Deep-Sequencing

SYNOPSIS: This is a notice of intent to negotiate on a sole source basis. The DEEP-SEQUENCING OF Prepared coral libraries at the University of Miami’s John P. Hussman Institute of Human Genomics (SC HIHG) This requirement is hereby synopsized in accordance with FAR 5.207 Preparation and Transmittal of Synopses:.

Action Code:

Date:

16 September 2024 Year:

2024 Contracting Office ZIP Code:

33149 Product or Service Code:

B510 Contracting Office Address:

4301 Rickenbacker Causeway, Key Biscayne, FL 33149 Subject:

Deep-Sequencing Proposed Solicitation Number:

TBD Closing Response Date:

17 September 2024 Contracting Officer:

Email:

Elizabeth.Perez@noaa.gov Contract Award and Solicitation Number:

Solicitation Number:

TBD Contract Number: To be determined at time of award.

Contract Award Dollar Amount:

10,629.00 Contract Line Item Number:

N/A Contract Award Date:

09/18/2024 Contractor:

University of Miami, Center for Genome Technology Description: This request is for the initiation of a contract with the University of Miami’s sequencing core at the John P. Hussman Institute of Human Genomics (SC HIHG) for which they will conduct sequencing on prepared genomic and transcriptomic libraries. These services are necessary to complete genomic and transcriptomic project deliverables, and to support NOAA AOML’s Omics initiatives.

The SC HIHG at the University of Miami offers MiSeq and NovaSeq X sequencing services, as well as having had previous experience with sequencing genomic and transcriptomic libraries prepared from coral species. These omics approaches will provide considerably more information for characterizing the microbiome and gene expression responses of experimental corals to lab-based stressors, increasing the chances of positive identification of disease-causing microbes and resilience gene mechanisms.

This will provide a new novel pathogen identification pipeline that will benefit AOML going forward with coral disease research, as well as provide critical data to evaluate the resilience of corals. This will be for analysis using three runs of Illumina MiSeq v3 PE300, one run of Illumina Novaseq X 25B PE150, and four runs of Qubit, Tapestation & qPCR per pool.

DELIVERABLE SCHEDULE: To be billed out incrementally as samples are sent in for analysis. Final date shall be no later than 09/17/2025 to allow for ample time of sample acquisition, shipment to SC HIHG, and delivery of subsequent data to AOML from SC HIHG.

TECHNICAL POINT OF CONTACT: Nicole Besemer Nicole.besemer@noaa.gov Emy Rodriguez emy.rodriguez@noaa.gov Only one source or brand name is reasonable available as detailed below:

The SC HIHG offers cost-effective and rapid MiSeq and NovaSeq X sequencing of prepared genomic and transcriptomic libraries. Using a vendor local to Miami allows us to rapidly sequence samples that are critical to high-value and time-sensitive projects, as well as graduate student timelines. Utilizing the SC HIHG will reduce chances of sample loss and degradation when shipping.

Samples are able to be transported from AOML to the facility in a 15-minute car ride, with samples dropped off and stored correctly immediately. This is a large benefit as these samples are irreplaceable (experiments cannot be repeated), and library preparation has Already invested thousands of dollars into these samples. Sequencing times are also must faster from sample drop off to data delivery relative to other sequencing providers, on the order of two to four weeks (versus months, as is common elsewhere).

Additionally, the SC HIHG has processed genomic and transcriptomic libraries prepared from coral samples in the past. This gives them the edge over other sequencing cores which have not sequenced these types of libraries before, as coral samples pose challenges related to PCR inhibition and nucleic acid degradation. Finally, the metatranscriptomic and metagenomic sequencing approach will provide far deeper insights into the microbiome and pathobiome of corals.

These will lay the basis for improving coral disease diagnostic methodologies which will place AOML at the forefront of this kind of research. (8) Destination information. 4301 Rickenbacker Causeway, Key Biscayne, FL 33149 (9) Delivery schedule. Incrementally as samples are sent to vendor. (10) Duration of the contract period. One year from date of award The proposed contract action is for services for which the Government intends to solicit and negotiate with only one source under authority of FAR 13.501.

Interested parties may identify their interest and capability to respond to the requirement or submit proposals. This notice of intent is not a request for competitive proposals. However, any firm that believes it an meet this requirement may provide written notification to the Contracting Officer. 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. Information received will normally be considered solely for the purpose of determining whether to conduct a competitive procurement.

Place of Contract Performance: University of Miami, Miller School of Medicine, Hussman Institute for Human Genomics Center for Genome Technology, Miami, Florida Set-aside Status: This Government intends this procurement to be a sole source award with no small business set aside.