droplet digital pcr competition overview
DESCRIPTION
Bio-Rad QX100™ Droplet Digital™ PCR System System designed specifically for digital PCR Sample partitioned into 20,000 droplets Unparalleled precision at +/- 10% 105 linear dynamic range (1 to 100,000 copies) Flexible assay format for running experiments Simple, yet elegant workflow Easy to use software Droplet Reader Droplet GeneratorTRANSCRIPT
Droplet Digital PCR Competition OverviewVersion 1.0 – November 16
Bio-Rad QX100™ Droplet Digital™ PCR System
System designed specifically for digital PCR Sample partitioned into 20,000 droplets Unparalleled precision at +/- 10% 105 linear dynamic range (1 to 100,000 copies) Flexible assay format for running experiments Simple, yet elegant workflow Easy to use software
Droplet GeneratorDroplet Reader
Digital PCR Competition
Life Technologies QuantStudio 12K Flex
Fluidigm EP1 System Biomark HD System
Raindance Technologies System TBD
Life TechnologiesQuantStudio 12K Flex Real Time PCR system
Combination of Viia7 and OpenArray technologies Real-time PCR: TaqMan array card (TLDA), 384-well block, Standard
or Fast 96-well blocks Digital PCR: OpenArray block
Promote several applications, including viral load, mutant sequence detection against wt background, GMO quality control, gene expression and genotyping
Stand-alone operation is possible with LCD touch screen, but data is not shown on the system, need software on computer
OpenArray Plates
Each plate is essentially a microarray chip Through-hole accepts 33 ± 1 nL of sample and supermix Reagents retained in through-holes via surface tension
OpenArray Plates
Plates come preloaded from Life Technologies, can be predesigned or custom
OpenArray Plate Loading
AccuFill System loads samples into plate, transfers samples from 384-well plates into OpenArray Plates
OpenArray Plate Preparation
Users have ~90 seconds to load samples before they begin to evaporate Contributes to ~50% dead volume compared to 30% with QX100
After loading the plate, apply adhesive lid, fill the case with immersion fluid, then plug and load 4 plates into holder
Running OpenArray Plates
Run up to 4 plates Software fits real-time PCR data to a Poisson statistical model
and displays digital results as copies-per-through-hole
OptiFlex System
QuantStudio uses the same optical system as the Viia7 White light LED, filter wheels and camera Claim unlimited flexibility for dye selection, but fluorescence
excitation and emission of real-time PCR dyes are limiting Only 2-targets for dPCR – Fam and Vic (ROX normalization)
Life Technology Claims on Throughput
Maximum resolution of 12,000 data points (4 plates) The system allows you to process up to 1,728 genotyping
samples and 2,304 samples for gene expression in an 8 hr day PCR offline using the Dual Flat Block 9700, process a total of
over 5,184 genotyping samples in one day Can generating up to 110,000 data points or more per 8 hour
day, completing your project in days rather than weeks
Higher Throughput Option Only For Genotyping
Requires the purchase of Twister 2 robot and several thermal cyclers
Digital PCR Sample Dilutions
Claim multiple sample dilutions possible for increased input dynamic range
We do not need sample dilutions because we use 20,000 droplets
Digital PCR Claims
Life Tech states you can detect as little as 1.5-fold changes in target quantities in singleplex reactions We can do 1.2-fold changes in multiplex reactions
They acknowledge precision is determined by the number of replicates Better confidence intervals with more replicates This approach forces the user to choose between throughput
(number of samples analyzed) versus experiment precision At most, run 12,888 partitions for a single sample, but it
will cost $600 and requires 400 μL of sample
Bio-Rad Versus Life Tech
Bio-Rad Life TechCost per sample $3.00 $150.00
Number of partitions 20,000 3072
Cost per data point (cents) 0.0001 5
Partition Volume 1 nL 33 nL
Sample volume 20 μL 100 μL# of chips to match 20,000
partitions 1 7
Sample Volume Required to match 20,000 partitions 20 μL 700 uL
Cost to match 20,000 partitions $3.00 $1,050
Dead Volume 30% 50%
Price $89,000 $190,000
ddPCR Versus Life Technologies
Sample partitioning into 20,000 droplets enables independent, PCR micro-reactions, resulting in unmatched precision, accuracy and sensitivity for quantification
ddPCR +/- 10% precision allows the ability to distinguish very small fold differences and detect low copy number targets
Low sample volume translates into reduced reagent and sample costs
Significantly lower cost per sample $3 vs $150 Flexible format is not determined by a microfluidic chip
layout, multiple independent experiments can be run with ddPCR
Serial dilutions are not required, eliminates pipetting error between dilutions and saving reagent and consumable costs
ddPCR Versus Life Technologies
Yes, you can perform real-time PCR and dPCR with one system, but it costs $190,000 for the dPCR upgrade and the need to have data from both approaches is redundant
The OpenArray technology was developed for high throughput, low volume real-time PCR and genotyping, not digital PCR
