of the federally funded research.

Since the intent is to procure this on a sole source basis, no solicitation will be posted to SAM.gov Contract Opportunities. The applicable NAICS code is 541380, with a $19M size standard. The PSC is B529. The authority for this action is FAR 6.302.1-1 Only One Responsible source, and no other supplies or services will satisfy agency requirements.

Interested persons may contact the Contracting Officer via email at millicent.covert@va.gov regarding this procurement. The determination to conduct a competitive procurement based on responses to this notice is solely within the discretion of the Contracting Officer.

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