Genetics, Molecular Profiling & Epidemiology of …...Genetics, Molecular Profiling & Epidemiology...
Transcript of Genetics, Molecular Profiling & Epidemiology of …...Genetics, Molecular Profiling & Epidemiology...
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Genetics, Molecular Profiling &
Epidemiology of Early Stage MelanomaWinship Cancer Institute
2016 Melanoma Conference
Atlanta, GA, Feb. 27, 2016
Sancy Leachman, M.D., Ph.D.
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Disclosures & Conflicts
• Myriad Genetics Laboratory – MSAB (honorarium), Early Access
Program for myPath & myRisk (limited number of free tests)
• Castle Biosciences – MSAB (honorarium)
• Apple Support – Research Kit Tools, Thought Leader Meeting, &
Marketing
• NOTE: Mole Mapper is free, open source, and no revenue is
being generated from sponsorships.
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Overview: Early Detection through Genetic & Epidemiologic
Tools
• Genetic tools: Identifying patients at-risk
• Epidemiologic Tools
– War on Melanoma Community Registry
– Mole Mapper iPhone App
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Melanoma Genetics & Genetic Testing
Germline – Blood tests that tell you how much risk the patient has of
developing a melanoma (predisposition testing)
Somatic – Tests that tell you how likely your patient’s tumor has of being a
melanoma (diagnostic testing)
Somatic – Tests that tell you how likely your patient’s melanoma
has of metastasizing (being a lethal melanoma—prognostic
testing)
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Context: Germline Testing of Highest Risk Patients for Early
Identification & Screening
Vulnerable Phenotype
Light skin, eyes, hair, family history
Freckles, Sunburns, immunosuppression
High-Risk
Red hair (MC1R homozygote); > 100 nevi;
>5 dysplastic nevi; personal hx MM; AKs,
BCCs, SCCs (genes & environment)
Highest/Syndromic
“Rule of Threes” and Other Cancers
CDKN2A (p16, ARF), CDK4, TERT,
POT1, XP, BAP1, PTEN
Risk Level
(relative to
Gen. Pop.)
30+X
4-8X
2X
Proportion of
Melanoma Population
0.2-2.0%
≈15-30%
Almost
everybody
else!?
Almost
everybody
else!?
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≥3 invasive melanomas
in blood relatives≥3 melanomas in an individual
≥3 melanoma + pancreatic
OR astrocytoma (*2) in FDRs
OR unusual associations:
Uveal melanoma, lung
adenocarcinoma,
mesothelioma,
paraganglioma, clear cell
renal carcinoma
Identifying Hereditary Melanoma: Consider the “Rule of Twos & Threes”
*Only 1 criteria needs to be met. Consideration should be
given to age at diagnosis, UV exposure, skin type, and
ethnicity, as there may be exceptions to the “Rule of Twos
& Threes.” Leachman, et al. JAAD 2009
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Germline genetic testing: Single genes, panels of genes, or exomeNGS, test sequencing?
• Single gene – when phenotype suggests a particular mutation
• Gene panel – perhaps better, if cost is no object
• Exome/Genome sequencing – interpretation difficult
• Testing order: based on phenotype, history, cost
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Navigating the Genetic Testing Options for
Hereditary Patients
Only Melanoma
+/- Pancreatic OR
+/- Astrocytoma
Melanoma
+ Uveal Melanoma OR
+ Lung Adenocarcinoma OR
+ Paraganglioma OR
+ Mesothelioma OR
+ Clear Cell Renal Carcinoma
Melanoma in special context
Multiple other cancers/signs
including:
• SCC/BCC
• Breast, Thyroid, Endometrial
• Prostate
• Renal
• Colon
CDKN2A
If Negative
CDK4If Negative
BAP1
If Negative
PANEL TEST
Work with Genetic Counseling
Assure Genes Associated with Observed Cancers
Are Contained in the Panel
Other Syndrome?
• Xeroderma pigmentosum
• Cowden
• Tumor-specific (e.g.
