Sample to Insight
The GeneReader:
A Complete NGS System for Your Lab, Live in 30 Days
Sylvain Cogne / Massimo Cerfeda Market Development Manager NGS, EMEA May 2017
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2016 Analyst & Investor Day
Sample to Insight
2016 Analyst & Investor Day 2
Customers want meaningful molecular insights
Moving from tools and components to solutions that provide valuable insights
BIOLOGICAL SAMPLE
VALUABLE MOLECULAR
INSIGHTS
Sample Technologies Assay Technologies
Bioinformatics Automation systems
SAMPLE TO INSIGHT SOLUTIONS
Faster Better More efficiently
Situation
Sample to Insight
Sample Sample Insight
QC
Library QC
Variant Confirmation
The GeneReader NGS Sample to Insight solution
The GeneReader™ NGS System is the first complete Sample to Insight® NGS solution designed for any lab to deliver actionable insights
Confidential
Sample to Insight
Confidential
Workflow overview – Template Sequencing
Sequencing by synthesis technology
Automated on GeneReader
1-3 Flowcells in parallel
16 samples per flowcell
16 million reads per flowcell
100-150 bp maximum read length
85% of bases > Q25
Continuous loading mode
Generate FASTQ files
Auto transfer to QCI-A
Sequencing
DNA Extraction
Target Enrichment
Clonal Amplification Library
Preparation
Analysis / Interpretation
GR 1.1 specifications
Sample to Insight
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• LIMS connectivity, iPad-based manual
• True ‘actionability’
The GeneReader NGS System is intended for Research Use Only. Not for use in diagnostic procedures
• Robust and consistent performance
• Bioinformatics & Reporting
Sample to Insight
The ultimate objective of NGS in molecular pathology
6 GeneReader NGS System PROM-10229-001
A full Sample Report in your hands
• Simple
• Actionable
• Yet comprehensive
Sample to Insight
Not a Sequencer---but a System
GeneReader NGS System PROM-9303-002 7
Nucleic Acid Extraction
Target Enrichment
Library Preparation
Next- Generation Sequencing
Data
Analysis Interpretation
QIAxcel QIAxcel
RGQ QC
GeneRead Assistant (iPad and App included) Support
Data Management
GeneRead Link and LIMS
QIAcube RGQ QIAcube GeneRead
QIAcube
GeneReader QCI-Analyze QCI-Interpret Automation
Sample to Insight
QIAGEN | qiagenbioinformatics.com | bioinformaticssupport@qiagen.com | qiagen.com | 2016 8
Designed, built and validated in collaboration with clinical labs
Customizable Reporting
ability to capture /persist internal annotations, integration into LIMS and EMR systems
Comprehensive Curation of Clinical Evidence
reported cases, drug labels, professional guidelines
Decision Support Software
classify variants, identify treatment options, and geographical clinical-trial matching
Treatment and Trial Identification
based upon levels of evidence, expected drug response, prognosis and lab defined rules
QCII – Intuitive and transparent variant interpretation
Sample to Insight
The QIAGEN Knowledge Base
Title, Location, Date 9
18+ years experience in content acquisition and ontology
Knowledge Base Findings
>13,000,000
>30,000
Publications
>340,000
Samples Analyzed
>20,000
Disease Classes
>30
Integrated Databases
>200
MDs, PhDs Automated &
Manual Curation
Sample to Insight
GeneRead Link
GeneReader NGS System PROM-9303-002 10
Workflow management solution for the GeneReader NGS System
Automated transfer of data from LIMS and of results back to LIMS
Electronic lab notebook for complete traceability
Full sample and workflow tracking
Result and QC score mgmt. with recommendation for actions
Minimal manual interaction for data handling
Sample to Insight
GeneRead Link
GeneReader NGS System PROM-9303-002 11
The entire workflow on one screen
Integrated Actionable Flexible Affordable Reliable
A B L H C
Workflow phases overview always visible
Work to do Samples waiting in this phase
Work in Progress Guided execution for sample batch
Results to Approve Based on
execution results and QC
Sample to Insight
