Oncomine Focus assay panel and Oncomine Knowledgebase ... · Oncomine Focus Assay 52 unique genes...
Transcript of Oncomine Focus assay panel and Oncomine Knowledgebase ... · Oncomine Focus Assay 52 unique genes...
Oncomine Focus assay panel and Oncomine Knowledgebase Reporter.
How it can help to identify relevant alteration
and early phase trials.
Dr Isabelle SOUBEYRAN Dr Emmanuel KHALIFA
Molecular Pathology Unit – Institut Bergonié – France
ESMO 2017- THERMO FISHER SCIENTIFIC SYMPOSIUM
• NGS panel for testing mutations, copy number variations and RNA alterations
• OKR to process NGS data and link it to trials • Our experience
MAIN TYPES OF MOLECULAR ALTERATION TO BE SCREENED
SINGLE NUCLEOTIDE VARIANT
COPY NUMBER VARIANT (CNV)
FUSION GENES
ALK
EML4
MICROLESIONS MACROLESIONS
FISH
Sanger
qPCR
CGH
Microtome
Nucleic Acid Extraction
Fusion Genes
CNV Copy Number Variation
SNV Single Nucleotide Variation
Conventional approach
Copy Number variant
FISH
Sanger
qPCR
CGH Nucleic Acid Extraction
Fusion Genes
Single Nucleotide Variant
NG
S
NGS approach
Oncomine Focus Assay
52 unique genes 269 amplicons in DNA panel, 271 amplicons in RNA panel
DNA Panel
RNA Panel
Hotspot genes, n=35 Fusion drivers, n=23 ALK RET ROS1 NTRK1 NTRK2 NTRK3 FGFR1 FGFR2 FGFR3 MET BRAF RAF1 ERG ETV1 ETV4 ETV5 ABL1 AKT3 AXL EGFR ERBB2 PDGFRA PPARG
Copy Number Variants, n=19 AKT1 ALK AR BRAF CDK4 CTNNB1 DDR2 EGFR ERBB2 ERBB3 ERBB4 ESR1 FGFR2 FGFR3 GNA11 GNAQ HRAS IDH1
IDH2 JAK1 JAK2 JAK3 KIT KRAS MAP2K1 MAP2K2 MET MTOR NRAS PDGFRA PIK3CA RAF1 RET ROS1 SMO
ALK AR BRAF CCND1 CDK4 CDK6 EGFR ERBB2 FGFR1 FGFR2
FGFR3 FGFR4 KIT KRAS MET MYC MYCN PDGFRA PIK3CA
Thermo Fisher All Rights Reserved For Research Use Only. Not for use in diagnostic procedures.
COPY NUMBER VARIATION DETECTION
Depth ratio: tumoral DNA/Bioinformatic baseline (48 XY patients)
Normalisation with reference genes Gender information+++ Tumoral cellularity+++
Detection threshold : At least 4 copies At least 10 amplicons involved
Ref. genes Chromosome
APC 5
BIRC2 11
BRCA1 17
DCUN1D1 3
MED12 X
NF1 17
ALK AR BRAF CCND1 CDK4 CDK6 EGFR ERBB2 FGFR1 FGFR2
FGFR3 FGFR4 KIT KRAS MET MYC MYCN PDGFRA PIK3CA
19 genes
*For Research Use Only. Not for use in diagnostic procedures.
Gene A Gene D primer 5’a
primer 3’d
Gene A Gene B
Amplicon AB primer 5’a
primer 3’b
1- DIRECT DETECTION OF 269 KNOWN TARGETED FUSION BREACKPOINTS
FUSION TRANSCRIPTS DETECTION: PRINCIPLES (AMPLISEQ STRATEGY)
Possibility to identify new fusion transcripts between genes included in the RNA panel
ALK RET ROS1 NTRK1 NTRK2 NTRK3 FGFR1 FGFR2 FGFR3 MET BRAF RAF1 ERG ETV1 ETV4 ETV5 ABL1 AKT3 AXL EGFR ERBB2 PDGFRA PPARG
2- IMBALANCE ASSAY PRINCIPLE (ALK, ROS1, RET and NTRK1)
Fusion partner
Driver oncogene
012345
Expression 5' Expression 3'
Oncogène driver
Partenaire defusion
5’ 3’
Fusion breakpoint
Oncogenic Fusion Transcript
012345
5' expression 3' expression
Driver oncogene
Fusion partnerReciprocal Fusion Transcript
Imbalance expression between the 5' assay and the 3' assay of the driver gene
5’ 3’
Confirmation for the fusion calls Improve sensitivity by providing indirect evidence of
a fusion other than those targeted by the panel *For Research Use Only. Not for use in diagnostic procedures.
