Advanced Assay
Design Software
for the iCycler iQ™ Detection System
Launch package
April 2002
Lab Devices Division
Molecular Biology Business Unit
NEW Design Software for the iCycler iQ System
Beacon Designer from PREMIER Biosoft International
Launch April 2002
Bio-Rad has become the recognized expert in the real-time PCR market by offering real solutions
to meet customers’ needs. We plan to solidify our strengths by offering the complete solution to
our customers with a truly advanced primer and probe design software product.
Designing assays with this software for experiments on the iQ system will result in success for
both customers in their laboratories and success for Bio-Rad in the marketplace. The real-time
PCR instrumentation market is growing by 50% in the coming year, and primer/probe design
packages directly support this growth.
Real-time PCR requires different design and assay conditions than traditional PCR due to the high
sensitivity of detection by the real-time PCR instrument. Performance on real-time instrumentation
is directly tied to how well the assays are designed. There is a great need for intuitive tools to
create the optimal assay. Currently, our customers must rely on field application specialists,
technical support, and competitor information to design their assays. By offering this design
software, we will give our customers the necessary tools and support to design for their assays.
We are excited to introduce Beacon Designer software, an advanced probe and primer design
software for real-time PCR assay design. This software does more than just design molecular
beacons. It also designs optimal TaqMan® probes and primers. Easy-to-use features make
designing for SNP detection effortless. It is unique in its ability to design for multiplex assays. The
software is the only one linked to the Web for quick sequence retrieval from Entrez and dbSNP
and the ability to BLAST sequences.
The software was introduced to the iCycler iQ Field Application Specialists at the 2002
International Sales Meeting in Puerto Rico. Those of you who have had the opportunity to betatest this new software have given great feedback. This product will be available for iQ customers
in April 2002. Please review the information and return the attached FAX back form by Friday,
April 5th, so we can plan for an effective launch.
Thank you!
Larissa, Shannon, Hilary, and Steve
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PRODUCT DESCRIPTION
Beacon Designer is a probe and primer design software that designs optimal primer sets
and probes for real-time PCR assays to be run on real-time PCR instruments, such as the
iCycler iQ. This software was created by PREMIER Biosoft and is currently offered through
their website www.premierbiosoft.com for $1885. Beacon Designer is one of many
scientific software packages PREMIER Biosoft offers, but this is the only one we will be
offering to our iQ customers. Bio-Rad will be distributing this product, and PREMIER
Biosoft’s name will remain on the product.
Why Beacon Designer?
We chose this particular design software because of its open platform- you can choose the type
of probe designed and the temperature parameters you need for your assay. The software
originally designed molecular beacons only. Now it contains new features for TaqMan, allelic
discrimination, and multiplex design. PREMIER Biosoft’s commitment to continually improve the
product and responsiveness to customer feedback means that features we need will be
incorporated in the future. In the software, you can select “Request Feature” which links you
directly to their website to give them immediate feedback on this product. This is a key feature for
improving the product.
Does this mean we promote molecular beacons over TaqMan?
No, because the iCycler iQ is an open platform system, we strive to meet all real-time PCR
needs. For most applications, customers prefer linear/TaqMan probes because they are easily
designed and synthesized, and produce robust results in real-time PCR assays. For some
applications, molecular beacons may be the preferable chemistry. Beacon Designer was
originally a program that designed molecular beacons only. Feedback from Bio-Rad R&D and
other customers helped define the need for a software program that also designed for TaqMan,
multiplex, and allelic discrimination assays. So PREMIER Biosoft incorporated these needed
new features to Beacon Designer, and we believe the design software will further improve with
feedback from our customers.
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KEY FEATURES
This software will be the first truly comprehensive primer and probe design package on the market
because it offers design of two probe types (TaqMan and molecular beacons) and offers the most
user flexibility in the design parameters. The software is distinguished in its ability to check the
cross-homologies of the amplicon sequence by the integration of NCBI website to BLAST
sequences and integration for direct retrieval of sequences from Entrez and dbSNP. Optimal
primers and probes are designed due to the calculations using nearest neighbor Santa Lucia
values and the evaluation of secondary structure of the primer and probe sequences.
Feature
This is the only software that designs
molecular beacons with accurate
calculations of arm and probe
sequence and display of structures.
The software designs optimal
linear/TaqMan probes, with more
flexible Tm parameters compared to
ABI Primer Express.
The algorithm provides the most
accurate Tm calculation for the
customers’ assays using nearest
neighbor, Santa Lucia values, taking
into account salt concentrations and
GC content.
This software designs TaqMan and
molecular beacon probes to detect
wildtype and mutant alleles.
This is the only software that designs
for multiplex by automatically
evaluating primers and probes for
cross homologies, with a graphical
display of structures.
This is the only software integrated to
the web so that sequences can be
retrieved immediately from Entrez
using accession numbers and from
dbSNP using assay IDs.
