mammaprint development of a diagnostic test · rna analysis for diagnostics @agendia mammaprint: a...

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

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

May 27, 2019 3





▪ Conclusions

May 27, 2019 4

Breast cancer

Good outcome(no metastases)

Poor outcome(metastases)

Similar clinical characteristics

Different disease outcome!

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)

MammaPrint and BluePrint support physicians and patients in cancer diagnosis and treatment plan

May 27, 2019 6

Cardoso et al, NEJM 2016; Whitworth et al, AnnSurgOncol 2017; Groenendijk et al, NPJ Br Cancer, 2019

MammaPrint from discovery to diagnostic test

May 27, 2019 7

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

MammaPrint developed using unbiased gene selection based on patient outcomes

May 27, 2019 8

70 best predicting genes to calculate the risk for distant recurrence

The Amsterdam 70-gene signature

Van ‘t Veer et al, Nature 2002

May 27, 2019 9

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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▪ Conclusions

May 27, 2019 12

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

May 27, 2019 13

DxTest

1. Discovery

2. Translation



5. Clinical Utility


Discovery- MammaPrint test

The Amsterdam 70-gene signature

Van ‘t Veer et al, Nature 2002

May 27, 2019 14

Translation- MammaPrint test

DxTest

1. Discovery

2. Translation



5. Clinical Utility


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



5. Clinical Utility


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

May 27, 2019 16

DxTest

1. Discovery

2. Translation



5. Clinical Utility


Analytical validity- MammaPrint test


17

Dx Test

1. Discovery

2. Translation



5. Clinical Utility


Clinical utility - MammaPrint test


Overall clinical concordance: 99.0%

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Dx Test

1. Discovery

2. Translation



5. Clinical Utility


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

May 27, 2019 19

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

May 27, 2019 21




▪ Translation of MammaPrint from a microarray- to NGS-based test

▪ Conclusions

May 27, 2019 22

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

May 27, 2019 23

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

May 27, 2019 24

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

25

DxTest

1. Discovery

2. Translation



5. Clinical Utility


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

May 27, 2019 26

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

May 27, 2019 27

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

May 27, 2019 28




▪ Translation of MammaPrint from a microarray- to NGS-based test

▪ Conclusions

May 27, 2019 29

Discovery

Diagnostic test

Moving from discovery to diagnostic application

requires a rigorous path

DxTest

1. Discovery

2. Translation



5. Clinical Utility


T H A N K Y O U

mammaprint development of a diagnostic test · rna analysis for diagnostics @agendia mammaprint: a...

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