Controlling Chaos in Oncology Testing

Transcription

1 HORIZON DISCOVERY Controlling Chaos in Oncology Testing 16 th March 2016 Brian Burke PhD

2 Disclaimer This Presentation does not constitute or form any part of an offer to sell, or invitation to purchase or apply for or enter into any contract or make any other commitment whatsoever in relation to, securities. Although reasonable care has been taken to ensure that the facts stated in this Presentation are accurate and that the opinions expressed are fair and reasonable, the contents of this Presentation have not been formally verified by Horizon Discovery plc (the Company ) or any other person. Accordingly, no representation or warranty, expressed or implied, is made as to the fairness, accuracy, completeness or correctness of the information and opinions contained in this Presentation and no reliance should be placed on such information or opinions. Further, the information in this Presentation is not complete and is subject to updating, revision, further verification and amendment. Neither the Company, nor any of its subsidiaries, nor any of its respective members, directors, officers or employees nor any other person accepts any liability whatsoever for any loss howsoever arising from any use of such information or opinions or otherwise arising in connection with this Presentation. Accordingly, information contained in the Presentation is being supplied to you solely for your information and may not be copied, reproduced or further distributed to any person or published in whole or in part, for any purpose. In particular, the distribution of this Presentation in certain jurisdictions may be restricted by law, and persons into whose possession this Presentation comes should inform themselves about, and observe, any such restrictions. Any failure to comply with these restrictions may constitute a violation of laws of any such jurisdiction. This Presentation includes certain forward-looking statements, estimates and projections with respect to the anticipated future performance of Horizon Discovery plc, its products and the markets in which it operates. Forward-looking statements involve risks and uncertainties. Actual events could differ materially from those projected herein and such statements, estimates and projections reflect the various assumptions made by the Company which assumptions may or may not prove to be correct. These forward-looking statements speak only as at the date of this Presentation. The Company expressly disclaims any obligation or undertaking to disseminate any updates or revisions to any forward-looking statements contained in the Presentation to reflect any change in the Company s expectations with regard thereto or any change in events, conditions or circumstances on which any such statements are based. No part of this Presentation, or the fact of its distribution, should form the basis of or be relied upon in connection with any contract or commitment or investment decision whatsoever. This Presentation does not constitute a recommendation regarding the securities of the Company. By participating in and/or accepting delivery of this Presentation you agree to be bound by the foregoing restrictions and the other terms of this disclaimer. 2

3 About Horizon Discovery Cell Line Builders Reference Standards 3

4 Value for money? Sensitivity? Data Analysis? Patient Safety THE PATIENT? Reimbursement Guidance and Proficiency Cost of Drug Development FDA CLIA CAP Pharma 4

5 Precision Medicine Development Pipeline Research & Development Assay Development Sample Screening Patient Stratification Clinical Studies Phase II & III CLIA Studies Patient Stratification On Market Companion Diagnostics Proficiency Testing/Ring Trials Acquisition of limited clinical samples Clinical Samples are heterogeneous and not quantitative Clinical Trial time lines and use of multiple partners/geographies can lead to drift in assay performance Outsourcing can make managing variation more difficult Unnecessary and sustained variability can affect Study performance New drugs rely on successful and effective adoption of diagnostics to ensure reimbursement Proficiency Testing benefits from samples that are quantitative and that permit preanalytical and analytical evaluation of diagnostic workflows CONFIDENTIAL 5 Research Use Only

6 Why are we here? Key Observations Assays are currently developed in silos There is no quick way to benchmark assays or platforms What makes a good assay in a development lab does not always translate In spite of the importance of diagnostics to Precision Medicine, they still remain an add on in many cases 6

7 WHY DO WE NEED REFERENCE STANDARDS?

8 Would you fly in a plane with an altimeter accurate to 10%? Heathrow 25m +/- 2.5m A Bumpy Landing Guangxi 690m +/- 69m Crash Landing 8848 m Tenzing 2860m +/- 286m Never Even Close!! 8

9 Percentage of Incorrect Results External Quality Assessment 40 EGFR Genotyping Errors External Quality Assessment EGFR Sample Tested Only 70% of laboratories passed the proficiency test. False -negatives and false-positives were the main sources of error. European Molecular Quality Network (EMQN) 9

10 Molecular Diagnostic Assay Biomarker Negative Biomarker False Negative No treatment No side-effects No treatment Shortened patients life Treatment with no benefit Patient suffers side-effects Biomarker False Positive Treatment Extended patients life Biomarker Positive As we push the limits of technology, the risk of false results will increase 10

