Applications in Genomics - PerkinElmer

Applications in Genomics
Enabling molecular diagnostics and improving the quality and efficiency of next
generation sequencing
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Genomics Tools
Research
Applied
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LabChipGX
Selected Partners & Customers
713/726
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Instrument features:
• Quantitative sizing of DNA and RNA
• Amenable to wide range of MDx assays
• Relevant assays in oncology, infectious disease
• Accurate automated sample concentration
• 96 and 384-well compatible
• Speed: 30 seconds per sample
• Walk-away fully automated workflow
• Integrated bar-code reader for sample tracking
• 21 CFR part 11 compliant software
“Compatible with ALL endpoint PCR assays”
“Less expensive than capillary electrophoresis”
“Simple workflow minimizes errors”
“Unparalleled throughput and resolution”
“Advanced software for analysis and data integrity”
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Sciclone G3
Engineered for Precision
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One system:
• Sciclone G3: 3 ‘engines’
Available with 3 head versions, heads can be
swapped by user
– 96 High Volume Head (HVH) disposable tips,
1-200ul volume range
Sciclone G3
– 384 Low Volume Head (LVH) disposable tips,
pin tool or fixed cannula,
0.5-25ul volume range\
– 384 nanoLitre Head (NLH) fixed cannula
0.1-5ul volume range
• All 3 instruments offer 20 deck positions,
compatible with all SBS format consumables
including;
– microtitre plates
– reagent reservoirs
– deepwell blocks
– tube racks
– disposable tips
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Sciclone G3 -Servo Gripper
Specification
• Servo Driven
• Grips
– Plates and filter plates
– Covers
– Tips
– Deepwell blocks and filter
blocks
Application
– Delidding and holding lid
during pipetting routine
– Plate stack/restack during
filtration application
– Barcode reading
– On deck consumables
management
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Specification
• Independent “Z” Control for single well access
– Fixed Cannula:
» 100µl syringe, 1-50µl cannula
– Disposable Tip
» 100µl or 250µl syringes, 100µl or 200µl tips
» 1000µl syringe, 1000µl tips
Sciclone G3 - Z8
– Z8 Volume Range:
» 0.5µl - 200 µl
» 5-1000µl
– Z8 Precision 200µl syringe
» 0.5µl – 5µl

Options
• Swappable heads
• Swappable arrays
• Bulk dispense
• Vacuum filtration
ti
• Positive pressure
• Magnet location
• Hyperstacks
• Enclosure
• Hepa and UV
And even more accessories……
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Additional Accessories
Pin Tools
Shakers
Tube Racks
Temp Control (piezo)
Reagent
Reservoirs
Tip Washing
‘bubbler style’
Tip Washing
‘ultrasonic style’
Active Locator
(precision)
Temp Control
(recirculating fluid)
Barcode Reader
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A true “multitool”…
but what was missing?...
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Tube to Plate Capability
Tube to plate solution providers…
Is there a better way?....
YES
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The Next “Big Thing” in Caliper Automation
Sciclone G3 with tube to plate
Faster, better, less consumable cost…
1) New Deck Cutout
—6 racks of 16 tubes
—Supports Vacutainer w/ other racks in dev.
—Filler panel restores locations
2)Built In BCR
—Scans Tubes Upon Loading
—Databases barcodes
—GUI will not allow misreads
3) Integrated sample submission GUI and tracking
software
4) PING sensor for non-contact liquid level
sensing (no need for electrostatic tips!!!)
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Tube Rack Barcoding
Built In Scanner
Optical Sensor
BCR Trigger
Holes
Slots for label exposure
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Error Proof GUI
Will not advance application until tubes are readable
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Coaxial
Cable
Control
Module
Sensor
24V
DC
Serial
port
•Liquid Level Detection
•Filter Plate Clogged Well Detection
•Consumable Identification
•Automated t Deck Teaching
•Located in head
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• Reformats tips at four tiers
Tip Reformatter Option
• Enables attachment of subgroups of 24
tips using std 96 tip mandrel
• 3x faster than Span 8’s
• Preserves 96 tip access
(12x faster than Span 8’s or forces
competition to use additional 96 ch head)
• SBS footprint
• Supports 300ul Thermo tips (shown)
• 384 version in development
Patent Pending
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Automated “walk-away” Immunoassay –
Sciclone G3
Multiplex immunoassay
Blood banking immunoassay tests using
3.5 Million Samples per year
•HIV
• HCV
• Chagas disease
• Transfer of 96 samples to a plate in 4 mins
(as opposed to others at 20 mins).
• 600-700 samples an 8 hour day with one Luminex reader
(8 analytes detected simultaneously per sample).
• Current method is 8 individual immunoassays.
• Multiplexing up to 100 analytes
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Nucleic Acid Fractionation
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Traditional Method
Manual Gels, Razor blades, Gel Extraction Kits
Automated Nucleic Acid
Fractionation
LabChip Approach
Automated Separation, Analysis & Purification
Preparative Microfluidics Separations
‣ Simple workflow
‣ Less than 5% CV
‣ Ready for NGS analysis
Manual gel and LabChip Comparison
• 30 min vs. 5-8 hours, automated vs. manual
• Safety: No razors or polyacrylamide
• Quantitative vs. qualitative bands
• Reproducible, accurate, sensitive results
• File sharing vs. dried gels
Load Analyze Collect
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Fractionation of Sheared gDNA
298bp +/- 12bp (4%)
Sheared human DNA
Fractionated Sample
• High collection efficiency of target range
– No excessive diffusion
– No post purification
– Single independent channel per
sample
• < 30 minute processing
• 4 samples processed simultaneously
• PCR compatible buffer
• Low input volume needed
• Why automated size selection?
– Tighter sizing facilitates assembly
– Increase average read lengths
– Improve process efficiency
– Reduce run-to-run variability
– Efficiency = $ and time
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Workflow
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LabChip Fractionation
Program Size
Run Assay
Size detection
window
A “current switch” drives desired
fragments into collection well.
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Software
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Software Collection in Process
Chip info and run status
Electropherogram
Virtual gel
Sizing ladder
Tabular data
Collected fragment highlighted
Genomic smear
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Illumina Pair End Sequencing
Fractionated material denatured and applied directly to flow cell without purification
327bp+/-16.2bp
(4.9%)
8.6ng total
Data courtesy of the Broad Institute
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No GC Bias of Fractionated Material
20 mins 6 hours
Caliper – LabChip
Broad – Gel slice
Data courtesy of the Broad Institute
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LabChip XT Instrument
Specifications
Weight:
4.5 kg
Power requirements: 100/110/230
VAC, 50/60 Hz
Power consumption:
600 V
Excitation Wavelength: 530 nm
PC Controller:
Included
Other features:
• Integrated analysis and extraction software
• Virtual gel, electropherogram, and tabular
data
• 2D barcode reader
• Status indicator and safety latch
• USB connectivity
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High Resolution DNA500 Assay
Specifications
Number of samples:
4 per chip
Range:
50 to 500 bp
Input volume:
10 ul plus
Input concentration:
25 – 250 ng/ul
Output volume:
10 to 20 ul
Highest resolution: +/- 5%
Run time to 500 bp:
30 minutes
Other features:
• Independent control of channels
• Disposable electrodes (no cross contamination)
• Waste recovery for precious samples
• Barcode sample tracking
• Physical or software sizing i ladder
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Collaborations and Projects
Partner & Advisory Board
• Exceptional beta test with Top 3 NGS provider
• Working opportunities with Pacific Biosciences,
Epicentre, Illumina, Fluidigm, Covartis and others
• Alpha sample evaluations with all major sequencing
centers
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Sciclone G3 - Swappable Heads
Air displacement heads
– 5-10 minutes swap time
– 4 thumb screws and
quick connect air and
electronics
– 96 High Volume
– 384 Low Volume
– 384 nanoLitre
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Sciclone G3 - Swappable Arrays
Arrays
• 96 and 384 fixed cannula and
disposable tip arrays can be
swapped on the fly in a method
• Can switch from 96 to 384 during
method
• Can switch from disposable tip to
fixed cannula in a method
• Provides an additional level of
pipetting flexibility
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Bulk Reagent Dispenser
Specification
• Eight channel syringe dispenser
• Independent syringe control
• 96 and 384 plate compatible
• Volume range 10 - 1,500ul
• Up to 4 units – depending on Z8 and
gripper accessory configuration
• Precision
– 10µl 2.2%CV
– 20µl 1.2%CV
– 40µl 1%CV
– 80µl

