Biomarkers Diagnostic Program

Final Agenda
C A M B R I D G E H E A LT H T E C H I N S T I T U T E S 1 1 t h A N N UA L
BIOMARKERS & DIAGNOSTICS

W OR L D
CONGRESS
2015
The Leading Annual Meeting Dedicated to Biomarkers

and Diagnostics Research and Implementation
MAY 5-7, 2015 | LOEWS PHIL ADELPHIA HOTEL | PHIL ADELPHIA, PA
Register today and network with 400 of your colleagues
F E AT U R E D S P E A K E R S
Raghu Kalluri
Chair, Cancer Biology

MD Anderson Cancer Center
Nicholas C. Dracopoli
Vice President
Johnson & Johnson
Marc Ladanyi
Chair, Molecular Oncology

Memorial Sloan-Kettering Cancer
Center
Michael E. Burczynski
Executive Director, Biomarkers

Bristol-Myers Squibb
Dennis J. Slamon
Chief, Hematology & Oncology

University of California, Los Angeles
M AY 5 - 6
Biomarkers for Patient Selection

Big Data for Personalized Medicine and
Biomarker Discovery NEW
Cell-Free Biomarkers and Diagnostics NEW
Predictive Cancer Biomarkers NEW
M AY 6 - 7
Kenneth Emancipator
Companion Diagnostics
Elaine Lyon
Clinical and Translational Biomarkers

in Drug Discovery
Director, Companion Diagnostics

Merck Research Labs
Medical Director
ARUP Laboratories
Alan T. Wright
Chief Medical Officer

Roche Diagnostics
Clinical NGS Testing NEW
Darrell R. Borger
Director, Biomarker Laboratory

Harvard Medical School
Monica Motwani
Precision Medicine Leader

AbbVie
Premier Sponsors:
SHORT COURSES
Fit-for-Purpose Biomarker Assay Development and Validation

Next-Generation Sequencing as a Clinical Test
Organized by:
Cambridge Healthtech Institute
BiomarkerWorldCongress.com
C O N F E R E N C E AT - A - G L A N C E
T2: Big Data for Personalized

Medicine and Biomarker Discovery
T1: Biomarkers for Patient Selection
T3: Cell-Free Biomarkers and

Diagnostics
T4: Predictive Cancer Biomarkers
Tuesday, May 5
7:00 am
Conference Registration and Morning Coffee
8:00-10:10
Implementing Precision Medicine
10:10-10:40
Coffee Break in the Exhibit Hall with Poster Viewing
10:40-12:00 pm
Implementing Precision Medicine (contd)
12:00-1:30
Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own
Big Data for Biomarker Discovery and Drug

Development
Circulating Tumor DNA as Biomarkers and

Diagnostics

Diagnostics
Big Data for Biomarker Discovery and Drug

Development (contd)

Diagnostics (contd)

Diagnostics (contd)
Exosomes and Microvesicles
NGS for Biomarker Discovery and Patient Selection
Circulating Biomarkers in Drug Discovery

(contd)
Genomic Data Analysis
microRNA and ncRNA
Predictive Cancer Biomarkers for Targeted

Therapy
Genomic Data Analysis (contd)
microRNA and ncRNA (contd)
Predictive Cancer Biomarkers for Targeted

Therapy (contd)
1:30-3:20
3:20-4:10
Refreshment Break in the Exhibit Hall with Poster Viewing
Big Data to Advance Personalized Medicine
4:10-5:00

(contd)
5:00-6:00
Welcome Reception in the Exhibit Hall with Poster Viewing
5:30
Short Course Registration
6:00-9:00
Dinner SC1: Fit-for-Purpose Biomarker Assay Development and Validation (*Separate registration required)
Big Data to Advance Personalized Medicine (contd)
Wednesday, May 6
7:30 am
Breakfast Presentations (Sponsorship Opportunities Available) or Morning Coffee
8:25-9:50
Predictive Cancer Biomarkers for Targeted Therapy
9:50-10:45
10:45-12:00 pm

(contd)
12:00
Close of Conference
T6: Clinical and Translational

Biomarkers in Drug Discovery
T5: Companion Diagnostics

11:00 am
T7: Clinical NGS Testing
Conference Registration
12:15-1:30 pm
Lunch on Your Own
Luncheon Presentation Sponsored by Quanterix
Luncheon Presentation Sponsored by NuGen
1:30-3:20
Companion Diagnostics Development and

Commercialization Strategies
Biomarkers in Drug Discovery Decision Making
NGS in the Clinic
3:20-4:25
Refreshment Break in the Exhibit Hall with Poster Viewing
4:25-5:40

Commercialization Strategies (contd)
5:45
Short Course Registration
6:00-9:00
Dinner SC2*: Next-Generation Sequencing as a Clinical Test (*Separate registration required)
Translational Biomarkers: From Discovery to the Clinic
NGS in the Clinic (contd)
Thursday, May 7
7:30 am
Breakfast Presentations (Sponsorship Opportunities Available) or Morning Coffee
8:25-9:50
Companion Diagnostics Case Studies
9:50-10:45
10:45-12:00
Companion Diagnostics Case Studies (contd)
12:00-1:30
Lunch on Your Own
1:30-2:50
Partnering and Collaborations
2:50
Close of Conference
Biomarker Assay Development and Validation
NGS-Driven Clinical Trials
Genomic Biomarker Discovery
NGS-Driven Clinical Trials (contd)
NGS Assay Development and Platforms
SPONSORS
Premier Sponsors
Corporate Sponsors
Corporate Support Sponsors
3 | BiomarkerWorldCongress.com
DINNER COURSES*
Tuesday, May 5, 6:00-9:00 pm
Wednesday, May 6, 6:00-9:00 pm
SC1: Fit-for-Purpose Biomarker Assay

Development and Validation
SC2: Next-Generation Sequencing

as a Clinical Test
Instructors:
John L. Allinson, FIBMS, Head, Biomarker Strategy, Drug
Development Services, LGC Group
Viswanath Devanarayan, Ph.D., Global Head & Senior Research
Fellow, Exploratory Statistics & Bioinformatics, AbbVie, Inc.
Instructors:
Seth Crosby, M.D., Director, Partnerships & Alliances,
Washington University School of Medicine
Avni Santani, Ph.D., Assistant Professor, Clinical Pathology,
University of Pennsylvania School of Medicine
This tutorial will provide recommendations on the fit-for-purpose best practices in

the development and validation of biomarker assays for exploratory or advanced
biomarker applications. Strategies for different applications at various phases
of biomarker development will be described. Key elements in the method of
development and validation will be illustrated with examples, including reference
to standard material, sample stability and collection integrity, validation and QC
samples, validity of reference standards, calibration curve fitting methods, method
optimization and feasibility studies. Special challenges in protein biomarker assays
will be discussed, including strategies for moving from biomarker panels in the
exploratory phase to the few markers chosen to support clinical trials, crossvalidation of biomarker assays, etc.
Next-Generation Sequencing (NGS) is used widely in clinical research for

the discovery of disease-associated genes, and the clinical community
is beginning to embrace this technology for diagnostic testing. The rapid
evolution of NGS technologies presents significant opportunities and
challenges for researchers and clinicians for improving health outcomes,
particularly with respect to an increased emphasis on personalized
and preventive medicine. Adoption of NGS in the clinical laboratory
setting requires the adoption of many processes and procedures, such
as the analytic and clinical validation of the test, CLIA certification/CAP
accreditation, standards for reference materials, availability for proficiency
testing, and questions regarding reimbursement and informed consent.
The success of NGS as a viable diagnostic modality depends on many
branches of the health care community working together. This session
will be informative and practical for the researcher and laboratorians who
are considering launching NGS as a clinical test.
Outline:

Introduction: Nomenclature, types of biomarker methods/assays,

method development and validation road-map, fundamental
validity, similarity and differences from PK assays and diagnostic
applications
Pre-analytical and bioanalytical elements: Target range, standards, validation
and QC samples, stability, matrix effect, specificity and relative selectivity
Calibration curve model selection, evaluation and weighting
Method feasibility and optimization with precision profiles
Evaluation of some pre-study validation characteristics such as precision,
bias, sensitivity and quantification limits
Use of sample controls for in-study performance monitoring and conformance
testing among laboratories
Special considerations for multiplex assays, cross-validation of assays, etc.
Method comparisons
*Separate Registration Required.
BiomarkerWorldCongress.com | 4
Biomarkers & Diagnostics World Congress 2015
D I S T I N G U I S H E D FA C U L T Y
John L. Allinson, FIBMS, Head, Biomarker Strategy, Drug
Development Services, LGC Group
Jiri Aubrecht, Pharm.D., Ph.D., Senior Director and Safety Biomarker
Group Lead, Drug Safety Research & Development, Pfizer
Nazneen Aziz, Ph.D., Chief Research Officer & Senior Vice President,
Phoenix Childrens Hospital
Mark S. Boguski, M.D., Ph.D., Associate Professor, Center for
Biomedical Informatics, Harvard Medical School
Matthias Holdhoff, M.D., Ph.D., Assistant Professor, Oncology,

Medicine and Neurosurgery, Brain Cancer Program, SKCCC, Johns
Hopkins University
Xiaolan Hu, Ph.D., Head, Genetically Defined Diseases,
Yoshiya Oda, Ph.D., President, Biomarkers and Personalized

Medicine Core Function Unit, Eisai
Gregory J. Opiteck, Ph.D., Senior Principal Scientist, Merck
Chris Huang, Ph.D., Principal Scientist, Systems Pharmacology &

Biomarkers, Immunology TA, Janssen R&D
Nickolas Papadopoulos, Ph.D., Professor, Ludwig Center, SKCCC,

Johns Hopkins University
Usman Iqbal, M.D., Senior Medical Affairs Leader, AstraZeneca
Abhijit A. Patel, M.D., Ph.D., Assistant Professor, Therapeutic

Radiology, Yale University School of Medicine
Darrell R. Borger, Ph.D., Director, Biomarker Laboratory,

Massachusetts General Hospital and Harvard Medical School
Shidong Jia, Ph.D., Scientist, Oncology Biomarker

Development, Genentech
Carrie Brodmerkel, Ph.D., Director, Immunology Biomarkers,

Johnson & Johnson
Bing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell

Biology, Thomas Jefferson University
Catherine Brownstein, Ph.D., Instructor, Pediatrics, Harvard Medical

School and Boston Childrens Hospital
Raghu Kalluri, M.D., Ph.D., Professor & Chair, Cancer Biology, MD

Anderson Cancer Center
Kenneth Buetow, Ph.D., Director, Computational Sciences and

Informatics Program for Complex Adaptive Systems; Professor,
School of Life Sciences, Arizona State University
Ann Kapoun, Ph.D., Vice President, Translational Medicine,

OncoMed Pharmaceuticals
Michael E. (Ransom) Burczynski, Ph.D., Executive Director,

Biomarker Technologies, Exploratory Clinical and Translational
Research, Bristol-Myers Squibb
James Novotny, Ph.D., Group Director, Pharmacodiagnostics,

Marc Ladanyi, M.D., William Ruane Chair in Molecular Oncology,

Molecular Diagnostics Service and Human Oncology &
Pathogenesis Program, Memorial Sloan-Kettering Cancer Center
Suso Platero, Ph.D., Director, Oncology Biomarkers,

