mammaprint development of a diagnostic test · rna analysis for diagnostics @agendia mammaprint: a...
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A G E N D I A . C O M
S y m p o s i u m v o o r p a t h o l o g i e - O L V A a l s t
2 7 M a y 2 0 1 9
Lorenza Mittempergher, PhD
Director Research Agendia
MammaPrint –Development of a diagnostic test
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May 27, 2019 2
Presentation outline
▪ Introduction on the MammaPrint test
▪ Development of a diagnostic test
▪ Translation of MammaPrint from a microarray- to a NGS-based test
▪ Conclusions
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May 27, 2019 3
Presentation outline
▪ Introduction on the MammaPrint test
▪ Development of a diagnostic test
▪ Translation of MammaPrint from a microarray- to a NGS-based test
▪ Conclusions
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Breast cancer
Good outcome(no metastases)
Poor outcome(metastases)
Similar clinical characteristics
Different disease outcome!
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RNA analysis for diagnostics @Agendia
MammaPrint: a diagnostic test that analysesthe RNA expression of 70 genes in breasttumors to predict if a patient has a High Risk(poor outcome) or a Low Risk (goodoutcome) for breast cancer recurrence
BluePrint: A diagnostic test that analysesthe RNA expression of 80 genes in breasttumors to identify functional molecularsubtypes for breast cancer (Luminal-type,HER2-type, Basal-type)
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MammaPrint and BluePrint support physicians and patients in cancer diagnosis and treatment plan
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Cardoso et al, NEJM 2016; Whitworth et al, AnnSurgOncol 2017; Groenendijk et al, NPJ Br Cancer, 2019
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MammaPrint from discovery to diagnostic test
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Work published in:Van ‘t Veer et al, Nature 2002Van den Vijver et al , NEJM 2002Glas et al, BMC Genomics 2006Cardoso et al, NEJM 2016
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MammaPrint developed using unbiased gene selection based on patient outcomes
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70 best predicting genes to calculate the risk for distant recurrence
The Amsterdam 70-gene signature
Van ‘t Veer et al, Nature 2002
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MammaPrint gives a binary test result: Low Risk or High Risk for distant recurrence
Genes
LOW
RIS
KH
IGH
RIS
K
Pati
ents
+1.000
-1.000
0.000
MammaPrint Index
LOW RISK~10% chance that the cancer will
recur within 10 years without additional adjuvant
chemotherapy
HIGH RISK~29% chance that the cancer will
recur within 10 years without additional adjuvant
chemotherapy
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Presentation outline
▪ Introduction on the MammaPrint test
▪ Development of a diagnostic test
▪ Translation of MammaPrint from a microarray- to a NGS-based test
▪ Conclusions
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DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Key elements in diagnostic test development
Reimbursement
AwarenessAcceptanceAdoption
Regulatory
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DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Discovery- MammaPrint test
The Amsterdam 70-gene signature
Van ‘t Veer et al, Nature 2002
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Translation- MammaPrint test
DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Software:• Algorithm• QC model
Low-complexity (70 genes plus controls)breast cancer “8 pack” (Agilent Technologies) prognosis array
Glas, BMC Genomics 2006
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DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Analytical validity- MammaPrint test
Challenge: if reproducibility is too low -> test fails, back to discovery
Performance
characteristicsoverall fresh FFPE
Precision* 98.2 % 99.0 % 97.3 %
Repeatability** 98.3 % 99.0 % 97.6 %
Reproducibility*** 97.3 % 97.9 % 96.6 %
*closeness of agreement between results of successive measurements of the same sample-> different operator/batches
**closeness of agreement between results of successive measurements of the same sample -> same operator/batches
***closeness of agreement between results of measurements of the same sample (control sample) under changes conditions
accurate but a low precision
very precise, but a low accuracy
Beumer et al, BCRT 2016
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DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Analytical validity- MammaPrint test
Beumer et al, BCRT 2016
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Dx Test
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Clinical utility - MammaPrint test
Beumer et al, BCRT 2016
Overall clinical concordance: 99.0%
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Dx Test
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Clinical utility - MammaPrint test
No statistical difference between Chemotherapy (CT) vs no chemotherapy (no CT) arms
Excellent survival with no chemotherapy for patients with clinically high risk features butgenomically low risk features (94.4%) --->Safe to forego chemotherapy! Improved quality of life!
Retel, BCRT 2011, Cardoso et al, NEMJ 2016
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Regulatory compliance- MammaPrint test
Laboratory accreditation/certification:- ISO certified – 13485: Medical Device manufacturing- US-CLIA- College of American Pathologist (CAP) certified- US-state licenses- GMP-compliant
Product clearances:- CE mark as IVDD- FDA cleared: 6 clearances obtained since launch of MammaPrint (2006)
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Key features of the MammaPrint test
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Presentation outline
▪ Introduction on the MammaPrint test
▪ Development of a diagnostic test
▪ Translation of MammaPrint from a microarray- to NGS-based test
▪ Conclusions
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Decentralization of the MammaPrint test:from a microarray test to a NGS test
▪ In order to offer an “in-house solution“ to hospitals▪ To have cost savings for health services thanks to local processing of the sample▪ To allow patient access in countries with ethical restriction for the exchange of patient material▪ Making sure that all patients get the same level of accurate diagnosis
MammaPrint BluePrint Breast Cancer Recurrence and Molecular Subtyping kitMammaPrint microarray test
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Same 70 genes (MammaPrint) but measured on different platforms
Intensity as measure ofexpression
Readcount as measure ofexpression
MIC
RO
AR
RA
Y
NG
S
Microarray versus NGS
Why NGS?
✓ Must be easy to use/implement as part of an existing workflow
✓ No or limited investment required for large hospitals (many hospitals have already NGS infrastructure in house)
✓ Good performance with FFPE tissue
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TissueAmplification and labeling
RNA isolationMicroarray hybridization
Datapreprocessing
Algorithm TissueLibrary and capture PrepRNA isolation MiSeq(Dx) Data
preprocessing
Algorithm
All steps performed @Agendia’s central lab Agendia cloud-ADAPTSteps performed @ local lab
Centralized workflow- Microarray at Agendia Decentralized workflow- NGS kit at local lab
Decentralization of the MammaPrint test
Patient report Patient report
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DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
Microarray - NGS Agendia concordance: 98%
NGS reproducibility: 98%
Microarray - NGS Agendiaequivalent clinical performance
Development of the MammaPrint NGS test @Agendia
Mittempergher et al, 2019, accepted manuscript in Journal of Molecular Diagnostics
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Beta-testing of the MammaPrint NGS test @Leuven Hospital and @Curie Institute
1. Pathology 2. RNA Isolation 3. Sample Preparation
4. Library Preparation 5. Target Enrichment 6. Sequencing 7. Data Interpretation
Microarray – NGS beta site concordance: 91%
NGS Agendia – NGS beta site concordance: 93%
Agendia cloud
ADAPT
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Onboarding process for new sites that want to use the Agendia NGS kit
This will allow a high and equal standard of MammaPrint (and BluePrint) genomic testing for breast cancer
in a decentralized setting
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Presentation outline
▪ Introduction on the MammaPrint test
▪ Development of a diagnostic test
▪ Translation of MammaPrint from a microarray- to NGS-based test
▪ Conclusions
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Discovery
Diagnostic test
Moving from discovery to diagnostic application
requires a rigorous path
DxTest
1. Discovery
2. Translation
3. Analytical validity
4. Clinical validity
5. Clinical Utility
6. Cost effectiveness
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T H A N K Y O U