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Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology

Cirdan
Cirdan

Personalised / Precision Medicine has revolutionized cancer treatment and, in parallel, is also deeply transforming the way we practice tissue pathology. The aim of this talk is to briefly review the status of molecular diagnostic tests applicable to tissues and cells, as well as the main technical and conceptual areas that, in my opinion, will be dictating the evolution of tissue pathology and its integration with the molecular era. These areas are, among others – a) digital pathology in the pipeline of therapeutic pathology; b) tissue-based NGS and its integration in routine diagnostics; c) the promise of liquid biopsy diagnostics and its necessary “partnership” with tissue molecular testing; d) Pathology IT, databases and bioinformatics; and e) the training of future tissue pathologists. In the process of this review, it may be apparent that a solid, integrated, morpho-molecular approach to pathology may serve our patients better.

1 of 150
Manuel Salto-Tellez, MD (LMS), FRCPath, FRCPI
Professor and Chair of Molecular Pathology
Clinical Consultant Pathologist
Deputy Director, Centre for Cancer Research and Cell Biology
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
MARCH 2011 – A MEETING OF MINDS
MARCH
2011
INTRODUCTION
2007
Salto-Tellez M. Clinical Chemistry 2007
•ANATOMICAL DIMENSION
•OF PATHOLOGY
ANATOMICAL / CLINICAL DIMENSION
OF PATHOLOGY (HISTOLOGY AND CYTOLOGY)
“… transforming pathology of the dead
into pathology of the living.”
Salto-Tellez M. Clinical Chemistry 2007
Paediatric
Sarcomas
Colorectal
Cancer
Lympho –
proliferative
Disorders
Lung Cancer Breast Cancer
TREATMENT AND/OR PROGNOSIS
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L D I M E N S I O N O F P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
TREATMENT AND/OR PROGNOSIS
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L D I M E N S I O N O F P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007
•ANATOMICAL / CLINICAL DIMENSION OF PATHOLOGY
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
•ANATOMICAL / CLINICAL / MOLECULAR DIMENSION OF PATHOLOGY
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
DIRECTOR'S CHALLENGE: TOWARD A MOLECULAR
CLASSIFICATION OF TUMORS
Release Date: January 20, 1999 RFA: CA-98-027
P.T. National Cancer Institute
PURPOSE - The Director of the National Cancer Institute (NCI)
challenges the scientific community to harness the power of
comprehensive molecular analysis technologies to make the
classification of tumors vastly more informative. This challenge is
intended to lay the groundwork for changing the basis of tumor
classification from morphological to molecular characteristics.
Dr Harold Varmus, 1999
Research and the World of Tissue Pathology
Molecular biomarkers used in clinical standard-
of-care decision making in colorectal cancer
Biomarker Purpose
Diagnostic
APC mutation detection
MMR protein expression (MSH2, MLH1, MSH6,
PMS2)
MSI (microsatellite instability) analysis
MMR mutation detection (MSH2, MLH1, MSH6,
PMS2)
BRAF mutation detection
MYH mutation detection
LKB1, SMAD4, BMPR1A, PTEN mutation detection
Diagnosis of FAP
Diagnosis of HNPCC
Diagnosis of MYH-associated polyposis
Diagnosis of harmartomatous polyp syndromes
Prognostic/Predictive
KRAS mutation analysis
BRAF mutation analysis
Thymidylate synthase protein expression
MSI
Gene expression signature
Molecular stratification for treatment with epidermal
growth factor receptor (EGFR) inhibitors
Identification of response to 5-FU
Identification of response to 5-FU
Prognostication
Van Schaeybroeck S, et al (Salto-Tellez M). Abeloff's Clinical Oncology. 5th edition; in press.
Molecular testing in breast cancer
American Society of Clinical Oncology/College
of American Pathologists Guideline
Recommendations for Human Epidermal Growth
Factor Receptor 2 Testing in Breast
Cancer - Antonio C. Wolff AC et al.
JCO Jan 1 2007: 118-145.
Boyle DP, et al. (Salto-Tellez M). Biochim Biophys Acta 2013;1835:230–42.
AKT1 mut in 2% of patients
AKT1 inhibitor AZD5363
Activating ERBB2 mut in 3% of patients
plasmaMATCH
BRCA1 and BRCA2 mut
PARP inhibitors.
ESR1 mut
Oral SERDs.
Molecular classification of
lung adenocarcinoma
Pao W & Hutchinson KE.
Nat Med 2012;18:349–51.
Lindeman NI et al.
J Mol Diagn. 2013 Jul;15(4):415-53.
Molecular testing in sarcomas & lymphomas
Molecular testing in malignant melanomas
GLIOMA TESTING
DNA QPCR
1P
19Q
PTEN
EGFR Amplification
DNA Sanger Sequencing
IDH 1 & 2
DNA Methylation
RNA QPCR
BRAF Translocations
EGFR v.3
NI-MPL Validation Strategy
Selected target therapeutics in
clinical oncology practice
Salto-Tellez M. In: Tan & Lynch’s Principles of Molecular Diagnostics and Personalized
Cancer Therapy, Lippincott Williams & Wilkins, 2012.
16
Revolution in Oncology
New Drugs for Targeted Therapy
Discovery Medicine 2014
32
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
TREATMENT AND/OR PROGNOSIS
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L D I M E N S I O N O F P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
A N A T O M I C A L - C L I N I C A L - M O L E C U L A R D I M E N S I O N
O F P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
Multiple Biomarker Analysis
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F
P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
Multiple Biomarker Analysis
Pharmacogenomics
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F
P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
Multiple Biomarker Analysis
Pharmacogenomics
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F
P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
Multiple Biomarker Analysis
Pharmacogenomics
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F
P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
Multiple Biomarker Analysis
Pharmacogenomics
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F
P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
TREATMENT AND/OR PROGNOSIS
Molecular
Detection
of
Translocations
Microsatellite
Instability
Analysis
KRAS/BRAF
Mutation Analysis
B & T cell
rearrangements
Specific
translocations Analysis
of
EGFR
Mutations
Analysis
of
C-kit
Mutations
HER2-neu
Status
Multiple Biomarker Analysis
Pharmacogenomics
SURG PATH
Diagnosis of
Paediatric
Sarcomas
SURG PATH
Diagnosis of
Colorectal
Cancer
SURG PATH
Diagnosis of
Lympho –
proliferative
Disorders
SURG PATH
Diagnosis of
Lung Cancer
SURG PATH
Diagnosis of
Breast Cancer
SURG PATH
Diagnosis of
Gastrointestinal
Stromal
Tumours
A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F
P A T H O L O G Y
Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
MARCH 2011 – A MEETING OF MINDS
MARCH
2011
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH
2011
SEPT
2011
Salto-Tellez, James & Hamilton.
