Clinical Utility of Droplet ddpcr, moving to diagnostics. Koen De Gelas, PhD, CRIG ddpcr mini symposium, 15/05/2018
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2 Clinical Utility of Droplet ddpcr, moving to diagnostics 2 Koen De Gelas, PhD, CRIG ddpcr mini symposium, 15/05/2018
3 Disclaimer Disclaimer: all consumables, instruments, applications and software covered in this presentation are intended for research use only, unless explicitely stated differently. 3
4 Bio-Rad, a true global company Headquarters Principal Manufacturing & Research Additional Key Locations 4
5 Our Businesses Bio-Rad is a $2B IVD company Life Sciences Droplet Digital PCR & Amplification Protein Electrophoresis Lab-Scale Chromatography Process Scale Separation Flow Cytometry Imaging and Analysis Clinical Diagnostics Diabetes Monitoring Quality Controls Autoimmune Testing Immunohematology HIV Testing 5
6 Droplet digital PCR
7 Droplet digital PCR 7
8 Landscape of Digital PCR Applications Single Cell Analysis Liquid Biopsy Oncology Agriculture/ Food ddpcr Gene Expression 8 Reference Standards Environmental Monitoring Infectious Disease
9 The road to diagnostics: advantages of ddpcr Superior precision, sensitivity, ease of use Different input matrices, including liquid biopsies Fast turn around time and throughput: up to 4x 96 samples / day Absolute measurement Highly reproducible, robust High potential to move into clinical diagnostics 9
10 ddpcr reproducibility Different days, different operators Day 1 Operator 1 Day 2 Operator 2 Day 3 Operator 3 30ng 3ng 0.3ng 0.03ng 10
11 Fractional Abundance (%) Fractional Abundance (%) ddpcr reproducibility Mutant % Different instruments DR1 DR2 DR3 Different users User 1 User 2 User 3 11
12 12 ddpcr reproducibility
13 The road to diagnostics: Introducing QXDx 13
14 QXDx TM instruments QXDx TM AutoDG QXDx TM Manual DG 14 Open Mode Systems: the system is capable of running both FDA-cleared, CE-IVD and home brew/in house assays
15 QXDx TM ddpcr Universal Kit ddpcr Universal Kit for QX200 AutoDG ddpcr Dx System 15 ddpcr Universal Kit for Qx200 ddpcr Dx System
16 QXDx TM ddpcr Universal Kit Validated kit Verified performance for ddpcr run GMP reagents Consistent reproducible quality Certificate of analysis provided with kit 16
17 17 Measuring major and deep molecular response in CML patients using ddpcr technology
18 BCR-ABL or Philadelphia translocation Chromosomal abnormality Chronic Myeloid Leukemia cells (CML) bcr Uncontrolled cell division bcr Variants: p190 p210(e13a2) p210(e14a2) p
19 CML is treatable but can remain chronic BCR-ABL tyrosine-kinase inhibitors (TKI) 1 st generation: Gleevec (Imatinib) 2 nd generation: Dasatinib, Nilotinib, Radotinib, Bosutinib 19 Blood : ; doi:
20 Current Paradigm testing qpcr Challenges with qpcr Quantitation dependent on laboratory skill level Most labs have a homebrew assay Dependent on standards (dilution series) High variation among labs Each lab is attributed a correction factor At low levels, qpcr is not as accurate as most would like. 20
21 Delivering a Better Way for BCR-ABL with ddpcr Monitoring Made Easy Leveraging Simplicity Driving patient outcomes Absolute Quantification Scalable Ease of Use Proven No Standard Curves Precision Accuracy Reproducibility High Throughput 8-48 Samples per Run Increased Sensitivity through multiwell testing Similar to qpcr Open Mode for Home Brew Assays Close Mode for CE-IVD Cleared Tests Thousands Systems Placed Worldwide Standard for National Measurement Institutes >2600 ddpcr Publications 21 >600 Liquid Biopsy Publications
22 QXDx TM BCR-ABL %IS kit Multiplex Design Absolute Quantitation Accuracy & Precision All Inclusive Reagents Automated Analysis Controls Correction factor for WHO-IS Detects p210 Major transcripts (e13a2, e14a2) Ability to count all BCR-ABL fusion gene present in the sample Absolute confidence in results at low %IS Ratios Calibrators aligned to WHO standards Automated thresholding, Result interpretation Hi, Low %IS controls Relate results to WHO-IS (CF = 0.93, kit dependent) 22