Breast or Colon)
FAMMM
Cutaneous Cancer SyndromeBAP-1 Pattern
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The Testing Process
Identify Candidates Using
“Rule of Twos & Threes”
Refer for Genetic
Counseling
Mutation
Does NOT
Desire
Testing
Desires Testing
Mutation of
Uncertain
Significance
No
Mutation
Manage Based on Family
History
• Add Other CA
Screening
• Test 1st Degree
• Select Family
Member with
Melanoma
• Preauthorize
• Send to a CLIA Lab
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Genetic Diagnostic Testing for Melanoma
• Fundamentally different than predisposition testing
– Purpose is to determine if a lesion is melanoma, not if the
individual is at risk for melanoma
– Performed on tissue, not blood
– Provides adjunctive measure to complement histology in
ambiguous cases
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Fluorescent In-Situ Hybridization (FISH)
• Two clinically available assays based on gene copy number
• Most studies on unambiguous lesions
– Sensitivity 87-94%; specificity 95-98%
• Less sensitivity in ambiguous lesions (43%)
• Subjective, requires specialized expertise
• Chromosomes: 6p25 (RREB1), 8q24 (MYC), 9p21
(CDKN2A/p16), 11q13 (CCND1), centromere (CEN9)
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Comparative Genomic Hybridization (CGH)
• Also detects chromosomal gains and losses
• Comparison between tumor DNA & control DNA to
evaluate entire genome
• Sensitivity & specificity not as well-characterized
• Most studies done on unambiguous cases
• Some subjectivity, but less than FISH
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Gene Expression Profiling (GEP): Quantitative Reverse
Transcription Polymerase Chain
Reaction
• Evaluates expression of RNA rather than mutations in
DNA
• Panel of 23 genes used
• Expression algorithm used to generate a score that falls
into a benign or malignant range
• Objective and quantitative
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Comparison of Diagnostic Genetic Tests for Melanoma
FISH CGH qRT-PCR
Advantages Minimal tissue
required; single-cell
resolution; can detect
translocations
Can assess all 23
chromosomes; no
proficiency in
fluorescent
microscopy required
Provides additional
diagnostic value in
discriminating benign
vs malignant lesions
Limitations Visualizes tiny
fraction of genome;
expertise
requirement
Can’t assess
intratumoral
heterogeneity;
dilution by stroma
New test,
publications in
progress; no
correlation with
outcome
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Genetic Prognostic Testing for Melanoma
• Fundamentally different than predisposition or diagnostic
testing
– Purpose is to determine if a lesion is a potentially deadly
melanoma
– Performed on tissue, not blood
– Provides adjunctive measure to complement histologic (e.g.,
Breslow depth) and other prognostic (e.g., sentinel node
biopsy) data
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• Evaluates risk of recurrence for cutaneous melanoma patients
• Separates tumors into Class 1 (less risk) and Class 2 (more risk)
• High positive predictive value for Class 2
• High negative predictive value for Class 1
• Allows improved risk stratification that supports consideration of
heightened follow-up (maybe adjuvant therapy in future)
Hodi, et al. 2010; Joseph, et al. 2014; Lyle, et al. 2014; Menzies, et al. 2014; Nishino, et al. 2014; Steinman,
et al. 2014; Del Vecchio, et al. 2015; Kaufman, et al. 2015; Tsai, et al. 2015
Gene Expression Profiling (GEP): Quantitative Reverse
Transcription Polymerase Chain
Reaction
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5-yr DMFS
Class 1 = 100%
Class 2 = 58%
Gerami, et al. Clin Cancer Res. 2015;21(1),175-183.
Distant Metastasis Free Survival
Class 1
(n=76)
Class 2
(n=141)
Events 14 71
5-yr DMFS 82% 46%
Class 1
Class 2
% fre
e o
f m
eta
sta
sis
100%
75%
50%
25%
0%
n=217
p<0.0001
Time (years)
1086420
Gerami, et al. J Am Acad Dermatol. 2015;72(5):780-5.e3.
Gene Expression Profiling (GEP): Class 1 and 2
Discriminates Risk of Recurrence
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Putting it all together: An integrated approach to “choice points”
in melanoma patients
Patient calls
with concern
Expedited
Appointment
Yes
Routine
Appointment
New
∆ing
Hx?No
History
Physical
• Risk assess
• FBSE
• Dermoscopy
Low/Moderate Risk
Education &
Appropriate F/U
High/Extreme Risk
Photography?
Biopsy?
Referral?
Photography?
• Total body
• Select nevi
• Combination
Biopsy? Referral?
Additional Imaging
• Confocal
• OCT
• Hyperspectral
Reassured
(Monitor)Benign or Equivocal Malignant
Consider 2nd Opinion
Consider Molecular Dx
*Excise
*Guidelines
*Multidisciplinary
Genetic
Counselor
Genetic
Testing?
Consider
Mol. Prog.
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Epidemiologic Tools: War on Melanoma Community Registry
• Walsh Family $$
• 25,000 Living Patients
• Patients, Family, Friends
• IRB-Approved
• Collaborative
• >4800 total
• >3500 Patients
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Early Detection: Oregon vs Schleswig-Holstein
Similar Populations, Different Health Care System
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The War Plan: A Statewide Population
Sciences Experiment!