Molecular Oncology, 2014 Oct;8(7):1163-8
Salto-Tellez & Kennedy.
Drug Discovery Today, 2015, in press.
Manpower
Technology Samples
Manpower
Technology Samples
RESEARCH DIAGNOSTICS
SAMPLES
HYBRID LABORATORY OPERATION
TECHNOLOGY
MANPOWER
Northern Ireland Molecular Pathology Laboratory (NI-MPL)
End to End Diagnostic and Research Service
Cutting Across Technologies and Infrastructures
Salto-Tellez, James & Hamilton. Molecular Oncology, 2014
Salto-Tellez, James & Hamilton.
Molecular Oncology, 2014 Oct;8(7):1163-8
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH
2011
SEPT
2011
Salto-Tellez, James & Hamilton.
Molecular Oncology, 2014 Oct;8(7):1163-8
Salto-Tellez & Kennedy.
Drug Discovery Today, 2015, in press.
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
MARCH
2011
SEPT
2011
MARCH
2012
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Salto-Tellez & Kennedy. Drug Discovery Today, 2015, in press.
100%
1%
Kern SE.
Why your new cancer biomarker
may never work: recurrent
patterns and remarkable diversity
in biomarker failures.
Cancer Res. 2012 Dec 1;72(23):6097-101
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
MARCH
2011
SEPT
2011
MARCH
2012
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
NEXT GENERATION SEQUENCINGHT GE ARRAYS / METHYL / CNV
IMAGING SCANNING LT TESTING (SEQ, Q-PCR)AUT NA EXTR
AUTOMATED IHCAUTOM. FISHAUTOMATED H+E
MICROSCOPYSAMPLE PREPARATION
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Level 1:
well-characterised
Level 2:
basic knowledge
Level 3:
hardly or no
knowledge
Full characterization (cell lines, KO models, WBs, etc)
REJECTYES NO
QUESTION 1: What is known about the AB?
QUESTION 2: Is there a good protocol
Technical: Antigen retreivals/Dilutions using Case controls and detecting expected expression
REJECTYES NO
QUESTION 3: Does it have the expected use – is it fit for purpose?
Diagnostic Genetic/molecular Therapeutic
Single? Panel?
Sensitivity and Specificity
against diagnostic target
Use of molecular
reference
standards
Follow strict
guidelines
REJECTACEPT AND INTRODUCE TO SERVICE
YES NO
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Digital Pathology &
Molecular Diagnostics
Tissue Hybridization-based
Testing
Extracted Nucleic Acid-based
Testing
Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
Gland-to-gland &
Intragland heterogeneity
QUANTITATION - ABSOLUTE AND RELATIVE
(HOUSE-KEEPING GENE)
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
JAN 2013 - CPA MOLECULAR DIAGNOSTIC ACCREDITATION
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
… to show our hospital that we are competent to perform diagnostics
… to show research agencies / charities that we perform research according to the
best standards
… to show industry our quality
S-CORT
(under review)
NATIONAL & EUROPEAN PROGRAMMES
€ 6M £2.5M £ 6M £3.5M £600K
ACCELERATOR
£3.9M TO BE CONFIRMED
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
JAN 2013 - CPA MOLECULAR DIAGNOSTIC ACCREDITATION
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
J Natl Cancer Inst. 2014 Jan;106(1):djt335. doi: 10.1093/jnci/djt335.
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
Genome Sequencing - FASTER
Sanger (capillary) sequencing
2015
? ~1day
?? $100
2005
~3 years
~$ 20million
2010
~1month
$9,500
(Illumina)
AML
Melanoma
Small-celllung
Breast
2008
~4 months
~$ 1.5million
Lung(NSS)
Cancer Genomics
2000
~10 years
~$ 3.5 billion
Myeloma
Hepatocellular
CLL
MouseAML
Next generation sequencing
Genome Sequencing - BROADER
102
104
106
108
1010
1012
1014
1016
Output
kbp / run
Capillary (Sanger)
Sequencing
Next Generation
Sequencing
(NGS)
2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011
454
pyroseq
Solexa/
Illumina
ABI
SOLID
Illumina
HiSeq
Technologies
Roche/454
Titanium
ABI
SOLID 3.0
ABI
capillary
Ion
Torrent
Genome Sequencing - CHEAPER
NGS Research Paradigm
Clinical samples
(best possible sample quality)
NGS ANALYSIS
(discovery – as broad as possible)
CONFIRMATION OF SELECTED FINDINGS
(orthogonal methods)
Selected Report of Results
Alvi (Salto-Tellez) et al. Oncotarget 2015 – Advanced Publication
Alvi (Salto-Tellez) et al. Oncotarget 2015 – Advanced Publication
Lawrence Ms et al. Nature. 2013 Jul 11;499(7457):214-8.
For most cancer types, this landscape consists of a small number of
“mountains” (genes altered in a high percentage of tumors) and a
much larger number of “hills” (genes altered infrequently).
To date, these studies have revealed ~140 genes that, when altered by
intragenic mutations, can promote or “drive” tumorigenesis. A typical
tumor contains two to eight of these “driver gene” mutations; the
remaining mutations are passengers that confer no selective growth
advantage.
Driver genes can be classified into 12 signaling pathways that regulate
three core cellular processes: cell fate, cell survival, and genome
maintenance.
Vogelstein et al. Science . 2013; 339(6127): 1546–1558.
NGS Research Paradigm
Clinical samples
(best possible sample quality)
NGS ANALYSIS
(discovery – as broad as possible)
CONFIRMATION OF SELECTED FINDINGS
(orthogonal methods)
Selected Report of Results
?
PLoS ONE 8(7): e69604. doi:10.1371/journal.pone.0069604
PLoS One. 2013 Jul 26;8(7):e69604. doi: 10.1371/journal.pone.0069604. Print 2013.
LUNG ADENOCARCINOMA
COLORECTAL CANCER
MALIGNAT MELANOMA
5 BIOINFORMATICS ANALYTICAL
SOFTWARES
CAN WE CONFIDENTLY DETECT WHAT IS CURRENTLY STANDARD
OF CARE? (EGFR, KRAS, BRAF)
CAN WE RELY ON THE INFORMATION GENERATED IN
OTHER KEY ONCOGENES (n=43)?
