B529--Prostate Cancer-Specific Sequencing Services

Description

{"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. \n\nBackground:\nFranklin 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.\nAim 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.\nAim 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.\n\nScope:\nVendor shall perform prostate cancer-specific sequencing for the SFVAHCS over a 3-year period. This includes:\nMinimum 30x and 60x coverage\nFFPE-compatible workflow\nTumor-normal matched sequencing\nFASTQ, BAM, VCF file delivery\nQuality metrics (Q30, coverage uniformity, etc.)\nSecure data transfer method\nPCR+ Human WGS - 30x v3_FFPE_DRAGEN - 150 Samples\nPCR+ Human WGS - 60x v3_FFPE_DRAGEN 150 Samples\n\nSpecific Tasks:\nPerform PCR+ Human WGS - 30x v3_FFPE_DRAGEN for 150 samples\nPerform PCR+ Human WGS - 60x v3_FFPE_DRAGEN for 150 samples\nEnsure anonymization and secure handling of all samples\nProvide tumor and normal genome sequencing specific to prostate cancer tissue\n\nThe 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: \n\nTissue 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.\n \nDownstream 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. \n\nCost 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.\n\nSince 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. \n\nInterested 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. \n\n"}