Digital PCR 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: Government Objectives
Representing Best Interests/Value to Govt
Comprehensive Land Claim Agreement: No
Vendor Name and Address: 
Bio-Rad Laboratories (Canada) Ltd.
1329 Meyerside Drive
Mississauga Ontario
Canada
L5T1C9
Nature of Requirements: 
Digital PCR System (ddPRC)

31029-133315/A
Allard, Ken
Telephone No. - (204) 983-4920 
Fax No. - (204) 983-7796

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.

Background:
Molecular genetics and genomics research at National Research
Council (NRC) - Saskatoon involves a broad suite of activities. 
Researchers apply genetic approaches using molecular tools,
conduct transgenic studies, investigate plant development and
physiology, characterise plant and conduct metagenomics studies
of microbial populations.  A common essential need in these
research projects is to quantify nucleic acids with high
precision, sensitivity, and specificity at a high throughput
level, as related to determining native- and trans-gene copy
number, detecting and quantifying genetic variants and target
nucleic acids in complex mixtures, and determining gene
expression levels.  These investigations often involve very
limited amounts of nucleic acid samples, as from micro-dissected
tissues.  The new emerging Digital PCR (dPCR) technology offers
very robust system for absolute quantification of nucleic acids
and is required to meet the research needs at PBI/NRC-Saskatoon.
Any interested supplier must demonstrate by way of a statement
of capabilities that its product/equipment/system meets the
following requirements:

Criteria for assessment of the Statement of Capabilities -
Minimum Essential Performance Specifications:

1. The dPCR system is of a "benchtop" scale must read samples in
standard 96-well format plates to enable incorporation into our
existing workflows and use standard thermocyclers already
present at NRC-Saskatoon. Existing workflows utilise a
temperature gradient PCR step to optimise assay conditions and
the requested new dPCR system must be able to incorporate a
temperature gradient PCR step.  The temperature gradient ability
must NOT require any additional pipetting or liquid handling
steps as these will introduce additional errors into the
experiment. 

2. The dPCR system must analyze 96 unique samples in less than 5
hours, including the steps of 1) partitioning of sample assays
into 12,000 to 20,000 reaction partitions, 2) PCR amplification
and 3) reading and scoring reaction partitions.  Note: This
requirement is necessary in order to analyze multiple samples at
once without introducing potential source of error by single
tube analyses. Also, these features are needed to meet sample
throughput requirements of the multiple users from several NRC
research programs as well as potential industrial partners at
Saskatoon.

3. This dPCR system should include droplet generator and droplet
reader. The droplet reader must incorporate a 96-well
auto-sampler so that unattended operation is possible to
maximize sample throughput. 
4. The dPCR system must produce 12,000 to 20,000 reaction
partitions per sample for 96 unique samples in 30 minutes or
less.

5. The dPCR system that is compatible with DNA binding
chemistries (e.g. Evagreen) as well as hydrolosis probe
chemistry using FAM and/or HEX dyes and  must detect
fluorescence signals corresponding to those derived from VIC-,
HEX-, Evagreen-, or FAM-labeled PCR probes.

6. The dPCR system must distinguish between gene copy number
variants of 11 vs. 10 and less using two or less sample assay
reactions of one reaction well each (equivalent to one chamber
or panel of a reaction chip) with an input of nucleic acid
template equivalent to 100 ng of plant or microbse' genomic DNA
or less so as to minimise amount of nucleic acid sample size
required per assay and cost of consumables. This ability must be
achieved without the need for a preamplification step which can
cause a significant measurement bias by distorting the abundance
and relative presence of target nucleic acids. 

7.  The dPCR system must enable gene expression analysis and
quantification of DNA copies with +/- 10% precision to meet the
requirements of the multiple users from several research
programs. The system must include gene expression module that
can analyze and produce accurate gene expression levels in the
sample. 

8. The dPCR system must detect a specific genetic variant at a
level as low as 0.001% abundance in a sample mixture that
includes other genetic variants, and enable a linear
quantification of this variant over four orders of magnitude of
abundance of this variant in a complex mixture of nucleic acids. 

9. The dPCR system must NOT require development of standard
curves or need an external calibrator to estimate relative
abundance of target nucleic acids, thereby minimizing the number
of samples to be prepared and analyzed.  Rather, the instrument
must generate digital data reflecting absolute quantification of
target nucleic acid abundance. 

10.  The digital PCR system must have a reaction partition
volume of 1 nL or less. 

11. The relative expanded uncertainty of the dPCR system from
the data for 20,000 reaction partitions is required to be 5% or
less to achieve the data precision required by the research
programs. 

