B529--Research Study Services and Support - RNA Sequencing

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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 New York Genome Center, Inc., located at 101 Avenue of the Americas, Floor 7, New York, New York, for the James J. Peters VA Medical Center (JJPVAMC, Bronx) for its RNA sequencing and bioinformatics analysis services. These services are essential to VA Merit award study under Dr. Fatemeh Haghighi, Ph.D.

Background:

The purpose of the contract is obtain services to perform genetic assays (RNA-seq) for the VA Merit-funded project entitled Identifying DNA Methylation Alterations of Chronic Effects Of Blast and Disturbed Sleep , awarded to Dr. Fatemeh Haghighi.

The Project involves human studies of blast-related TBI using blood specimens. In particular, the method employed in these studies involves ultra-high through-put Next Generation Sequencing (NGS) platform for processing of RNA specimens on a genome scale. These assays are performed in specialized genomics facilities/genomics centers using the Illumina Inc. technology. The goal of this Project is to analyze RNA expression in 466 RNA blood samples from humans with chronic blast exposure. For transcriptional studies, we will use a method called RNA-seq. The results of these RNA-seq studies will be used to gain a better understanding of gene expression abnormalities associated with mild blast-related TBI, and further to identify biomarkers of TBI.

Scope of Work:

This assay requires using highly specialized Illumina, Inc. sequencing technologies. VA will perform RNA extraction from blood specimens and will deliver samples to the Contractor. Upon receipt of samples from VA, the Contractor shall first perform quality control (QC) analysis of the delivered RNA samples using Bioanalyzer (Agilent). The Contractor shall then perform whole genome transcription sequencing analysis (RNA-seq) for 466 total blood samples. The Contractor shall provide initial bioinformatics analysis of the data, which consists of alignment of sequencing reads to the human genome. The specimens that are needed to be analyzed by RNA-seq assay RNA isolated from human blood are prone to degradation at temperatures higher than -80 C and should be kept frozen on dry ice.

Specific Tasks & Deliverables:

The Contractor will perform the sequencing and bioinformatics analysis.

The Project will be discussed in detail via teleconference before samples are sent to the contractor, during which the parties will discuss and review the activities of the contract. Topics will include the overall project management plan and schedule, and contractor will that all required personnel are in place.

The Contractor will designate point of contact(s) for prompt administration and administrative duties and responsibilities during this contract.

The Contractor will communicate on the status of ongoing analyses (i.e. quality control, sequencing, and bioinformatics analysis).

In the course of the contract, the Contractor will provide description of any problems anticipated or encountered, and their resolution or non-resolution.

Using RNA, Contractor will perform library preparation for RNA sequencing via KAPA TOTAL with a minimum of 2ug total, DNase-treated RNA as input required.

RNA samples that will be utilized are in a total volume of 15ul to 30ul DEPC treated H20, with absorbance values of OD260/280= >1.9.

Sample quality will be ascertained by BioAnalyzer (or equivalent) with a RIN value >= 6. As such, the Contractor performs quality control (QC) analysis of the RNA. In case one or more RNA samples fail Contractor s QC, the Contractor should inform Dr. Haghighi. Contractor is not exempt from charges incurred due to failed experiments through no fault of Contractor. Any samples deemed by Contractor to be insufficient, invalid, or degraded to the point of being unusable may be returned at Dr. Haghighi s request. Contractor may elect to charge a fee at its standard rates for expenses related to sample preparation, quality testing, and shipping fees for each returned sample. Samples that yield data outside Contractor s quality metrics due to circumstances beyond the control of Contractor are not the responsibility of Contractor. Contractor does not guarantee results.

The Contractor will perform total RNA sequencing for 466 blood RNA specimens. The sequence should be performed using the Illumina Sequencing technology for blood samples. The sequencing shall be performed using paired-end method for total RNA sequencing. For all RNA samples that pass QC, the sequencing stage shall be completed.

The Contractor shall provide initial bioinformatics analysis of the data, which consists of alignment of the sequence reads to human genome and the below deliverables:

Alignment of raw reads using STAR aligner

Quality control using RSeQC and Picard (%GC, %duplicates, gene body coverage, unsupervised clustering, library complexity, etc.)

Picard MarkDuplicates

Gene quantification using featureCounts

Gene annotation using Gencode

Normalize count matrix with DESeq2

Differential expression with DESeq2

Transcript quantification with Kallisto GENOTYPING ANALYSIS

Delivery of raw data

Contractor Requirements:

1. Capability. Contractor shall be capable of performing Tasks and Deliverables as outlined above.

2. Proximity. The biological samples used for this contract have been collected over several years of interagency collaborations by DoD and VA involving Warfighter and Veteran participants with exposures to blast overpressure and are irreplaceable. First, these biological samples (i.e., RNA samples) are highly sensitive to temperature changes and must be processed by a genome facility located within the New York metropolitan area within a driving radius of 1 hour (average time). The reason for this requirement is that the samples to be sequenced are sensitive to temperature and should be kept frozen at -80°C using dry ice. The Principal Investigators (PIs) of the studies, or the members of PIs laboratories at the JJPVAMC can easily deliver the samples to the Contractor. Due to the requirement to maintain temperature control, physical integrity of the samples, and chain of custody, transportation of the samples outside this specified radius will not meet our requirements and would pose increased risks of damage to or loss of the samples.

3. Data Integration. Data integration is essential for this requirement. Under Contract 36C24E18C007, NYGC provided RNA sequencing services of which data generated is correlated to the new requirement and is necessary for integration. In order to prevent batch effects and control for study/experiment-wise error in the data, it is required that the same laboratory/genome facility is used for this contract.

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 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.