2 NGS PLATFORMS
PLoS One. 2013 Jul 26;8(7):e69604. doi: 10.1371/journal.pone.0069604. Print 2013.
J Pathol. 2014 Sep;234(1):5-10. doi: 10.1002/path.4365.
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
PREPARATIONS FOR 1ST
CLINICAL TRIAL
PTEN MAP2K1(MEK) EGFR KRAS
NRAS BRAF PIK3CA ERBB2
MET PIK3R1
Multiplicom - MErCuRIC specific MASTR assay:
257 amplicons in 4 plexes covering all coding exons of the 10 genes.
Of the 257, 21 are control amplicons to allow for gene deletions / amplifications.
The average length of the amplicons is 198 bp ranging from 124 to 255 bp.
The evaluation of the performance of the assay (MiSeq) resulted in 100% coverage of all targets, a
higher than 97% on target reads and higher than 99% of all amplicons within 20% of mean
coverage
PI – DR SANDRA VAN SCHAEYBROECK
Representation of uniform coverage of the MErCuRIC MASTR assay
Currently, only part of exon 9 of ERBB2 is covered suboptimally.
The low covered region is 30 bp in size located at the 5’ end of exon 9.
It is unlikely that this low coverage will lead to false negative results
since no mutations are reported in the COSMIC database for this DNA fragment.
Aiming to avoid amplification of the MAP2K1 pseudogenes on chromosome 8p21.
The MiSeq sequencing data showed that only MAP2K1 specific amplicons were
amplified and hence no pseudogene amplicons.
Schematic presentation of the complete workflow of the MErCuRIC
MASTR assay .
The resulting amplicon library can be sequenced on MiSeq and PGM.
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
SOLID TUMOURS - LEVELS OF TESTING
CLASS 4
HUMAN CANCER
COMPREHENSIVE
200-400
CLASS 1
ACTIONABLE
MUTATIONS
6-12
CLASS 3
Tumour
COMPREHENSIVE50-200
CLASS 2
CLINICALLY
RELEVANT
20-50
Dx DiscoveryClinical
Trials
Getting from raw sequencing data to accurate and timely curation
of clinically actionable variants and reporting in a user
friendly format for our ordering physicians continues to
be a significant challenge for complex molecular testing.
M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3
M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3
Is this an activating or inactivating mutation?
Does this mutation engender sensitivity to specific targeted therapeutics?
How to select therapy in case of multiple genomics alterations?
M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3
“Managing levels of (un)certainty”
M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3
The Need for Analytical Redundancy - Courtesy of – Dr Richie Soong, NUS
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
2,000 CRC
transcriptomics
Validation of WES
& RNA-Seq
Validation of
WGS
Ion Torrent Illumina iScan Affymetrix Illumina MiSeq Illumina NextSeq
MOLECULAR PATHOLOGY PROGRAMME – GENOMICS
Ion Torrent Illumina iScan Affymetrix Illumina MiSeq Illumina NextSeq
MOLECULAR PATHOLOGY PROGRAMME – GENOMICS
Hamilton P (Salto-Tellez M). Oncotarget 2015 (advanced publication)
% Tumour cells is critical
Total number of cells is critical
Tumour cells ? Tumour cells ?
Breast Cancer % Tumour Estimates
PathXL – QUB – BHSCT internal assessment, 2015
PathXL – QUB – BHSCT internal assessment, 2015
Variation in % Tumor Cell
Evaluation in Lung Cancer
Smits AJJ et al. Modern Pathology 27, 168-174 (February 2014)
Variation in % Tumor Cell
Evaluation in Colorectal Cancer
Viray, et al. Arch Pathol Lab Med. 2013;137:1545–154
Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
FIG 11. (A) COMPARISON OF AUTOMATED TUMOUR NUCLEI COUNTS AND PERCENTAGE
TUMOUR VALUES (Y-AXIS), AGAINST BENCHMARK DATA ON TUMOR % SHOWING STRONG
CORRELATION, MAPPING CLOSELY TO ACTUAL TUMOR CELL PERCENTAGE VALUES. (B) THE
SAME SCATTERPLOT AS (A) BUT SUPERIMPOSING THE RANGE OF PATHOLOGY ESTIMATES (RED
CIRCLES) AGAINST THE BENCHMARK DATA.
Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
Initiation
Implementation
phase
*Led by Prof Louise Jones. Includes molecular pathology representation from
BRC-GMC centres. Consultation with Joint Molecular Pathology Group
Joint Molecular Pathology working group
Main program
WS 1: upstream tumour
handling
WS 2: tumour
processing, fixative,
embedding
WS 3: tumour
assessment
WS 5: DNA
quantification and
quality assessment
WS 4: DNA extraction
WS 6: Library
preparation and
sequencing
EXPERIMENTAL PATHWAY
SOPdevelopmentgroup
Initiation
Implementation
phase
*Led by Prof Louise Jones. Includes molecular pathology representation from
BRC-GMC centres. Consultation with Joint Molecular Pathology Group
Main program
WS 3: tumour
assessment
EXPERIMENTAL PATHWAY
SOPdevelopmentgroup
Joint Molecular Pathology working group
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
Generators of DNA & RNA
clinical sample collections
Generators of archival
clinical tissue collection
( … )
Clinical Diagnosis Research Availability
Providers of samples
to tissue repositories
Research Availability
Frozen
Tissue
Repository
Clinical Diagnosis Research Availability
DNA RNA
( … )
Conventional Pathologist Molecular Diagnostician
Dr Jackie James
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
THE PROPOSAL
£3.9M
1.
To create a “common digital pathology language” across the members of the proposal
2.
To use digital pathology to describe tumour heterogeneity and cancer immunology
3.
To improve the efficiency of NGS through digital pathology pre-analytical interventions
4.
To develop “a common digital pathology platform” for the UK
5.
To create a structure of Clinical Fellowships /MSc in different aspects of Molecular Pathology
(Including liquid biopsy pathology, lung digital pathology and
the pathology of early-phase clinical trials)
Cancer immunology is a branch of immunology that studies
interactions between the immune system and cancer cells.
It is a growing field of research (and increasingly diagnostics)
that aims to discover innovative cancer immunotherapies
and immune companion diagnostics to treat and retard
progression of the disease.