The OpenArray format forces a compromise between precision and sample throughput
You must order chips pre-loaded with primers and probes, so assay flexibility is limited and the experiment is locked
Fluidigm BioMark HD System
Integrated Fluidic Circuitry (IFC) technology Microfluidic plates with varying throughput (~$360/plate)
Real-time PCR: 48 samples x 48 assays (2034 rxns) 96 samples x 96 assays (9216 rxns), 192 samples x 24 SNPs
Digital PCR: 12 samples X 765 partitions (9180 rxns), 48 samples x 770 partitions (39,960 rxns)
Promote gene expression, single cell analysis, genotyping, NGS sample preparation, CNV
Fluidigm Sells 2 Systems
Biomark HD system – includes integrated cycler and real-time detection camera. It costs $240K
EP1 System – separate thermal cycler and camera, can’t be used for single cell gene expression. It costs $100K
BioMark HD System EP1 System
Integrated Fluidic Circuitry (IFC) technology
Microfluidic chip that uses pressure to move liquids and nano-scale valves to trap samples into small wells
Sample Sample InputsInputs
ChipChipIHS Underneath ChipIHS Underneath Chip
Pressure AccumulatorPressure Accumulator
RC – Reaction ChamberIV – Interface valveCV – Containment Valve
Inside Chip
IFC Chip Loading
Sample CDNA or DNA concentration: 1/5,000 nl Target concentration: 1,000
greater, or 1/5nl
Workflow Part 1
Prime. Prime chip in IFC controller to close interface valves, preventing premature mixing of samples and assays (10 min)
Transfer. Pipette samples premixed with master mix and primer, probes into separate sample inlets on frame of the chip 12.765 Chip – minimum load 4 ul per well 48.770 Chip – minimum load 8 ul per well
IFC Controller
Workflow Part 2
Load samples. Place the chip back on IFC controller, and pressure load assay into reaction chambers (40 minutes)
Run. Place chip on BioMark HD System for thermal cycling and fluorescence detection, OR place chip in FC1 cycler for PCR and then into EP1 reader
Analyze. Software automatically counts and reports the number of positives for each reporter, provides color coded heat maps
Results
Fluidigm
Focused much more on single cell gene expression and high throughput/low volume screening
Fluidigm
Trying to adapt, instead of develop technology for digital PCR Fewer partitions per sample negatively impacts precision
For more precision, need to run panel replicates
Panels of 765 wells
Bio-Rad Versus Fluidigm
Bio-Rad FluidigmCost per sample $3.00 $30.00
Number of Partitions 20,000 765
Cost per data point (cents) 0.0001 4
Partition volume 1 nL 6 nL
Sample volume 20 μL 10 μL per well
# of chips req for 20,000 partitions
1 2 (for 12.765 chip)
Sample Volume req 20 μL 240 uL
Cost $2.38 $720
Dead Volume 30% 50%
Price $89,000 $240,000
ddPCR Versus Fluidigm
Sample partitioning into 20,000 droplets enables independent, PCR micro-reactions, resulting in unmatched precision, accuracy and sensitivity for quantification
ddPCR +/- 10% precision allows the ability to distinguish very small fold differences and detect low copy number targets
Low sample volume translates into reduced reagent and sample costs
Significantly lower cost per sample $3 vs $30 Flexible format is not determined by a microfluidic chip
layout, multiple independent experiments can be run with ddPCR
ddPCR Versus Fluidigm
Yes, you can perform real-time PCR and dPCR with one system, but it costs $240,000 for the BioMark HD1 and the need to have data from both approaches is redundant
IFC format was developed for high throughput, low volume real-time PCR and genotyping, not digital PCR
IFC format forces a compromise between precision and sample throughput
Changing throughput on Fluidigm system requires chip and hardware modifications
We have the ability to optimize reactions using a gradient
Raindance
Small, venture-backed company
Raindance Also Uses Droplets
Raindance System
System combines pre-made primer droplets with sample droplets, creating many million drops of partitioned sample, each drop has one of 20,000 different primers
PCR is carried out in standard TC 20,000 independent amplifications from a single sample
Raindance
Researchers are not currently using Raindance technology to quantify target DNA based on a digital readout
Raindance
RDT 1000 is a high-priced (~$225K) droplet generator for next generation sequencing sample preparation. The RDT 1000 does not analyze gene targets in droplets like the Bio-Rad system
New system (Thunderstorm) enables 8 primer libraries by 96 samples
Lowered chip price from ~$600 down to ~$150 This is a per sample price New pre-made libraries
Pre-Made Primer Libraries
Targeting Next Gen Sequencing Sample Prep
Raindance Is Working on Digital PCR
Bio-Rad Versus Raindance
The ability to produce 100K to 1M droplets does not give Raindance an advantage for ddPCR Generating and reading more droplets can improve statistical
analysis for rare mutant detection, but for CNV, allelic discrimination and gene expression there is limited benefit to analyzing that many droplets
We expect the Raindance system to be very expensive if they “fit” digital PCR into their current format and system