QIAact panel portfolio: maximum actionability within 30 days
Title, Location, Date 12
Actionable Insights Tumor Panel
Lung DNA &
compr. Fusions Panel
Myeloid Leukemia Panel BRCA 1/2 Panel
Custom Panel
Based on QIAGEN knowledge base, enabling maximum actionability Verified from sample to insight, enabling any lab to go live within 30 days
Integrated Actionable Flexible Affordable Reliable
A B L H C
Sample to Insight
Every GR assay undergoes rigid sample to insight verification
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Systematic Sample-to-Insight verification by multiple experiments, Instruments, users and sites and reviewed on Subsystem and undergo System approval, before going to release
Sample to Insight
QIAact BRCA precision study
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Very good reproducibility between batches, operators and systems
Sample to Insight
Robust data of the workflow (HotSpot Panel)
PROM-10667-001 USCAP March 2017 For Research Use Only; Now available in the US with NEW chemistry 15
Achieved consistently high performance regardless of variables* in:
• Sample batch
• Operator and experience level
• Instrument and site
• Plexing (1-10 samples per flow cell)
* 3 batches of Horizon material, 3 sites/instruments, 3 operators
Sample to Insight
Chr Gene Variant
Expected Allelic Frequency (ddPCR Range)*
GeneReader (Actioanable Insights Tumor Panel) Observed
frequency*
(Standard Deviation)
Average Coverage
3rdParty Verification
(ddPCR)**
7p12 EGFR L858R 1.00%
(0.6-1.4%)
1.29%
(0.29%) 6,195 0.98
7p12 EGFR ΔE746 - A750 1.00%
(0.6-1.4%)
1.28%
(0.12%) 10,340 1.09
7p12 EGFR T790M 1.00%
(0.6-1.4%)
0.97%
(0.04%) 1,226 1.00
7p12 EGFR V769 -
D770insASV
1.00%
(0.6-1.4%)
0.86%
(0.01%) 4,351 0.89
12p12.1 KRAS G12D 1.30%
(0.78-1.82%)
1.32%
(0.39%) 10,527 1.22
1p13.2 NRAS Q61K 1.30%
(0.78-1.82%)
1.64%
(0.12%) 11,757 1,25
1p13.2 NRAS A59T 1.30%
(0.78-1.82%)
1.34%
(0.08%) 10,552 1.20
3q26.3 PIK3CA E545K 1.30%
(0.78-1.82%)
1.58%
(0.05%) 36,384 1.41
Liquid Biopsy Data with Equally Rigorous Testing
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cfDNA samples at ~1%
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*: 6-plex
Accurately, consistently and robustly detecting cfDNA at 1% sensitivity per design specification
PROM-10622-001 Precision Medicine Webinar For Research Use Only; Now available in the US with NEW chemistry
Sample to Insight
Our data quality exceeds latest Palmetto standards
PROM-10622-001 Precision Medicine Webinar For Research Use Only; Now available in the US with NEW 17
Sample to Insight
QIAact panel portfolio: maximum actionability within 30 days
Title, Location, Date 18
Actionable Insights Tumor Panel
Lung DNA &
compr. Fusions Panel
Myeloid Leukemia Panel BRCA 1/2 Panel
Custom Panel
Based on QIAGEN knowledge base, enabling maximum actionability Verified from sample to insight, enabling any lab to go live within 30 days
Integrated Actionable Flexible Affordable Reliable
A B L H C
Sample to Insight
Most actionable panel for first-line testing
GeneReader NGS System PROM-9303-002 19
• KRAS
• NRAS
• KIT
• BRAF
• PDGFRA
• ALK
• EGFR
• ERBB2
• PIK3CA
• ERBB3
• ESR1
• RAF1
Targeting solid tumors with:
• Highest prevalence
• Greatest need for testing
• Variants associated with actionable insights 12 genes
QIAGEN
Knowledge Base
Lung Breast
Ovarian Colorectal
Melanoma
Sample to Insight
QIAact Lung Panel on GeneReader NGS System
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Number of Variants
Genes QIAact Lung DNA Panel VOIs QIAact AIT V2 VOIs
NRAS 20 41
NTRK1 3 0
DDR2 2 0
ALK 30 39
RAF1 0 2
PIK3CA 14 167
PDGFRA 1 47
KIT 17 257
RICTOR (CNV) 0
ROS1 3 0
ESR1 6 11
EGFR 325 (+CNV) 466
MET 20 (+CNV) 0
BRAF 22 157
FGFR1 (CNV) 0
PTEN 1 0
KRAS 66 152
ERBB3 0 10
AKT1 1 0
MAP2K1 14 0
ERBB2 4 (+CNV) 62
Total Variants 549 1411
QIAact Lung panel covers more Lung relevant variants
Sample to Insight
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Thank you Questions?