$3.9M to develop Digital Pathology in the UK
BELFAST
Manpower, IT,
Instrumentation
EPITHELIAL
INTERROGATION
Training
SOUTHAMPTON
Manpower, IT
Instrumentation
CANCER IMMUNE
INTERROGATION
TrainingMARSDEN
Manpower
WGS QA/QC
Training
CRUK DIGITAL MOLECULAR PATHOLOGY & TRAINING NETWORK
UCL Neuro
Manpower
Training
Leicester
Lung Ca
Training
Newcastle
Clin Trials
Training
Manchester
Liq Bx
Training
Pagès (Galon) N Engl J Med 353;25, 2005 Galon. Science. 2006;313(5795):1960-4.
Fridman (Galon). Nat Rev Cancer 2012 Galon. J Pathol 2014; 232: 199–209
Cancer Immunology and
Tissue Hybridization Assays
Multiplexing
Subcellular localization
Spatial localization
(topography or
Immune contexture)
Quantitation
http://www.perkinelmer.co.uk/Catalog/Product/ID/VECTRA
CD3 quantitation – validation experiments
CD3 quantitation – validation experiments
CD3 quantitation – validation experiments
Time
PercentSurvival
CHEMOTHERAPY
GENOMIC TARGETED THERAPY
IMMUNE CHECKPOINT THERAPY
COMBINATION OF IMMUNE CHECKPOINT THERAPY
AND GENOMIC TARGETED THERAPY
Sharma & Allison. Cell 161, April 9, 2015
14 1 26 7 17 24 1 15 19 18 2 16 13 22 11 3 3 12 5 28 9 8 4 27 6 23
TP53 1 3 2 0 0 1 1 2 1 0 2 1 0 0 0 2 2 1 1 0 2 1 1 2 3 0
APC 1 0 0 1 0 1 0 0 1 0 0 0 0 0 2 0 2 1 1 0 0 2 0 0 0 0
BRAF 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 1 1
KIT 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 1 1
MET 0 1 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0
SMD4 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
FBXW7 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0
KRAS 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
MSI S S S S H S S S S S S S S H S S H H H H H H H H
Alvi & Salto-Tellez. 2015, in preparation
Alvi & Salto-Tellez. 2015, in preparation
64%27%
PD-L1 IHC -- Test validation
PD-L1 Scoring
Cell type
(epithelial
vs
immune
vs
stromal)
Percentage of + cells
(in each type)
Subcellular localization
Topographic localization
(i.e. immune contexture)
Alvi & Salto-Tellez. 2015, in preparation
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
REGIONAL, FULLY COMMISSIONED
MOLECULAR DIAGNOSTIC SERVICE
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE
OCT 2015: PRECISON MEDICINE CATAPULT CENTRE OF EXCELLENCE
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
Creating the leading
Precision Medicine
Ecosystem in the world
Catapult.org.uk@PMCatapult
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology
Salto-Tellez & Kennedy. Drug Discovery Today, 2015, in press.
INDUSTRIAL-ACADEMIC PARTNERSHIPS
PRE-CLINICAL
RESEARCH
PRODUCT /
TECHNOLOGY
DEVELOPMENT
Our mission is to improve patient care through the development of:
1. Biomarkers for prognosis, prediction and markers of response
2. Biologically determined targeted therapies.
INDUSTRIAL-ACADEMIC PARTNERSHIPS
CLINICAL & PRE-CLINICAL
RESEARCH
PRODUCT /
TECHNOLOGY
DEVELOPMENT
Our mission is to improve patient care through the development of:
1. Biomarkers for prognosis, prediction and markers of response
2. Biologically determined targeted therapies.
INDUSTRIAL-ACADEMIC PARTNERSHIPS
CLINICAL & PRE-CLINICAL
RESEARCH
PRODUCT /
TECHNOLOGY
DEVELOPMENT
Our mission is to improve patient care through the development of:
1. Biomarkers for prognosis, prediction and markers of response
2. Biologically determined targeted therapies.
INDUSTRIAL-ACADEMIC PARTNERSHIPS
CLINICAL & PRE-CLINICAL
RESEARCH
PRODUCT /
TECHNOLOGY
DEVELOPMENT
PRODUCT /
TECHNOLOGY
ADOPTION
Our mission is to improve patient care through the development of:
1. Biomarkers for prognosis, prediction and markers of response
2. Biologically determined targeted therapies.
INDUSTRIAL-ACADEMIC PARTNERSHIPS
CLINICAL & PRE-
CLINICAL RESEARCH
PRODUCT &
TECHNOLOGY
DEVELOPMENT
PRODUCT &
TECHNOLOGY ADOPTION
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE
OCT 2015: PRECISON MEDICINE CATAPULT CENTRE OF EXCELLENCE
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
MARCH 2011 – A MEETING OF MINDS
SEPT 2011 – A HYBRID, INTEGRATED MODEL
MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL
FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
CPA MOLECULAR DIAGNOSTIC ACCREDITATION
JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST
FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS
2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST
2014: TEACHING IN MOLECULAR PATHOLOGY
JAN 2015: RENEWAL OF NI BIOBANK FUNDING
APRIL 2015: CR-UK ACCELERATOR AWARD
OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE
OCT 2015: PRECISON MEDICINE CATAPULT CENTRE OF EXCELLENCE
?
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
BIOBANKINGLGF
CCRCB - PM
BIOINF., DP (LAB), OFFICESGF
MOL PATH / MOL DX LAB1ST F
BIOMARKER DISCOVERY PROG.2ND F
TARG. DRUG DISCOVERY PROG.3RD F
MST, PH, JJ
RK
?
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
?
MARCH
2011
SEPT
2011
MARCH
2012
FROM
MARCH
2012
JAN
2013
JAN
2014
FROM
JAN 2014
2014
JAN
2015
APR
2015
OCT
2015
INTEGRATION…
… OF TISSUE PATHOLOGY WITH MOLECULAR PATHOLOGY
… OF TECHNOLOGY PLATFORMS, IT SYSTEMS AND MATERIALS (BIOBANKS)
… OF TALENT, THROUGH TRAINING
… OF DIAGNOSTICS AND RESEARCH, THROUGH COMMON RESOURCES & LABS
… OF HEALTHCARE AND ACADEMIA WITH INDUSTRY, THROUGH QUALITY
NORTHERN IRELAND Inc.