Relative representation of the 23 driver oncogenes in Oncomine Focus Fusion panel
0.0
5.0
10.0
15.0
20.0
25.0 ALKRETROS1NTRK1NTRK2NTRK3FGFR1FGFR2FGFR3METBRAFRAF1ERGETV1ETV4ETV5ABL1AKT3AXLERBB2PDGFRAPPARG
*For Research Use Only. Not for use in diagnostic procedures.
Relative histotype representation in Oncomine Focus Fusion panel
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10
15
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25
30
35
40
45
nb FT in histotype N = 269 FT
Oncomine Fusion panel optimized for NSCLC, CNS and thyroid tumor testing *For Research Use Only. Not for use in diagnostic procedures.
Oncomine Knowledge Base Reporter
• Efficient and intuitive tool for screening clinical trials
• Updated several times a year • Allows to filter according to type of cancer,
gene and trials
*For Research Use Only. Not for use in diagnostic procedures.
ION REPORTER CNV detection RNA alteration detection
OVAT
Selection of predefined pathogenic variants (Thermofisher database)
Oncomine Knowledge Base Reporter
Edition of clinical trials available
Tumoral sample information entry
TORRENT SUITE SERVER
Annotated vcf Bam files
Raw data
SNV detection
Option 1 : Automatic interpretation of predefined variants with OVAT
ION REPORTER CNV detection RNA alteration detection
OVAT
Selection of predefined pathogenic variants (Thermofisher database)
Oncomine Knowledge Base Reporter
Edition of clinical trials available
Tumoral sample information entry
TORRENT SUITE SERVER
Annotated vcf Bam files
Raw data
SNV detection
Option 2 : Manual interpretation of pathogenicity by the biologist
Biological interpretation and validation of variants Evaluation of pathogenicity
Oncomine Knowledge Base Reporter Functions and settings
Allows to upload variant file filtered by OVAT (automatic interpretation)
Allows to interrogate relevance of gene alteration (manual interpretation)
Option tools to filter trials according to country/center availability
Thermo Fisher All Rights Reserved
For Research Use Only. Not for use in diagnostic procedures.
OKR Example of Met alteration
Administrations approvals Trials available
Thermo Fisher All Rights Reserved For Research Use Only. Not for use in diagnostic procedures.
Clinical trial description
Thermo Fisher All Rights Reserved For Research Use Only. Not for use in diagnostic procedures.