GeneReader NGS System PROM-9303-002
Sample to Insight
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Additionals
GeneReader NGS System PROM-9303-002
Sample to Insight
DNA Extraction
Confidential
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Workflow overview – target enrichment
Gene Panels – focus on the genomic region of interest
Target Enrichment
Clonal
Amplification Sequencing Library
Preparation
Analysis / Interpretation
GR 1.0 specifications as shared in May 2016
QIAact V2.0 Assay technology
Sample to Insight
Actionable Insights Tumor Panel RAS sample study
GeneReader NGS System PROM-9303-002 24
Outstanding coverage achieved even with challenging FFPE samples
Parameter Detail
Instrument 3 GeneReader NGS Systems
Reagents GeneReader Reagents
Bioinformatics solution QCI-Analyze, QCI-Interpret
Sample number and type 43 FFPE Colorectal Cancer (CRC) samples
Sample age 3 to 20 years
Sample quality Highly fragmented DNA
Variant insight coverage 98.6% of bases covered at >500x 99.8% of bases covered at >200x
Integrated Actionable Flexible Affordable Reliable
A B L H C
Sample to Insight
Parameter Detail
Instrument 5 GeneReader NGS Systems
Reagents GeneReader Reagents
Bioinformatics solution QCI-Analyze, QCI-Interpret
Sample number and type 39 FFPE Colorectal Cancer (CRC) samples
Sample age 3 to 20 years
Sample quality Highly fragmented DNA
Amplicon coverage 94.45% of bases covered at >500x 97.27% of bases covered at >200x Variant insight coverage 99.36% of bases covered at >500x 99.89% of bases covered at >200x
QIAact V2.0 - RAS Sample Study
Note: Positive samples included into the study have all been confirmed with Sanger sequencing and passed Quantimize <0.04. ) For the repeat study performed with updated sequencing chemistry, four wildtype samples were not available anymore reducing the sample number to 39 compared to results shown earlier.
Outstanding coverage achieved even with challenging FFPE samples
Sample to Insight
QIAact V2.0 - RAS concordance study with therascreen
Confidential
RAS agreement study
>5% Ras variant Allele Frequency Cutoff
therascreen PCR and Pyro Assays (1)
+ (MT) –(WT) Total
GeneReader NGS System (2)
+ (MT) 14 0 14
– (WT) 0 25 25
Total 14 25 39
Note: (1) If KRAS status regarded as mutant (MT) as identified by either therascreen KRAS PCR Assay or by therascreen RAS Extension Pyro Assay.
(2) Variants from codons 12, 13, 59, 61, 117, 146 contained in established QIAGEN therascreen assays are called.
100 % Agreement between GeneReader NGS System and QIAGEN therascreen PCR
& Pyro Assays
Sample to Insight
QIAact BRCA 1/2 Panel: not just for Inherited Breast Cancer
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Cancer Types Mutation Types
NCCN/SGO Guidelines on Testing
Clinical Actionability
• Breast
• Ovarian
• Germline
• Somatic
• All patients with Ovarian
• Patients with high-risk Breast Cancer
• PARP inhibitor
• Active trials for somatic
mutations
Need to detect mutations in blood & FFPE and in multiple cancer types
Sample to Insight
QIAact BRCA Performance on GeneReader NGS System
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QIAact BRCA 1/2
On GeneReader NGS System
VAF cut off >=5% (in FFPE)
ROI full exons + 20bp flanking
True Positives 274
False Positives 0
False Negatives 0
PPV 100 %
Sensitivity 100 %
Accuracy 100%
Coverage of ROI 98.84% @ 5% LAF
99.84% @ 10% LAF
showing 100% PPV and PPA @ VAF of 5%
Sample to Insight
QCI Provides Clear Insights Into Variant Pathogenicity
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Variant list screen shows overview of validated variants
Colour coded classification of variants
Complete transparency of classification evidence
Actionable variants highlighted
QIAGEN-AZ confidential
Sample to Insight
QCI Provides Clear Insights Into Variant Pathogenicity
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See approved drugs from EMA, FDA, ESMO, ASCO and NCCN (configurable)
See clinical trials specific to geographical location
QIAGEN-AZ confidential
Sample to Insight
QIAact Lung All-in-One Assay – need for test consolidation
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Complex genetic changes.
Examples:
Point mutation: EGFR T790M Large deletion: MET: exon 14 CNV: ALK
Fusion: RET, ROS1
Tests typically deployed:
• PCR
• IHC
• FISH
• Array
Need for one single assay that includes all the results
Sample to Insight
QIAact Lung DNA Panel Specifications
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KPI Specification
Actionable mutations 100% (~ 550)
SNV Detection Yes
Small Indel Detection (<6 bp) Yes Large Indel Detection (<18 bp) Yes
CNV Yes
VAF Threshold 5% (FFPE), <1% (LB)
Specificity >90%
Variant Coverage >1000x 99%; >100x 99% UMIs
Fusion Yes (via RNA Seq)
Sample to Insight
QIAact Lung RNA Panel for the GeneReader NGS System
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Fusions of Interests
QIAact Lung RNA Panel
Total number of genes 72
Total number of 5‘ partners 60
Total number of 3‘ partners 14
Total number of fusions 77
Frequency cut off 20% tumor cells in wild type background
QIAact Lung DNA Panel + QIAact Lung RNA Panel
= QIAact Lung All-in-One Assay