Illumina HiSeq upgrade kits and MiSeq Instrument - Saskatoon, SK

Trade Agreement: NAFTA/AIT/Canada-Peru FTA/Canada-Colombia FTA
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: 
Illumina HiSeq upgrade kits and MiSeq Instrument - Saskatoon, SK

31029-124007/A
Holt, Judy
Telephone No. - (306) 975-4051 (    )
Fax No. - (306) 975-5397

National Research Council Canada, Saskatoon, has a requirement
for supply of an Illumina HiSeq 2000, two Illumina HiSeq 2500
upgrade kits and an Illumina MiSeq instrument.

BACKGROUND:
One of the main objectives of the NRC Saskatoon is the
development of technologies for improving wheat, oilseed and
pulse crop germplasm.  NRC Saskatoon is a centre of excellence
for establishing advanced molecular biology, genetics and
genomics technologies in the DNA Technologies Laboratory to
further the rapid development of improved germplasm in wheat and
other crops.

Important projects at NRC Saskatoon are the Canadian Triticum
Advancement through Genomics (CTAG) project and Genomics
Assisted Breeding (GAB) project of the NRC Wheat Flagship
initiative.  The CTAG project includes sequencing of over 7,000
large insert BAC clones that comprise the entire length of a
single chromosome, as part of the Canadian component of the
International Wheat Genome Sequencing Consortium (IWGSC)
project.  Additionally, both projects are engaged in the
sequencing of regions of the wheat genome that are enriched for
expressed genes; a.k.a. exome sequencing together with de novo
whole genome sequencing activities in these very large and
complex polyploid genomes.  As well a range of deep gene
expression profiling using RNA sequencing is also planned for
both projects. The projects together with the genome sequencing
requirements of other Brassica and pulse crops genomics projects
have significantly increased the high throughput sequencing
requirements of NRC Saskatoon.  In addition to major genome
sequencing efforts in multiple crops the platforms also
accommodate a range of other applications required by NRC
Saskatoon researchers.  These include 1) re-sequencing of
targeted genomes for SNP discovery and mutation detection; 2)
the genome wide detection of epigenetic DNA methylation
modifications via the sequencing of bisulphite-treated DNA; 3)
very deep tag-based gene expression (DGE); 4) small RNA sequence
profiling; 5) Chromatin Immunoprecipitation Sequencing studies
of protein-DNA or RNA interactions (ChIP-Seq); and 6)
metagenomic sequencing.

A key aspect of all this work is the high-throughput and high
quality nature of the sequence data to best accommodate the
requirements of project milestones.  To meet the increased
demands of the projects described above we require the
capability of new sequencing instruments and upgrades to
existing platforms that will integrate seamlessly into the
laboratory and the existing bioinformatics architecture.

Sole Source Justification 
(d) Only one supplier is capable of performing the work.

The Illumina HiSeq 2000 platform is a unique and fully
integrated platform that uses a unique and proprietary massively
parallel sequencing-by-synthesis technology for genetic analysis
and functional genomics.  The platform is a 2nd generation
Illumina platform consists of the,HiSeq 2000 analyzer and a
suite of data collection and analysis software, and dedicated
consumables.  The much increased data throughput and unique
qualities of the sequence data produced from the HiSeq 2000 and
the associated 2500 upgrade means that the activities described
for the different projects can be comfortably achieved in
complex plant genomes such as wheat, Brassica, pulse, and other
crops.   Additionally, the range of applications (Items 1-6 in
the Background) required by NRC scientists will be accommodated
by the platform.  Importantly the new HiSeq 2000 will be fully
compatible with the existing HiSeq 2000 sequencing and
bioinformatics infrastructure at NRC Saskatoon and thus will
require little additional support to be fully operational in the
shortest possible timeframe.  The HiSeq 2500 upgrade is a
dedicated upgrade feature to the HiSeq 2000 platform that
enables the flexibility of shorter run times (24 hours rather
than 10 days) for HiSeq platform while still yielding 100bp
paired read lengths at high capacity and quality.  The MiSeq is
a standalone instrument utilizing the same proprietary
sequencing chemistry and data output format as the HiSeq but is
capable of short runs with up to 250bp high quality (70% reads
>Q30 scores) paired read lengths with 300bp paired read
capability in mid-2013.  It is the only platform currently
capable of such runs and the data will be invaluable to bridge
regions of low complexity commonly found in large plant genomes.
 The MiSeq instrument is also capable of running in short read
mode to rapidly assess the quality of sequencing libraries to be
run on the HiSeq 2000 platforms.  It is the only sequencing
platform that will enable this degree of library quality control
assessment for the Illumina HiSeq platforms.  The MiSeq will
also be fully compatible with the existing HiSeq 2000 sequencing
and bioinformatics infrastructure at NRC Saskatoon and thus will
require little additional support to be fully operational in the
shortest possible timeframe.

GCR Exemption
(d)	Only one supplier, person or firm is capable of performing
the contract.

AIT Article 506
12 (b)	to ensure compatibility with existing products, to
recognize exclusive rights, such as
exclusive licences, copyright and patent rights, or to maintain
specialized products that must
be maintained by the manufacturer or its representative.

NAFTA Article 1016
2 (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;

WTO-AGP Article XV
1 (b)   when, for works of art or for reasons connected with
protection of exclusive rights, such as patents or copyrights,
or in the absence of competition for technical reasons, the
products or services can be supplied only by a particular
supplier and no reasonable alternative or substitute exists;

Only known supplier
Illumina Canada Inc
5200 Illumina Way
San Diego
California
92123

Estimated Value - $834,292.94 Cdn
Delivery Date: Above-mentioned

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with one firm only as identified above. Should you have any
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