GLOBAL ANALYSIS IN THE CONTEXT OF BIP PROTOCOL
AT BERGONIE INSTITUTE
(about the 300 first samples screened by Oncomine Focus assay)
BERGONIE INSTITUTE PROFILING (BIP) TRIAL TYPE PROMOTOR TARGETS DRUG NAMES
MOST Umbrella Centre Léon Bérard
ABL1, KIT, PDGFRA/B, DDR1/2, CSF1R
Nilotinib
PIK3CA, PIK3R1, AKT12, mTOR, TSC1/2,
PTEN Everolimus
VEGFR1-3, PDGFRB, FLT3, BRAF (non
V600), CRAF, KRAS, RET
Sorafenib
ERBB2 Lapatinib
VEGFR1-3, PDGFRA/B, KIT Pazopanib
AcSé Crizotinib Basket
Unicancer
ALK1, ROS1, MET Crizotinib
AcSé Vemurafénib
Basket BRAF Vemurafénib
STRTRK-2 Basket IGNYTA Inc NTRK1-3, ALK1, ROS1 Entrectinib
LOXO-101 Basket LOXO Oncology NTRK1-3 Larotrectinib
KIDES Basket Orion FGFR1-4, VEGFR1-3 ODM203
JNJ-42756493 Basket Janssen RD FGFR1-4 Erdafitinib
BET-1155121 Basket GSK Ampli N-MYC GSK525762
MEDIOLA Basket AstraZeneca BRCA / PDL1 MEDI4736 + Olaparib
GSK-2118436 Basket GlaxoSmithKline BRAF Dabrafenib
• Goal : Identify relevant molecular alterations in cancer research
• High throughput analysis : NGS Oncomine Focus assay
• Inclusion criteria :
Solid malignant tumor or hematological malignancy
Advanced disease Performance status < 2 Measurable disease
according to RECIST 1.1
02468
1012141618
Repartition of histological types in our series(%)
4 tumor types representing 52% of the samples
DESCRIPTIVE ANALYSIS of ALTERATIONS AND GLOBAL YIELD IN BIP PROTOCOL
0.02.04.06.08.0
10.012.014.016.018.0
73% 23% 4%
Mutations
Amplifications
RNA alterations
Patie
nt (
%)
45.3 33 37.6
0
50
Oncomine focus assay global yield
All Somatic alterations Novel somatic alterations Actionable alterations
Alteration types distribution %
Tumor recruitment versus Histotype fusion panel representation
05
1015202530354045
• Panel under-exploited for thyroid and CNS fusion detection in our series
0
5
10
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NSCLC CERVIX COLORECTAL ENDOMETRIAL GASTRIC OVARIAN PANCREAS SARCOMA BREAST UROTHELIAL
Yield by tumoral type (all somatic alterations)
Histotype recruitment (%) Histotype contribution to global yield (%)
COMPARATIVE YIELD OF RELEVANT ALTERATIONS: BY TUMORAL TYPE
COMPARATIVE YIELD OF RELEVANT ALTERATIONS: PRIMARY VERSUS METASTATIC SITES
0
50
100
150
200
Primary site Metastatic site
Number of samplesscreened
Number of samples withat least one actionablealteration
300
82
4 0
50
100
150
200
250
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350
All tumor sequenced Complementary CGH Actionable Targets detected by CGH
Is CGH-array has additional value to Oncomine Focus assay to screen tumors?
4/82 cases : - PTEN homoz del - AKT2/VEGFA amp - AR amp - BRCA2 homoz del
Conclusion : In our series, CGH-array yields up only few additional relevant alteration when no new targetable alteration is detected by Oncomine Focus panel
*For Research Use Only. Not for use in diagnostic procedures.
COMPARATIVE YIELD OF ACTIONABLE ALTERATIONS: ONCOMINEFOCUS ASSAY VERSUS 426 GENES PANEL
426 genes panel (568 tumors) Oncomine focus assay (52 genes) on 300 tumors
Tumors screened: n=300
Tumors with at least one relevant alteration: n=136 (37,6%)
*For Research Use Only. Not for use in diagnostic procedures.
Take home messages
– Globally Oncomine focus panel yield allows to identify > 37% of tumors with at least 1 actionable alteration
– The RNA panel is optimized for non epidermoid NSCLC theranostic screening
– Under-exploitment of panel in our series – Screening yield in a trial depends on panel volume as number of
potential drugs available – Oncomine Knowledge base Reporter is an efficient and intuitive
tool for screening clinical trials
THANKS
Dr Emmanuel Khalifa Dr Benjamin Bonhomme Félix Lefort Magali Philips Isabelle Hostein Gaelle Pérot Jennifer Chiron Mathilde Beunardeau Céline Auzanneau
Molecular Pathology Lab
Larry Blanchard Mélanie Muller Laetitia Nègre-Mayeur Agnès Ribeiro Marie-Cécile Blard Marlène Boucheix Nathalie Mérillon-Tortevoie Charlotte Primois Léa Ries Ghislaine Sierankowski
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