Janssen Pharmaceuticals
Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity
(an MPLN company)
Deepak Rajpal, Ph.D., Director, Computational
Biology, GlaxoSmithKline
Mitch Raponi, Ph.D., Senior Director, Molecular Diagnostics,
Clovis Oncology
Carolina Rizo, Ph.D., MBA, Director, Business Development, Roche
Molecular Systems
James Cai, Ph.D., Head, Data Science, Roche
Andrea H. Lauber, Ph.D., Executive Director, Business Development,

Clinical Biomarkers and Pharmacodiagnostics, Bristol-Myers Squibb
Wolfgang Sadee, Dr.rer.nat., Professor & Director, College of

Medicine Center for Pharmacogenomics, The Ohio State University
Ken Chang, Ph.D., Clinical Assay Development & Outsourcing

Lead, Merck
Eunice Lee, Ph.D., Division of Immunology and Hematology Devices,

Office of In Vitro Diagnostics and Radiological Health, CDRH, FDA
Avni Santani, Ph.D., Assistant Professor, Clinical Pathology,

University of Pennsylvania School of Medicine
Clark Chen, M.D., Ph.D., Associate Professor and Chief, Stereotactic

and Radiosurgery; Vice-Chairman, Academic Affairs, Neurosurgery,
University of California, San Diego
Bin Li, Ph.D., Associate Director, Computational Biology, Takeda
Nadeem Sarwar, Ph.D., Vice President & Global Head, Genetics &
Human Biology, Eisai
Rong Chen, Ph.D., Director, Clinical Genome Informatics, Genetics

and Genomic Sciences, Icahn School of Medicine at Mount Sinai
Seth Crosby, M.D., Director, Partnerships & Alliances, Washington
University School of Medicine
Viswanath Devanarayan, Ph.D., Global Head & Senior Research
Fellow, Exploratory Statistics & Bioinformatics, AbbVie, Inc.
Nicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson
& Johnson
Paula Eason, Ph.D., Scientific Program Manager, Cancer Division
of Research Partnerships, Foundation for the National Institutes
of Health
Daniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling
Core, National Cancer Institute, NIH
Kenneth Emancipator, M.D., Executive Medical Director, Molecular
Biomarkers and Diagnostics, Merck Research Laboratories
Helen Fernandes, Ph.D., Associate Professor, Pathology and
Laboratory Medicine, Weill Cornell Medical College
Andrea Ferreira-Gonzalez, Ph.D., Professor and Chair, Division of
Molecular Diagnostics; Director, Molecular Diagnostics Laboratory,
Department of Pathology, Virginia Commonwealth University
Ming-Lin Liu, M.D., Ph.D., Research Assistant Professor,

Dermatology, Perelman School of Medicine, University
of Pennsylvania
Hui Ling, M.D., Ph.D., Odyssey Fellow, Experimental Therapeutics,
MD Anderson Cancer Center
Tracy Lively, Ph.D., Deputy Associate Director, Cancer Diagnosis
Program, National Cancer Institute, NIH
Johan Luthman, D.D.S., Ph.D., Vice President, Clinical
Neuroscience, Eisai
Rajyalakshmi Luthra, Ph.D., Director, Molecular Diagnostic
Laboratory; Professor, Pathology and Laboratory Medicine, MD
Elaine Lyon, Ph.D., Medical Director, Molecular Genetics and
Genomics, ARUP Laboratories; Associate Professor, University
of Utah School of Medicine; Past President, Association for
Molecular Pathology
Subha Madhavan, Ph.D., Associate Professor and Director,
Innovation Center for Biomedical Informatics; Director, Clinical
Research Informatics, Lombardi Comprehensive Cancer Center,
Georgetown University
G. Mike Makrigiorgos, Ph.D., Professor, Radiation Oncology, DanaFarber Cancer Institute, Harvard Medical School
Nikoletta Sidiropoulos, M.D., Medical Director, Genomic Medicine

Program, University of Vermont
Dennis J. Slamon, M.D., Ph.D., Chief, Hematology & Oncology,
The David Geffen School of Medicine, University of California,
Los Angeles
David Smith, Ph.D., Professor, Laboratory Medicine & Pathology,
Mayo Clinic
Sharon Sokolowski, MS, Senior Principal Scientist, Pfizer Global
Research & Development
Joan Sopczynski, Ph.D., Senior Manager, Predictive Informatics,
Business Insights, R&D Business Technology, Pfizer
George Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine
and Pathology, Mayo Clinic
John A. Wagner, M.D., Ph.D., Senior Vice President & Head, Global
Clinical and Translational Sciences, Takeda Pharmaceuticals
I-Ming Wang, Ph.D., Principal Scientist, Genetics and
Pharmacogenomics, Merck Research Labs
Liling Warren, Ph.D., Senior Scientific Investigator, GlaxoSmithKline
Shrikant Mane, Ph.D., Director, Yale Center for Genome Analysis
Anton Wellstein, M.D., Ph.D., Professor, Oncology, Pharmacology

and Medicine, Georgetown University Medical School; Associate
Director, Basic Science, Lombardi Comprehensive Cancer Center
William B. Mattes, Ph.D., DABT, Director, Division of Systems

Biology, National Center for Toxicological Research, US Food and
Drug Administration
David T.W. Wong, D.M.D., DMSc, Felix & Mildred Yip Professor and
Associate Dean of Research, UCLA School of Dentistry; Director,
Center for Oral/Head & Neck Oncology Research
Ron Mazumder, Ph.D., MBA, Global Head, R&D and Operations,

Janssen Diagnostics, Janssen Pharmaceutical Companies of
Johnson & Johnson
Alan T. Wright, M.D., CMO, Roche Diagnostics Corporation
Stephen T. Furlong, Ph.D., Safety Science Lead, AstraZeneca
Ian McCaffery, Ph.D., Head, Companion Diagnostic

Development, Genentech
Zhongming Zhao, Ph.D., Professor, Biomedical Informatics, Cancer

Biology and Psychiatry, Vanderbilt University School of Medicine
Peter S. Gargalovic, Ph.D., Principal Scientist, Cardiovascular Drug

Discovery Biology, Bristol-Myers Squibb
Jason Merker, M.D., Ph.D., Assistant Professor, Pathology, Stanford

University Medical Center
Jaya Goyal, Ph.D., Director, Translational Sciences, Value-Based

Medicine, Biogen Idec
Jennifer J.D. Morrissette, Ph.D., Clinical Director, Center for

Personalized Diagnostics, University of Pennsylvania School
of Medicine
James M. Ford, M.D., Associate Professor, Medicine (Oncology) and

Genetics; Director, Stanford Clinical Cancer Genomics Program,
Stanford University School of Medicine
Yasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and
Personalized Medicine, Eisai
Birgit Funke, Ph.D., Assistant Professor, Pathology, MGH/Harvard
Medical School; Director, Clinical Research and Development,
Laboratory for Molecular Medicine, Partners HealthCare
George A. Green IV, Ph.D., Group Director, Pharmacodiagnostic

Center of Excellence, Bristol-Myers Squibb
Steven Gutman, M.D., Myraqa Strategic Advisor, Illumina, Inc.
Christos Hatzis, Ph.D., Assistant Professor, Medicine, and Director,
Bioinformatics, Breast Medical Oncology, Yale University School
of Medicine
Monica Motwani, Ph.D., Translational Oncology & Precision

Medicine Leader, Oncology Discovery, AbbVie
Aejaz Nasir, M.D., MPhil, Fellow, College of American Pathologists;
Senior Medical Advisor & Surgical Pathology Lead, Molecular Solid
Tumor & Anatomic Pathologist, Tailored Therapeutics, Diagnostic &
Experimental Pathology, Eli Lilly and Company
Xuemei Zhao, Ph.D., Principal Scientist, Molecular Biomarkers and

Diagnostics Laboratory, Merck
S p o n s o r s h i p, E x h i b i t & L e a d G e n e r at i o n O p p o r t u n i t i e s
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prospects. Sponsorship allows you to achieve your objectives before, during, and long after the event. Any sponsorship can be customized to meet
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cooperative marketing efforts by CHI, and more.
Breakfast & Luncheon Podium Presentations

Opportunity includes a 30-minute podium presentation. Boxed
lunches are delivered into the main session room, which guarantees
audience attendance and participation. A limited number of
presentations are available for sponsorship and they will sell out
quickly. Sign on early to secure your talk!
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conference pre-registration list for an evening of
networking at the hotel or at a choice local venue. CHI will
extend invitations and deliver prospects, helping you to
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will be customized according to sponsors objectives, i.e.:
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Conference Venue and Hotel:
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Phone: 215-627-1200
Reservations: Go to the travel page of biomarkerworldcongress.com
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BiomarkerWorldCongress.com | 6
M AY 5 - 6
Biomarkers for Patient Selection

TUESDAY, MAY 5
11:30 Operationally Identifying Pharmacogenetic Variants
7:00 am Conference Registration and Morning Coffee
Merck has undertaken an enterprise change management initiative to understand

the sources of complexity and cost in identifying functionally relevant PGx
variation. Finding the inflection points between cost and complexity was key.
Merck has now moved to a fully standardized analytical platform which delivers
consistent and high quality PGx data on a time scale that is impactful to the
decision-making process. Therefore, we are in keeping with a customercentric model, while reducing demands on operational processes and
information systems.
Implementing Precision Medicine

8:00 Chairpersons Opening Remarks
8:10 Companion Diagnostics A New Take on Medical Value

Companion diagnostics are proving value by targeting, monitoring and directing
personalized therapies. In the future, companion diagnostics will expand to
include both biochemical and physical measurements. Testing can be discrete,
periodic or continuous with analyzers that may be remote, worn or implanted. Just
as advancements in biochemistry and pharmacology have driven therapeutics,
innovations in measurement techniques will revolutionize healthcare.
8:35 Understanding Disease Heterogeneity, Status, Trajectory

and Treatment Response to Enable Patient Stratification
Jaya Goyal, Ph.D., Director, Translational Sciences, Value-Based
Medicine, Biogen Idec
Gregory J. Opiteck, Ph.D., Senior Principal Scientist, Merck
12:00 pm Luncheon Presentation:

Role of Biomarkers in Improving the Success
Rate of Early Oncology Drug Development
Sponsored by
Kamala Maddali, DVM, Ph.D., Director, Scientific

Development, Quest Diagnostics Clinical Trials
Biomarkers have contributed to the advancement of targeted therapies and
the rise of personalized medicine which optimize the probability of success in
early oncology drug development. This presentation will cover various oncology
case studies on the role of biomarkers: in patient selection strategies including
Companion Diagnostics to stratify patients who will benefit from the clinical trial,
as predictive biomarkers to predict patient outcomes, and in predicting toxicity,
efficacy, and drug dosage to ensure that critical endpoints are achieved.
9:00 Quantitative Immunohistochemistry for Effective Breast

Cancer Patient Stratification
Hallgeir Rui, M.D., Ph.D., Cancer Biology & Pathology, Thomas Jefferson
University
1:30 Chairpersons Remarks
9:25 Multiplexed Biomarkers: Transitioning

from Discovery to the Clinic
Sponsored by
Robert Neely, Ph.D., Research Investigator,

Bioanalytical Sciences, Bristol-Myers Squibb
With the developing need of multiple biomarkers in clinical programs, the need
for multiplexed platforms has increased considerably. Multiplexing analytes will
save time and sample; however, it will lead to an increase in analytical factors
that will need to be assessed during method development and validation. The
two most widely used platforms for multiple analyte screening are either a bead
based or a planar format. This talk will focus on these platforms and highlight the
technical challenges that can arise in a multiplex assay. Specifically, it will focus on
the analytical rigor needed to transition from discovery to the clinic.
9:55 Q&A with the Speakers

