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.