5 (4?) (2?) TISSUE PATHOLOGY SERVICES
REGIONAL MOLECULAR PATHOLOGY DX SERVICE
NI-MPL
PRECISION MEDICINE CATAPULT
INVEST NI
A SINGLE, INTEGRATED, HOLLISTIC INFORMATION
AND DIAGNOSTIC IMAGING SYSTEM FOR NI
Tom Simms Memorial Fund
Tom Simms Memorial Fund
Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology

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Manuel Salto-Tellez on Personalised medicine and the future of tissue pathology

  • 1. Manuel Salto-Tellez, MD (LMS), FRCPath, FRCPI Professor and Chair of Molecular Pathology Clinical Consultant Pathologist Deputy Director, Centre for Cancer Research and Cell Biology
  • 4. MARCH 2011 – A MEETING OF MINDS MARCH 2011
  • 6. •ANATOMICAL DIMENSION •OF PATHOLOGY ANATOMICAL / CLINICAL DIMENSION OF PATHOLOGY (HISTOLOGY AND CYTOLOGY) “… transforming pathology of the dead into pathology of the living.” Salto-Tellez M. Clinical Chemistry 2007
  • 7. Paediatric Sarcomas Colorectal Cancer Lympho – proliferative Disorders Lung Cancer Breast Cancer TREATMENT AND/OR PROGNOSIS Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007
  • 8. SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer TREATMENT AND/OR PROGNOSIS SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007
  • 9. •ANATOMICAL / CLINICAL DIMENSION OF PATHOLOGY Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 10. •ANATOMICAL / CLINICAL / MOLECULAR DIMENSION OF PATHOLOGY Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 11. DIRECTOR'S CHALLENGE: TOWARD A MOLECULAR CLASSIFICATION OF TUMORS Release Date: January 20, 1999 RFA: CA-98-027 P.T. National Cancer Institute PURPOSE - The Director of the National Cancer Institute (NCI) challenges the scientific community to harness the power of comprehensive molecular analysis technologies to make the classification of tumors vastly more informative. This challenge is intended to lay the groundwork for changing the basis of tumor classification from morphological to molecular characteristics. Dr Harold Varmus, 1999 Research and the World of Tissue Pathology
  • 12. Molecular biomarkers used in clinical standard- of-care decision making in colorectal cancer Biomarker Purpose Diagnostic APC mutation detection MMR protein expression (MSH2, MLH1, MSH6, PMS2) MSI (microsatellite instability) analysis MMR mutation detection (MSH2, MLH1, MSH6, PMS2) BRAF mutation detection MYH mutation detection LKB1, SMAD4, BMPR1A, PTEN mutation detection Diagnosis of FAP Diagnosis of HNPCC Diagnosis of MYH-associated polyposis Diagnosis of harmartomatous polyp syndromes Prognostic/Predictive KRAS mutation analysis BRAF mutation analysis Thymidylate synthase protein expression MSI Gene expression signature Molecular stratification for treatment with epidermal growth factor receptor (EGFR) inhibitors Identification of response to 5-FU Identification of response to 5-FU Prognostication Van Schaeybroeck S, et al (Salto-Tellez M). Abeloff's Clinical Oncology. 5th edition; in press.
  • 13. Molecular testing in breast cancer American Society of Clinical Oncology/College of American Pathologists Guideline Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in Breast Cancer - Antonio C. Wolff AC et al. JCO Jan 1 2007: 118-145. Boyle DP, et al. (Salto-Tellez M). Biochim Biophys Acta 2013;1835:230–42. AKT1 mut in 2% of patients AKT1 inhibitor AZD5363 Activating ERBB2 mut in 3% of patients plasmaMATCH BRCA1 and BRCA2 mut PARP inhibitors. ESR1 mut Oral SERDs.
  • 14. Molecular classification of lung adenocarcinoma Pao W & Hutchinson KE. Nat Med 2012;18:349–51. Lindeman NI et al. J Mol Diagn. 2013 Jul;15(4):415-53.
  • 15. Molecular testing in sarcomas & lymphomas
  • 16. Molecular testing in malignant melanomas
  • 17. GLIOMA TESTING DNA QPCR 1P 19Q PTEN EGFR Amplification DNA Sanger Sequencing IDH 1 & 2 DNA Methylation RNA QPCR BRAF Translocations EGFR v.3 NI-MPL Validation Strategy
  • 18. Selected target therapeutics in clinical oncology practice Salto-Tellez M. In: Tan & Lynch’s Principles of Molecular Diagnostics and Personalized Cancer Therapy, Lippincott Williams & Wilkins, 2012. 16
  • 19. Revolution in Oncology New Drugs for Targeted Therapy Discovery Medicine 2014 32
  • 20. SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer TREATMENT AND/OR PROGNOSIS SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 21. TREATMENT AND/OR PROGNOSIS SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status A N A T O M I C A L - C L I N I C A L - M O L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 22. TREATMENT AND/OR PROGNOSIS Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status Multiple Biomarker Analysis SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 23. TREATMENT AND/OR PROGNOSIS Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status Multiple Biomarker Analysis Pharmacogenomics SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 24. TREATMENT AND/OR PROGNOSIS Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status Multiple Biomarker Analysis Pharmacogenomics SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 25. TREATMENT AND/OR PROGNOSIS Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status Multiple Biomarker Analysis Pharmacogenomics SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 26. TREATMENT AND/OR PROGNOSIS Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status Multiple Biomarker Analysis Pharmacogenomics SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 27. TREATMENT AND/OR PROGNOSIS Molecular Detection of Translocations Microsatellite Instability Analysis KRAS/BRAF Mutation Analysis B & T cell rearrangements Specific translocations Analysis of EGFR Mutations Analysis of C-kit Mutations HER2-neu Status Multiple Biomarker Analysis Pharmacogenomics SURG PATH Diagnosis of Paediatric Sarcomas SURG PATH Diagnosis of Colorectal Cancer SURG PATH Diagnosis of Lympho – proliferative Disorders SURG PATH Diagnosis of Lung Cancer SURG PATH Diagnosis of Breast Cancer SURG PATH Diagnosis of Gastrointestinal Stromal Tumours A N A T O M I C A L - C L I N I C A L – MO L E C U L A R D I M E N S I O N O F P A T H O L O G Y Salto-Tellez M. Clinical Chemistry 2007 Jul;53(7):1188-90Salto-Tellez M. Clinical Chemistry 2007
  • 28. MARCH 2011 – A MEETING OF MINDS MARCH 2011
  • 29. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2011 SEPT 2011 Salto-Tellez, James & Hamilton. Molecular Oncology, 2014 Oct;8(7):1163-8 Salto-Tellez & Kennedy. Drug Discovery Today, 2015, in press.