10:10 Coffee Break in the Exhibit Hall with Poster Viewing
10:40 Precision Medicine and Biomarker Development at the NCI
Tracy Lively, Ph.D., Deputy Associate Director, Cancer Diagnosis
Program, National Cancer Institute, NIH
The development of predictive markers to guide the use of emerging targeted
therapeutic agents requires new approaches to both clinical trials and correlative
laboratory science. This talk will present NCIs experience with novel trial designs,
the Exceptional Responders initiative and more effective approaches to the
integration of biomarker development into cancer therapy trials.
11:05 Talk Title to be Announced

Carrie Brodmerkel, Ph.D., Director, Immunology Biomarkers, Johnson &
Johnson
1:35 Application of NGS for Biomarker Discovery and Patient

Selection
2:00 Phoenix Childrens Hospital to Address the Unmet Need:

Slow Progress in Pediatric Drug Development
The need for new drugs in pediatric cancer is acute. Virtually no new therapy
has been introduced in the past two decades. Treatment for relapsed patients is
lower than in adults yet a large number of childhood cancer patients will relapse.
In stark contrast to the rapid introduction of targeted therapies in adults more
effective therapies are unavailable in pediatric cancer. PCH will focus on genomic
analysis to better understand disease mechanisms to develop new therapeutics
for pediatric cancer.
2:25 A General Approach to the Discovery and Translation of

Multi-Gene Biomarkers in Drug Discovery and Therapy
Wolfgang Sadee, Dr.rer.nat., Professor & Director, College of Medicine
Center for Pharmacogenomics, The Ohio State University
Extensive genetics/genomics studies have yet to account for the estimated
heritability of complex traits, including diseases and their treatments. Our
discovery pipeline encompasses detailed molecular genetics of target genes
to avoid use of surrogate markers and large-scale data analytics to reveal
phenotype associations involving gene-gene-environment interactions.
Discovering frequent regulatory variants in key genes often under positive
selection, we are now in a position to develop clinically relevant biomarker
panels, demonstrated with examples.
2:50 A Novel Phospho-Proteomic Diagnostic

for Patient Stratification and Therapy
Selection for Breast Cancer
Sponsored by
8:55 The Impact of Multiplexed Genotyping in Directing Cancer

Care and a Role for Combining Genotype with Histology for
Biomarker Discovery
Glenn Hoke, Ph.D., Executive Vice President and

COO, Theranostics Health, Inc.
Darrell R. Borger, Ph.D., Director, Biomarker Laboratory, Massachusetts

General Hospital and Harvard Medical School
The TheraLink Assay for Breast Cancer, a commercially available CAP/CLIA test,
measures the proteomic signature in patients cancer, to provide the activation
status for multiple drug targets. Designed for use in the routine clinical setting, this
molecular diagnostic assay can identify which patients are more likely to respond
to a particular molecularly targeted therapy. Case studies and the design of a
prospective trial will be presented.
Our laboratory has conducted clinical genotyping in a large academic hospital

for 7 years, and we have started to evaluate its impact on expanding targeted
therapy options for cancer patients. With the integration of next-generation
sequencing technologies, more complex genotypes are now being identified.
Subsequently, the integration of histological testing may provide important
perspective into the biological function of unknown variants and the ability to
identify new biomarkers of response.
3:20 Refreshment Break in the Exhibit Hall with Poster Viewing

4:10 Utility of Targeted NGS Panels for Cancer in an Academic
Molecular Pathology Laboratory
Helen Fernandes, Ph.D., Associate Professor, Pathology and Laboratory
Medicine, Weill Cornell Medical College
The utility of targeted next-generation sequencing-based assays for identification
of genomic variants has made significant advances in the field of molecular
oncology. Testing panels and platforms have enabled clinical molecular pathology
laboratories to expand their testing menu to include NGS assays that can provide
information for a more reliable prediction of personalized cancer therapies.
Additionally, the assays can identify relevant genes that may have implications for
enrollment of the patient in clinical trials. This presentation will focus on the issues
involved for optimal performance and implementation characteristics of assays
for the identification of somatic variants in solid tumors in an academic molecular
pathology laboratory.
4:35 Patient Stratification in Oncology Using

NGS: An Application of the PATH Analytics
Platform to AML Patients from TCGA
Sponsored by
Scott Marshall, Ph.D., Managing Director, Analytics,

Precision for Medicine
Molecular heterogeneity in tumors is expected to impact prognosis and response
to therapy, and the ability to stratify patients based on their underlying molecular
profiles can improve outcomes. The transformation of high-dimensional genomic
data into personalized treatments requires cutting-edge science and advanced
analytics. To help biopharmaceutical companies realize this goal, Precision for
Medicine has developed the PATH Analytics Platform, a multi-modal platform
designed to accelerate research on biomarker discovery and patient stratification
by combining advanced Bayesian analytics and real-time data exploration.
5:00-6:00 Welcome Reception in the Exhibit Hall with Poster

Viewing
9:20 From Discovery Through

Commercialization of Personalized Multiplex
Biomarker Assays
Sponsored by
Al Akowitz, Ph.D., Vice President, Strategic Sales, Meso Scale Discovery

10:45 Genomic Markers Associated with Pathologic Complete
Response and Resistance in Triple Negative Breast Cancer
Christos Hatzis, Ph.D., Assistant Professor, Medicine, and Director,
Bioinformatics, Breast Medical Oncology, Yale University School of
Medicine
Efforts to develop transcriptional predictors of chemotherapy sensitivity in triple
negative breast cancer (TNBC) have been met with limited success due to the
heterogeneity of this disease. We explored whether genomic differences in the
exomes of extremely chemotherapy sensitive and highly chemotherapy resistant
TNBC cases could provide clues of chemosensitivity. Although a few genes show
response-associated mutational patterns, the chemoresistant cases appear to
have higher mutational load and subclonal heterogeneity, suggesting that higher
DNA diversity may be associated with chemotherapy resistance. Interestingly,
resistant tumors show characteristic mutational spectrum shifts that may suggest
heterogeneous branch evolution. These broad measures of genomic diversity
could show promise as markers of resistance to chemotherapy.
11:10 Comprehensive Translational Research to Identify Predictive

Biomarkers of Lenvatinib in the Preclinical and Clinical Study
Yasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and Personalized
Medicine, Eisai
This presentation will cover: 1) systems biology to identify biomarker candidates
for Lenvatinib using the cancer cell line panel, 2) translational research to test
biomarker candidates in multiple Phase II trials, and 3) biomarker correlative
analysis in Phase III trial.
5:30 Short Course Registration
11:35 Identification of Independent Primary Lung Tumors and

Intrapulmonary Metastases Using DNA Junctions
6:00-9:00 pm Dinner Short Course*
George Vasmatzis, Ph.D., Assistant Professor, Laboratory Medicine and

Pathology, Mayo Clinic
SC1: Fit-for-Purpose Biomarker Assay Development and Validation

*Separate registration required
WEDNESDAY, MAY 6
7:30 am Breakfast Presentation (Sponsorship Opportunity
Available) or Morning Coffee

8:30 Use of Biomarkers for Decision-Making in Breast Cancer

Therapy
Dennis J. Slamon, M.D., Ph.D., Chief, Hematology & Oncology, The David
Geffen School of Medicine, University of California, Los Angeles
Distinguishing independent primary tumors from intrapulmonary metastases

in non-small-cell carcinoma remains a clinical dilemma with significant clinical
implications. Using next-generation DNA sequencing, we developed a
chromosomal rearrangement-based approach to differentiate multiple primary
tumors from metastasis. Tumor specimens from patients with known independent
primary tumors and metastatic lesions were used for lineage test development,
which was then applied to multifocal cases. Lung tumors predicted to be
independent primary tumors based on different histologic subtype did not share
any genomic rearrangements. In cases of lung primary tumor and paired distant
metastasis, shared rearrangements were identified in all cases, emphasizing
the patient specificity of identified breakpoints. Concordance between
histology and genomic data occurred in the majority of cases. Discrepant cases
were resolved by genome sequencing. A diagnostic lineage test based on
genomic rearrangements from mate-pair sequencing demonstrates promise for
distinguishing independent primary from metastatic disease in lung cancer.
12:00 pm Close of Conference
M AY 5 - 6
Big Data for Personalized Medicine and

Biomarker Discovery
TUESDAY, MAY 5
Big Data in Biomarker Discovery and Drug

Development
Nicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson &
Johnson
8:10 Big Data and Small Trials: Translating Biological Data into
Clinical Biomarkers
Nicholas C. Dracopoli, Ph.D., Vice President, Janssen R&D, Johnson &
Johnson
All of the companion diagnostic tests approved by the FDA for use in oncology
are for driver mutations in genes involved in signal transduction pathways.
These tests are for single analytes predicting the functional status of the
drug target or pathway. There are no approved companion diagnostics for
drugs that work through alternative mechanisms such as chemotherapy or
immunomodulation. This presentation will discuss why so few biomarkers have
been developed and why we have mostly failed to develop molecular profiles
that predict drug response.
8:35 Applying Data Science in Translational Clinical Research

James Cai, Ph.D., Head, Data Science, Roche
The intelligent use of Big Data has transformed many industries. It also
presents numerous opportunities for pharmaceutical companies as we collect
more genomic Big Data directly from patients. In this talk I will outline a Data
Science model that emphasizes mixed-capability teams and impact on science
and business decisions. I will discuss how quantitative analytical skills, agile
programming, novel technologies and business acumen all contribute to this
model. I will illustrate with examples where Data Science was applied to clinical
research resulting in new scientific insights and better business decisions.
9:00 Using Clinical and Real World Data for Biomarker Discovery
in Precision Medicine
Joan Sopczynski, Ph.D., Senior Manager, Predictive Informatics,
Business Insights, R&D Business Technology, Pfizer
Real world and clinical trial databases consist of large patient data sets that can
be explored for biological insights. Examples will be presented describing the
analysis of this patient data for biomarker identification and disease knowledge.
Methods used to analyze the data, including the application of machine learning
techniques, will be described highlighting their ability to identify biomarkers
distinguishing patient populations.
9:25 Biology Driven Strategies to Discover

Novel Biomarkers and Predictive Markers
from Genomic Sequencing Data
Sponsored by
Ashley Van Zeeland, Ph.D., CEO, Cypher Genomics

The adoption of genomic sequencing beyond targeted panels in clinical
development has been impeded by the difficulty of discovering a signal from
the noise in small clinical studies. This presentation will describe, and present
results from, a comprehensive, biology-based approach that can identify novel
biomarkers from whole exome or whole genome sequencing data from the small
sample sizes that are typical of drug development and lead to the development of
novel companion diagnostic products.

