Download Corporate Template 4:3 for Internal Use

Personalized Medicine Research Solutions
Andy Felton Ph.D.
Vice President Marketing & Product Management
Clinical Sequencing Division
The world leader in serving science
Overview
• Platforms
• Ion AmpliSeq™ & Oncomine™ Assays for Oncology
Research
• New FFPE Direct Reagent
• Liquid Biopsy Solutions
• In Development – Immune Response Assays
Platforms
Ion Torrent NGS Cancer Research Tools
THE ONCOMINE™
KNOWLEDGEBASE
Ion AmpliSeq™
Technology*
Ion Torrent™
Systems*
Ion Torrent™ NGS platform:
Pre-NGS sample prep:
• Custom / pre-designed
panels
• Hundreds of gene variants
per sample in single run
• Low input amounts
•
•
•
•
•
Minimal sample input
Fast turnaround times
Enables reproducible results
Enables accurate performance
All in a single run
*For Research Use Only. Not for use in diagnostic procedures.
* Clinical research trials are not referring to any of the products presented in these slides.
Compendia
Bioinformatics
One of the world’s largest
curated cancer genomic
database:
• Public sources
• Peer reviewed literature
• Published clinical research
trials *
Solid Tumor Driver Variant Map
Legend:
Copy gain
Copy loss
Hotspot
Deleterious
Gene fusion
Bladder
Breast
Colorectal
Endometrial
Esophageal
Gastric
GIST
Glioblastoma
Head and Neck
Kidney
Liver
Melanoma
Mesothelioma
NSCLC
Osteosarcoma
Ovarian
Pancreas
Prostate
Basal Cell
SCLC
Sarcoma
Testicular
Thyroid
Gene variants
0.01
>0.30
Oncomine™ Focus Assay
Intelligent design includes hotspot SNV and indels, CNVs and gene fusions
Categorized by somatic alteration type
52
Categorized by potential relevance
genes
35 Hotspot genes
Labels
19 Focal CNV gains
Guidelines
23 Fusion drivers
Drug Targets
43
Clinical Trials
>400(US)
*For Research Use Only. Not for use in diagnostic procedures.
12
9
Oncomine Comprehensive Assay*
143 genes: Several used in multiple applications
(hotspot, CNV, driver fusion)
Categorized by somatic alteration type
143
Categorized by potential relevance
genes
73 Hotspot genes
Labels
49 Focal CNV gains
Guidelines
26 Full CDS for DEL
mutations & CNV loss
Drug Targets
72
Clinical Trials
>450(US)
22 Fusion drivers
*For Research Use Only. Not for use in diagnostic procedures.
12
9
Oncomine Knowledgebase Reporter: Variant Summary Table
For Research Use Only. Not for use in diagnostic procedures.
National Cancer Institute-Molecular Analysis for Therapy Choice (MATCH)
Phase I technical results – June 2016
• 795 patients enrolled for screening in the first 3 months -739 core
needle biopsies sequenced with 87% success rate
• 9.5% of the 13% which were not sequenced had no tumor present at
all, giving an effective 97.5 % success rate
• Optional fine needle aspirates, 97% of the samples were successfully
sequenced - mandatory
in Phase II providing a projected 98.6%
Goals
success rate based on Phase I analysis
1Mickey
Williams, PhD, Frederick National Laboratory for Cancer Research
http://www.cancer.gov/about-cancer/treatment/clinical-trials/nci-supported/nci-match
Expanding Menu of Panels and Assays for Cancer Research
Oncomine™ Assays
Ion AmpliSeq™ Panels
Robust results with limited sample input & simple
automatable workflows
•
Informed by the Oncomine™ Knowledgebase
•
Single workflow for DNA and RNA
•
Pre-designed or Custom-design options
•
•
Primer pools only
Complete solution containing Primer Pools plus Library,
Templating and Sequencing kits
•
Cancer Hotspot
Panel v2
Comprehensive
Cancer Panel
Colon and Lung
Research Panel v2
50 Genes
400 Genes
22 Genes& Fusions
BRCA1 and
BRCA2 Panel
RNA Fusion
Research Panel
TP53 Panel
Complete coverage
of coding exons and
exon-intron boundaries
AML Panel
> 70 fusion transcripts
White Glove
Oncomine™
Comprehensive
Assay
Exons and UTRs
Custom Panels
21 Genes
For Research Use only. Not for use in diagnostic procedures.
Oncomine™
Focus Assay
Our Vision for the Future: Oncomine Universal Dx Product
•
One workflow to deliver results across many biomarkers enabled by targeted NGS
•
One Test – all answers for patient stratification to available targeted therapies
Oncomine™ Focus
Assay*
Oncomine™ Universal
Dx Test*
Oncomine™ Universal
Dx Test*
RUO
Early Development
IUO
Registration Trials
IVD
Companion Diagnostics
2015
Solid tumor
sample
2016
Oncomine™ IVD
Assay
Sample report
The content provided herein may relate to products that have not been officially released and is subject to change without notice.
“For investigational use only. The performance characteristics of this product have not been established."