Vacuum Plate Filtration
Specification
– Vacuum manifold – applies
vacuum from below plate
• Compatible with 96 & 384
• Compatible with all major filter plate
applications and manufacturers
Qiagen, Millipore, Promega
Applications
– RNA & DNA Purification
– Radiometric filter binding assays
– SPE
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Positive Pressure Plate Filtration
Specification
– Positive pressure manifold -
applies positive pressure onto
plate from above, manifold
attaches to head – pressure
control available within software
• Compatible with 96 & 384
• Compatible with all major filter plate
applications and manufacturers
Qiagen, Millipore, Promega
Applications
– RNA & DNA Purification
– Radiometric filter binding assays
– SPE
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Magnetic bead separation
Specification
• Magnetic bead separation based assay
chemistries
i
• Compatible with 96 & 384
• Compatible with all major magnetic bead
applications and manufacturers Agencourt,
Promega etc…
Applications
– RNA & DNA Purification
– Protein purification
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HyperStak Plate/Tip Rack Storage
•FILO Stack Storage
•40 Plate Capacity
•Only Caliper Provides Nested 384 tips!
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Tip Reformatter -video
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How to Create a Deck Layout
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Methods and Instructions
Drag & Drop Instructions
Mix
Aspirate
Dispense
Begin Loop End Loop Begin
Concurrent
End
Concurrent
If, Then..
Do While..
Call Method
Execute Path
Move Material
(Twister II)
Email
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Example of Command: Aspirate
Step 1
Step 2
Step 3
Step 4
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Excel & VB Integration
Read Cell
Run VBA
Write Cell
Run Excel Macro
Examples:
Write Barcode File
Save Workbook
•Front End Interface
• Third Part Device Integration
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Liquid Classes
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Dedicated Operator Interface
• Single point of system
operation, status monitoring,
error notification and
recovery
• Application completion
display
• System status t indicators
• Real time view of variables
and parameters
• Editing variables and
parameters
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Enhanced error recovery
• Alarm resolution - Single point
of control for error recovery
• Display time elapsed since an
alarm was raised
• Customizable error recovery by
calling a method
• Ability to start from a selected
line after error
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Final
Cutting edge innovations
- “PING!”, Tip Reformatter, Smart Tube Racks, Concurrency
Industry leading flexibility & performance
- EZ swap heads, swap on fly arrays, Bulk Dispense,
HyperStaks, controls Twister II, pos pressure filtration
- tight CV’s across all pipetting & dispense options
Ease to use software
- Highly Graphical
- Powerful integration i of Excel and VBA
A strategy of differentiation in a commodity market of liquid handlers…
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Sciclone G3 Control Software
• 3 Security Levels
• “Administrator”
• “Developer”
• “Operator”
• Dedicated Operator Interface
• Enhanced Error Recovery
• High Flexibility to Method developer
• Concurrency, controls Twister II
• Same Software for Sciclone and Zephyr
• Parallel control of multiple peripherals
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