Post on 21-Jun-2020
Laboratory Medicine Program
“Next-Gen” Pathology: Integrating New Technologies
Sylvia L. Asa, MD, PhD
Pathologist-in-Chief Medical Director
Laboratory Medicine Program University Health Network
Laboratory Medicine Program
What Is Pathology?
• Pathology, from the greek πάθος, pathos, “feeling, suffering” and λογία, logia “study of”
• the study and diagnosis of disease through examination of organs, tissues, bodily fluids, and whole bodies
Laboratory Medicine Program
The Origins of Pathology
• The Autopsy • Dates back to ancient Egypt and Greece • The tool of the Physician-Scientist
– To identify the cause of death – To explain signs and symptoms of disease
Laboratory Medicine Program
The First Clinical Applications
• Surgical pathology by surgeons • Laboratory hematology by hematologists • Biochemistry in nephrology and endocrinology • Microbiology in infectious diseases
Louis DN and Young RH: Keen Minds to Explore
the Dark Continents of Disease 2011
Laboratory Medicine Program
What Has Pathology Become? • Laboratory-based clinical testing
– Focus on QA/QC/GLP
• Microscope-based anatomical pathology • Custodianship of patient samples on behalf of
patient • Representative of patient in Quality of Care
events (M&M rounds) • Minimal or no patient contact
Laboratory Medicine Program
The Pathology Diagnosis
• The pathological diagnosis is the gold standard that indicates the presence or absence of disease, the type of disease, and its classification
• Therapeutic decisions are based on the pathology diagnosis – a misdiagnosis can result in unnecessary, harmful and
aggressive therapy or inadequate treatment
Laboratory Medicine Program
BREAST
• Atypia on breast core needle biopsies: reproducibility and significance.
• The impact of inter-observer variation in pathological assessment of node-negative breast cancer on clinical risk assessment and patient selection for adjuvant systemic treatment.
• Inter-observer reproducibility of HER2 immunohistochemical assessment and concordance with fluorescent in situ hybridization (FISH): pathologist assessment compared to quantitative image analysis
Morphologic Pathology is an Interpretive Discipline
Laboratory Medicine Program
Morphologic Pathology is an Interpretive Discipline
GENITOURINARY
• Interobserver variability between expert urologic pathologists for extraprostatic extension and surgical margin status in radical prostatectomy specimens
• Intraobserver and interobserver variability of fuhrman and modified fuhrman grading systems for conventional renal cell carcinoma
• Intra- and interobserver reproducibility of interpretation of immunohistochemical stains of prostate cancer
Laboratory Medicine Program
What Does This Mean for Patients?
• Is the diagnosis right? • Is the treatment right? • Is the prognosis right? • Was the trial right? • Are the data reliable?