Massive Public Education CampaignProviders Skin Care Services Lay Public
Grass Roots AND Top-Down
Discovery of Suspicious Lesions
Screening & Biopsy If Needed
Early Stage Removal If Needed
Expansion To Other States
Experimental Design
Baseline Measures:
• Obstacles
• Tumor Depth/Stage
• Cost
• Comparison to controls
Repeated MeasuresSuccessful
Unsu
cce
ssfu
l
Refine & Repeat
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A Massive Campaign Requires A Massive Army
Melanoma Community RegistryPatients Family Friends
Education:
• Symposia
• Curriculum
• Outreach
Activism:
• Legislation
• Community Events
• Fundraising
Research:
• Questionnaires
• Imaging
• Phone Apps
• New Tests
Novel Application Of Volunteerism Tools
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Over 800 Participants
• 126 Volunteers
• 21 Providers
• 18 from registry
Pilot Experiment: Skin Cancer Research Expo and Sun Safety
Event, May 30, 2015
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Melanoma Community Registry
• 127 New Registrants Enrolled
• 244 Risk & Phenotype Question-
naires Completed
Skin Cancer Research Expo and Sun Safety Event
May 30, 2015
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Knight BioLibrary
• 162 blood draws
• 810 - 26 ml vials
• 2,400 aliquots
Skin Cancer Research Expo and Sun Safety Event
May 30, 2015
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Skin Checks and
Sun safety
• 247 screened
• 55 recommended
biopsies
• 4 possible melanoma
• 5 possible SCC
• 13 possible basal
cells
• 55 toured DermSpectra
Skin Cancer Research Expo and Sun Safety Event
May 30, 2015
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Research Demos/Info
• Knight Clinical Trials – 50
ppl
• Tan Meter – 175 ppl
• Mole Mapper – 20
downloaded app
• OCTRI – 65 healthy
controls
Skin Cancer Research Expo and Sun Safety Event
May 30, 2015
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Social Media
- 45 social posts on
Facebook, Twitter, &
- Reached 105,608
users across all
Platforms
- 15,000 saw our top Post
- 1500 “re-engagements” (re-tweets,
comments, shares, etc.)
- 1400 clicks to our registry & sites
- 600 YouTube views
Skin Cancer Research Expo and Sun Safety Event
May 30, 2015
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Preliminary Data: The Registry Wants to
Participate
Opportunities to Participate:
I want to attend educational
conferences
I want to attend focus groups to
provide my opinion about
questionnaire development or
other documents for participants.
I want to attend melanoma-
centric events
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Preliminary Data: The Registry Will Participate
In Research
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Where do the patients come from?
Oregon Health & Science University (OHSU)
31%
Providence Health & Systems20%
Kaiser Permanente11%
Legacy Health9%
Other22%
Veterans Administration2%
I prefer not to provide access to this information
electronically, but I will provide records as hard-
copy2%
I prefer not to privide access to this information
3%
Other7%
Q19: HEALTH CARE SYSTEMS THAT HAVE MY ELECTRONIC MEDIAL RECORDS INCLUDE:
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War on Melanoma Community Registry: Representative
Participants for Research
62%
24%
3%
1%3%
7%
Q26: What was your Stage of Melanoma (n=1162)
In Situ Stage I or II Stage III Stage III In transit Stage IV Don't know
• Representative categories of
patients
• Controls included
• Eager to participate
• A tool to better understand
melanoma at every level
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Mole Mapper: A tool within a tool
• Dream: To make this app OUR app, to facilitate mole
tracking and collaboration worldwide!
FAQ’s:Cannot diagnose melanoma or make
recommendations for care
Can measure & track nevi
Available in iTunes Store (NOT PLUS)
Part of Apple’s ResearchKit Suite of
Apps
Android version in development
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For “The People:” Provide a free, quantitative
mole-tracking tool
Short-Term Goals for the Mole Mapper App
For Providers
& Patients:
Facilitate
productive clinic
visits
Participant
Clinician Researcher
For Researchers:
Conduct a large-
scale,
crowdsourced,
research study
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Design: Current Work Flow
Mole Map
Keep Data
On Phone
No back-up
Sage
Bio-
network
OHSU War
on
Melanoma
Cohort
Consent
to Share
Data
Strip Identifiers
De-Identified
Data
PHILinkers Image Analysis
& Challenges
Human Research
Citizen Science
Optimization
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Challenges for the Development of a Melanoma Research App:
Legal & Regulatory
Bureau of Consumer
Protectionhttps://www.ftc.gov/news-
events/press-releases/2015/02/ftc-
cracks-down-marketers-
melanoma-detection-apps
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Challenges: Clinical Research App Development is Complex
App
Launch
OHSU
Developer
Dan Webster
Sage
Bionetworks
ResearchKit
Thought
Leaders
Team Effort:
• OHSU Leadership
• Knight Leadership
• Clinical Trials/CTSA
• Dermatology
• Strategic Communications
• Social Media
• IRB
• Contracts
• Legal Affairs
• ITG Security
• Technology Transfer
• Outside consultants
• Funding
• Modification for ResearchKit
• Specifications
• Testing
• Pre-launch Meetings
• Guidance
• Prioritization
• Publicity
• Essential
Collaborator
• Back-end
• Big-data
Oct. 15!
