384 Well Clean
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Transcript of 384 Well Clean
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384 well PCR Cleanup Application
Launch package
January 24, 2003
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Page 2
Index
Technology Page
Overview PCR 3
Overview PCR Cleanup 4
Whatman Protocol 5
Protocol Automation 6
Product
System Components 7
Pricing/Packaging 8
Competitor Comparison
Whatman Performance Data 9
Performance Comparison 10Protocol Time Comparison 11
Value Page
Features/Benefits 12
Customer
Customer ID 13
Market Sizing 14
Product Positioning 15
Marketing Support
Sample Information 16
Advertising Plan 17
Trade Show Plan 18
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Page 3
PCR Overview
Capable of greater than a Billion
fold replication of a DNA sequence
of interest
Necessary to create enough DNA to
perform:
Hybridization assays
(i.e. microarray)
Sequencing
SNP detection methods
Genotyping
cDNA library construction
PCR has been the most powerful
and widely used molecular biology
technique for the past 30 years
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Whatman 384 PCR Cleanup Procedure
Add Binding Buffer
PCR Product (5-30ul)
384 Well DNABinding Plate
2 x Wash with
90ul wash buffer
X 384
Add Elution Buffer
(10ul-50ul)
Centrifuge Filter
2.5 min @ 1800xg
Bind
Centrifuge Filter
5 min @ 1800xg
Wash
Elute
Centrifuge Collect
2.5 min @ 1800xg
Incubate
(1 min @ RT)
384 WellCollection Plate Collect
Waste - 384 Deep WellCollection Plate
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Protocol Automation
Demonstrated adaptability shown with
an in-house automated liquid handler(Biomek 2000)
Adaptation to other laboratory
instrumentation will be case specific
(no universal solution)
SBS compatible platesThings to consider:
Pipetting speeds - Semi-viscous buffers require careful pipetting during
delivery, mix & transfer steps
Disposables - Customer specific PCR tubes & pipette tips will have an
effect on liquid handling parameters (pipetting heights/speeds, mixing& transfer steps)
Molecular Biology Precautions - Routine cleaning of processing
equipment and lab surfaces will reduce the risk of unwanted amplicon
contamination. Use of aeresol resistant pipette tips is recommended.
Biomek 2000
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System Components
Upstream Accessories
96-well PCR Plates (7705-1901)
384-well PCR Plates (7705-1305)
Heat seals (7704-0002 or 7704-0003)
Downstream 384-Well Accessories
384-well black polystyrene plates (7701-2100) - fluorescent measurements
384-well white polystyrene plates (7701-3100) - chemiluminescent measurements
384-well 0.45u hydrophilic PVDF filterplate (7700-2106) - media support plate forcustomer specific dye terminator cleanup
384-well PCR Cleanup Components
384-well DNA Binding Plate (7700-2110)
384-well 400ul Waste Collection Plate (7701-5400)
384-well 100ul Collection Plate (7701-1100)Adhesive plate seals (7704-0001)
Equipment required
Centrifuge with microplate holder (2.3 inch stack height)
Automated Liquid Handling System & associated disposables
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Page 8
Pricing
Package Weights
7700-2110 384-well DNA Binding Plate 50 790
7701-5400 384-well 400ul Waste Collection Plate 25 143
7701-1100 384-well 100ul Collection Plate 50 110
7704-0001 Adhesive plate seals 100 44
List Price/Prep 0.06
Cat # Description Height cm Weight k Length cm Width cm
7700-2110 DNA Binding Plate 13 4.31 43.18 14.24
7701-1100 Uniplt 384 Well 100ul 14 2.86 44.45 17.78
7701-5400 Uniplt 384 Well 400 ul 14 2.86 44.45 17.78
7704-0001 Adhesive Plate Seal 5.08 0.34 20.32 11.43
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Pricing in Euros
Package Weights
Cat Num Description Plates/Case Price/Case
7700-2110 384-well DNA Binding Plate 50 1,304
7701-5400 384-well 400ul Waste Collection Plate 25 240
7701-1100 384-well 100ul Collection Plate 50 182
7704-0001 Adhesive plate seals 100 73
List Price/Prep E 0.06
Cat # Description Height cm Weight k Length cm Width cm
7700-2110 DNA Binding Plate 13 4.31 43.18 14.24
7701-1100 Uniplt 384 Well 100ul 14 2.86 44.45 17.78
7701-5400 Uniplt 384 Well 400 ul 14 2.86 44.45 17.78
7704-0001 Adhesive Plate Seal 5.08 0.34 20.32 11.43
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Performance DataCapillary Sequencing
Purified 1.8kb product sequenced
using big dye chemistry
Non-cross talk
Alternating positive & negative cleanups re-amplified to
detect low levels of cross contamination
Development Run - Yield / Recovery / Reproducibility
0.00
0.50
1.00
1.50
2.00
2.50
3.00
3.50
4.00
4.50
5.00
213bp A melogeni n 500bp pGE M 1. 9k b pG EM
PCR Product
DNAQuantity(ug/w
ell)
86.0%
88.0%
90.0%
92.0%
94.0%
96.0%
98.0%
100.0%
%Recovery
Crude Input (ug)
DNA Yield (ug)
% Recovery
7.36%
CV
5.15%
CV
7.41%
CV
DNA Recovery & Consistency
3 Different PCR product sizes purified &
quantified (n=24)
384 well PCR Cleanup - Adjunct Study
0
1
2
3
4
5
6
7
8
9
10
0 2 4 6 8 10
HS DNA Input (ug/wel l)
DNAYield(ug/we
ll)
Standard PCR
2% DMSO
1.5M Betaine
0.1% Glycerol
DNA Binding Capacity
Varying levels of DNA Input purified and
quantified. Study also shows comparison of
PCR reactions containing typical adjucts
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Competitor Performance Comparison
Parameter Whatman Millipore Telechem=CPG=Genetix
Sample requirements 5-30ul PCR reaction (split
or concentrate if needed)
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Liquid handling pipette headMethod #
plates
8 channel* 384 channel**
2 1:25:10 21:30Whatman
4 2:36:50 29:30
Millipore 1 51:00 28:002 1:33:30 25:30CPG/Telechem/
Genetix 4 2:51:30 35:30*based on internal Biomek 2000 testing
**estimated times
Competitor Time Comparison
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Features384 well
Bind-wash-elute chemistry
Centrifuge processing protocol
SBS compatible microplates
Sample volumes 5-30ul
High recovery of low MW PCR
products
Robust to various PCR adjuncts
Uses DNA Binding plate
Bulk Component Purchase
Benefits Increased throughput, decreased cost
Simple method
No phenol / chloroform / alcohol extractions
Provides highly purified DNA.