  • 32. Northern Ireland Molecular Pathology Laboratory (NI-MPL) End to End Diagnostic and Research Service Cutting Across Technologies and Infrastructures Salto-Tellez, James & Hamilton. Molecular Oncology, 2014 Salto-Tellez, James & Hamilton. Molecular Oncology, 2014 Oct;8(7):1163-8
  • 33. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2011 SEPT 2011 Salto-Tellez, James & Hamilton. Molecular Oncology, 2014 Oct;8(7):1163-8 Salto-Tellez & Kennedy. Drug Discovery Today, 2015, in press.
  • 34. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL MARCH 2011 SEPT 2011 MARCH 2012
  • 37. Salto-Tellez & Kennedy. Drug Discovery Today, 2015, in press. 100% 1% Kern SE. Why your new cancer biomarker may never work: recurrent patterns and remarkable diversity in biomarker failures. Cancer Res. 2012 Dec 1;72(23):6097-101
  • 38. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL MARCH 2011 SEPT 2011 MARCH 2012
  • 39. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012
  • 40. NEXT GENERATION SEQUENCINGHT GE ARRAYS / METHYL / CNV IMAGING SCANNING LT TESTING (SEQ, Q-PCR)AUT NA EXTR AUTOMATED IHCAUTOM. FISHAUTOMATED H+E MICROSCOPYSAMPLE PREPARATION
  • 43. Level 1: well-characterised Level 2: basic knowledge Level 3: hardly or no knowledge Full characterization (cell lines, KO models, WBs, etc) REJECTYES NO QUESTION 1: What is known about the AB? QUESTION 2: Is there a good protocol Technical: Antigen retreivals/Dilutions using Case controls and detecting expected expression REJECTYES NO QUESTION 3: Does it have the expected use – is it fit for purpose? Diagnostic Genetic/molecular Therapeutic Single? Panel? Sensitivity and Specificity against diagnostic target Use of molecular reference standards Follow strict guidelines REJECTACEPT AND INTRODUCE TO SERVICE YES NO
  • 45. Digital Pathology & Molecular Diagnostics Tissue Hybridization-based Testing Extracted Nucleic Acid-based Testing
  • 46. Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
  • 47. Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
  • 48. Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press
  • 49. Bingham V, (Salto-Tellez M) McQuaid S. Human Pathology. 2015, In Press Gland-to-gland & Intragland heterogeneity QUANTITATION - ABSOLUTE AND RELATIVE (HOUSE-KEEPING GENE)
  • 50. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012
  • 51. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS JAN 2013 - CPA MOLECULAR DIAGNOSTIC ACCREDITATION MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013
  • 53. … to show our hospital that we are competent to perform diagnostics … to show research agencies / charities that we perform research according to the best standards … to show industry our quality S-CORT (under review) NATIONAL & EUROPEAN PROGRAMMES € 6M £2.5M £ 6M £3.5M £600K ACCELERATOR £3.9M TO BE CONFIRMED
  • 54. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS JAN 2013 - CPA MOLECULAR DIAGNOSTIC ACCREDITATION MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013
  • 55. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014
  • 57. J Natl Cancer Inst. 2014 Jan;106(1):djt335. doi: 10.1093/jnci/djt335.
  • 58. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014
  • 59. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014
  • 60. Genome Sequencing - FASTER Sanger (capillary) sequencing 2015 ? ~1day ?? $100 2005 ~3 years ~$ 20million 2010 ~1month $9,500 (Illumina) AML Melanoma Small-celllung Breast 2008 ~4 months ~$ 1.5million Lung(NSS) Cancer Genomics 2000 ~10 years ~$ 3.5 billion Myeloma Hepatocellular CLL MouseAML Next generation sequencing
  • 61. Genome Sequencing - BROADER 102 104 106 108 1010 1012 1014 1016 Output kbp / run Capillary (Sanger) Sequencing Next Generation Sequencing (NGS) 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 454 pyroseq Solexa/ Illumina ABI SOLID Illumina HiSeq Technologies Roche/454 Titanium ABI SOLID 3.0 ABI capillary Ion Torrent
  • 63. NGS Research Paradigm Clinical samples (best possible sample quality) NGS ANALYSIS (discovery – as broad as possible) CONFIRMATION OF SELECTED FINDINGS (orthogonal methods) Selected Report of Results
  • 64. Alvi (Salto-Tellez) et al. Oncotarget 2015 – Advanced Publication
  • 65. Alvi (Salto-Tellez) et al. Oncotarget 2015 – Advanced Publication
  • 66. Lawrence Ms et al. Nature. 2013 Jul 11;499(7457):214-8.
  • 67. For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors) and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance. Vogelstein et al. Science . 2013; 339(6127): 1546–1558.
  • 68. NGS Research Paradigm Clinical samples (best possible sample quality) NGS ANALYSIS (discovery – as broad as possible) CONFIRMATION OF SELECTED FINDINGS (orthogonal methods) Selected Report of Results ?
  • 69. PLoS ONE 8(7): e69604. doi:10.1371/journal.pone.0069604 PLoS One. 2013 Jul 26;8(7):e69604. doi: 10.1371/journal.pone.0069604. Print 2013.
  • 70. LUNG ADENOCARCINOMA COLORECTAL CANCER MALIGNAT MELANOMA 5 BIOINFORMATICS ANALYTICAL SOFTWARES CAN WE CONFIDENTLY DETECT WHAT IS CURRENTLY STANDARD OF CARE? (EGFR, KRAS, BRAF) CAN WE RELY ON THE INFORMATION GENERATED IN OTHER KEY ONCOGENES (n=43)? 2 NGS PLATFORMS PLoS One. 2013 Jul 26;8(7):e69604. doi: 10.1371/journal.pone.0069604. Print 2013.
  • 71. J Pathol. 2014 Sep;234(1):5-10. doi: 10.1002/path.4365.
  • 72. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 PREPARATIONS FOR 1ST CLINICAL TRIAL
  • 73. PTEN MAP2K1(MEK) EGFR KRAS NRAS BRAF PIK3CA ERBB2 MET PIK3R1 Multiplicom - MErCuRIC specific MASTR assay: 257 amplicons in 4 plexes covering all coding exons of the 10 genes. Of the 257, 21 are control amplicons to allow for gene deletions / amplifications. The average length of the amplicons is 198 bp ranging from 124 to 255 bp. The evaluation of the performance of the assay (MiSeq) resulted in 100% coverage of all targets, a higher than 97% on target reads and higher than 99% of all amplicons within 20% of mean coverage PI – DR SANDRA VAN SCHAEYBROECK
  • 74. Representation of uniform coverage of the MErCuRIC MASTR assay
  • 75. Currently, only part of exon 9 of ERBB2 is covered suboptimally. The low covered region is 30 bp in size located at the 5’ end of exon 9. It is unlikely that this low coverage will lead to false negative results since no mutations are reported in the COSMIC database for this DNA fragment.