The uniquely integrated BLAST
feature automatically screens for the
major cross-homologies of the
amplicon sequence.
Benefit
This gives the customer more
options for their assay design.
The customer is in control of the
design.
The software designs truly
optimized primers for molecular
beacon and TaqMan assays.
The customer can choose the best
assay design to promote specificity
for allelic discrimination.
The customer can accelerate time to
results for an optimized multiplex
assay.
The customer can begin design
immediately, without having to
modify the sequence.
This ensures specificity of the
product amplified from the designed
probes and primers.
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COMPETITIVE ANALYSIS
The major competitors are Applied Biosystems (ABI) and Roche, who offer both real-time
instruments and probe design software. The software offered is seen as completing the package
of support to the customer from assay design to assay detection on the real-time instruments. The
ABI Primer Express is widely recognized and accepted by its users, and it is used as a major
selling feature. Roche launched their design package this year, which also completes their realtime PCR package.
Roche Light Cycler Probe Design Software v. 1
$1000
This software can only design one type of probe, which works only on the Roche system. It can
design for two types of assay- 1) quantitation and 2) mutation analysis. The software has welldesigned interface, very easy to use, and the user can print a detailed report. The major
weakness is that this probe works well only on their system.
Applied Biosystems Primer Express v. 2
$5000
This software can design two types of probes, TaqMan and TaqMan MGB probes. TaqMan MGB
probes can be designed on this software only and bought only through Applied Biosystem. The
software program displays features and sequences in a good format that is easy to view. The
software designs for quantitation and allelic discrimination, but for allelic discrimination, the user
has to evaluate the probe sequences himself. Manual is very large. The major weakness is that
the user is restricted to the temperature parameters of Applied Biosystems, so program is very
inflexible.
PREMIER Biosoft Beacon Designer v. 2 $1885/ Bio-Rad Laboratories $1485
This software can design molecular beacons, unlike the other programs, and also TaqMan probes.
The user may set the design parameters, with much more flexibility than Primer Express.
Interface is simple, and streamlined so that a novice can have optimized primers and probes
designed for him for quantitation, allelic discrimination, and multiplex assays. The major
weaknesses are that the export of results is not as sophisticated, and the adjustments of user
sequences is not as visual as the other two programs. However, PREMIER Biosoft’s commitment
to improve this product and free upgrades will overcome these weaknesses.
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COMPETITIVE ANALYSIS
PREMIER
Biosoft
Beacon
Designer
Price in USD
Applied Biosystems
Primer Express
Roche Applied
Science
Light Cycler
$1885, $1485
for iQ
customers
$5000, included with
system
$1000
YES
YES
NO
YES
NO
NO
Designs TaqMan Probes
Designs molecular beacons
Designs for SNPanalysis
YES
YES
YES
Multiplex function to check for crosshomologies
YES
NO
NO
Integrated to web
YES
NO
NO
Tm calculations using Santa Lucia
values
YES
NO
NO
BLAST sequences
YES
NO
NO
Input of sequences directly from
Entrez and dbSNP
Flexible Tm Parameters
YES
NO
NO
YES
NO
YES
NO
YES
YES
YES
YES
YES
Can annotate sequences
Results page
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TARGET COG, PROPOSED PRICING STRATEGY
Suggested List Price
Cost of Goods
PREMIER
Biosoft’s Price
$1485 USD
$1010 USD
$1885 USD
The primary intent in offering this product is to generate increased sales of the iCycler iQ system by
offering the complete iQ package with design software. The opportunity to bundle Beacon Designer
software with new iCycler iQ sales enables us to increase the value of our real-time PCR detection
system. New competitors in the instrument market, such as the Corbett Rotogene, Cepheid
SmartCycler, and the Stratagene MX4000 do not offer probe/primer design software. Our main
competitors Roche and Applied Biosystems do offer design software to accompany their instruments,
which increases the perceived value of their system. However, both offer limited design software. We
can maintain a competitive edge by offering the complete iQ system, one that offers support
from assay design to assay detection.
We extend this same support to the existing iCycler iQ customer base by offering this product at a
discounted price from PREMIER Biosoft’s list price. This increases the value of being an iQ user. We
strive to help customers succeed in their scientific efforts using our instrument, and now we have
design software to aid in their efforts. Furthermore, the service demand on our field application
specialists and technical support will be alleviated because customers will have more control in
optimizing their assays. Design software will be a great benefit to Bio-Rad and our customers.
Our distribution agreement with PREMIER Biosoft allows us to offer the Beacon Designer software
only to iQ customers because we offer a customer base that would benefit from this software. We gain
from this agreement because we are able to offer advanced design software that will continue to
improve with feedback from our customers. In addition, we have the opportunity to work with a
company that believes in being responsive to the needs of the researcher.
