AN11--Multi-Omics Sequencing Services (Research Study Support)

Page 3 of 3 Page 1 of 3 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 one (1) year with NOVOGENE CORPORATION INC, located at 2921 Stockton Blvd Ste 1810, Sacramento, California, 95817-2305, for the VA Pittsburgh Healthcare System for its multi-omics sequencing and analysis services to support VA-funded study. Background: Degenerative cervical myelopathy (DCM) is the most common cause of spinal cord dysfunction and poses a significant health burden in Veterans. However early detection is a significant challenge, leading to the current study aimed at identifying diagnostic biomarkers that will inform treatment more targeted and individualized treatment strategies. This study will employ three different discovery-based untargeted omics tools to identify blood metabolites, circulating plasma proteins, and global transcriptional profiles of blood cells. Scope of Work: The current study is a multi-omics project with the following unique restraints: (1) small pilot funding (less than 50K for the entire project), (2) short-time frame (pilot funding is received and must be used within the same fiscal year, by September 30, 2026), and the lab performing the study is a clinical research lab that is uniquely situated to recruit and evaluate the specific Veteran population but lacking in the necessary equipment and skill sets (high-order wet lab molecular biology and biochemistry expertise that is required to perform initial sample processing in-house and bioinformatics expertise needed for data analysis). A fourth complication is the inherent variability in sample processing of a relatively small number of patients (no room for removal of outliers) and fact that each omics type must be comparable across samples collected at different time points based on pre-operative scheduling. Briefly, the basic workflow is that multiple blood samples will be collected from each patient (n=40) using blood tubes specific for each of the three omics types (to preserve the specific molecule types for each) - which will be a total of 120 samples that will be stored until ready for processing. They must all be processed together in one large batch to allow for comparability, and the sheer number alone makes doing initial steps in-house impossible for this clinical lab. A high throughput core or company is thus required as a matter of reasonable logistics. We reached out to several different cores at the University of Pittsburgh. These cores do not accept blood samples. We would need to perform the preprocessing of each sample ourselves, which as stated above is not feasible. There is also no single core to perform all three omics, and none of the omics cores can perform the post-analysis required to transform the numbers into meaningful scientific findings that we ca then interpret in the context of clinical relevance. We nonetheless did our due diligence and met with several cores and two different scientific experts to determine the feasibility of using these core services. We would minimally need four cores, aloin with a collaborative laboratory with necessary equipment and expertise to perform the study outside of a company. Justification for Sole Source: Novogene is a recognized leader in the field of genomics, but unlike similar competitive giants that are specialized in a single omics service, Novogene can provide a complete pipeline for the study s multi-omics needs, including sample prep (from human blood) and complete data analysis (as opposed to software to be used for analysis, for example). With over 25 years of experience managing large data set studies, the Principal Investigator is highly familiar with the technical variability that would lead to data that is essentially useless. While designing the pipeline for this study, he considered the various logistical issues, including how to reduce variability among batches) as well as the practicality of performing the study within the allotted time frame and budget. Because Novogene will perform the RNA extraction, for example, there will not be a need to purchase those kits that would be required if they were to do this in-house. Novogene is low cost, because they are high throughput. It would cost more per sample if VA attempted to do each early processing step themselves. Additionally, each of the omics services provided are discovery-based. So, while many companies can perform mass spectrometry, not many companies can perform O-link proteomics specifically or shotgun metabolomics (over 40,000 unique metabolites will be interrogated) as opposed to a smaller panel of metabolites. The hypothesis is that there is a set of macromolecules that can define progressive spinal disease in such a way as to distinguish it from similar non-progressive spinal cord disease that would allow for better and earlier diagnostics and importantly more specialized treatments aimed at targeting the underlying causes. This requires a large net for this pilot study and simultaneous ability to detect extremely subtle variations between similar spinal cord diseases, in contrast to more widely different experimental sets (such as normal versus cancer for example). No other company was found to be a reasonable alternative for the study without either reducing the scope and/or compromising the data quality. Specific Tasks & Deliverables: The Contractor shall be capable of providing ALL the following: 1. Extract metabolites from human plasma and run omics/ provide raw and analyzed data + left-over samples for verifying findings in the lab 2. Extract proteins from human plasma and run O-link mass/spec + analysis/provide raw and analyzed data + left-over samples for verifying findings in the lab 3. Isolate RNA from human whole blood, perform poly-A enrichment and QC, construct library and process RNA samples, perform sequencing/provide raw and analyzed data + left-over samples for verifying findings in the lab 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 541714, with a 1000 employee size standard. The PSC is AN41. 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.