Physician-patient
treatment decision
New solutions for FFPE sample handling
Introducing Ion AmpliSeq Direct FFPE DNA Protocol
•
Fast and easy one-tube, two-step
protocol using Direct Reagent
that eliminates the requirement for
deparaffinization and purification
•
DNA is prepared in 30 min with only
10 min hands-on time
•
DNA lysate can either be quantified or
used directly for Ion AmpliSeq targeted
sequencing
Demonstration video:
https://www.youtube.com/watch?v=x8Rb50oHRug
For Research Use Only. Not for use in diagnostic procedures.
Excellent Coverage Uniformity Across Challenging Sample Types
Performance of Ion AmpliSeq high-content gene panel* across different tissues and varied
amounts of input Ion AmpliSeq Direct FFPE DNA lysate (2-75 ng)
30
100%
25
Sample DNA Yield (ng/µL)
20
60%
15
40%
10
20%
5
0
Uniformity of Base Coverage
80%
0%
Liver Liver Lung Lung Colon Colon Liver Liver Lung Lung Colon Colon
11cm2
cm2
0.25cm2
0.25 cm2
FFPE Samples
Uniformity of base coverage >95%
*134 gene targets 2,530 primer pairs
For Research Use Only. Not for use in diagnostic procedures.
DNA yield measured using
InvitrogenTM QubitTM 3.0 Fluorometer
and Qubit ds HS Assay Kit.
Peripheral Monitoring
New Oncomine Lung cell free DNA assay
Breast and Colon panels in late stage development
New library method for targeted
sequencing of key variants from
single tube of banked blood
research sample
Gene List
ALK
BRAF
EGFR
ERBB2
KRAS
MAP2K1
MET
NRAS
PIK3CA
ROS1
TP53
Increased sensitivity to detect
rare variants present down to
0.1% in cfDNA
Covering key hotspot mutations in
11 genes
157 Cosmic Hotspots
T790M Included
For Research Use only. Not for use in diagnostic procedures.
Variant calls from FFPE vs Plasma (late stage lung cancer)
Samples Variant
FFPE
Plasma
1
EGFR-L858R 71.42%
2.62%
2
TP53-R158L
51.89%
4.32%
3
MET-T1010I
KRAS-G12C
43.87%
34.62%
51.75%
0.28%
4
N/A
No detection
No detection
5
EGFR-L858R 58.44%
MET-T1010I
41.93%
TP53-Y220C 35.54%
7.28%
48.72%
1.93%
6
TP53-R158L
1.26%
10.19%
Circulating Tumor Cell & Cell Free DNA Analysis with Cynvenio Liquid Biopsy
Immunomagnetic capture of CTC’s from single blood research tube enables CTC
analysis without whole genome amplification as well as cfDNA and germline
comparison
•
•
•
•
Circulating tumor DNA (ctDNA) isolation
Circulating tumour cells (CTCs) enrichment
via the Cynvenio CTC Platform
NGS sequencing assays for both CTC DNA
and ctDNA analysis
Unique workflows to get results from both
ctDNA and CTCs from one sample, in one
analysis
One
sample
ctDNA and CTC
protocols
NGS on one chip
For Research Use only. Not for use in diagnostic procedures.
Analysis
Immuno-Oncology
Immuno-Oncology Field Expanding Rapidly
>500 Immuno-Oncology clinical trials registered
Seizing the future in oncology (2015)
For Research Use only. Not for use in diagnostic procedures.
In Development
400 gene AmpliSeq Gene Expression Assay* Enables Accurate Stratification
Robust panel design strategy to
enable a unique molecular signature
development
0.20
Expert content selection
0.15
≥ 200 Publications
0.10
Large data sources
Clinical researchers from
leading cancer centers and
academic medical centers
Key Opinion Leaders
*The content provided herein may relate to products that have not
been officially released and is subject to change without notice.
Squ.highTIL_53-3
Squ.highTIL_53-1
Squ.highTIL_53-2
Squ.lowTIL_63-1
Squ.lowTIL_63-2
Squ.lowTIL_63-3
Squ.lowTIL_57-1
Squ.lowTIL_57-2
Squ.lowTIL_57-3
Ade.lowTIL_59-3
Ade.lowTIL_59-1
Ade.lowTIL_59-2
Ade.lowTIL_61-1
Ade.lowTIL_61-2
Ade.lowTIL_61-3
Ade.highTIL_51-3
Ade.highTIL_51-1
Ade.highTIL_51-2
Ade.highTIL_55-3
Ade.highTIL_55-1
Ade.highTIL_55-2
Ade.highTIL_49-1
Ade.highTIL_49-2
Ade.highTIL_49-3
0.05
0.00
Oncomine™ Knowledgebase
1-correlation
Primary Literature
Immuno-oncology panel segregates
high TIL tumor samples
For Research Use only. Not for use in diagnostic procedures.
A Mission We’re Proud Of
We enable our customers to make the world
healthier, cleaner and safer
© 2016 Thermo Fisher Scientific Inc. All rights reserved. All trademarks are the property of Thermo Fisher Scientific and its
subsidiaries unless otherwise specified.