Laboratory Medicine Program
Pathology 2000-2010
Laboratory Medicine Program
Challenges for 2020
• Volume – aging population – higher sensitivity for early disease
• Demand – sophisticated knowledgeable population – Culture of “instant gratification”
• New technologies – genomics – proteomics – informatics – robotics ‘tissue soup’ instead of tissue
11
Laboratory Medicine Program
The Challenge for 2020
• Faster • Better
– Higher quality – Personalized
• Cheaper
• Innovative
Laboratory Medicine Program
The New Paradigm: Faster
• Pathology must be faster – “Same Day” diagnosis
– Automation
– 24/7 labs
Laboratory Medicine Program
The New Paradigm: Faster • Speech-recognition integrated with LIS means instant reporting without the need for dictatyping
Laboratory Medicine Program
• Synoptic Reporting – Complete
• Standardized formats (CAP checklists) – Adaptable and flexible
• No more verbose reports that no one reads! – Database technology
• Statistics collection • Administrative tracking • QA monitoring • Academic data mining
The New Paradigm: Better
Laboratory Medicine Program
What Is “Correct”? • Objective classification by
– mRNA expression – DNA sequencing – Response to therapy
The New Paradigm: Better
Laboratory Medicine Program
Technologic Advances: “omics”
HT-Sequencing DNA
Microarray Expression Profiling
RNA
Mass Spectrometry Protein
Metabolomics
Laboratory Medicine Program
The New Paradigm: Better • Subspecialty Pathology
– All cases reported by a pathologist with expertise in the specific subspecialty required
– Benefits: • Better quality and faster patient care • Fiscal responsibility: 1 pathologist per case • Pathologist satisfaction – enhanced academic excellence
– Challenges: • Requirement for appropriate staffing in all areas and
redundancy
Laboratory Medicine Program 19
Digital Pathology • Whole slide imaging
• A disruptive enabling technology
Laboratory Medicine Program
Digital Pathology Enables
• Remote access
• Multiple viewers
• Immediate access to the right pathologist at the right time
Laboratory Medicine Program
Computer-Assisted Diagnostics
Digital Pathology Enables
• Automated analysis of: – Measurement – Mitoses – Ki67 LI – Other IHC
• intensity • distribution
– Her2 FISH – Hematology
• Cellavision
• QA of technical quality – Section thickness – Stain quality
? Need for Westgard rules in AP?
Laboratory Medicine Program
• Novel approaches to address issues of inter- and intra-observer variability
GENIE© (GENetic Imagery Exploration) is a GP software system that builds automatic feature extraction algorithms for image analysis, utilizing spectral and spatial signatures of the images
“GENIE© can recognize benign and malignant areas in H&E-stained slides and does not have intra- or inter-observer variation”
Digital Pathology Enables
Laboratory Medicine Program
A Disruptive Technology
In a time of drastic change it is the learners who inherit
the future. The learned usually find themselves
equipped to live in a world that no longer exists.
Eric Hoffer
Laboratory Medicine Program
Requirements for Full Adoption
• Workflow integration – From the lab to the pathologist
• LIS integration – Barcodes – Slide tracking and retrieval
Laboratory Medicine Program
Critical Requirement
$$$ Business Case • Reduced microscope budget • Analysis of time spent
– Finding slides – Matching slides to case – Shipping slides – Retrieving slides for post-hoc review
Laboratory Medicine Program
Informatics: The LIS
26
• LIS as part of the e-chart
• LIS e-orders and processes
• Specimen tracking and management
• Integration of lab data from all disciplines into a consolidated report
Laboratory Medicine Program
• Patient-Centred Care
• Individualized diagnostics
• Targeted therapies
All based on “omics”
Will “omics” replace pathology?
27
The New Paradigm: Personalized
Laboratory Medicine Program
Targeted Therapies • Hormone receptors in breast cancer • Herceptin
DP does it better ……
Laboratory Medicine Program
EGF-R Rx in Lung and Colon Cancer
Laboratory Medicine Program
And When It Doesn’t Work?