10:40 Building and Leveraging Clinical and EHR Data Stack to

Optimize Clinical Development and Patient Outcomes
Usman Iqbal, M.D., Senior Medical Affairs Leader, AstraZeneca
Big Data analysis of clinical outcomes, genetic profiles and tissue morphology is
a big driver of personalized medicine. However, different elements of Big Data
have different applications and considerations in personalized medicine. This
presentation will focus on the development and application of the Real World
Evidence category of Big Data and how innovative platforms linking clinical
and EHRs platform can strategically optimize patient segmentation, clinical
development and health outcomes.
11:05 Exploring Clinical Transcriptomics for Biomarkers

Deepak Rajpal, Ph.D., Director, Computational Biology, GlaxoSmithKline
We will share our experience from a case study on clinical transcriptomics in
a dermatology indication space to understand disease resolution following
therapeutic intervention.
11:30 Translational Biomarker Identification for Patient

Stratification and Disease Indication Selection through Big Data
Bin Li, Ph.D., Associate Director, Computational Biology, Takeda
We implemented a tranSmart-based translational infrastructure, with globally
normalized molecular profiling data (~1600 GEO studies) and manually curated
patient information (~200 GEO studies). Also, a PLSR-based modeling framework
was designed and implemented, using a special splitting strategy and canonical
pathways to capture robust information for biomarker discovery. Combining these
efforts, we were able to build drug-sensitivity predictive models for SOC drugs,
and to successfully re-predict these drugs FDA-approved cancer indications.
12:00 pm Luncheon Presentation (Sponsorship Opportunity

Available) or Lunch on Your Own
Big Data to Advance Personalized Medicine

Rong Chen, Ph.D., Director, Clinical Genome Informatics, Genetics and
Genomic Sciences, Icahn School of Medicine at Mount Sinai
1:35 The Opportunities and Challenges of Biomarker-Driven,

Targeted Therapies
Mark S. Boguski, M.D., Ph.D., Associate Professor, Center for Biomedical
Informatics, Harvard Medical School
2:00 Using Big Data to Interpret Personal Genomes for Disease

Variant Discovery, Precision Medicine and Novel Therapeutics
Rong Chen, Ph.D., Director, Clinical Genome Informatics, Genetics and
Genomic Sciences, Icahn School of Medicine at Mount Sinai
Hundreds of thousands of individuals have been sequenced and released into
public repositories, providing an exciting resource for the discovery of disease
variants and therapeutic targets. This presentation will describe how we built
a knowledge base through 100,000 exomes, millions of literatures, protein
structures, and post-translational modification sites, and developed applications
to interpret sequencing cohorts and biobank data for disease variant discovery,
diagnosis and novel therapeutics. I will discuss how we interpret exomes and
RNA-Seq data for personalized cancer therapeutic reports.
2:25 Data Science Platforms for Molecularly-Targeted Therapy

and Personalized Medicine Research
Subha Madhavan, Ph.D., Associate Professor and Director, Innovation
Center for Biomedical Informatics; Director, Clinical Research Informatics,
Lombardi Comprehensive Cancer Center, Georgetown University
G-DOC Plus is an enhanced web platform that uses cloud computing and other
advanced computational tools to handle NGS and medical images so that they
can be analyzed in the full context of other omics and clinical information to drive
personalized medicine research. G-DOC Plus tools have been leveraged in the
cancer and non-cancer realms for hypothesis generation in precision medicine
and translational research.
2:50 The Developmental Neuropsychiatry Program at BCH: Using

Big Data for Personalized Medicine and Biomarker Discovery
Catherine Brownstein, Ph.D., Instructor, Pediatrics, Harvard Medical
School and Boston Childrens Hospital
Genomic Data Analysis

8:30 Big Data Experiment What Does Whole Genome

Sequencing Tell Us?
Chris Huang, Ph.D., Principal Scientist, Systems Pharmacology &
Biomarkers, Immunology TA, Janssen R&D
Boston Childrens Hospital is developing the infrastructure needed for largescale psychiatric research and treatment discovery with the creation of the
Developmental Neuropsychiatry Program (DNP). This new center is in a unique
position to improve psychiatric care through precision genetic medicine. The
DNP is working towards faster and more accurate diagnosis through assessment
of a patients phenotype, MRI results and neurophysiology, in combination
with next-generation sequencing and gene discovery. The goal is targeted
prescribing and increased possibilities for investigational therapies. The DNP is
investigating therapeutics to prevent schizophrenia by working with the youngest
patients, creating neuronal cell cultures to identify cell autonomous effects, and
constructing models of neural networks. The DNP also has cutting-edge research
in assessing response to medication and outcomes in the context of their
genotype and phenotype. The Clinical Pharmacogenomics Program is working
with the Psychiatry Department to study the relationship between genotype and
reported adverse drug reactions. Another research study is enrolling patients
to identify behavioral and brain biomarkers linked to psychotic illness. Finally,
groundbreaking research out of two Harvard laboratories has created a novel
all-optical electrophysiology platform to rapidly screen drugs for functional effects
in human neurons.
8:55 Hypothesis-Free Versus Hypothesis-Driven Approaches to

Predictive Modeling of Genomic Data
Next-generation sequencing (NGS) technologies have enabled investigators to

sequence thousands of tumor genomes. Correspondingly, personal genomics
and personalized medicine is emerging as a new research field. In this talk, I will
first present the identification of actionable mutations through our melanoma
whole genome sequencing and characterization of mutational changes
associated with drug resistance in EGFR-mutant lung cancer cell lines. Then, I
will introduce our recently developed bioinformatics methods for identification of
cancer genes from NGS data.
4:10 Catalyzing Delivery of Novel and Targeted Therapeutics from

Human Genetics to Patients
Janna Hutz, Ph.D., Director and Head, Quantitative Genetics and
Bioinformatics, Eisai
4:35 Realizing Personalized Medicine through Application of a

Next-Generation Cyber Capability to See the Emergent Whole in
Big Data
Kenneth Buetow, Ph.D., Director, Computational Sciences and
Informatics Program for Complex Adaptive Systems; Professor, School of
Life Sciences, Arizona State University
Data Science has the capacity to provide the needed tools to tackle the unique
challenges generated by personalized medicine. Arizona State Universitys (ASU)
Complex Adaptive Systems team is building a first generation Data Science
research platform the Next Generation Cyber Capability (NGCC). The ASU
NGCC composed of hardware, software and people transforms Big Data
to information and creates the evidence necessary to enable personalized
medicine. The NGCC permits data points to be evaluated in concert using
Big Data analytic frameworks thereby identifying an emergent, coherent
whole. Biologic network analysis represents one such promising integrative
approach. These networks account for the individual heterogeneity in underlying
etiology as well as the interaction of diverse events necessary to generate
complex phenotypes.

Viewing
WEDNESDAY, MAY 6
Viswanath Devanarayan, Ph.D., Global Head & Senior Research Fellow,

Exploratory Statistics & Bioinformatics, AbbVie, Inc.
Modeling of genomics Big Data to predict phenotypes of interest typically
involved a variety of machine/statistical-learning methods. Hypothesis-free
approach entails taking a totally unbiased approach by building the optimal
predictive signatures from the whole genome data. Hypothesis-driven
approaches tend to focus the predictive modeling efforts to only a subset of
the whole genome that is previously known to be implicated to the phenotype,
for example, from disease and target based pathway analysis. We will compare
the results and relative benefits from these two approaches using traditional
microarray as well as RNA-Seq data from neuroblastoma patients.
9:20 Application of Next-Generation Sequencing to Identify

Actionable Mutations and Cancer Driver Genes
Zhongming Zhao, Ph.D., Professor, Biomedical Informatics, Cancer
Biology and Psychiatry, Vanderbilt University School of Medicine

10:45 Systems Genetics Approaches in Drug Discovery
Peter S. Gargalovic, Ph.D., Principal Scientist, Cardiovascular Drug
Discovery Biology, Bristol-Myers Squibb
Evolution of high-throughput analytical methodologies and lowering of the cost is
now allowing an unprecedented access to genomic and phenotypic information
across large clinical and pre-clinical population studies. Today R&D is faced with a
challenge to implement effective ways to leverage the available population data
and provide guidance for drug discovery and development. Systems genetics
is emerging as a novel cutting edge approach to interrogate complex disease
population data. This presentation will highlight the concepts and show examples
of its application to drug discovery.
11:10 Recent Advancement in Mendelian Genomics and Data

Management at Yale Center for Genome Analysis
The Yale Center for Genome Analysis (YCGA) is one of the leaders in the
identification of disease-causing DNA variants. In the last four years, the use of
next-gen sequencing has led to the publication of >150 articles in peer-reviewed
journals including >25 in high-profile journals such as Science, Nature, Cell,
New England Journal of Medicine and Nature Genetics, reporting new variants
in various disorders, including hypertension, autism, several types of cancers,
Gaucher disease, skin disorders and cortical malfunctions, all using exome
analysis. In 2010, YCGA became part of the NHGRI supported Yale Center for
Mendelian Genomics (YCMG), which is one of three centers in the U.S. that
together form the Centers for Mendelian Genomics. The primary goal of this
consortium is to use NGS and computational approaches to discover the genes
and variants that underlie Mendelian conditions on a collaborative basis and at no
cost to the investigator. The presentation will focus on recent discoveries made
at YCGA, its computer infrastructure and the current challenges and solutions
developed for data analysis and management.

M AY 5 - 6
Cell-Free Biomarkers and Diagnostics

TUESDAY, MAY 5

Diagnostics

Medicine and Neurosurgery, Brain Cancer Program, Sidney Kimmel
Comprehensive Cancer Center, Johns Hopkins
8:35 Detection of Somatic Mutations in Biological Fluids in the

Management of Cancer
Nickolas Papadopoulos, Ph.D., Professor, Ludwig Center, SKCCC, Johns
Hopkins University
Somatic mutations are cancer-specific biomarkers that reveal the presence of
cancer when present in cell-free DNA or DNA derived from biological fluids. The
number of circulating tumor DNA molecules with somatic mutations is very low
compared to that of DNA molecules with wild type sequence and requires very
sensitive methods for their detection. Here we discuss our efforts for developing
such methods, studies for their validation, and their clinical applications.
9:00 cfDNA Ultra-Rare Allele Detection and Discovery

Sponsored by

10:40 Ultrasensitive Measurement of Circulating Tumor DNA to
Assess Treatment Response and Resistance
Abhijit A. Patel, M.D., Ph.D., Assistant Professor, Therapeutic Radiology,
Yale University School of Medicine
Our group has developed an ultrasensitive, multi-target assay that can identify
and quantify mutant ctDNA using novel error-suppression techniques applied
to next-generation sequencing data. Broad coverage of mutation hotspots and
warm-spots allows detection of ctDNA without prior knowledge of the tumors
mutation profile. Clinical examples will be presented in which this approach
is used to noninvasively monitor changes in ctDNA levels in response to
treatment and to track the emergence of mutations that confer resistance to
targeted therapies.
11:05 Single-Tube Enrichment of Mutations in Cancer Gene

Panels from Circulating DNA, Using COLD-PCR Prior to Targeted
Amplicon Resequencing
Targeted re-sequencing of mutations in cancer-relevant genes provides
opportunities for fine-tuning cancer therapy and follow-up during treatment,
by examining mutations in tumors and bio-fluids. However, a major technical
11:30 Panel Discussion

Moderator: G. Mike Makrigiorgos, Harvard Medical School
9:25 Presentation to be Announced
limitation has been the lack of sensitivity of cancer re-sequencing panels for
mutations below 1-2% abundance, which is frequently the case for circulating
DNA. We present a newly developed method via which mutations in numerous
amplicons are first enriched via COLD-PCR in a single-tube reaction, prior to
targeted re-sequencing. Using this approach, mutations of 0.01-0.1% abundance
can be detected via next-generation sequencing.

