Genome Sequencer System

Trade Agreement: NAFTA/AIT/Canada FTAs with Peru/Colombia/Panama Tendering Procedures: Generally only one firm has been invited to bid Attachment: None Non-Competitive Procurement Strategy: Exclusive Rights Comprehensive Land Claim Agreement: No Vendor Name and Address: Illumina Canada, Inc. 5200 Illumina Way San Diego California United States 92122 Nature of Requirements: Genome Sequencer System

W0114-145087/A Semple, Patrick Telephone No. - (613) 530-3117 ( ) Fax No. - (613) 545-8067

1. 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.

2. Requirement: Genome Sequencing Sequencing System

The Royal Military College of Canada (RMC) located in Kingston, ON has a requirement for the supply, delivery, installation, and training of a MiSeq Genome Sequencing System manufactured by Illumina Canada Inc., to the Royal Military College (RMC) of Canada, Kingston, ON, before March 31, 2014.

The Environmental Toxicology and Endocrinology Laboratory of the Royal Military College of Canada leads several genomics-related research projects, especially focused on transcriptomics and epigenetics. The Environmental Toxicology and Endocrinology Laboratory works in collaboration with researchers from the Department of National Defense, Environment Canada, and Fisheries and Oceans Canada.

RMC requires to purchase a transcriptome sequencer for research. After careful consideration of all instruments currently available on the Canadian market, only the Illumina Mi-Seq platform has all the needed requirements to fit RMC's research needs. The main goal of the Environmental Toxicology and Endocrinology Laboratory is to decipher the molecular mechanisms of action of environmental pollutants in vertebrates. Due to the limitations in assessing 1-3 gene(s) at the time using real-time RT-PCR (simplex or multiplex) or to use sequenced genome animals to develop microarray platforms, the development of de novo libraries of sequence data from the whole transcriptome of treated animals have become the most economic and rapid approach in aquatic ecotoxicogenomics. Illumina MiSeq has developed the most robust technology that shows success in several papers published in the field of aquatic toxicology. The MiSeq system offers an accurate benchtop sequencer which is user friendly that integrates amplification, sequencing and data analysis in one instrument. This ease of use and the versatile applications allowed with the MiSeq will allow the equipment to be efficiently used by multiple labs, including the Environmental Science Group of the Royal Military College of Canada. The Environmental Toxicology and Endocrinology Laboratory is currently developing pioneer research in epigenetics in non-mammalian species which require the sequencing of a wide variety of samples. All together, the rapidity, the accuracy, the ease of use, the versatility, the robustness, and the chemistry technology engineering make the MiSeq the ideal system to meet all the requirements.

3. Criteria for assessment of the Statement of Capabilities (Minimum Essential Requirements)

Due to the nature of RMC's research of working with massive genome sizes, it is imperative that the instrument is fast, efficient and highly accurate in order to keep up with the large amount of samples that must be processed. The Sequencer System must:

- produce an average of 25 million high-quality filtered reads - generate over 50 million paired end reads of up to 300 bases pairs for each read - produce 15 Gb of high quality data output per run in as little as a 4 hour run - do competitive nucleotide addition with a proprietary reversible terminator technology which allows for highly accurate sequencing even through homopolymeric regions - The system must be able to be run remotely on the internet with a standard web browser using a cloud computing environment as well as have the ability to stream data to the cloud eliminating the need for onsite data storage and dedicated analysis computers.

The Sequencer System must offer the flexibility to do transcriptome sequencing, targeted sequencing and small RNA sequencing.

4. Applicability of the trade agreements to the procurement

This procurement is subject to the following trade agreement(s)

Agreement on Internal trade (AIT) North American Free Trade Agreement (NAFTA) Canada FTAs with Peru/Colombia/Panama

5. Justification for the Pre-Identified Supplier

The Illumina MiSeq system is the only system that meets all the above essential requirements. In aquatic molecular biology. The Illumina Mi-Seq System is one of the most used systems (Mehinto et al., 2012 Frontiers in Genetics, 3(62) 1-10). Illumina's sequencing by synthesis (SBS) chemistry is the demonstrated leader in data accuracy, a quality that is essential when dealing with vast number of samples. For comparison and continuity sake, it is crucial that RMC uses the same system as their research colleagues to allow compatible data output in order to allow metagenomics analysis. Lastly, Illumina is the only system that enables Users the ability to monitor their Mi-Seq run remotely on the internet with a standard web browser using BaseSpace, a cloud computing environment as well as stream the data to BaseSpace eliminating the need for onsite data storage and dedicated analysis computers. BaseSpace also provides instant, web-based data management, archival, analysis, and sharing capabilities. Being a Federal and Military University with restricted access after normal working hours, this Mi-Seq feature is required to allow personal to work on their dataset when the laboratory is closed.

6. Government Contract Regulations Exception

The following exception to the Government Contracts Regulations is invoked for this procurement under subsection: subsection 6(d) - "only one person is capable of performing the work".

7. Limited Tendering Reasons

The following limited tendering reasons are invoked under the

Agreement on Internal Trade (AIT) - Article 506-12 (b); Where there is an absence of competition for technical reasons and the goods or services can be supplied only by a particular supplier and no alternative or substitute exists.

North American Free Trade Agreement (NAFTA) - Article 1016: Limited Tendering Procedures; (b) where, for works of art, or for reasons connected with the protection of patents, copyrights or other exclusive rights, or proprietary information or where there is an absence of competition for technical reasons, the goods or services can be supplied only by a particular supplier and no reasonable alternative or substitute exists;

8. Period of the Proposed Delivery Date

The equipment must be delivered on or before March 31, 2014.

9. Cost estimate of the proposed contract

The estimated value of the contract, including option(s), is $100,000.00 - $150,000.00 (GST/HST extra).

10. Name and address of the pre-identified supplier

Illumina Canada Inc. 5200 Illumina Way San Diego California United States , 92122

11. 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.

12. Closing date for a submission of a statement of capabilities is Tuesday, 31th December 2013, at 14:00 Eastern Standard Time

13. Inquiries and submission of statements of capabilities

Inquiries and statements of capabilities are to be directed to

Patrick Semple Intern Officer Public Works and Government Services Canada, Acquisitions Branch 86 Clarence Street, Kingston, Ontario, K7L 1X3 Telephone: 613-530-3117 Facsimile: 613-545-8067 E-mail address: patrick.semple@pwgsc.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.