• K-ras mutations in Colon Cancer
Laboratory Medicine Program
What About Next-Gen Sequencing? The Genome Institute at Washington University: Software • BLASTaid – A simple interface for byte indexing a WU-BLAST multi-part report for faster access. • BreakDancer – WashU structural variant (SV) detection algorithm for paired-end data. • CMDS – WashU algorithm for identifying recurrent DNA copy number changes. • cnvHMM – WashU copy number variant (CNV) detection algorithm for Illumina/Solexa data. • ComComb – WashU algorithm for identifying common combinations of mutations across tumor types. • EXOR – Filters mutually exclusive alignment events and defines a position-specific reciprocal best alignment set. • FASTAParse – A light-weight parsing module for handling FASTA formatted sequence within larger perl applications. • Gen Bell – Calculates Bell’s polynomials. • GSTAT – WashU analysis tools • Miropeats – Displays DNA sequence similarity information graphically. • MuSiC – The MuSiC suite is a set of tools aimed at determining the significance of somatic mutations discovered within a given cohort
of cancer samples, incorporating the cohort's alignment data, variant lists and any relevant clinical data. • Overgo Maker – Output overgo sequences ready for ordering from a fasta input file. • Pairoscope – WashU tool for visualizing SVs from Illumina/Solexa paired-end reads. • PathScan – WashU algorithm that assesses significance of gene groups by Boolean tagging each gene as mutated or not mutated. • Pathway Tools – WashU annotation tools. • PolyScan – Automatic indel and SNP detection to the analysis of human re-sequencing data. • R Functions for Correlation Analysis – Some of the functions we use with R. • Semblance – Assess a genome assembly by comparison to finished clones. • SomaticSniper – WashU somatic SNV detection algorithm for whole genome resequencing data. • SWT – WashU Sliding Window Tool for detecting copy number variants from Illumina/Solexa data. • TIGRA_SV – Tigra_sv is a program that conducts targeted local assembly of structural variation (SV) using the iterative graph routing
assembly (TIGRA) algorithm. • UR – A Class Framework and Object/ Relational Mapper (ORM) for Perl. • VarScan – Somatic and germline variant detection for massively parallel sequencing
Laboratory Medicine Program
The Future of Pathology?
$15.00 each $1000.00 each
Laboratory Medicine Program
Epigenetic Control: Can it Override the Genotype?
N Engl J Med. 2007 Feb 15;356(7):731-3
Laboratory Medicine Program
BRAF Mutations in Melanocytes
• ̃80% of benign nevi (? early event) • 50% of cutaneous melanoma
– Both superficial spreading and nodular – Non-overlapping with NRAS mutations
• Epidemiologic evidence of UV-induction – Not supported by T→A transversion – ? Secondary effect of UV damage e.g. ROS
• Not in acral melanoma (Kit mutations) • Not in ocular melanoma (GNAQ or GNA11) • Not in mucosal melanoma (Kit, ? CDKN2A)
Laboratory Medicine Program
BRAF Inhibition in Melanoma
• Sorafenib – Failed in phase III clinical trial
• Vemurafenib – Success in pivotal phase III study (BRIM-3)
• OS 84% cf 64% with dacarbazine • Estimated median PFS 5.3 mo cf 1.6 mo on dacarbazine
– licensed by the US FDA as Zelboraf for the treatment of metastatic melanoma in August 2011
Laboratory Medicine Program
• Most common genetic event in thyroid cancer
• Diagnostic marker of PTC • Genotype-phenotype correlations
– BRAFV600E in classical variant PTC (40-50%) – BRAFK601E in FVPTC (rare) – VK600-1E deletion (BRAFVK600-1E) in solid variant (single case)
• Prognostic significance controversial
BRAF Mutation in Thyroid Cancer
Laboratory Medicine Program
BRAF Kinase Inhibition Arrests Thyroid Cancer Growth In Vivo
Salvatore G et al, Clin Cancer Res 2006;12:1623-9
However ………
Clinical trials have
failed to show
effectiveness of
BRAF inhibitors
in thyroid cancer
Laboratory Medicine Program
The Importance of Informatics
• Not just to collect data • Not just to analyze data • Not just to report data
The Importance of Data Integration
• To collect, analyze and report integrated data
in the clinical context
Laboratory Medicine Program
What Is Anatomical Pathology?
• Integrative morphology-based interpretation
Gross Morphology
Chemistry on a glass slide
Immunoassay on a glass slide
Laboratory Medicine Program
What About Academia?
