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Transcript of Non-profit research institute and world’s leading biobank.
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Non-profit research institute and world’s leading biobank
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Copying Leads to “Spelling Mistakes”
Some Diversity Enables Us To Resist Infectious Disease
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99.6%identical
0.4%unique
Science magazine’s “Breakthrough of the Year” in 2007
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90% chance that they do (freq. > 1%)Gabriel et al. Science, 2002
Compare two chromosomes from any two people
Only ~ 1 in 1000 bases differ
Do these same sites show variation in other people?
Most Genetic Variation is Shared Among Us All
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Out of Africa
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Measuring Genetic Variation is Now Possible, Comprehensive and Cost Effective
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Heart Disease, Diabetes Cancer, Obesity
All known single Gene diseases
~2,000
Don’t we already know about many Human Disease Genes?
Multi-Gene Diseases
Impact onPublic Health
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GWAS Studies
Manolio et al. (2008) J. Cli. Inv. 118(5):1590
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Maher, B. (2008) Nature 456
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Many Differences in the Way Individuals Respond to Rx Drugs are Clear Already
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CYP2C19
$8 Billion inAnnual Sales
Prasugrel Just Approved by FDA
Plavix Plavix*
liver
Plavix Must Be Activated in the Liver
Alternative Drug
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Tamoxifen is a Pro-Drug
7-10% of Women do not activate Tamoxifen
Alternative: aromatase inhibitors
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Genome-informed medicine will not be widelyAdopted until it is demonstrated to work in the clinic
How data are provided to patient and doctor will Be critical determinants of successful adoption (i.e. what’s the right system?)
Goal is to Determine Whether Using Personal Genome Information Will Be Useful In Medicine?
Correlations in Observational Data
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Observational Data Can Be Useful
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“American Family Study”
“We desperately need, in this country, a large-scale, prospective, population-based cohort study. And we need to enroll at a minimum half a million people. We would need to have their environmental exposures carefully monitored and recorded, their DNA information recorded, their electronic medical records included, and have them consented for all sorts of other follow-ups.”
June 6, 2008 Interview with Science Magazine
Dr. Francis Collins
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FreeResearch study
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2 million sites of variation
2,000 sites of knownRelevance to drug action
The CPMC Uses Two “GeneChips”
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D-MET Coverage
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Coriell GenomeCenter
CLIA!
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Education of Medical Professionals
Input From Medical Professionals
“Don’t even tell me it’s a wart.”
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Who can participate and how are they recruited?
Eligibility:You must be at least 18 years oldYou must have an email address and access to the internet
Recruitment Mechanisms:Community-based recruitmentCancer Clinic-based recruitmentPrimary Care-based recruitment
Community and
Employer
Cancer
ChronicDisease
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The CPMC Web Portal
cpmc.coriell.org
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Jane Doe
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Collection of Detailed Family, Medical History, Medication, Lifestyle and Demographic Info
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What information do we collect?All cohorts: MFLQ
Demographic InformationMedical HistoryMedicationsFamily HistoryLifestyle InformationGenetic Knowledge assessment
Cancer Cohorts:Cancer Registry DataCancer-related health recordsPrescribing Records
Primary Care Cohorts:Electronic Health RecordsPrescribing Records
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Who decides what genetic information is reported?
Informed Cohort Oversight Board (ICOB), an external advisory board. Composed of scientists, medical professionals, ethicist, community members.
Vote on whether conditions are potentially actionable.
Meet at least twice a year. New results then reported toall participants.
Actions completely transparent. RNR Foundation
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CPMC Risk Reporting
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CPMC Process Overview
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Genetic Variant/Disease SelectionSearch Public Databases for
published GWASNHGRI GWAS catalogue; HuGENet™; PubMed
Generate list of Health Condition/Genetic variant papers
Selection criteria for Genetic Variant:
•Replicated associations•Adequately sized studies•On Affymetrix 6.0 GeneChip (currently)
Final list of Health Condition/Genetic variants
Selection of Health Condition:
•Health conditions only (no Traits)•Is disease potentially ‘actionable’?•Assess by review of medical society policies and recommendations
Prepare Document with Health Condition and a Genetic Variant Summaries for submission to ICOB
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CPMC Risk Reporting
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Risk Estimation
Evaluate Study Design and Size Select study that will provide most representative and valid risk estimates
Assess Study Quality Evaluate methods used for determining phenotype and genotype
If study reports relative risk – report risks directly
If study reports odds ratios – estimate relative risk and report estimated risks
Step 1: Study Selection
Step 2: Risk Determination
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Study Selection
PubMed &
HuG
ENet TM
Select studies
from highest
tier
If more than one paper
qualifies then select the
largest study
Hierarchy of Study Designs
Meta-Analysis of Prospective Studies
Individual Prospective Study
Meta-Analysis of Case-Control Studies
Individual Population-Based Case-Control Study
Individual Case-Control Study (not population based)
Study Quality • Disease Assessment Carried out consistently? Objective? Clinically accepted definition?
