Synopsis: Notice of Intent to Award a Sole-Source Contract

Announcement Number:  NRMAD000-21-00679

Project Title:  DNA Sequencing data to complete secondary PCR of amplicons, library normalization, MiSeq sequencing in support of the NOAA’s Omics Strategic Plan.

The US Department of Commerce (DOC), National Oceanic and Atmospheric Administration (NOAA), Oceanic and Atmospheric Research (OAR), Atlantic Oceanographic and Meteorological Laboratory (AOML) intends to negotiate on a sole source basis, under the statutory authority of FAR 13.106-1(b)(1)(i), with Michigan State University, Research Technology Support Facility Genomics Core

to complete secondary PCR of 1,500 amplicons, library normalization, quality control of libraries, MiSeq sequencing, and provide the sequence data files to NOAA/AOML/Ocean Chemistry and Ecosystems Division via a secured FTP account.

The Atlantic Oceanographic and Meteorological Laboratory/Ocean Chemistry and Ecosystems Division is seeking DNA sequencing to identify fish and microbial sequences in samples collected from the 2019 and 2021 Southeast Area Mapping and Assessment Program (SEAMAP) cruises. This sequence data will be used to measure biodiversity of multiple taxonomic groups in the Gulf of Mexico and to support ecosystem-based fisheries management. This is a part of NOAA OAR’s ’Omics Strategic Plan.

Sole Source Justification

DNA sequencing analysis is highly sensitive to the sequencing facility used. In particular, AOML’s Ocean Chemistry and Ecosystems Division’s DNA samples are prepared with Fluidigm adapters added to both ends of the DNA molecule in the first-step PCR; the Michigan State University’s Genomics Core is uniquely qualified and is the only sequencing service provider who will perform the second-step PCR on DNA molecules with Fluidigm adapters.   The second-step is critical and the Michigan State University has the capability of providing this service and producing quality results that meet the Code of Federal Regulations.   They are the only known source with these capabilities.  

The AOML/ Ocean Chemistry and Ecosystems Division will submit 1,500 primary PCR products prepared in their lab for completion of library preparation by secondary PCR and sequencing.  The Michigan State University, Research Technology Support Facility Genomics Core will perform secondary PCR using dual-indexed, Illumina compatible primers to complete library synthesis. The primers used target the Fluidigm CS1/CS2 oligomers at the ends of the primary PCR products.  The Amplicon libraries will be normalized using Invitrogen DNA Normalization Plate and product recovered from the plate pooled. Submissions will be divided into four (4) pools. Pools will go through QC’d and quantified using a combination of Qubit dsDNA, Agilent 4200 TapeStation High Sensitivity DNA1000 and Invitrogen Collibri Illumina Library Quantification qPCR kits.  Each pool will be loaded on one (1) MiSeq v2 Standard flow cell (4 runs total). Sequencing will be performed in a 2x250bp paired end format using a 500 cyle v2 reagent cartridge. Custom sequencing primers complementary to the CS1/CS2 oligomer sequences will be added to appropriate wells of the reagent cartridge. Total expected out is 8 - 10 million read pairs per flowcell.   Sequence data will be demultiplexed and converted to FastQ format and will be delivered to the AOML/ Ocean Chemistry and Ecosystems Division via a private, secure FTP account.    The two-step PCR option for the Michigan State Genomics Core’s “other amplicons” service allows us to use any PCR primers we need and make modifications to the primers.  No other service provides this level of flexibility.  

Special Notice

This special notice is not a solicitation for competitive quotes, nor will one be posted on Contract Opportunities. However, if an interested party believes that it is capable of meeting the requirements and be in compliance with the above justification, they may submit substantiating documentation in writing within the open period of this notice. Responses can be sent via e-mail to [email protected].   Documentation will be evaluated solely for the purpose of determining whether or not to conduct this procurement on a competitive basis. A determination by the Government not to conduct a competitive procurement, based upon response to this notice, is solely within the discretion of the Government. Oral communications are not acceptable in response to this notice.

All responsible sources may submit a Capability Statement in accordance with the solicitation, which shall be considered by the agency if received on or before 11:00 AM EDT on June 26, 2021. The Capability Statement must contain material in sufficient detail to allow NOAA to determine if the party can meet all of the requirements.

All electronic correspondence shall have the subject line read: Announcement Number:  

Project Title:  DNA Sequencing data to complete secondary PCR of amplicons, library normalization, MiSeq sequencing in support of the NOAA’s Omics Strategic Plan

It is the Contractor’s sole responsibility to ensure that any correspondence, transmitted to the specified Government representative(s) is received prior to the due date specified herein.

The Government representative(s) will verify receipt of your email, if notification is not received within 24 hours of your email,

DOC/NOAA/OAR/AOML requires that all contractors doing business with this office be registered with the System for Award Management (SAM). No award can be made to a company not registered in SAM. For additional information and to register in SAM, please access the following web site: www.sam.gov. To register, all contractors must have a Dun and Bradstreet number (DUNS). A DUNS may be acquired free of charge by contacting Dun and Bradstreet at http://www.dnb.com/eupdate or by telephone at (800)333-0505.

The notice will remain open from 6/23/2021 to 6/26/2021.