  • 76. Aiming to avoid amplification of the MAP2K1 pseudogenes on chromosome 8p21. The MiSeq sequencing data showed that only MAP2K1 specific amplicons were amplified and hence no pseudogene amplicons.
  • 77. Schematic presentation of the complete workflow of the MErCuRIC MASTR assay . The resulting amplicon library can be sequenced on MiSeq and PGM.
  • 79. SOLID TUMOURS - LEVELS OF TESTING CLASS 4 HUMAN CANCER COMPREHENSIVE 200-400 CLASS 1 ACTIONABLE MUTATIONS 6-12 CLASS 3 Tumour COMPREHENSIVE50-200 CLASS 2 CLINICALLY RELEVANT 20-50 Dx DiscoveryClinical Trials
  • 80. Getting from raw sequencing data to accurate and timely curation of clinically actionable variants and reporting in a user friendly format for our ordering physicians continues to be a significant challenge for complex molecular testing.
  • 81. M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3
  • 82. M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3 Is this an activating or inactivating mutation? Does this mutation engender sensitivity to specific targeted therapeutics? How to select therapy in case of multiple genomics alterations?
  • 83. M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3 “Managing levels of (un)certainty”
  • 84. M O L E C U L A R O N C O L O G Y 8 ( 2 0 1 4 ) 8 5 9 - 8 7 3
  • 85. The Need for Analytical Redundancy - Courtesy of – Dr Richie Soong, NUS
  • 86. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014
  • 87. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014
  • 89. 2,000 CRC transcriptomics Validation of WES & RNA-Seq Validation of WGS Ion Torrent Illumina iScan Affymetrix Illumina MiSeq Illumina NextSeq MOLECULAR PATHOLOGY PROGRAMME – GENOMICS
  • 90. Ion Torrent Illumina iScan Affymetrix Illumina MiSeq Illumina NextSeq MOLECULAR PATHOLOGY PROGRAMME – GENOMICS Hamilton P (Salto-Tellez M). Oncotarget 2015 (advanced publication)
  • 91. % Tumour cells is critical Total number of cells is critical Tumour cells ? Tumour cells ?
  • 92. Breast Cancer % Tumour Estimates PathXL – QUB – BHSCT internal assessment, 2015 PathXL – QUB – BHSCT internal assessment, 2015
  • 93. Variation in % Tumor Cell Evaluation in Lung Cancer Smits AJJ et al. Modern Pathology 27, 168-174 (February 2014)
  • 94. Variation in % Tumor Cell Evaluation in Colorectal Cancer Viray, et al. Arch Pathol Lab Med. 2013;137:1545–154
  • 95. Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
  • 96. Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
  • 97. FIG 11. (A) COMPARISON OF AUTOMATED TUMOUR NUCLEI COUNTS AND PERCENTAGE TUMOUR VALUES (Y-AXIS), AGAINST BENCHMARK DATA ON TUMOR % SHOWING STRONG CORRELATION, MAPPING CLOSELY TO ACTUAL TUMOR CELL PERCENTAGE VALUES. (B) THE SAME SCATTERPLOT AS (A) BUT SUPERIMPOSING THE RANGE OF PATHOLOGY ESTIMATES (RED CIRCLES) AGAINST THE BENCHMARK DATA. Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
  • 98. Oncotarget 2015, minor revisionsOncotarget 2015, advanced publication
  • 99. Initiation Implementation phase *Led by Prof Louise Jones. Includes molecular pathology representation from BRC-GMC centres. Consultation with Joint Molecular Pathology Group Joint Molecular Pathology working group Main program WS 1: upstream tumour handling WS 2: tumour processing, fixative, embedding WS 3: tumour assessment WS 5: DNA quantification and quality assessment WS 4: DNA extraction WS 6: Library preparation and sequencing EXPERIMENTAL PATHWAY SOPdevelopmentgroup
  • 100. Initiation Implementation phase *Led by Prof Louise Jones. Includes molecular pathology representation from BRC-GMC centres. Consultation with Joint Molecular Pathology Group Main program WS 3: tumour assessment EXPERIMENTAL PATHWAY SOPdevelopmentgroup Joint Molecular Pathology working group
  • 101. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014
  • 102. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014
  • 104. Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
  • 105. Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
  • 106. Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
  • 107. Flynn C, (Salto-Tellez M) .J Clin Pathol. 2014 Jul;67(7):632-6.
  • 108. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014
  • 109. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015
  • 110. Generators of DNA & RNA clinical sample collections Generators of archival clinical tissue collection ( … ) Clinical Diagnosis Research Availability Providers of samples to tissue repositories Research Availability Frozen Tissue Repository Clinical Diagnosis Research Availability DNA RNA ( … ) Conventional Pathologist Molecular Diagnostician Dr Jackie James
  • 111. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015
  • 112. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015
  • 113. THE PROPOSAL £3.9M 1. To create a “common digital pathology language” across the members of the proposal 2. To use digital pathology to describe tumour heterogeneity and cancer immunology 3. To improve the efficiency of NGS through digital pathology pre-analytical interventions 4. To develop “a common digital pathology platform” for the UK 5. To create a structure of Clinical Fellowships /MSc in different aspects of Molecular Pathology (Including liquid biopsy pathology, lung digital pathology and the pathology of early-phase clinical trials)
  • 114. Cancer immunology is a branch of immunology that studies interactions between the immune system and cancer cells. It is a growing field of research (and increasingly diagnostics) that aims to discover innovative cancer immunotherapies and immune companion diagnostics to treat and retard progression of the disease.
  • 115. $3.9M to develop Digital Pathology in the UK BELFAST Manpower, IT, Instrumentation EPITHELIAL INTERROGATION Training SOUTHAMPTON Manpower, IT Instrumentation CANCER IMMUNE INTERROGATION TrainingMARSDEN Manpower WGS QA/QC Training CRUK DIGITAL MOLECULAR PATHOLOGY & TRAINING NETWORK UCL Neuro Manpower Training Leicester Lung Ca Training Newcastle Clin Trials Training Manchester Liq Bx Training
  • 116. Pagès (Galon) N Engl J Med 353;25, 2005 Galon. Science. 2006;313(5795):1960-4.