11 Sources of Variability Tumour sample As lower allelic frequencies increase in clinical relevance, workflows become more fallible Reference Materials Action Analysis DNA extraction Variant Calling/ Confidence Scoring DNA Quantification Library Preparation Sequencing Alignment/Mapping 11

12 HOW DO WE BUILD REFERENCE STANDARDS?

13 Not All Controls are Created Equal! Horizon uses highly characterised cell lines to build reference standards This gives us highly defined building blocks to create reference standards which reflect the biology of the patient. Better still, these reference standards are consistent and evergreen! Horizon has developed manufacturing processes that allow for consistent, long term production of reference standards NORMAL CELL NORMAL CELLS MUTANT CELLS SINGLE MUTATION Products Services Drugs MUTATED CELL PATIENT IN A TEST TUBE 13

14 Formats available PRE-ANALYTIC ANALYTIC cfdna Representative genomic DNA fragmented to bp Validated allelic frequencies to 0.01% Genomic DNA Precise allelic frequencies from % Extensively validated 50ng/μl FFPE Precise allelic frequencies from % Validated quantities of DNA in FFPE FFPE IHC Validated by Quantitative Digital Pathology (QDP) Quantified levels of protein expression (low to high) Formalin Compromised DNA Three tiers of formalin treatment: low, medium and high Validated by Tapescreen assay Multiplex DNA for NGS Multiple mutations in a single sample Extensively validated 50ng/μl FFPE FISH Hard-to-source biomarkers available Renewable source of positive and negative cells FFPE RNA Hard-to-source biomarkers available Consistent and reproducible 14

15 Covering all Diagnostic Modalities NGS Oncology Panels Q-Seq Coverage of TruSeq, AmpliSeq, and more Real Time PCR EGFR, KRAS, BRAF Exomes Genome in a Bottle Immuno-Oncology PD-L1 Liquid Biopsies Cell free DNA Reference Standards RNAseq NEW NSCLC Fusion Control. 15

16 NEXT GENERATION SEQUENCING

17 NGS: Massive Opportunity vs Massive Variability Accuracy ranked highest in importance for users of next-generation sequencing systems. NOTE: Based on a survey of 108 end users. SOURCE: Frost & Sullivan 17

18 One Sample Three Platforms - 80% Agreement # SNPs (% of SNPs detected) Platform #1 Platform #2 Platform #3 SOURCE: GIAB Slides

19 One Data Set Five Bioinformatic Workflows - 60% Agreement O Rawe et al. Genome Medicine 2013, 5:28 SOURCE: GIAB Slides

20 Horizon NGS Philosophy Deployment NGS technology is one of the key advances in the diagnostic space, promising greater breadth of data with more tangible pricing points HDx led the adoption of a more direct approach to assessing the performance of NGS platforms in the oncology space HDx enables key variables such as allele frequency, effects of formalin or genotype specific effects to be investigated directly Horizon is now extending this to structural variants and increasing customization around formalin 20

21 Multi-Gene Multiplex Case Study for IonTorrent / Ampliseq gdna Source: Horizon Discovery Partner A Partner B Partner C Partner D Horizon Discovery Partner D FFPE Platform: QX100 Droplet Digital PCR System AmpliSeq Cancer Panel Ampliseq Cancer Hotspot Panel v2 Ampliseq Cancer Hotspot Panel v2 (Average of 8 runs) Ampliseq Panel QX100 Droplet Digital PCR System Ampliseq Sequencing Depth N/A x Average 5000x 2000X N/A Gene Mutation Expected Observed mutant ratio Observed mutant ratio BRAF V600E KIT D816V EGFR ΔE746 - A Not detected Not detected EGFR L858R EGFR T790M Not detected Not detected EGFR G719S KRAS G13D KRAS G12D Not detected NRAS Q61K PIK3CA H1047R PIK3CA E545K Difficulty in detecting the lower allelic frequencies in FFPE sample 21

22 Case Study Data for Tru-Q NGS Reference Standards 5% blend 2.5% blend 1.3% blend Gene Source: Platform: Mutation Horizon Diagnostics Predicted % N/A Horizon Diagnostics Observed % QX100 Droplet Digital PCR System Partner Ion Torrent BRAF V600M EGFR T790M EGFR L858R EGFR L861Q KIT D816V KRAS G12A KRAS G12R NRAS Q61K Horizon Diagnostics Predicted % N/A Horizon Diagnostics Observed % QX100 Droplet Digital PCR System Partner Ion Torrent Horizon Diagnostics Predicted % N/A Horizon Diagnostics Observed % QX100 Droplet Digital PCR System Partner Ion Torrent missing missing missing missing missing missing Specific and Sensitive down to 5% allelic frequency Specific and Sensitive down to 2.5% allelic frequency Not sensitive to detect down to 1% for all variants 22