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Post-Launch Challenges: A Three-Year Plan for Success
• Intensive & ongoing needs analysis, team building
• Optimized data flow
• Nurturing the cohort
• De-bugging, improved usability
• Evolving/Adding “new features” functionality
• Development & release process, including Android
• Serving outside collaborators
• Obtaining preliminary data
• Writing grants/proposals
• Business plan for sustainability
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Progress: What does the App do now?
• Map Measure Monitor Monthly
“Map, Measure, and Monitor Moles Monthly”
Monitor Monthly
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Informed Consent Is Required Before Data Release Occurs:
Novel Process
Go through formal consent on app
Pass test to demonstrate understanding
of risks and benefits
(Courtesy of John Wilbanks &
Sage Bionetworks)
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Data: Includes Baseline Demographic and Risk Questions
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Data: How much interest has been generated for
Mole Mapper?
0
5,000
10,000
15,000
20,000
25,000
30,000
35,000
10/23 11/3 11/9 11/16 11/24 12/7 1/7 2/4 2/19
Mole Mapper Stats
App Store Views Downloads Registrants Moles Measured
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Data: Building a Cohort of Thousands in Months (4 months)
8,019 App Downloads
2,204 Consented Participants
2,787 Mole Measurements & Mole Photos
~13% of participants are melanoma
patients/survivors, ~27% with family history
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Data: Mole Size Is Consistent with Clinical Experience
0.0
0.5
1.0
1.5
2.0
2.5
3.0
3.5
4.0
4.5
5.0
5.5
6.0
6.5
7.0
7.5
8.0
8.5
9.0
9.5
10.0
10.5
11.0
11.5
12.0
12.5
13.0
13.5
14.0
14.5
15.0
0
25
50
75
100
125
150
175
200
225
Mole Diameter (mm)
Num
ber
of M
ole
Mea
sure
men
ts
Mole Measurement Distribution
Average Mole Size: 3.83mm
1 std. deviation larger:
5.97mm
in keeping with 6mm “eraser”
recommendation for vigilance
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Data: User Comments
The dashboard helped me discover my
statistically significant “Ugly Duckling”:
7.1 mm fried-egg on my back
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Citizen Science: Patient-Driven Improvements
“Sometimes it’s hard
to take pictures and
keep the reference
next to the mole”
Participant
Clinician Researcher
“I don’t always have
a coin on me for
measuring”
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Provide a free, melanoma triage tool - maybe
a diagnostic tool?
Opportunities: Long-Term Goals for the Mole Mapper App
Reduce
unnecessary
patient visits
and detect
melanoma
earlier
Participant
Clinician Researcher
Optimize and
automate image
analysis for diagnostic
purposes?
Incorporate advanced
imaging tools and
algorithms?
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Opportunities: Data will be “open-sourced” to qualified
researchers worldwide
48
Participant
Clinician Researcher
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Opportunities: Cohort will be “crowd-sourced” to contribute
data worldwide
Participant
Clinician Researcher
Chemoprevention Trial?
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Summary: Germline Genetic Testing to Identify Patients at
Highest Risk for Screening
• Identify the highest risk individuals
• Unlikely you will find many of these patients
• Likely the tests will have changed between now and the
time you identify them
• Identify a genetic counselor in your area and refer, work
with them to assure appropriate follow-up
• Refer to a registry: [email protected]
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• Diagnostic genetic testing to assess likelihood that a
lesion is malignant
– FISH, CGH, qRT-PCR available
– Little outcome data on any
– Little data on ambiguous lesions
– Can help to guide surgical removal & treatment
• Prognostic genetic testing to assess likelihood that a
lesion is deadly
– qRT-PCR available
– Growing data to support (David Lawson)
– Can help to guide follow-up
Summary: Diagnostic & Prognostic Genetic Testing to Identify
Patients Needing Additional
Care
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• The next era of cancer care will emphasize prevention and
early detection
• Engaging patients through a registry/app is powerful
• It takes a village
• To Join/refer: “War on Melanoma”
• Try the App: www.molemapper.org and provide feedback
• Contact me: [email protected]
• Together we can make this happen!
Summary: Epidemiologic and Technologic Tools Can
Contribute Directly to Research Efforts
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Acknowledgements!
Dan & Courtney Webster
Stephen Friend
Andrew Trister
Divya Nag
Jeff Williams
Lisa Domenico
Berwick Baker Edelson Guild
Norris
Edison Eberting
Gershenwald
Olbricht Rigel
Kashani Tumeh
Kirkwood Swetter
Kean
Zone Halpern
Geller
Weinstock
Thought
Leaders