MiSeq Sequencing System

Trade Agreement: NAFTA/AIT/Canada FTAs with Peru/Colombia/Panama
Tendering Procedures: All interested suppliers may submit a 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: 
MiSeq Sequencing System

01896-140251/A
Perkins, Bill
Telephone No. - (204) 983-0275
Fax No. - (204) 983-7796

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:  MiSeq Sequencing System

The Department of Agriculture and Agri-Food Canada's (AAFC)
Research Center in Brandon, MB has a requirement for the supply,
delivery, installation, and training of one (1) MiSeq System, to
Brandon Research Centre, Brandon, MB, on or before March 31,
2014.

The current team of genomic researchers in Winnipeg and Brandon
manage a diverse portfolio of projects, which are funded through
multiple sources including Growing Forward (A-Base), Canadian
Crop Genomics Initiative, Agricultural Development Fund, Western
Grains Research Foundation and other industrial collaborators.

Due to the limitations of modern breeding programs a common
theme among many of these projects is an interest in identifying
and capturing diversity from not only within crop species but
also from wild relatives. The state of the art for such projects
is the development of libraries of sequence data from multiple
germplasm sources that are mined for both genes underlying
traits of interest and associated nucleotide variation that is
used in marker development. Such objectives have become economic
with the rapid improvements in sequencing technology, in
particular Illumina have been the forefront of this technology
development and the MiSeq represents the latest advance in this
area, offering an accurate benchtop sequencer with minimal
hands-on requirement 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. We are
currently leading novel research in epigenetics which require
the sequencing of a wide variety of templates such as small RNA,
RNASeq, methylome and degradome. The MiSeq and its associated
chemistry provide the essential tools to perform all of this
research.

Illumina MiSeq system is the world's most accurate and fast
sequencer using a proprietary technology that is protected by an
interlocking system of patents, copyright and industrial secrets.


3.  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 system meets the following requirements:

·	System must be a single integrated instrument with a small
footprint of less than 2 square feet and capable of performing
clonal (cluster) amplification, Next Generation sequencing and
data analysis without requiring emulsion PCR
·	System must be a single flow cell system with adjustable read
length from 36 to 300 bp
·	System must be able to perform single-end, paired-end and
mate-pair read with the following turnaround time (including
cluster generation, sequencing and basecalling with quality
scores), throughput and quality criteria:

o	Paired-end reads of 2 X 250 bp in 39 hours with a minimum of
7.5 Gb generating a minimum of 24 M filtered reads with more
than 75% of the bases higher than Q30 (quality score)
o	Paired-end reads of 2 X 300 bp in 65 hours with a minimum of
13.2 Gb generating a minimum of 44 M filtered reads with more
than 70% of the bases higher than Q30 (quality score)

o	Single-end read of 1 X36 bp in 4 hours with a minimum of 540
Mb generating a minimum of 12 M filtered reads with more than
90% of the bases higher than Q30 (quality score)

·	System must offer the flexibility to perform and analyze:
o	Resequencing
o	De novo sequencing
o	Targeted sequencing
o	Small RNA sequencing
o	mRNA sequencing
o	Sequencing of bisulfite-converted DNA 
o	Library quality control

·	System must produce the following standard output file
formats: fastq, bam, text (CSV)

·	System must be compatible with ready-to-use kits for the
following applications using the following sample sizes:

o	DNA sequencing of single-end, paired-end and mate-pair reads
with 1 ng to 1 ìg DNA
o	RNA sequencing of total RNA (0.1-4 ìg), mRNA (10-400 ng) and
small RNA (1 ìg total or 10-50 ng microRNA)
o	Sample multiplexing of up to 96 indices for DNA 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)





5.  Justification for the Pre-Identified Supplier

The Illumina MiSeq System is a unique and proprietary system.
Illumina is the only distributor of the MiSeq system. The MiSeq
system's wide flexibility with regards to applications is the
only one capable of generating all of the data required by the
projects. It is the only bench top sequencing system capable of
automated paired-end reads and up to 15 Gb per run, delivering
over 600 bases of sequence information which represent the
required throughput. It is also the only system in the market
that can sequence small RNA, an essential application for our
projects which also include methylome and degradome analyses,
methods supported by the MiSeq. The MiSeq is the only next
generation sequencer that integrates amplification (no emulsion
PCR), sequencing and data analysis into one instrument, with a
simplified interface and workflow that will allow multiple users
to operate the system. The MiSeq instrument is also capable of
running in short read mode to rapidly assess the quality of the
sequencing libraries. Further, the MiSeq utilises the same
chemistry and generates the same type of data that will ensure
compatibility with current protocols and analysis pipelines
developed at AAFC. Advantageous attributes of the MiSeq includes
fastest turnaround time from library prep to data generation
while still maintaining Illumina's reputation for accurate high
quality sequence data and, data analysis support provided by
Illumina in the form of real-time analysis software, which
provides fully optimized analysis solutions for resequencing,
custom amplicon assays and small RNA sequencing.


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
$130,000.00 - $135,000.00 (GST/HST extra).	






10.  Name and address of the pre-identified supplier

Illumina Canada Inc.
44 Chipman Hill Suite 1000 
Saint John, New Brunswick
E2L 2A9
Canada


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

The closing date and time for accepting statements of
capabilities is: Monday, November 18, 2013, 2:00 Central
Standard Time (CST)


13.  Inquiries and submission of statements of capabilities

Inquiries and statements of capabilities are to be directed to:

Bill Perkins 
Supply Specialist 
Public Works and Government Services Canada
100-167 Lombard Avenue, Winnipeg, MB R3C 2Z1

Telephone:	 (204) 983-0275
Facsimile:	 (204) 983-7796
E-mail:	 bill.perkins@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.