23 Clinical Validation Using Horizon s NGS Process Standard Case Study: CLIA Validation of AltheaDx Oncology Panel 150 (AOP 150) using HDx Reference Standards Concordance with dpcr, average six IonTorrent PGM NGS runs 23

24 Routine Assay Monitoring Results from a commercially-available NGS-based Oncology Panel evaluated using Horizon s Quantitative Multiplex Reference Standard (QMRS) in FFPE format; collected over a period of 8 months. 24

25 MOVING AWAY FROM THE INVASIVE

26 ctdna Low Copy Number Reference Standard Five Mutant Multiplex in six formats developed containing all the following EGFR mutations: T790M L861Q G719S L858R ΔE746- A750 Six multiplex reference standards defined by copy number: Mutant copies in 5,000 total EGFR copies (0.5% Mutant Allele Burden) Mutant copies in 50,000 total EGFR copies (0.05% Mutant Allele Burden) Mutant copies in 5,000 total EGFR copies (1.0% Mutant Allele Burden) Mutant copies in 50,000 total EGFR copies (0.1% Mutant Allele Burden) Mutant copies in 5,000 total EGFR copies (2.0% Mutant Allele Burden) Mutant copies in 50,000 total EGFR copies (0.2% Mutant Allele Burden) 26

27 ctdna Assay Verification Down to 0.05% Allelic Frequency 25 Mutant copies in 50,000 total EGFR copies EGFR Multiplex #1 #2 Wild Type Effective mutant allele frequency 0.5% 0.05% 0% Expected Observed Expected Observed Expected Observed ΔE746-A Mutant Copies per 5000 Total Copies G719S L858R L861Q T790M Concentration (Total Copies EGFR per µl) Manufacturing performance is excellent in spite of limitations of some probe sets 27

28 Fragmented K-Ras and N-Ras Reference Standards Gene Mutation Allelic Frequency K-Ras G12C 50% 5% 1% 0.1% N-Ras Q61K 50% 5% 1% 0.1% K-Ras G12C N-Ras Q61K WT 50% 5% 1% 0.1% 50% 5% 1% 0.1% 28

29 Assay development and validation Fragmented Multiplex Reference Standards Multiplex 1 Multiplex 2 Gene Mutation Allelic Frequency EGFR L861Q 7.1% K-Ras G12C 10% N-Ras A146T 10% PI3K3CA E545K 10%% Gene Mutation Allelic Frequency EGFR % EGFR T790M 7.7% N-Ras G12D 10% N-Ras Q61K 10% N-Ras K117N 10% 29 29

30 Fragmented K-Ras and N-Ras Reference Standards Gene Mutation Allelic Frequency K-Ras G12C 50% 5% 1% 0.1% N-Ras Q61K 50% 5% 1% 0.1% 30

31 What do the cfdna Standards look like? Expected Allelic Frequency (AF%) Gene Variant 5% Multiplex I 1% Multiplex I 0.1% Multiplex I 100% WT Multiplex I EGFR L858R EGFR ΔE746 - A EGFR T790M EGFR V769 - D770insASV KRAS G12D NRAS Q61K NRAS A59T PIK3CA E545K

32 cfdna Reference Standards 5% - 0.1% 1% Multiplex I cfdna Reference Standard assessed using Droplet Digital PCR (blue), Ion Torrent (orange) and MiSeq (grey). All assays utilized amplicon-based enrichment. Figure 1: Example trace showing the fragment sizes collected by D1000 DNA ScreenTape assay, comparing cfdna HDx Reference Standards (Red and Green traces) to cfdna extracted from human plasma (Blue trace). cfdna from human plasma was provided by CareDx,Inc. Leftmost peaks-internal marker for the assay. Rightmost peaksfragmented materials. 32

33 HDx Reference Standards Every Assay, Every Run, Every Confidence MDx/NGS Labs Support workflow analysis and setup Provision of positive reference standard for everyday run control ISH Labs FISH and IHC applications External reference standard to ensure workflow integrity Universal across time, across platforms, across operators and across geographies 33

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