  • 117. Fridman (Galon). Nat Rev Cancer 2012 Galon. J Pathol 2014; 232: 199–209
  • 118. Cancer Immunology and Tissue Hybridization Assays Multiplexing Subcellular localization Spatial localization (topography or Immune contexture) Quantitation http://www.perkinelmer.co.uk/Catalog/Product/ID/VECTRA
  • 119. CD3 quantitation – validation experiments
  • 120. CD3 quantitation – validation experiments
  • 121. CD3 quantitation – validation experiments
  • 122. Time PercentSurvival CHEMOTHERAPY GENOMIC TARGETED THERAPY IMMUNE CHECKPOINT THERAPY COMBINATION OF IMMUNE CHECKPOINT THERAPY AND GENOMIC TARGETED THERAPY Sharma & Allison. Cell 161, April 9, 2015
  • 123. 14 1 26 7 17 24 1 15 19 18 2 16 13 22 11 3 3 12 5 28 9 8 4 27 6 23 TP53 1 3 2 0 0 1 1 2 1 0 2 1 0 0 0 2 2 1 1 0 2 1 1 2 3 0 APC 1 0 0 1 0 1 0 0 1 0 0 0 0 0 2 0 2 1 1 0 0 2 0 0 0 0 BRAF 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 1 1 KIT 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 1 1 1 0 1 1 MET 0 1 0 0 0 0 0 0 0 1 0 0 1 1 0 0 0 0 0 0 0 0 1 0 0 0 SMD4 0 1 1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 FBXW7 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 KRAS 0 0 0 1 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 MSI S S S S H S S S S S S S S H S S H H H H H H H H Alvi & Salto-Tellez. 2015, in preparation
  • 124. Alvi & Salto-Tellez. 2015, in preparation 64%27%
  • 125. PD-L1 IHC -- Test validation PD-L1 Scoring Cell type (epithelial vs immune vs stromal) Percentage of + cells (in each type) Subcellular localization Topographic localization (i.e. immune contexture)
  • 126. Alvi & Salto-Tellez. 2015, in preparation
  • 128. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015
  • 129. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015
  • 131. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015
  • 132. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE OCT 2015: PRECISON MEDICINE CATAPULT CENTRE OF EXCELLENCE MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015
  • 133. Creating the leading Precision Medicine Ecosystem in the world Catapult.org.uk@PMCatapult
  • 136. Salto-Tellez & Kennedy. Drug Discovery Today, 2015, in press.
  • 137. INDUSTRIAL-ACADEMIC PARTNERSHIPS PRE-CLINICAL RESEARCH PRODUCT / TECHNOLOGY DEVELOPMENT Our mission is to improve patient care through the development of: 1. Biomarkers for prognosis, prediction and markers of response 2. Biologically determined targeted therapies.
  • 138. INDUSTRIAL-ACADEMIC PARTNERSHIPS CLINICAL & PRE-CLINICAL RESEARCH PRODUCT / TECHNOLOGY DEVELOPMENT Our mission is to improve patient care through the development of: 1. Biomarkers for prognosis, prediction and markers of response 2. Biologically determined targeted therapies.
  • 139. INDUSTRIAL-ACADEMIC PARTNERSHIPS CLINICAL & PRE-CLINICAL RESEARCH PRODUCT / TECHNOLOGY DEVELOPMENT Our mission is to improve patient care through the development of: 1. Biomarkers for prognosis, prediction and markers of response 2. Biologically determined targeted therapies.
  • 140. INDUSTRIAL-ACADEMIC PARTNERSHIPS CLINICAL & PRE-CLINICAL RESEARCH PRODUCT / TECHNOLOGY DEVELOPMENT PRODUCT / TECHNOLOGY ADOPTION Our mission is to improve patient care through the development of: 1. Biomarkers for prognosis, prediction and markers of response 2. Biologically determined targeted therapies.
  • 141. INDUSTRIAL-ACADEMIC PARTNERSHIPS CLINICAL & PRE- CLINICAL RESEARCH PRODUCT & TECHNOLOGY DEVELOPMENT PRODUCT & TECHNOLOGY ADOPTION
  • 142. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE OCT 2015: PRECISON MEDICINE CATAPULT CENTRE OF EXCELLENCE MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015
  • 143. MARCH 2011 – A MEETING OF MINDS SEPT 2011 – A HYBRID, INTEGRATED MODEL MARCH 2012 – NI-MPL1 BECOMES FULLY OPERATIONAL FROM MARCH 2012: PUBLICATIONS (1) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS CPA MOLECULAR DIAGNOSTIC ACCREDITATION JAN 2014: INDUSTRY (1) – ALMAC DIAGNOSTICS & DDRD TEST FROM JAN 2014: PUBLICATIONS (2) – THE BROAD SPECTRUM OF MOLECULAR DIAGNOSTICS 2014: INDUSTRY (2) – PATH XL & TISSUEMARK TEST 2014: TEACHING IN MOLECULAR PATHOLOGY JAN 2015: RENEWAL OF NI BIOBANK FUNDING APRIL 2015: CR-UK ACCELERATOR AWARD OCT 2015: A REGIONAL, FULLY COMMISSIONED MOLECULAR DIAGNOSTIC SERVICE OCT 2015: PRECISON MEDICINE CATAPULT CENTRE OF EXCELLENCE ? MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015
  • 144. BIOBANKINGLGF CCRCB - PM BIOINF., DP (LAB), OFFICESGF MOL PATH / MOL DX LAB1ST F BIOMARKER DISCOVERY PROG.2ND F TARG. DRUG DISCOVERY PROG.3RD F MST, PH, JJ RK ? MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015
  • 145. ? MARCH 2011 SEPT 2011 MARCH 2012 FROM MARCH 2012 JAN 2013 JAN 2014 FROM JAN 2014 2014 JAN 2015 APR 2015 OCT 2015 INTEGRATION… … OF TISSUE PATHOLOGY WITH MOLECULAR PATHOLOGY … OF TECHNOLOGY PLATFORMS, IT SYSTEMS AND MATERIALS (BIOBANKS) … OF TALENT, THROUGH TRAINING … OF DIAGNOSTICS AND RESEARCH, THROUGH COMMON RESOURCES & LABS … OF HEALTHCARE AND ACADEMIA WITH INDUSTRY, THROUGH QUALITY
  • 147. 5 (4?) (2?) TISSUE PATHOLOGY SERVICES REGIONAL MOLECULAR PATHOLOGY DX SERVICE NI-MPL PRECISION MEDICINE CATAPULT INVEST NI A SINGLE, INTEGRATED, HOLLISTIC INFORMATION AND DIAGNOSTIC IMAGING SYSTEM FOR NI