Exosomes and Microvesicles

1:35 The Biology and Functional Contribution of Exosomes in

Cancer Progression and Metastasis
2:00 Characterization of Endothelial Microvesicles in Preclinical

Species and Application to Drug Development
Sharon Sokolowski, MS, Senior Principal Scientist, Pfizer Global
Research & Development
Microvesicles (0.5 1M) in the peripheral blood of preclinical species have been
evaluated as potential biomarkers of vascular perturbation or injury. Validation
steps were completed to more fully characterize and understand the changes
observed in peripheral blood microvesicle absolute counts in normal, dosed and
diseased animals. While taking into consideration the advantages and caveats
of microvesicle evaluation with current methods and instrumentation, application
of microvesicles as safety and efficacy biomarkers during drug development
was explored.
2:25 Extracellular Vesicles (EV) as a Molecular Diagnostic

Platform
Clark Chen, M.D., Ph.D., Associate Professor and Chief, Stereotactic
and Radiosurgery; Vice-Chairman, Academic Affairs, Neurosurgery,
University of California, San Diego
Extracellular vesicles (EVs) are cell-secreted vesicles that range 30-2,000
nm in size. These vesicles are secreted by both normal and neoplastic
cells. Physiologically, EVs serve multiple critical biologic functions, including
cellular remodeling, intracellular communication, modulation of the tumor
microenvironment, and regulation of immune function. Because EVs contain
genetic and proteomic contents that reflect the cell of origin, it is possible to
detect tumor-specific material in EVs secreted by cancer cells. Importantly,
EVs secreted by cancer cells transgress anatomic compartments and can be
detected in the blood, cerebrospinal fluid and other bio-fluids of cancer patients.
In this context, there is a growing interest in analyzing EVs from the bio-fluid of
cancer patients as a means of disease diagnosis and therapeutic monitoring.
This talk will focus on the development of EVs as a diagnostic platform for the
most common form of brain cancer, glioblastoma, and discuss potential clinical
translational opportunities.
2:50 Novel Role of Microvesicles in Cardiovascular Diseases

Ming-Lin Liu, M.D., Ph.D., Research Assistant Professor, Dermatology,
Perelman School of Medicine, University of Pennslyvania
Circulating Biomarkers in Drug Development

4:10 Translational Circulating Biomarker Research for Drug
Development
Yoshiya Oda, Ph.D., President, Biomarkers and Personalized Medicine
Core Function Unit, Eisai
Biomarkers can play very important roles for drug development because
biomarkers can show the data for target engagement, target modulation, patient
stratification and drug efficacy. As a sample source of biomarkers, tissue is an
issue, because the amount of tissue is very limited and it is hard to obtain biopsy
samples in certain disease areas. Circulating biomarkers in serum/plasma are very
practical and patient-friendly. Several real examples about proteins, lipids and
miRNAs as circulating biomarkers will be shown during the presentation.
4:35 Next Generation Sequencing of Circulating

Tumor Cells from the CELLSEARCH System
Sponsored by
Charles Saginario, Scientist, CRS Labs,

Janssen Diagnostics

Viewing
WEDNESDAY, MAY 6
microRNA and ncRNA

Associate Dean of Research, UCLA School of Dentistry; Director, Center
for Oral/Head & Neck Oncology Research
8:30 Application of miR-Based Biomarkers in Diagnosis and

Management of Liver Injury in Human Subjects
Jiri Aubrecht, Pharm.D., Ph.D., Senior Director and Safety Biomarker
Group Lead, Drug Safety Research & Development, Pfizer
8:55 3UTR SNPs that are Targets for A-I RNA Editing Control
IGF1R mRNA Expression Levels in High-Risk Neuroblastoma
Danika Johnston, Ph.D., Research Associate, The Childrens Hospital of
Philadelphia
9:20 Exploration of Circulating Non-Coding RNAs as Cancer

Biomarkers
Hui Ling, M.D., Ph.D., Odyssey Fellow, Experimental Therapeutics, MD
10:45 Salivary Extracellular Non-Coding RNA Biomarkers

Associate Dean of Research, UCLA School of Dentistry; Director, Center
for Oral/Head & Neck Oncology Research
Extracellular RNAs (exRNAs) in human bodily fluids are emerging as effective
biomarkers for detection of diseases. Saliva, as the most accessible and noninvasive bodily fluid, has been shown to harbor exRNA biomarkers for human
diseases including cancer. Using high-throughput RNA-Seq, we conducted an
in-depth bioinformatic analysis of non-coding RNAs (ncRNAs) in human cell
free saliva (CFS) of healthy subjects with a focus on microRNAs (miRNAs), piwiinteracting RNAs (piRNAs) and circular RNAs (circRNAs) reporting the unusual
abundance of piRNA and the first demonstration of circRNA in a bodily fluid.
11:10 MicroRNAs in Mediating Tumor Angiogenesis, Drug

Resistance and Autophagy Responses in Human Cancers
Bing-Hua Jiang, Ph.D., Professor, Pathology, Anatomy and Cell Biology,
Thomas Jefferson University
Our recent study demonstrates that a number of microRNAs (miRNAs) are
downregulated in several kinds of human cancers including ovarian, breast,
lung, colon and glioma; and that levels of miRNA suppression are associated
with cancer development and drug resistance. To understand the mechanism,
we found that several different kinds of miRNAs are involved in tumor growth,
angiogenesis, drug resistance and autophagy responses through HER2, EGFR,
IGF-IR and ATG14 pathways. The miRNA suppression is regulated by DNA
methylation and reactive oxygen species.
11:35 Liquid Biopsies to Monitor Disease Progression and

Therapeutic Response in Cancer
Anton Wellstein, M.D., Ph.D., Professor, Oncology, Pharmacology and
Medicine, Georgetown University Medical School; Associate Director,
Basic Science, Lombardi Comprehensive Cancer Center
Clinically detectable cancer should be considered as a systemic disease. Cancer
tissue analysis provides a snapshot of the makeup of the local disease and/or
metastases that is limited by physical access to cancerous sites. In contrast, serial
blood samples provide a source of biomarkers that can reveal real-time changes
due to altered disease stage and/or treatment responses. The utility of circulating
microRNAs will be discussed.
M AY 5 - 6
Predictive Cancer Biomarkers

TUESDAY, MAY 5

Diagnostics
Medicine and Neurosurgery, Brain Cancer Program, Sidney Kimmel
Comprehensive Cancer Center, Johns Hopkins
8:35 Detection of Somatic Mutations in Biological Fluids in the

Management of Cancer
Nickolas Papadopoulos, Ph.D., Professor, Ludwig Center, SKCCC, Johns
Hopkins University
Somatic mutations are cancer specific biomarkers that reveal the presence of
cancer when present in cell-free DNA or DNA derived from biological fluids. The
number of circulating tumor DNA molecules with somatic mutations is very low
compared to that of DNA molecules with wild-type sequence and requires very
sensitive methods for their detection. Here we discuss our efforts for developing
such methods, studies for their validation, and their clinical applications.
9:00 cfDNA Ultra-Rare Allele Detection and Discovery

9:25 Pharmacodynamic Assessment of Drug
Response by Monitoring Mutational Load in
Urinary Circulating Tumor DNA
Sponsored by
Mark Erlander, Ph.D., CSO, Trovagene

The concept of liquid biopsies is expanding to include urine as a specimen type.
Using Precision Cancer MonitoringSM (PCM) platform for quantitative ctDNA
analysis at a single copy level, we demonstrate that drug-induced immediate early
changes in ctDNA mutational load correlate with tumor burden and treatment
response. As a non-invasive specimen, urine enables frequent monitoring of
ctDNA, and this accessibility can be applied to investigating mechanisms of action
of targeted therapeutics and, ultimately, cancer management.

10:40 Ultrasensitive Measurement of Circulating Tumor DNA to
Assess Treatment Response and Resistance
Abhijit A. Patel, M.D., Ph.D., Assistant Professor, Therapeutic Radiology,
Yale University School of Medicine
Our group has developed an ultrasensitive, multi-target assay that can identify
and quantify mutant ctDNA using novel error-suppression techniques applied
to next-generation sequencing data. Broad coverage of mutation hotspots and
warm-spots allows detection of ctDNA without prior knowledge of the tumors
mutation profile. Clinical examples will be presented in which this approach
is used to noninvasively monitor changes in ctDNA levels in response to
treatment and to track the emergence of mutations that confer resistance to
targeted therapies.
11:05 Single-Tube Enrichment of Mutations in Cancer Gene

Panels from Circulating DNA, Using COLD-PCR Prior to Targeted
Amplicon Resequencing
Targeted re-sequencing of mutations in cancer-relevant genes provides
opportunities for fine-tuning cancer therapy and follow-up during treatment,
by examining mutations in tumors and bio-fluids. However, a major technical
limitation has been the lack of sensitivity of cancer re-sequencing panels for
mutations below 1-2% abundance, which is frequently the case for circulating
DNA. We present a newly developed method via which mutations in numerous
amplicons are first enriched via COLD-PCR in a single-tube reaction, prior to
targeted re-sequencing. Using this approach, mutations of 0.01-0.1% abundance
can be detected via next-generation sequencing.
11:30 Panel Discussion

Moderator: G. Mike Makrigiorgos, Harvard Medical School


1:35 Application of NGS for Biomarker Discovery and Patient
Selection
2:00 Phoenix Childrens Hospital to Address the Unmet Need:

Slow Progress in Pediatric Drug Development
The need for new drugs in pediatric cancer is acute. Virtually no new therapy
has been introduced in the past two decades. Treatment for relapsed patients is
lower than in adults yet a large number of childhood cancer patients will relapse.
In stark contrast to the rapid introduction of targeted therapies in adults more
effective therapies are unavailable in pediatric cancer. PCH will focus on genomic
analysis to better understand disease mechanisms to develop new therapeutics
for pediatric cancer.
2:25 A General Approach to the Discovery and Translation of

Multi-Gene Biomarkers in Drug Discovery and Therapy
Wolfgang Sadee, Dr.rer.nat., Professor & Director, College of Medicine
Center for Pharmacogenomics, The Ohio State University
Extensive genetics/genomics studies have yet to account for the estimated
heritability of complex traits, including diseases and their treatments. Our
discovery pipeline encompasses detailed molecular genetics of target genes
to avoid use of surrogate markers and large-scale data analytics to reveal
phenotype associations involving gene-gene-environment interactions.
Discovering frequent regulatory variants in key genes often under positive
selection, we are now in a position to develop clinically relevant biomarker
panels, demonstrated with examples.
2:50 A Novel Phospho-Proteomic Diagnostic for

Patient Stratification and Therapy Selection for
Breast Cancer
Sponsored by
Glenn Hoke, Ph.D., Executive Vice President and COO,

Theranostics Health, Inc.

4:10 Utility of Targeted NGS Panels for Cancer in an Academic
Molecular Pathology Laboratory
Helen Fernandes, Ph.D., Associate Professor, Pathology and Laboratory
Medicine, Weill Cornell Medical College
The utility of targeted next-generation sequencing-based assays for identification
of genomic variants has made significant advances in the field of molecular
oncology. Testing panels and platforms have enabled clinical molecular pathology
laboratories to expand their testing menu to include NGS assays that can provide
information for a more reliable prediction of personalized cancer therapies.
Additionally, the assays can identify relevant genes that may have implications for
enrollment of the patient in clinical trials. This presentation will focus on the issues
involved for optimal performance and implementation characteristics of assays
for the identification of somatic variants in solid tumors in an academic molecular
pathology laboratory.
4:35 Patient Stratification in Oncology Using

NGS: An Application of the PATH Analytics
Platform to AML Patients from TCGA
Sponsored by
Scott Marshall, Ph.D., Managing Director, Analytics,

Precision for Medicine
Molecular heterogeneity in tumors is expected to impact prognosis and response
to therapy, and the ability to stratify patients based on their underlying molecular
profiles can improve outcomes. The transformation of high-dimensional genomic
data into personalized treatments requires cutting-edge science and advanced
analytics. To help biopharmaceutical companies realize this goal, Precision for
Medicine has developed the PATH Analytics Platform, a multi-modal platform
designed to accelerate research on biomarker discovery and patient stratification
by combining advanced Bayesian analytics and real-time data exploration.