Laboratory Medicine Program
Garbage In – Garbage Out
• We have the technical capacity to produce low quality data from low quality analytes with unprecedented efficiency
• We arrive at the wrong answer with unprecedented speed
Laboratory Medicine Program
The New Paradigm: Innovative • Pathology / Laboratory Medicine
– critical players in ensuring highest quality translational research:
• The right specimen, the right test, the right interpretation
• Biobanking in Translational Research – Value is in technical & diagnostic excellence of specimens
Challenge: • Balance legal, regulatory & institutional requirements
for Diagnostic Tissue vs Biobanking of Research Tissue Cheung, Martin & Asa, CMAJ 2013;185(2):135-9
Laboratory Medicine Program
Clinical Laboratory
Patient X
Diagnostic stained slides
Diagnostic paraffin blocks
Patient X
Diagnostic frozen
material
Research Biobank
Research frozen
material
Research paraffin blocks
Diagnostic wet tissue(post-sampling)
Diagnostic wet tissue(pre-sampling)
Archived diagnostic tissue
Excess diagnostic tissue
Research stained slides
Weeks
Years
Post-retention excess diagnostic tissue
Research wet tissue from research-only
procedure
Patient X
Laboratory Medicine Program 44
• To provide the right diagnosis
• To provide the right material
• To provide the right leads
• To provide the right experiments
• To evaluate the consequences of genetic manipulation
The Expanding Role of Lab Medicine
Laboratory Medicine Program
Where Are We Heading? • Predictive genetics/epigenetics will define
individual risk and prognosis
• Targeted prevention
• Monitoring for onset with multimodal biomarkers
• Targeted therapies based on host genetics and epigenetics
• Signatures of stage-specific progression
• Mechanisms of escape
Laboratory Medicine Program
The Uncontestable Trends • Clinicians want increasingly detailed, reliable
and relevant information from specimen analyses that can be translated into optimal treatments
• Pathology must re-educate and re-invent itself if it is to maintain the central role it plays as the ultimate arbiter of treatment
“As is your pathology, so goes your clinical care”
Sir William Osler
Laboratory Medicine Program
The New Paradigm • Pathology labs must be faster and better
– QA is the sine qua non
• Pathology reports must be comprehensive – Incorporation of molecular, biochemical and other data
is critical to the consultative value of the report
• Pathology data must be synoptic and database-oriented
• Pathology must be innovative
Laboratory Medicine Program
The Virtual Autopsy
Laboratory Medicine Program After “The Anatomy Lecture of Dr. Nicolaes Tulp” – Rembrandt, 1632
(Courtesy of Dr. Carlos Cordón, New York, USA)
Laboratory Medicine Program
2020 Vision
• Large automated core laboratories • Electronic support for specimen tracking
and handling, QMS • Highly subspecialized teams providing a
matrix of subject and technical expertise – Biochemistry - Microbiology – Hematology, Transfusion & Hematopathology – Subspecialty Anatomical Pathology – HLA - Molecular/Genetics
“Blurring the lines between AP and CP”
Laboratory Medicine Program
Critical Elements
• Specimen tracking
• Specimen ID
What next?
• Patient ID
Laboratory Medicine Program
• Specimen tracking • Workload tracking
and personnel • Supplies and
equipment • QA processes
“………sophisticated refrigerators and Radio Frequency Identification (RFID) technology will be able to monitor the products household members use, create shopping lists, and even communicate with other networked devices to arrange deliveries”
Laboratory Management in the Electronic Era
Laboratory Medicine Program
Comprehensive integrated reports including: • Incorporation and integration of clinical,
radiologic, and biochemical data • Germline SNPs and mutations
– predisposition, metabolic profiles
• Tumor or tissue somatic events – morphologic, immunohistochemical, flow
cytometric, cytogenetic and molecular data
• Immunologic responses
Laboratory Data Management in the “Next-Gen” Era
Laboratory Medicine Program
Digital radiology
Digital cardiology
Family and medical history Electronic medical record
PATHOLOGY: the centre of Personalized
Cancer Medicine
Endoscopy
2020 Pathology
Laboratory Medicine Program
2020 Pathologist
Laboratory Medicine Program
The Future of Pathology
The best way to predict the future is to invent it
Alan Kay