• Genotyping Are methods valid? Carried out consistently?
•Population Stratification Could risk estimates be biased?
Select Paper
Perform Updated
Search for ICOB
approved SNPs
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Example: CAD and SNP rs1333049
no
no
CDKN2A/CDKN2B rs1333049
RR Estimates (95% CI)
GG* 1 CG 1.29 (1.22 , 1.37) CC 1.67 (1.48, 1.87)
(Circulation 2008; 117:1675-1684)
Hierarchy of Study Designs
Meta-Analysis of Prospective Studies
Individual Prospective Study
Meta-Analysis of Case-Control Studies
Individual Population-Based Case-Control Study
Individual Case-Control Study (not population based)
*reference group
yes
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EXAMPLE
How do participants learn about their results?
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Participant Risk Summaries include Non-genetic Risks
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Potentially Actionable Conditions
Prostate cancer
Colon cancer
Melanoma
Coronary artery disease
Type 2 diabetes
Type 1 diabetes
Age-related macular degeneration
Hemochromatosis
Inflammatory bowel disease
Obesity CYP2D6
As of6-10-09
Lupus
Rheumatoid Arthritis
CYP2C9
CYP2C19
VKORC1
Complex Disease Drug Metabolism
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Pharmacogenomics Advisory Panel
Dr. Issam Zineh
Office of Clinical Pharmacology
FDA
CYP2D6-Tamoxifen
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Genetic Counselors available at no cost
What Do My Results Mean?
In person or by phone
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Nearly all states represented in the CPMC
10,000 Participants by 2010
Ultimate goal of 100,000
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Minority Participation and Outreach
U.S. Senator Robert Menendez
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Franklin Institute of Philadelphia
Reverend Floyd White of Camden, NJ
PRWT and Cherokee Pharmaceuticals
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What do participants do after viewing their results?
• They can invite their physician or members of their family to register to view their personal risk information through the web portal
• They may decide to make changes to their lifestyle to try to lower their risk of the health condition.
• They may decide to talk to their physician about their risk of the health condition.
• They can request genetic counseling at CPMC to discuss their risks, at no charge
• CPMC will send them period emails asking them to log onto their web portal account and complete short questionnaires about what they did with their results
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What research will be done with CPMC data?
• CPMC scientists, health researchers and biostatisticians will determine whether giving people information about their genetic risk alters their health behavior or their health.
– Outcome surveys, annual MFLQ, medical records
• CPMC scientists will assess the genetic knowledge of CPMC participants during the course of their participation in the study.
– Voluntary genetic knowledge survey
• The broader scientific community will have access to genotypic and phenotypic data from those individuals who opt to release their de-identified data for biomedical research.
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Coronary Artery Disease Survey Via Portal at 3 and 12 months
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Health Outcomes Behavioral Outcomes
Communication
Risk perception
Changes in behavior
Newly diagnosed CAD
MI
Angina
Bypass surgery
Surveys, Annual medical history updates, And EMRs
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Recent Federal Grants
Web-based educational content for physicians (Mary Daly at Fox Chase)
CPMC Participant Behavior Upon Receiving Genome Info. (Reed Peyritz at Penn)
•U01 trial will examine patient lifestyle changes and physician behavior
(assessed by coded tests/procedures/referrals) when the physicians have
or have not received training in genomic medicine.
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Study Aims• Assess motivations to participate in the CPMC and
perceptions of the utility of personalized medicine– Recruit potential “early adopters” to complete an anonymous survey
from among those who sign up to attend a CPMC enrollment event
• Explore participant understanding of personalized genomic disease risk results, intended and actual use of information and educational needs of individuals receiving results– Interview with CPMC participants (n=60)
• Develop possibly recommendations for the ethical offering of personalized genomic disease risk assessment
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Perceptions of Benefits of CPMC
% agreeing or strongly agreeing
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Perceptions of Risks of CPMC% agreeing or strongly agreeing
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Nature, November 6th, 2008
“Coriell study is leading by example…”
CPMC Praised in Nature Article
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HHS Visits Coriell“pioneers in the field of personalized medicine”
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Federal HHS Secretary Michael Leavitt Commissioned white paper
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For-Profit Personal Genome Companies
Will profile your genome for $1000 - $2500
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Contrasts between the CPMC study and some for profit DTC companies
No charge to study participants
Genetic counseling provided
A research study to determine whether genome Data is useful clinically
Direct engagement of hospital partners
Risk reporting based on family history, Demographics, lifestyle and genetics
IRB approved and monitored
Return of only potentially actionable results
Recruitment of underserved minorities
Collection of rich set of medical data over time
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Difficult Ethical, Legal and Social Issues
Ensuring genetic privacy
Anxiety associated with a genetic prognosis
How will doctors use the information?
Education of Participants, Doctors, Nurses and genetic counselors
Insurance Companies
EMRs!
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The Alternative
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cpmc.coriell.org
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