Easy downstream sample retrieval.
Complete elimination of well to well
contamination. Efficient volume recovery
Compatible with automated liquid handling
equipment
No sample concentration or dilution needed for
typical 384 PCR samples
Able to meet the demands of genomics customers
Compatible with lab specific PCR chemistries
Adaptable to binding nucleic acid from many
sample sources
Economic benefit for large genome centers and
custom kit manufacturers
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Target Customers
Genomics OEM PotentialsKit companies: Qiagen
Amersham BioRad
Promega
Gentra
Genetix
Eppendorf
Applied Biosystems
Stratagene
Mackerey Nagle
Invitrogen Roche
Edge
Princeton Separations
Instrument companies: Perkin Elmer
Tecan
Beckman
Gilson
Zymark Brandel
Genomic InstitutionsUS: Albert Einstein College of Medicine
Baylor College of Medicine The Chromosome 21 Mapping and
Sequencing Consortium
Center for Genetics in Medicine
Genoscope
GTC Sequencing Center
Cold Spring Harbor
Joint Genome Institute, U.S.
Department of Energy
Stanford DNA Sequencing AndTechnology Development Center
Stanford Human Genome Center
The Institute for Genome Research
University of Utah Genome Center
University of Oklahoma Advanced
Genome Technology Center
University of Texas, Southwestern
Medical Center
University of Washington GenomeCenter
The Institute for Systems Biology
Whitehead Institute for Biomedical
Research
Washington University
Europe: Gesellschaft fur
Biotechnologische ForschungmbH
InstituteforMolecular
Biotechnology, Jena, Germany
Max Planck Institute for
Molecular Genetics
Sanger Center
Finland Genome Research
Center
Asia: Human Genome Center, Institute
of Genetics, Chinese Academy of
Sciences
National YangMing University
Genome Research Ceter
Japan: Keio Uiversity School of
Medicine, Tokyo
Japan Science and Technology
Corporation
RIKEN Genome Sciences Center
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Target Market / Sizing
WW Market Size for PCR Clean up Kits ($M)
0.0
5.0
10.0
15.0
20.0
25.0
30.0
2000 2001 2002 2003 2004 2005 2006 2007
Sample Capacity of Thermal Cyclers Acquired 1998-2000
(Source PhorTech Thermocycler Mkt Survey)
0
10
20
3040
50
60
70
384 96 48 24
Sample Capacity
%o
fTHermalCyclersin
Installed
Base
The WW market for PCRClean up kits is estimated
at $15M in 2003 with
forecasted growth rate of
9% per year.
The shift to 384 well
PCR plates, starting in
2000, is gainingmomentum and leading
to demand for 384 well
PCR clean up.
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Product Positioning
The 384 well PCR Clean up product is intended for use in
large genomic research institutions performing millions ofPCR reactions per year.
Bulk Product
Primary market research suggests that these large genome
centers will fine tune their own protocol and set up their own
automation systems, thereby requiring bulk components as
opposed to turnkey kits. Specific examples of this preference
include Sanger Center, Cold Spring Harbor and the Finland
Genome Research Center.
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Samples & Inventory
Sample plates and accessories can be ordered separately
Or as a 2 plate set
Cat Num Description Units/Case
s7700-2110 384-well DNA Binding Plate 1 plate
s7701-5400 384-well 400ul Waste Collection Plate 1 plate
s7701-1100 384-well 100ul Collection Plate 1 plate
s7704-0001 Adhesive plate seals 1 seals
Cat Num Description Units/Case
s7905-0004 384-well PCR Clean up sample pack 768 reactions
The protocol and buffer formulations are available at the
Whatman web site locations
Technical Support/Protocols/ApplicationsProtocols
Technical Support/Applications/Laboratory Filtration-Microplates/Technical Papers