By Jean-Claude Marshall YouTube: http://goo.gl/5go1vt

1. Incorporating Personalized Medicine in
Community Hospital Systems
Catholic Health Initiatives’
Center for Translational Research
July 17, 2013

2. CHI: 5th Largest Hospital Network in US
Strength in Numbers
§ 5th largest US network
§ 86 acute care hospitals in 18 states
§ 40 LTC facilities
§ 85,000 employees
§ 2,900 physicians and midlevel providers
§ Diverse markets with 90% ranked #1 or #2
§ $15B in assets, $12B in annual revenue
§ FY 2012 – provided $715M+ in charity care

3. Personalized Medicine
§ What is it?
§ Personalized medicine is the use of new
methods of molecular analysis to better
manage a patient’s disease or predisposition
toward a disease… approaches may include
genetic screening programs that more precisely
diagnose diseases and their sub-types, or help
physicians select the type and dose of
medication best suited to a certain group of
patients. – Personalized Medicine Coalition

4. CHI Institute for Research
Innovation
Center
for
Clinical
Trials
-­‐
Clinical
Trial
recruitment
and
management
across
CHI
Center
for
Healthcare
Innova4on
(CHCI)
-­‐
Next
Gen
healthcare
delivery
-­‐ Mul-­‐center
Bio-­‐Repository
for
specimen
collecon
across
CHI
network
-­‐ CLIA
cerfied
laboratory
for
personalized
medicine
-­‐ Research
Laboratory
for
IP
generaon
Center
for
Transla4onal
Research
(CTR)
Biostascs/Data
Analycs
-­‐
Electronic
Medical
Record
links

5. Bio-Repository Network
§ Responsible for scientific oversight of collection process and storage, project
specifications
§ Installation of full time employee at individual sites
across the CHI
§ Responsible for patient recruitment and sample
processing/storage
§ Uniform collection procedures
§ Regulatory Guidance - WIRB protocol approval
§ Dedicated staff to facilitate sample collection, storage
and shipment
§ Annotated biospecimens with clinical and
longitudinal data (up to 10 years)
§ Single software solution for:
q Chain of custody tracking from consent to
storage
q Data capture from downstream molecular
analyses
q Querying capabilities to define cohorts
5

6. Best Practices:
Biospecimen Collection Overview

7. Cloud-based Informatics:
Network Strength
Data
Warehouse
CCR
CTR
Research
Data
Analysis

8. Physician Engagement
§ CHI is a community based hospital system
§ Physician engagement includes:
q education of local physicians in bio molecular
assays, including next generation sequencing
q Partnership to investigate clinically relevant
questions from inside the CHI system
q Proposed projects for grant/venture capital
funding through a variety of mechanisms

9. CHI Discovery Research Network
CTR working with
Physicians in their
communities
§ Hypothesis-driven
Research
§ Research Partnering
§ Education
Discovery
Research
Network
Biospecimen
Procurement
Program
Infrastructure
Support
IP
Generaon
Hypothesis
Development
Translaonal
Research
Laboratory
Specimen
and
Data
Access

10. Next Generation Sequencing (NGS)
§ Current generation of technology allows for
sequencing of the whole genome of a patient,
or a patient tumor sample
§ Derived from technology used to do the first
human genome sequencing project
§ That project took years, and millions of dollars
§ Current turn around time is 6 to 8 weeks for an
entire genome to be sequenced, turn around
times continue to decrease as do costs

11. Data Tsunami
§ Data storage and subsequent analysis is rapidly
becoming a bottleneck for most NGS labs
§ Single gene sequencing produces files of 10’s
to 100 KB in size
§ Exome sequencing produces ~10 GB file size
per run
§ Full genome sequencing produces file sizes on
the order of ~100 GB
§ Accompanying data analysis is time
consuming and requires specialized training
and software

12. Personalized Report
§ Personalized
report generated
from the exome
sequencing of
our patient
§ Can be tailored
to individual
physician
preferences

13. Clinical Trial #1 Eligibility

14. Patients Like Me

15. Challenges for NGS
§ Input requirements can be difficult to meet
with FFPE, especially FNA
§ Physicians leery of what information they
will get, quantity of information a problem
§ Clear, concise physician reports required
§ Current turn around times too long for full
exome sequencing, better for targeted

16. Opportunities for NGS
§ True implementation of personalized
treatment based on biology not phenotype
or even histology
§ Preservation of precious tissue by
integrating multiple tests into one assay
§ Longitudinal examination of a patients
primary, recurrence and resistant disease
§ Becoming more necessary with additional
targeted therapies and clinical trials

17. Therapies targeting the EGFR pathway
17
EGFR = Epidermal Growth Factor Receptor
Selected QIAGEN partners:
therascreen KRAS test
BKM120
Afatinib
Zelboraf

18. Patient Testing
§ First available test at CTR, for KRAS, codon 12,13,61
§ Reporting clinical outcome for the use of EGFR
inhibitors (panitumumab, cetuximab)
§ Predominantly used for colorectal cancers as per
guidelines (National Comprehensive Cancer Network)
§ 30-35% of patients have KRAS mutation, predictive for
lack of response to EGFR targeting
§ Cost of EGFR targeting: $30,000 for 8 weeks treatment
§ FFPE samples, typically from FNA
§ We also see lung cancer and metastatic samples

19. Thank you.