Viewing
for 7 years, and we have started to evaluate its impact on expanding targeted
therapy options for cancer patients. With the integration of next-generation
sequencing technologies, more complex genotypes are now being identified.
Subsequently, the integration of histological testing may provide important
perspective into the biological function of unknown variants and the ability to
identify new biomarkers of response.
9:20 From Discovery Through

Commercialization of Personalized Multiplex
Biomarker Assays
Sponsored by
Al Akowitz, Ph.D., Vice President, Strategic Sales, Meso Scale Discovery

10:45 Genomic Markers Associated with Pathologic Complete
Response and Resistance in Triple Negative Breast Cancer
Christos Hatzis, Ph.D., Assistant Professor, Medicine; Director,
Bioinformatics, Breast Medical Oncology, Yale University School of
Medicine
Efforts to develop transcriptional predictors of chemotherapy sensitivity in triple
negative breast cancer (TNBC) have been met with limited success due to the
heterogeneity of this disease. We explored whether genomic differences in the
exomes of extremely chemotherapy sensitive and highly chemotherapy resistant
TNBC cases could provide clues of chemosensitivity. Although a few genes show
response-associated mutational patterns, the chemoresistant cases appear to
have higher mutational load and subclonal heterogeneity, suggesting that higher
DNA diversity may be associated with chemotherapy resistance. Interestingly,
resistant tumors show characteristic mutational spectrum shifts that may suggest
heterogeneous branch evolution. These broad measures of genomic diversity
could show promise as markers of resistance to chemotherapy.
11:10 Comprehensive Translational Research to Identify Predictive

Biomarkers of Lenvatinib in the Preclinical and Clinical Study
Yasuhiro Funahashi, Ph.D., Senior Director, Biomarkers and Personalized
Medicine, Eisai
This presentation will cover: 1) systems biology to identify biomarker candidates
for Lenvatinib using the cancer cell line panel, 2) translational research to test
biomarker candidates in multiple Phase II trials, and 3) biomarker correlative
analysis in Phase III trial.
11:35 Identification of Independent Primary Lung Tumors and

Intrapulmonary Metastases Using DNA Junctions


WEDNESDAY, MAY 6

8:30 Use of Biomarkers for Decision-Making in Breast Cancer

Therapy
Dennis J. Slamon, M.D., Ph.D., Chief, Hematology & Oncology, The David
Geffen School of Medicine, University of California, Los Angeles
8:55 The Impact of Multiplexed Genotyping in Directing Cancer

Care and a Role for Combining Genotype with Histology for
Biomarker Discovery
Darrell R. Borger, Ph.D., Director, Biomarker Laboratory, Massachusetts
General Hospital and Harvard Medical School
Our laboratory has conducted clinical genotyping in a large academic hospital
Distinguishing independent primary tumors from intrapulmonary metastases

in non-small-cell carcinoma remains a clinical dilemma with significant clinical
implications. Using next-generation DNA sequencing, we developed a
chromosomal rearrangement-based approach to differentiate multiple primary
tumors from metastasis. Tumor specimens from patients with known independent
primary tumors and metastatic lesions were used for lineage test development,
which was then applied to multifocal cases. Lung tumors predicted to be
independent primary tumors based on different histologic subtype did not share
any genomic rearrangements. In cases of lung primary tumor and paired distant
metastasis, shared rearrangements were identified in all cases, emphasizing
the patient specificity of identified breakpoints. Concordance between
histology and genomic data occurred in the majority of cases. Discrepant cases
were resolved by genome sequencing. A diagnostic lineage test based on
genomic rearrangements from mate-pair sequencing demonstrates promise for
distinguishing independent primary from metastatic disease in lung cancer.
M AY 6 - 7
Companion Diagnostics
WEDNESDAY, MAY 6
4:50 Companion Diagnostics Immunoassay and Other Wet

Markers Method Development and Choice of Platform
Challenges and Considerations
11:00 am Conference Registration
John L. Allinson, FIBMS, Head, Biomarker Strategy, Drug Development

Services, LGC Group
12:15 pm Lunch on Your Own

Commercialization Strategies
1:35 Making Disciplined Decisions in Companion Diagnostic

Development Using Clinical Epidemiologic Techniques
Choosing which biomarker to develop as a companion diagnostic, choosing
a cutoff, and even deciding whether or not a companion diagnostic should be
co-developed with a therapeutic often provokes spirited discussions within
pharmaceutical companies. However, these discussions need not involve high
drama. This presentation will demonstrate a few simple, well-established clinical
epidemiologic techniques which can guide rational, disciplined decisions.
Examples of the application of these techniques will also be presented.
2:00 The Role of Companion Diagnostics in Improving Patient

Care
Carolina Rizo, Ph.D., MBA, Director, Business Development, Roche
Molecular Systems
Companion diagnostics is becoming a key element in cancer treatment. In this
talk, I will: 1) discuss the importance of standardized testing due to variability
observed in EQA schemes, 2) review the differences in test methodologies
and the resulting impact on patient selection, 3) describe the value of clinical
validation with a CDx and advantages it may bring to the drug registration
process, and 4) evaluate how future technologies (liquid biopsies) may play a role
in patient selection and management. I will show how companion diagnostics is
improving patient care and will continue doing so.
2:25 Dollars and Sense: Making the Most of Companion

Diagnostics
Steven Gutman, M.D., Myraqa Strategic Advisor, Illumina, Inc.
Companion diagnostics are now commonly being evaluated early in the drug
development process as important tools to reduce the cost of clinical trials and to
improve study outcomes. These tests are also being used to ensure the clinically
effective and cost effective use of new drugs. FDA review of these products
appears to be flexible and least burdensome and third party payers generally
have been willing to pay for these tests although not at the same premium as for
drugs. With this background in mind, this talk will address the gaps that exist in
the value proposition for companion diagnostics.
2:50 Diagnostics Partnering to Realize Combined

Drug-Diagnostics Strategies
Sponsored by
Rolf Ehrnstrm, Scientific Advisor, Diagnostics

Partnering, Thermo Fisher Scientific

4:25 Tissue and Time: Perspectives on Companion Diagnostic
Development
Ron Mazumder, Ph.D., MBA, Global Head, R&D and Operations, Janssen
Diagnostics, Janssen Pharmaceutical Companies of Johnson & Johnson
This talk will look at potential development of companion diagnostics in the wet
biomarker space. Consideration will be given to: 1) range of analytical platforms
available and factors that influence their choice, 2) development program from
original research method through to accredited diagnostic the technical
challenges and requirements, 3) different applications of the research and
diagnostic assays during a drug development program, and 4) overall project
design requirements from the sponsor, diagnostic and contract research
organization to deliver a successful outcome.
5:15 Regulatory Perspective on in vitro Companion Diagnostic

Devices
Eunice Lee, Ph.D., Division of Immunology and Hematology Devices,
Office of In Vitro Diagnostics and Radiological Health, CDRH, FDA
Since the approval of the HercepTest in 1998, significant strides have been
made to establish a regulatory structure for companion diagnostic devices in
the US. Companion diagnostics are defined as devices that provide information
that is essential for the safe and effective use of a corresponding therapeutic.
I will describe the current regulatory model for companion diagnostics, and
share some lessons learned from successful co-development programs from
the device perspective. My talk will also highlight considerations for validating
the performance of in vitro diagnostics, and discuss potential challenges to the
regulatory model for companion diagnostics in the future.

SC2: Next-Generation Sequencing as a Clinical Test
THURSDAY, MAY 7
7:30am Breakfast Presentation: Next Generation
in Situ Hybridization (ISH) and
Immunohistochemistry (IHC)
Sponsored by
Sven Mller, Ph.D., Manager, R&D, ISH pharmDx,

Dako - an Agilent Technology company
The need for solid tumor biomarkers to be confirmed in context of tissue
morphology calls for routine involvement of slide based techniques like IHC and
ISH. The major drawbacks of these methods relates to a qualitative readout and
a slow turn-around time, respectively. Based on Dako, an Agilent Technologies
Companys long term IHC and ISH expertise we are bringing these technologies
to the next level, enabling us to continue being a One Stop Shop in IHC and
ISH solutions for pharma partners - from early development to IVD class III
kits. The symposium focuses on game changing improvements of the ISH and
IHC technologies.
Companion Diagnostics Case Studies

James Novotny, Ph.D., Group Director, Pharmacodiagnostics, BristolMyers Squibb
8:30 Translational and Companion Diagnostic Strategies: A Case

Study of Development of a PI3K-Beta Inhibitor
Monica Motwani, Ph.D., Director, Precision Medicine & Diagnostics,
GlaxoSmithKline
In the era of precision medicine, efficient development and implementation of
biomarker and companion diagnostic strategies in clinical studies is a key to
being successful. This talk will discuss the PI3K beta inhibitor development as
an example to illustrate various steps in the development and implementation of
these strategies in clinic.
8:55 Evaluation of PD-L1 as a Potential Companion Diagnostic for

Nivolumab, a Novel Immune Checkpoint Inhibitor for the
Treatment of Cancer
James Novotny, Ph.D., Group Director, Pharmacodiagnostics, BristolMyers Squibb
PD-L1 expression has been documented on a wide variety of solid tumors, and
PD-L1 positivity may correlate with response from treatment with PD-1 pathway
inhibitors. Nivolumab is a fully human IgG4 PD-1 immune checkpoint inhibitor
antibody that selectively prevents interaction with PD-L1 and PD-L2, thereby
inhibiting the downregulation of antitumor T cell function. BMS has engaged in
a comprehensive analytical and clinical evaluation of PD-L1 expression by IHC
in order to determine the association between expression and clinical outcome
for Nivolumab.
9:20 A New Paradigm for Precision Oncology:

A Shared Vision for Universal Oncology Testing
Sponsored by
John Leite, Ph.D., Vice President, Oncology Market

Development, Oncology, Illumina
The rapid evolution of high-accuracy and high-throughput genomic technologies
has created unprecedented opportunities for translational and clinical applications
in cancer. Next-generation sequencing approaches now allow the interrogation
of germline and somatic variation associated with malignancy across DNA and
RNA sequence, structural variation, and epigenetic changes in many tissue types
including blood. Potential applications span the continuum of cancer care, from
inherited risk assessment and early detection to prediction of treatment response
and recurrence monitoring.
the PARP inhibitor Rucaparib. This approach is being prospectively tested in

the ARIEL (Assessment of Rucaparib In ovarian cancEr triaLs) program and will
be described.
11:35 Developing Biomarkers for Use in Patient Selection in Early

Phase Clinical Trials
Ann Kapoun, Ph.D., Vice President, Translational Medicine, OncoMed
Pharmaceuticals
This presentation will cover: 1) incorporating predictive biomarkers into early
stage R&D to ensure each clinical candidate has a complimentary biomarker
when it reaches the clinic, 2) embedding personalized medicine strategies into
drug discovery to fast-track CDx programs, and 3) prospective and retrospective
predictive biomarker case studies for Anti-Notch1 and for Tarextumab
clinical programs.
12:00 pm Enjoy Lunch on Your Own