12. The dPCR system must generate 12,000 to 20,000 reaction
partitions from a 20 microlitre sample reaction volume.

13. The dPCR system must NOT require use of specialized liquid
handling equipment or robotic liquid handlers that would
typically require specialized training and a dedicated
technician to operate since the system will be used by numerous
researchers from multiple programs.

14. The dPCR system must generate and assay reaction partition
in a manner that minimize the dead volume of the partition
holder and reader to <25% starting reaction volume. 

15. The system must use low cost consumables, which amounts to
less than $3.00 per sample.

16. The system must include all the needed software for
operation and analysis.

17. The system can detect one copy of target sequence in a DNA
sample. 

18. The system's software can perform and report various results
such as absolute concentration, copy number variation and ratio
analysis (for gene expression analysis).


Applicability of  the Trade Agreements to this Procurement

This procurement is subject to the following trade agreements:

Agreement on International Trade (AIT)
North American Free Trade Agreement (NAFTA)
Canada - Chile Free Trade Agreement (CCFTA)
Canada - Peru Free Trade Agreement (CPFTA)

Government Contracts  Regulations  Exceptions:

The following exception(s) to the Government Contracts
Regulations is (are) invoked for this procurement under
subsection: Government Contract Regulations, Part 1, Section
6(d) only one supplier (person or firm) is capable of performing
the contract.

Exclusions and/or Limited Tendering Reasons:

The following exclusions and/or 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 exist.

North American Free Trade Agreement (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.

Canada - Chile Free Trade Agreement (CCFTA) - Article Kbis-09 -
1(b) where, for works of art, or for reasons connected with
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.

Canada - Peru Free Trade Agreement (CPFTA) - Article 1409 1(b)
iii - due to the absence of competition for technical reasons.

Justification of Preselected Supplier:

The Bio-RadQX200 Droplet Digital PCR (dPCR) system is the only
system currently available that meets the throughput needs and
required high levels of precision, sensitivity, and specificity
of the research requirements at NRC-Saskatoon.  This is the only
system that offers and compatible with DNA binding chemistries
(e.g. EvaGreen) as well as hydrolosis probe chemistry using FAM
and HEX dyes. It is able to process samples in 96 well format in
a short time-frame, fitting throughput needs and existing
workflows' assay optimisation methods employing thermocyclers
already present at NRC-Saskatoon.  The QX200 dPCR system can
generate 20,000 reaction partitions for each sample processed,
providing for a unique level of robust statistical analysis in
combination with the 96 sample throughput level.  The QX200 dPCR
system achieves this high level of reaction partitions while
requiring only a small amount of nucleic acid sample size,
thereby making it the only system for analysing samples with
very limiting quantities, such as from microdissected single
cell embryos and small tissues.  Alternative systems consume
large quantities of sample input to reach comparable numbers of
partitions and cannot achieve the required throughput needs and
assay optimization capabilities as the dQX200 ddPCR system. 
This common resource piece of equipment will be used by
operators from multiple labs with various levels of training;
thus the system must not involve specialized liquid handling
equipment or robotics for preparation or processing of samples,
which would necessitate specialized training for multiple users
or the assignment of a dedicated technician for operation which
would limit accessibility and use of the system.  The QX200 dPCR
system does not require specialized liquid handling equipment or
robotics for preparation or processing of samples, and
furthermore is compatible with existing thermocylcing systems
and methodology at NRC-Saskatoon. These, combined with its
analytical ability, low sample processing cost and throughput
rate make it the only system that meets all the 1-18 performance
and specification requirements of dPCR system (as outlined in
the document) for research needs at NRC-Saskatoon.

NAME AND ADDRESS OF THE PRE-IDENTIFIED SUPPLIER:

The QX200 ddPCR manufactured by Bio-Rad Laboratories (Canada)
Ltd is the only known instrument meeting all specifications
essential to the requirement as listed above. 

For this reason, it is proposed to negotiate this requirement
with: 

Bio-Rad Laboratories (Canada) Ltd.
1329 Meyerside Drive
Mississauga Ontario
Canada
L5T1C9

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.


DELIVERY DATE

The equipment must be delivered on or before February 1, 2014 







INQUIRIES AND SUBMISSION OF STATEMENTS OF CAPABILITIES
Inquiries and statement of capabilities are to be directed to: 

Ken Allard 
Supply Specialist | Spécialiste en approvisionnement 
Acquisitions-Winnipeg | Approvisionnements - Winnipeg 
Public Works and Government Services Canada 
Travaux publics et Services Gouvernementaux Canada 
Suite 100 - 167 Lombard Ave., P.O. Box 1408, Winnipeg MB R3C 2Z1 
Email - ken.allard@pwgsc-tpsgc.gc.ca 
Tel/Tél - (204) 983 4920 
Fax/Téléc - (204) 983 7796 




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.