MARKETING POSITION AND SALES STRATEGY
The target customer will be current and new iCycler iQ users. iQ customers currently rely on the field
application specialists, technical notes, and competitor software and technical notes for information on
how to design probes for their real-time assay. Often times, they rely on the competitor’s inferior
information regarding probe design.
Current iQ customers are familiar with the complexity and time for assay design. There is a need to
further support these customers with advanced design software to facilitate their assay design needs.
Now, customers will be able to design their assays in minutes with Beacon Designer. You will be able
to offer this software at a price with a significant discount from the vendor’s list.
New iQ customers need a software program that maximizes the range and flexibility of our system.
This software offers more than what the competitors’ offer, and PREMIER Biosoft’s commitment to
continuous improvement ensures this design software will remain superior. By packaging this design
software with the iQ system, you will be able offer the new customer a complete iQ package of support
from assay design to assay detection.
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ORDERING INFORMATION
Catalog# 170-8734
iCycler iQ Beacon Designer Probe/Primer Design Software
Product Code
1441
NOTE: This is a product available to iQ customers only.
1)
An iQ serial number will be required to activate the product.
2)
Each purchase allows three activation keys for three installs of the software.
SPECIFICATIONS
The software runs on Windows NT / 98 / 2000 / ME / XP and Mac OS X 10.1. Beacon Designer
requires web access for full functionality of the features.
The customer will receive a CD-ROM and instructions with a registration number. The demo
version of the software is downloaded from the CD-ROM. The demo version generates a
Machine ID for your computer and requires an activation key to convert it to a workable version.


To obtain an activation key, the customer will have to email/fax/call PREMIER Biosoft
with the registration number, Machine ID, and serial number of the iQ to obtain the
activation key.
The customer is given up to three activation keys for three Machine IDs/computers.
This means a customer can install up to three copies of the software.
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PROMOTION PLAN
PROMOTION PLAN
Print Advertising
Bio-Rad will not directly advertise this software product by itself. It is a product that will help
promote the iCycler iQ Detection System as a complete package from assay design to assay
detection. The iQ print campaign for 2002 will include the design software as part of the iQ
complete package. This will run in Quarter 2 of 2002 in April 18th and 19th issues of Science and
Nature.
Sales Literature
The main point of sale piece/ promotional literature will be a two-sided 8.5’’ by 11’’ page. Front will
have key selling points of the design software. Back will have the features, comparison to
competitor info, and product ordering information. In addition to this, there will be a Quick Guide to
using Beacon Designer, which outlines how to use the main features of this software. This will be
the Bio-Rad signature piece to go with the PREMIER Biosoft product.
For Amplification Group shared literature, the, the Complete iQ point of sale piece/promotional
literature will contain information on the complete package offered for the iQ system- optical
system, thermal cycler, reagents, and the design software. Also, the design software will also be
part of the new iQ family brochure, containing point of sale pieces for all products offered for the
iQ. Both of these will be available in Quarter 2 of 2002.
Web Based Advertising/Promotion
The iCycler website (www.bio-rad.com/iCycler) will feature a new “What’s New Section” which will
have a link to Probe/Primer Design Software. This will open up the page for Beacon Designer with
key points, Features section, Quick Guide section with figures, Competitor Section, and Ordering
Information.
Available Materials
The powerpoint presentation of Beacon Designer from the 2002 sales meeting is posted on
Livelink. An informative and brief multimedia tour of the software can be viewed and/or
downloaded from the PREMIER website (www.premierbiosoft.com). This clear and informative
multimedia tour is the most comprehensive way to become familiar with the software.
FAX BACK form is attached
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FAX BACK
Bio-Rad Laboratories
To: Larissa Tan
Fax: (510) 741-5811
Life Science Group
2000 Alfred Nobel Drive
Hercules, CA 94547
Tel: (510) 741-6336
From:
Date:
Thank you for taking the time to learn about the Probe and Primer Design Software- Beacon
Designer. This product will be an exciting new feature to promote the iCycler iQ Detection
System as a complete package to meet all needs of the real-time PCR instrument user. Please
fill out the information listed below to help us ensure a successful launch and support your sales
needs.
Product Launch
When will you launch this product?
How many will you need, and when will you need them?
Number/month:
Date:
Sales forecast for 6 months (number of units)
April
May
July
August
June
September
Preliminary Promotion Plans
How do you plan to launch the Probe/Primer Design Software?
Training
The multimedia tour provided by PREMIER Biosoft for Beacon Designer is an informative training
tool for the software. Would you like more training, like a web conference for this product?
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Regional Competitive Information
Who is your main competitor?
Which instrument?
Which design software?
________
Are there any other competitors in probe design software that you expect to see? (Please
describe)
Please indicate any questions or comments you have regarding the Beacon Designer
Probe/Primer Design Software?
Thank you!
Larissa Tan
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