23 BCR-ABL cps Principle of the Test Blood extraction RNA conversion cdna thermal cycling ddpcr ABL cps
24 Test Signatures Goal CE-IVD (2 Wells) Deep Molecular Response CE-IVD (4 Wells) Deep Molecular Response LOQ MR 4.7 (0.002% IS) MR 5.0 (0.001% IS) LOD MR 4.7 (0.002% IS) MR 5.0 (0.001% IS) Scalable, Flexible & Reproducible solutions to enable Clinical research/trials and TKI stoppage studies. 24
25 25 QXDx TM BCR-ABL %IS kit
26 More content for ddpcr (research use only) PrimePCR ddpcr assays Multiplex screening kits Expert design assays Hematology assays Custom design assays RUO 26
27 PrimePCR ddpcr assay look up tool RUO 27
28 28 Bio-rad.com/web/MultiplexKits
29 ddpcr Multiplex Mutation Screening Kits RUO 29 Bio-rad.com/web/MultiplexKits
30 Droplet Digital PCR ddpcr Assays for Hematologic malignancies Assay Name KIT D816V JAK2 V617F FLT3 D835Y FLT3 D835H FLT3 D835V FLT3 D835E IDH1 R132C IDH1 R132H IDH1 R132G IDH1 R132S IDH1 R132L Unique Assay ID dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv dhsamdv RUO 30
31 Droplet Digital PCR ddpcr Assays for Hematologic malignancies Assay Name IDH2 R140Q IDH2 R172K IDH2 R172M IDH2 R172W MPL W515K MPL W515K MPL W515L PML RARA Unique Assay ID dhsamdv dhsamdv dhsamdv dhsamdv dhsamds dhsamds dhsamdv dhsacpe dhsacpe RUO 31
32 32 RUO
33 Assay design tool RUO 33
34 Conclusion Proven Bio-Rad ddpcr technology Sensitive, reproducible, robust Leverage ddpcr characteristics for entering the clinical diagnostic market Building Bio-Rad QXDx TM product line CE-IVD instruments, consumables and BCR-ABL %IS kit 34 Bio-Rad PrimePCR assays Assay content available for own validation / accreditation and lab developed tests
35 35 One
36 One One more thing... 36
37 One QX One TM ddpcr system 37
38 Instrument Architecture User Interaction Waste Oil 2 bottles Touchscreen computer DR Oil DG Oil Probes DG Oil EvaGreen 2 bottles each Read Plates 38 Wireless keyboard & track pad (optional) RFID Scanner New Plates
39 QX One TM ddpcr system System integration / High throughput: automated, walk away, 7 plates, continuous feeding 4 colour multiplexing + gradient run: advanced analysis capabilities, optimize custom assays Seamless integration: compatible with existing chemistries, CFR21 part 11 Ease of use: on board touch screen, live data preview, RFID consumables, IQ/OQ/PQ 39
40 QX One TM ddpcr system 4 channel fluorescence detection FAM, HEX, CY5, CY5.5 Scatter channel Measure droplet size Normalisation per well using instrument calibration curve Increased accuracy & precision 40
41 Concentration Uniformity Concentration Variation < 5% Concentration Variation < 2% 41 1 plate each, 3-lot supermix test, S.aureus
42 New Analysis Tool Tilt Correction Example of a nonorthogonal 2D amplitude plot (IDH2 R140Q mutation detection duplex) Tilt correction option allows for easier threshold setting 42
43 FAM CY5 Data Preview Copy Number 4-Plex HEX CY5.5 CCND1 (FAM), REN (HEX), PLAU (Cy5), SORL1 (Cy5.5) 4 targets in one well is the new standard 43
44 CY5 FAM Data Preview Copy Number 8-Plex 8 targets in one well is possible HEX 44 CY5.5
45 FAM CY5 Data Preview Mutation Screening Multiplex NRAS G12 (G12D gblock) EGFR Ex19del (COSM6223 gblock) HEX Screening assay detects G12A, G12C, G12D, G12R, G12S, G12V CY5.5 Screening assay detects >15 EGFR exon 19 deletions 45 ~ cp/μl wt concentration, merged well data
46 FAM Cy5 R&D Data on a Discriminating KRAS G12/13 Multiplex Kit G12C G12V G12A G12D G12R WT G12S HEX Cy5.5 46
47 One QX One TM ddpcr system We write the future of ddpcr 47
48 48 One
49 Difference between WHO and Golden Setting a CF for ddpcr y = x R² = y = x R² = WHO Actual vs Golden Lot CF = 10 Md = 0.93 WHO Bias Plot Golden Lot WHO Data Log Mean of WHO-IS and our values 49 WHO-IS
50 WHO-IS validation 5 kit lots tested WHO-IS primary materials used as samples 3 calibrator and control lots tested Regression performed with WHO-IS expected values vs ddpcr IS results Metric Minimum Maximum Measured m r intercept Correction Factor (CF) =
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