George A. Green IV, Ph.D., Group Director, Pharmacodiagnostic
Center of Excellence, Bristol-Myers Squibb
1:35 Creating and Managing the Multiple Interfaces of Drug/
Diagnostic Co-Development
George A. Green IV, Ph.D., Group Director, Pharmacodiagnostic Center
of Excellence, Bristol-Myers Squibb
Many pharmaceutical companies are using an external partnering model to
pursue co-development of drugs and diagnostic products. This approach
provides access to diverse biomarkers, technology and platforms, as well as
diagnostic manufacturing and commercialization expertise, thus maximizing
diagnostic development capabilities. External partnering creates multiple
interfaces of functions both within and between the drug and diagnostic
companies. We will explore some of the challenges that accompany these
interfaces, their management and implications, along with ideas for optimizing the
virtual diagnostic company model for the Rx/Dx co-development environment.
2:25 Innovative Strategies and Progress in Translational

Biomarkers in Clinical Oncology through Public-Private
Partnerships

Ian McCaffery, Ph.D., Head, Companion Diagnostic Development,
Genentech
11:10 Development of a Homologous Recombination Deficiency

(HRD) Companion Diagnostic Test for Selecting High Grade
Ovarian Cancer Patients Likely to Respond to the PARP Inhibitor
Rucaparib
Mitch Raponi, Ph.D., Senior Director, Molecular Diagnostics, Clovis
Oncology
PARP inhibitors are active in patients whose tumors exhibit homologous
recombination deficiency (HRD), and pathogenic mutations in the tumor
suppressor gene BRCA (a key player in the HR pathway) is a predictor of PARPi
efficacy. However, multiple mechanisms can result in HRD, which in turn leads
to a BRCAness phenotype. A comprehensive genomic sequencing-based HRD
test has been developed to identify a patient population who will benefit from
Paula Eason, Ph.D., Scientific Program Manager, Cancer Division of

Research Partnerships, Foundation for the National Institutes of Health
The continual need for development of biomarkers with robust clinical utility
is an ongoing challenge for all cancer types. Incorporation of prognostic and
predictive biomarkers into clinical trial strategies and therapeutic decision-making
is essential to disentangle the complexities of the pathogenic process, drug
pharmacodynamics, and tumor heterogeneity. Success will require strategic
partnerships and alliances between public and private sectors to share resources,
risks, experience and expertise, and to align multiple stakeholder incentives to
support and accelerate sustainable innovation.
2:50 Close of Conference
2 0 1 5 B I O M A RK E R S WO RL D C O N G RE S S M E D I A PA RT N E R S
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M AY 6 - 7
Clinical and Translational

Biomarkers in Drug Discovery
WEDNESDAY, MAY 6
2:50 Ultrasensitive Measurement of IL-17 in

Psoriasis Patients

12:15 pm Luncheon Presentation: Ultrasensitive
Multiplexed Cytokine Measurements
Cathy Soderstrom, Senior Scientist, Regulated

Biomarkers Group, Pfizer Groton
Sponsored by
Mark Roskey, Ph.D., Vice President & General Manager,

Applications and Reagents, Quanterix Corporation
The normal healthy range for many cytokines is very close to the limit of detection
of conventional immunoassay measurement techniques. Ultra-sensitive Simoa
technology measures biomarkers in blood at extremely low levels of detection,
allowing researchers to measure both healthy and sick subjects with confidence.
Multiplex cytokine panels allow users to achieve similar sensitivity with each
marker in a multiplex panel as they would if they were to test individual assays.
Biomarkers in Drug Discovery Decision-Making

Michael E. (Ransom) Burczynski, Ph.D., Executive Director, Biomarker
Technologies, Exploratory Clinical and Translational Research, BristolMyers Squibb
1:35 Enabling Robust Biomarker-Driven Decision-Making in Drug

Development: Key Factors and Considerations
Michael E. (Ransom) Burczynski, Ph.D., Executive Director, Biomarker
Technologies, Exploratory Clinical and Translational Research, BristolMyers Squibb
Prospective biomarker testing strategies in the clinic benefit from multiple
perspectives including those of discovery biologists, translational scientists,
biomarker technologists, physicians, statisticians, bioinformaticians and
operational personnel. Studies designed from these perspectives enable
teams to combine biomarker data across platforms from sufficiently powered,
feasible-to-execute clinical studies that can potentially 1) elucidate disease
pathophysiology, 2) confirm mechanism of action, 3) demonstrate target
engagement, 4) confirm dose-dependent pharmacodynamic effects and even 5)
determine if efficacy/safety profiles are enhanced in certain molecularly defined
subsets of patients. In addition, judicious sampling in those same studies for
future exploratory research can ultimately yield a biorepository of great value for
identifying new disease indications, drug targets, biomarkers and other valueadded information to the R&D organization in the future. Early definition of the
biomarker strategy, coupled with a system that permits flexible re-evaluation of
the strategy in light of new information, provides an optimal scenario for executing
biomarker studies in the clinic. Finally, committing to objectively assessing each
biomarker studys success and impact in the overall decision-making around a
candidate drugs development permits a return-on-investment (ROI) calculation
that can help refine future biomarker strategies to ensure only the most highly
informative biomarker approaches and methodologies are employed. The
present talk will review the basic tenets of a robust biomarker evaluation process
and illustrate several biomarker study approaches in this paradigm that have led
to rapid data generation, analysis and interpretation to support key decisions
during the early clinical development of candidate therapies.
2:00 Who Owns Biomarker Qualification and Surrogate

Endpoints?
John A. Wagner, M.D., Ph.D., Senior Vice President & Head, Global
Clinical and Translational Sciences, Takeda Pharmaceuticals

Suso Platero, Ph.D., Director, Oncology Biomarkers, Janssen
Pharmaceuticals
Sponsored by
Translational Biomarkers:
From Discovery to the Clinic
Johan Luthman, D.D.S., Ph.D., Vice President, Clinical Neuroscience, Eisai
4:30 Current Status for AD Biomarkers: From Mice to Men to

Trials and Clinical Practice
Johan Luthman, D.D.S., Ph.D., Vice President, Clinical Neuroscience, Eisai
Alzheimers disease (AD) is a clear illustration of the introduction of biomarkers
that has entirely changed the way drug R&D is executed, but also shows the
challenges of addressing remaining hurdles. In AD research, biomarkers are
now applied to translate animal data to early clinical studies, as well as to both
identify and stage the disease in clinical trials. For example, biomarkers have
become critical for diagnosis of AD pre-dementia. Moreover, demonstration of
the presence of AD pathology using biomarkers has become central for drug
trial stratification and enrichment strategies. Several modalities of AD biomarkers,
imaging (e.g. MRI and PET), bio-fluid (e.g. CSF measures) and functional,
are available for which there are different, but also commonly overlapping
applications. At the same time, for many AD biomarkers considerable work
remains in obtaining sufficient data on assay performance, clinical qualification
for the intended context of use, standardization of use and regulatory approval
before one can fully implement them in clinical trials and practice. In addition, it
is also important to note the possibilities for operational implementation as well
as the general acceptance and commercial potential of various AD biomarker
modalities varies considerably. Commonly there are also differing opinions
between academic and industrial scientists and regulators of what constitutes
satisfactory validation and qualification for use of AD biomarkers as stand-alone
or companion diagnostics, or as supportive outcome measures in clinical trials.
4:55 Approaches to Biomarkers that can Translate the

Stubbornness of Fortune
William B. Mattes, Ph.D., DABT, Director, Division of Systems Biology,
National Center for Toxicological Research, US Food and Drug
Administration
The terms biomarker and translational are all too often abused buzzwords; to
have practical meaning for public health a certain rigor must be applied to their
use. Per the Working Group definition a biomarker should be a characteristic
that is objectively measured and to that end the assay used to measure it should
be robust and validated for performance characteristics. Research in many
laboratories, including ours, focuses on potential biomarkers, but that distinction
should not be forgotten. Furthermore, the biomarker should be an indicator of
normal biological processes, pathogenic processes, or pharmacologic responses
to a therapeutic intervention; the implication is that the context of use need
be explicitly defined. This is the process of qualification, to be distinguished
from analytical validation. To be truly translational a biomarker needs to satisfy
the above criteria and be qualified in at least two experimental settings, such
as measuring liver injury in rodents and in humans. Of course, that means the
assay must be validated for performance in the biological media obtained from
the different settings. More difficult for the translational qualification is the reality
that experimental designs in non-clinical and clinical investigations are too often
vastly different. Approaches to address these challenges and examples will
be discussed.
5:20 Understanding IMiDS: Mechanism, Differentiation and

Biomarkers
9:20 SOMAmer Reagents and the SOMAscanTM

Assay, Tools for Real-Time Biology
Patrick R. Hagner, Ph.D., Scientist, Translational Development, Celgene
Andy Keys, Associate Director, Sales,

North America, SomaLogic
SomaLogics proteomic tools have found broad success in R&D applications
including: biomarker discovery and diagnostics development, target validation
in pre-clinical and clinical research; pharmacology in cells, tissues, and clinical
samples; and custom assay development. We offer tools from broad biomarker
discovery to developing single detection reagents.

9:35 The Impact of Preanalytical Variables on

Biomarker Research
THURSDAY, MAY 7
Sponsored by
Sponsored by

IHC technologies.
Biomarker Assay Development and Validation

Ken Chang, Ph.D., Clinical Assay Development & Outsourcing Lead,
Merck
8:30 Development and Validation of a Clinical Biomarker Assay

to Quantitate Thymic Stromal Lymphopoietin in Human Plasma at
Sub-pg/mL level
Sponsored by
David Craft, Ph.D., Senior Manager Sciences,

Preanalytical Systems, Becton Dickson & Company
The use of biomarkers can potentially improve the efficiency of the drug
development process. The preanalytical phase has great potential for errors.
This presentation will focus on the potential impact of sample handling on RNA,
proteins, cells within blood / tissue and how this variability can be controlled.
Genomic Biomarker Discovery

10:45 Discover Genomic Biomarkers for Assisting Vaccine
Research and Development
I-Ming Wang, Ph.D., Principal Scientist, Genetics and
Pharmacogenomics, Merck Research Labs
This presentation describes our integrated analysis of immune response to
infection and vaccination by a genome-wide blood gene expression approach.
Our main goal is to determine prediction rules governing the immune systems
behavior under different conditions. Proof-of-concept human and non-human
primate genomic studies were conducted to identify potential accessible
biomarkers for predicting vaccine response/safety and disease susceptibility to
infection. Harvesting results from these efforts and applying them in the clinical
setting should significantly enhance our capacity for future vaccine development.
11:10 Drug Target Validation in Concert with Clinical Development

Liling Warren, Ph.D., Senior Scientific Investigator, GlaxoSmithKline
Xuemei Zhao, Ph.D., Principal Scientist, Molecular Biomarkers and

Diagnostics Laboratory, Merck
11:35 Novel Biomarker Approaches for Pathologic Angiogenesis

in Human Cancers
TSLP is an attractive therapeutic target for the treatment of allergic diseases, and
plasma TSLP is a potential biomarker in the development of therapeutic agents.
We developed and validated an ultra-sensitive electrochemiluminescence assay
for measurement of TSLP in plasma with a lower limit of quantitation of 0.12 pg/mL,
which allowed the quantitation of TSLP in approximately 90% of human plasma
samples tested. The assay demonstrated excellent performance characteristics.
The validated TSLP assay enables assessment of circulating TSLP as a patient
selection marker in the development of therapeutics to treat atopic diseases.
Aejaz Nasir, M.D., MPhil, Fellow, College of American Pathologists;

