SPECIAL NOTICE
99 -- RNA Sequencing on 87 frozen samples and 16 matched plasma samples
- Notice Date
- 7/23/2021 12:54:56 PM
- Notice Type
- Special Notice
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- NATIONAL INSTITUTES OF HEALTH NIDA Bethesda MD 20892 USA
- ZIP Code
- 20892
- Response Due
- 8/2/2021 6:00:00 AM
- Archive Date
- 08/17/2021
- Point of Contact
- Alexander Beraud, Phone: 3014436677, Kenneth Goodling, Phone: 3014436677
- E-Mail Address
-
alexander.beraud@nih.gov, kgoodlin@nida.nih.gov
(alexander.beraud@nih.gov, kgoodlin@nida.nih.gov)
- Description
- INTRODUCTION THIS IS A PRE-SOLICITATION NON-COMPETITIVE (NOTICE OF INTENT) SYNOPSIS TO AWARD A CONTRACT WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION (INCLUDING BRAND-NAME). The National Institute on Drug Abuse (NIDA), Office of Acquisitions intends to solicit by a request for quotation from New York Genome Center (NYGC) for award on or around August 16, 2021. The purpose of this Acquisition is to characterize both coding gene expression and transposable element expression on 87 frozen and 16 matched plasma brain tumor/glioma samples.� NORTH AMERICAN INDUSTRY CLASSIFICATION SYSTEM (NAICS) CODE and SET ASIDE STATUS The intended procurement is classified under NAICS code 541380 with a Size Standard of $16.5 Million. This acquisition is NOT set aside for small businesses. REGULATORY AUTHORITY This acquisition is conducted under the authority of the Federal Acquisition Regulation (FAR) Part 13�Simplified Acquisition Procedures. Contracts awarded using FAR Part 13�Simplified Acquisition Procedures are exempt from the requirements of FAR Part 6�Competition Requirements. FAR Subpart 13.106-1 (b) Soliciting from a single source provides that: For purchases not exceeding the simplified acquisition threshold, Contracting officers may solicit from one source IF the contracting officer determines that the circumstances of the contract action deem only one source reasonably available (e.g., urgency, exclusive licensing agreements, brand-name OR industrial mobilization). The resultant contract will include all applicable provisions and clauses in effect through the Federal Acquisition Circular (FAC) 2020-01 dated November 12, 2019. DESCRIPTION OF REQUIREMENT PURPOSE AND OBJECTIVES: The purpose of this study is to explore the association of ERV gene expression, identification of loci from which these genes are expressed in glioma tissues. Identification of the expressed elements will provide new therapeutic approaches for these tumors. The NINDS Office of the Clinical Director (OCD) and Surgical Neurology Branch (SNB) will work with the contractor to characterize both coding gene expression and transposable element expression on 87 frozen and 16 matched plasma brain tumor/glioma samples. The samples are to be processed with a custom fragmentation protocol (kappa) that allows for both analyses to be performed so that bulk RNA-Seq analysis can be done in addition to transposable element expression. This type of sequencing can only be done by the New York Genome Center due to custom fragmentation adopted and library preparation steps needed for transposable element (ie HERV) analysis. The objective of this acquisition is to provide NIDA-NRB with maintenance and repair services to support the operation of the MRI scanner and ensure continued high-quality imaging performance of the scanner to support research in drug addiction. PROJECT REQUIREMENTS: Contractor shall provide: Extraction:� Fresh Frozen Tissue / Tumor Extraction:� Fresh Frozen Tissue / Normal RNA Sequencing:� Library Prep: Kapa Total, 350bp; NovaSeq, 2x100Coverage/Reads: 50M; Analysis: ESS (Stranded RNA - Star, FeatureCounts, DESeq2, Kallisto, Sleuth, FusionCatcher and STAR fusion) Salient characteristics RNA Somatic Deliverables: Expected number of reads per sample as specified in the service description >80% of bases sequenced with a quality score above Q30 BAM format file with corresponding BAI index file Tables of splice junction and non-canonical alignments Quality control metrics Raw count matrix with all genes and samples Normalized count matrix Regularized count matrix FusionCatcher table Quantity: RNA Sequencing on 103 Samples (87 Tumor / 16 Normal) CONTRACTING WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION (INCLUDING BRAND-NAME) DETERMINATION In accordance with FAR part 10, market research was conducted to reach this determination. Specifically, contacts with knowledgeable individuals both in industry and Government, as well as reviews of available product literature, revealed no other sources. Finally, a review of the GSA Advantage, Dynamic Small Business Search, and previous government acquisitions returned no results that meet all of the requirements of RNA Sequencing and Fragmentations. Therefore, only NYGC is capable of meeting the needs of this requirement. NYGC has optimized a custom kappa preparation kit per target fragmentation time that in turn produces fragmented lengths of target that allow for both traditional RNA-Seq analysis and TE-Seq (i.e., ERV) analysis. This was a bi-lateral endeavor where various fragmentation times were trialed, and the resulting target lengths sequenced by NYGC and the data analyzed by NINDS. Where after, NINDS mutually decided on a fragmentation time and target length that was a good compromise to use. When it was attempted by an internal core here at NIH the results could not be duplicated; emphasizing the expertise required to successfully do. There is inherent risk in posting this order request to any provider as there are no assurances a provider other than NYGC will be able to perform this customized step with success on their first attempt. NYGC has now been running this customized protocol routinely for NINDS and continues to deliver high quality data. The intended source is: New York Genome Center 101 6th Ave New York, NY 10013 United States of America CLOSING STATEMENT THIS SYNOPSIS IS NOT A REQUEST FOR COMPETITIVE PROPOSALS. However, interested parties may identify their interest and capability to respond to this notice. A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. All responsible sources may submit a capability statement, proposal, or quotation which shall be considered by the agency. The information received will normally be considered solely for the purposes of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement. Responses to this notice shall contain sufficient information to establish the interested parties' bona-fide capabilities for fulfilling the requirement and include: unit price, list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov. All responses must be received by the closing date and time of this announcement and must reference the solicitation number, 75N95021R00054. Responses must be submitted electronically to Alexander Beraud, Contract Specialist, at alexander.beraud@nih.gov. U.S. Mail and Fax responses will not be accepted. �
- Web Link
-
SAM.gov Permalink
(https://beta.sam.gov/opp/e212c8e884ee4da6a19fc1e214a58826/view)
- Place of Performance
- Address: New York, NY 10013, USA
- Zip Code: 10013
- Country: USA
- Zip Code: 10013
- Record
- SN06071646-F 20210725/210723230113 (samdaily.us)
- Source
-
SAM.gov Link to This Notice
(may not be valid after Archive Date)
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