Fish genome and transcriptome sequencing

Trade Agreement: NONE
Tendering Procedures: Generally only one firm has been invited to bid
Non-Competitive Procurement Strategy: Government Objectives Representing Best Interests/Value to Govt
Comprehensive Land Claim Agreement: No
Vendor Name and Address: 
Vertebrate Genome Laboratory
The Rockefeller University
1230 York Avenue
New York New York
United States
10065
Nature of Requirements: 


Title: Fish genome and transcriptome sequencing

Advance Contract Award Notice (ACAN)
An ACAN is a public notice indicating to the supplier community that a department or agency intends to award a contract for goods, services or construction to a pre-identified supplier, thereby allowing other suppliers to signal their interest in bidding, by submitting a statement of capabilities. If no supplier submits a statement of capabilities that meets the requirements set out in the ACAN, on or before the closing date stated in the ACAN, the contracting officer may then proceed with the award to the pre-identified supplier.

Definition of the Requirement
Title: Fish genome and transcriptome sequencing
The Department of Fisheries and Oceans (DFO) has a requirement for chromosome-level genome sequencing, assembly, and annotation for four marine species of commercial and ecological value.
Fisheries and Oceans Canada’s requires the sequencing of several animal genomes (Lumpfish, Rainbow Smelt, Cunner, and Snow Crab) to provide baseline genomic information on genomic architecture, genes of adaptive interest, and population genomics to better inform stock structure and gene flow to meet program-specific needs related to aquaculture and marine conservation area design and monitoring.
The samples are currently stored in uniquely identified vials frozen in liquid nitrogen and preserved at -80°C. High molecular weight DNA will need to be extracted by the contractor prior to sequencing and optical mapping.
The genomics facility must have the ability to extract ultrapure, very high molecular weight DNA (>100Kb) via agarose plug extraction to ensure DNA of sufficient length is available for single molecule real-time sequencing, optical mapping, and chromatin conformation capture. The facility must be equipped to purify extracted DNA, and perform library preparation for 10X linked read sequencing on a NovaSeq 6000 sequencer at a minimum of 50X depth, Pacbio continuous long reads at a minimum depth of 50X, Bionano optical mapping at a depth of 100X, and HiC chromatin conformation capture at a minimum depth of 50X to ensure a complete, chromosome-level, phased genome assembly per species. Assembly of each genome using all combined sequencing techniques will be necessary as well. 
After genome sequencing and assembly by the contractor, the contractor will be responsible for submission of raw sequences and assembly files to NCBI but will also provide all raw, intermediary, and final files to DFO project leads for on-site curation.  
Tasks:
- Extraction of high molecular weight DNA via agarose plug method and DNA quality control
- Library preparation and sequencing of phased 10X linked reads, phased Pacbio continuous long reads, high-coverage optical mapping, and HiC chromatin conformation capture
- Phased genome assembly using all combined sequencing technologies, per species
- All raw, intermediary, and final assembly files submitted to NCBI and transferred to DFO project leads.
Criteria for assessment of the Statement of Capabilities (Minimum Essential Requirements)
- Any interested supplier must demonstrate by way of a statement of capabilities that its product/equipment/system meets the following requirements:
- Capability to perform very high molecular weight DNA extractions (ideally via agarose plug extraction)
- Library preparation for current high throughput DNA sequencing methods, including 10X linked reads, Illumina NovaSeq, PacBio long read sequencing, Bionano optical mapping, and HiC chromatin conformation capture
- Established protocols and algorithms for complex phased genome assembly using each of the aforementioned technologies 
- Computing power required to assemble large genomes using complex algorithms (typically at least 256-500Gb of RAM)
- Capability of high-throughput genetic analysis and data management for multiple genomes
Justification for the Pre-Identified Supplier 
VGL has developed the most effective and streamlined pipeline for error-free de-novo genome sequencing available. No alternative service providers offer the same in-house services for genome sequencing, assembly and scaffolding that specifically use the platforms available at VGL and that are required to meet DFO’s needs for a highly accurate and complete reference genomes. 
Government Contracts Regulations (GCRs) Exception and Limited Tendering Reasons
The following exception to the Government Contracts Regulations is invoked for this procurement under subsection 6(d) - only one person is capable of performing the work.
The Vertebrate Genome Laboratory (VGL) is the only facility in North America with the technical capacity to sequence full genomes on this scale, including: extract DNA of sufficient quality for combined 10X/Pacbio sequencing, optical mapping, and chromatin conformation capture; conduct library preparation and sequencing of 10X, Pacbio, Bionano optical mapping, and HiC chromatin conformation capture; assembly of complex eukaryotic genomes using each of the aforementioned technologies; and storing, processing and tracking the data. The VGL currently has the technical capacity and necessary equipment to perform agarose plug extractions, the equipment necessary for each sequencing technology, algorithms to merge multiple data types (without errors) and create phased genome assemblies, and the ability to curate the large amount of raw data produced from these genome sequences.
Ownership of Intellectual Property 
Ownership of any Foreground Intellectual Property arising out of the proposed contract will vest in the Contractor.

-Canada intends to retain ownership of any Foreground Intellectual Property arising out of the proposed contract on the basis that the main purpose of the contract is to generate knowledge and information for public dissemination.
Period of the Proposed Contract
The period of the proposed contract is from date of award to March 31, 2020.

Cost Estimate
The estimated limitation of the proposed contract is $56,000.00 USD plus tax.

Name and address of the pre-identified supplier 
Vertebrate Genome Laboratory
The Rockefeller University
1230 York Avenue
New York, NY
Suppliers' right to submit a statement of capabilities 

Suppliers who consider themselves fully qualified and available to provide the goods, services or construction services described in the ACAN may submit a statement of capabilities in writing to the contact person identified in this notice on or before the closing date of this notice. The statement of capabilities must clearly demonstrate how the supplier meets the advertised requirements.
Closing date for a submission of a statement of capabilities 

The closing date and time for accepting statements of capabilities is:
December 20, 2019 at 2:00 p.m. NST
 
Inquiries and submission of statements of capabilities 
Inquiries and statements of capabilities are to be directed to: 
Janice Baird, Supply Specialist 
Public Services and Procurement Canada
John Cabot Building 
10 Barter’s Hill
St. John’s, NL
Telephone:  709-682-1588
Facsimile:  709-772-4603
E-mail: janice.baird@pwgsc-tpsgc.gc.ca


Delivery Date: Above-mentioned

You are hereby notified that the government intends to negotiate with one firm only as identified above. Should you have any questions concerning this requirement, contact the contracting officer identified above.

An Advance Contract Award Notice (ACAN) allows departments and agencies to post a notice, for no less than fifteen (15) calendar days, indicating to the supplier community that it intends to award a good, service or construction contract to a pre-identified contractor. If no other supplier submits, on or before the closing date, a Statement of Capabilities that meets the requirements set out in the ACAN, the contracting authority may then proceed with the award.  However, should a Statement of Capabilities be found to meet the requirements set out in the ACAN, then the contracting authority will proceed to a full tendering process.

Suppliers who consider themselves fully qualified and available to provide the services/goods described herein, may submit a statement of capabilities in writing to the contact person identified in this Notice on or before the closing date of this Notice. The statement of capabilities must clearly demonstrate how the supplier meets the advertised requirements.

The PWGSC file number, the contracting officer's name and the closing date of the ACAN must appear on the outside of the envelope in block letters or, in the case of a facsimile transmission, on the covering page.

The Crown retains the right to negotiate with suppliers on any procurement.

Documents may be submitted in either official language of Canada.