Senior Medical Advisor & Surgical Pathology Lead, Molecular Solid
Tumor & Anatomic Pathologist, Tailored Therapeutics, Diagnostic &
Experimental Pathology, Eli Lilly and Company
8:55 Fit-For-Purpose in situ Analytical Validation of NGS

Mutation Profiling in FFPE Tissue
Ken Chang, Ph.D., Clinical Assay Development & Outsourcing Lead,
Merck
We have developed a Concordance Calculator to quantify reproducibility
of multi-variant calls among Next-Generation Sequencing (NGS) replicates
(same gDNA with different library preparations). This novel approach also
allowed us to eliminate many different technical artifacts including Post Tissue
Collection Modifications (PTCM) such as deamination and oxidation artifacts. We
then developed a Fit-for-Purpose in situ analytical validation strategy using
RainDance ThunderBolts Cancer Panel to include part of the analytical validation
directly on each and every clinical sample. This strategy also involves using a set
of normal FFPE tissue samples to eliminate panel/library prep/pipeline specific
artifacts. The detail of this novel analytical validation approach will be discussed
in detail.
12:00 pm Luncheon Presentation:

Reagent Qualification and Platform Selection
Considerations for Single and Multiplex
Biomarker Analysis in Support of Clinical Studies
Sponsored by
Afshin Safavi, Ph.D., Founder and CSO, BioAgilytix Labs

Biomarker analysis has become a common practice by many pharmaceutical
companies to support PK/PD modeling. The reliability of outcomes is heavily
influenced by the quality of the reagents and commercial kits as well as the
selection of bioanalytical platform. Case studies will be presented to highlight
the key bioanalytical considerations involved in running successful biomarker
analyses in support of clinical studies with consideration to platform selection and
critical reagents as well as kit selection.

1:35 Creating and Managing the Multiple Interfaces of Drug/

Diagnostic Co-Development
Many pharmaceutical companies are using an external partnering model to
pursue co-development of drugs and diagnostic products. This approach
provides access to diverse biomarkers, technology and platforms, as well as
diagnostic manufacturing and commercialization expertise, thus maximizing
diagnostic development capabilities. External partnering creates multiple
interfaces of functions both within and between the drug and diagnostic
companies. We will explore some of the challenges that accompany these
interfaces, their management and implications, along with ideas for optimizing the
virtual diagnostic company model for the Rx/Dx co-development environment.
2:25 Innovative Strategies and Progress in Translational

Biomarkers in Clinical Oncology through Public-Private
Partnerships
Paula Eason, Ph.D., Scientific Program Manager, Cancer Division of
Research Partnerships, Foundation for the National Institutes of Health
The continual need for development of biomarkers with robust clinical utility
is an ongoing challenge for all cancer types. Incorporation of prognostic and
predictive biomarkers into clinical trial strategies and therapeutic decision-making
is essential to disentangle the complexities of the pathogenic process, drug
pharmacodynamics, and tumor heterogeneity. Success will require strategic
partnerships and alliances between public and private sectors to share resources,
risks, experience and expertise, and to align multiple stakeholder incentives to
support and accelerate sustainable innovation.
M AY 6 - 7
Clinical NGS Testing

WEDNESDAY, MAY 6
2:50 Clinical NGS: Moving from Gene Panels to Exome

Sequencing
Birgit Funke, Ph.D., Assistant Professor, Pathology, MGH/Harvard

Medical School; Director, Clinical Research and Development,
Laboratory for Molecular Medicine, Partners HealthCare
12:15 pm Luncheon Presentation: Enriching Nucleic Sponsored by

Acids for Next-Generation Sequencing Analyses
of SNPs, CNVs, Gene Fusions and More
Joe Don Heath, Ph.D., Vice President, Market Development Diagnostics,
NuGEN
The novel Single Primer Enrichment Technology (SPET) and how it differs from
existing target enrichment methods will be described. Sensitive variant detection
from genomic DNA derived from fresh and FFPE tissues using 344 cancer-related
genes will be demonstrated as well as utilization of SPET as a rapid, cost-effective
screening tool for discovery of novel fusions and detection of known fusions with
a panel of 500 cancer genes implicated in fusions events.
NGS in the Clinic

1:35 Using Genome Sequencing in the Clinical Setting

Jason Merker, M.D., Ph.D., Assistant Professor, Pathology, Stanford
University Medical Center
Genome sequencing is increasingly being applied in clinical practice for the
diagnosis of unexplained heritable disease. I will describe our experience with
establishing a clinical genomics service at an academic medical center. I will
then discuss the benefits and challenges identified during our initial efforts
to use genome sequencing to identify the molecular etiology in patients with
unexplained hereditary cancer risk.
2:00 The Realities of Implementing Clinical Genomic Testing: The

Good, the Bad and the Ugly
Optimizing the implementation of clinical genomic testing goes much beyond
rigorous test validation. Generating genomic information and integrating it
into clinical care requires collaboration between several divisions within the
laboratory, clinicians, both physicians and ancillary care providers, as well as
bioinformaticians, computational biologists, and information systems experts. This
presentation will address key logistical elements that should be considered in an
effort to optimize the clinical implementation of genomic medicine.
2:25 Laboratory-Developed Tests in the Genomic Medicine

Era: Validation, Regulation and Challenges Faced by New
Technologies and Clinical Applications
Andrea Ferreira-Gonzalez, Ph.D., Professor and Chair, Division of
Molecular Diagnostics; Director, Molecular Diagnostics Laboratory,
Department of Pathology, Virginia Commonwealth University
Laboratory-developed tests are those tests developed, validated and performed
by clinical laboratories. There are standards and regulations in place for the
validation of these tests before they are introduced into clinical practice. This
presentation will discuss the process of validation under the current regulatory
framework, and regulatory challenges posed by new technologies such as NGS
and its clinical applications.
NGS is increasingly used in the clinic, most commonly in the form of targeted
gene panels that are custom tailored for specific diseases. This paradigm cannot
keep up with the accelerating pace of novel discoveries, making static gene
panels suboptimal for many disorders. As the quality of exome capture kits is
improving, the nature of targeted panels is beginning to change from a static,
stand-alone assay to a set of genes that is interrogated from an underlying
exome assay.

4:25 Clinical Impact of NGS Multi-Gene Panels in Diagnosis and
Management of Hereditary Cancer Syndromes
James M. Ford, M.D., Associate Professor, Medicine (Oncology) and
Genetics, and Director, Stanford Clinical Cancer Genomics Program,
Stanford University School of Medicine
Next-generation sequencing-based panels assaying multiple hereditary cancer
risk genes are entering clinical use; however, little is known about their yield or
effect on clinical management of patients. We have sequenced germline DNA
samples from over 400 patients with personal and family histories of breast and
ovarian cancer, but without BRCA1/2 mutations, and found ~10% carry potentially
pathogenic mutations in other cancer susceptibility genes. Challenges include
return of genetic information to patients, clinical management, screening
and risk-reducing interventions in individuals with mutations in moderatepenetrance genes and high-penetrance genes in non-syndromic families, and
incidental findings.
4:50 Clinical NGS for Solid Tumor Testing

Rajyalakshmi Luthra, Ph.D., Director, Molecular Diagnostic Laboratory;
Professor, Pathology and Laboratory Medicine, MD Anderson Cancer
Center
5:15 Defining Clinical Utility for Genomic Testing
Supported by
Elaine Lyon, Ph.D., Medical Director, Molecular

Genetics and Genomics, ARUP Laboratories;
Associate Professor, University of Utah School of
Medicine; Past President, Association for Molecular Pathology
In addition to showing analytical and clinical validity, clinical laboratories are being
asked to demonstrate clinical utility, or how their tests are useful in treating or
managing disease. Traditional models such as large case/control studies are not
feasible for rare variants identified by genomic sequencing. Alternative methods
and models are needed to establish appropriate standards for molecular tests.
This presentation will discuss unique challenges for molecular tests, and the need
for novel solutions.

THURSDAY, MAY 7
Sponsored by
11:35 Supporting Clinical Trials and Clinical Decision-Making

through Genomic Sequencing

IHC technologies.
NGS-Driven Clinical Trials

Daniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core,
National Cancer Institute, NIH
8:30 MSK-IMPACT: Clinical Experience with High Volume

Hybrid Capture-Based Next-Generation Sequencing to Enable
Personalized Oncology and Prepopulate Genetically Informed
Clinical Trials
Marc Ladanyi, M.D., William Ruane Chair in Molecular Oncology,
Molecular Diagnostics Service and Human Oncology & Pathogenesis
Program, Memorial Sloan-Kettering Cancer Center
8:55 Bringing the Power of Genomics and Next-Generation

Sequencing to the NCI Clinical Trials
Daniel Edelman, Ph.D., Core Manager, Clinical Molecular Profiling Core,
National Cancer Institute, NIH
9:20 Purpose-built Targeted Sequencing

Technology to Discover Gene Fusions, SNPs
and CNVs in Clinically Relevant Samples
Supported by
Thon de Boer, Ph.D., Technical Product Manager,

ArcherDX, Inc.
Anchored Multiplex PCR (AMP) is a target enrichment technology for NGS-based
biomarker discovery. AMP accurately detects germline and somatic mutations
such as gene fusions, SNPs, indels, and copy number changes from as little as
80pg total nucleic acid. This talk will highlight the various applications of AMP and
the companion analysis software that enables detection of various gene fusions
down to 0.1% simulated tumor cellularity.

10:45 Opportunities and Challenges for NGS-Based Clinical Trials
Jamie L. Platt, Ph.D., Vice President, Genomic Solutions, Geneuity (an
MPLN company)
The requirements and challenges for NGS-based diagnostics are different from
those for NGS-based clinical trials. The evolving technology and regulatory
landscapes present increased opportunity for utilizing NGS in clinical trials;
however, a thorough understanding of workflow challenges, technical limitations
and data analysis is required for optimal success. The key challenges in NGSbased clinical trials will be discussed, and opportunities around assay validation,
companion diagnostics, data analysis, genomic annotation and supporting
services will be highlighted.
11:10 Considerations for the Use of Comprehensive Genomic

Profiling in Oncology Clinical Care and Clinical Trials
Matthew Hawryluk, Ph.D., Senior Director, Corporate & Business
Development, Foundation Medicine Inc
Oncology has engaged cancer as a disease of the genome, informed by an
increased understanding of the genomic alterations that drive patient tumors.
Foundation Medicine addressed the scientific, technical and practical challenges
in developing a comprehensive cancer genomic profiling test based on nextgeneration sequencing (NGS), enabling the development of targeted therapies
in the trial setting and helping appropriately identify patients in routine care. The
approach advances novel treatment paradigms and accelerates progress toward
truly personalized medicine.
Jennifer J.D. Morrissette, Ph.D., Clinical Director, Center for Personalized

Diagnostics, University of Pennsylvania School of Medicine
Rapid advancements in next-generation sequencing (NGS) have opened the
door for unprecedented diagnostic capabilities. While these technologies make
it feasible to sequence large genomic regions in very short periods of time, the
overall utility is limited by the variety of targets and validation of custom assays to
support immediate clinical needs. This presentation will focus on the clinical utility
of genomic testing and will highlight two areas of impact. The first section will
highlight the impact of genomic mutation detection on patient care and decision
making. The second section will focus on the laboratory effort to support clinical
trials, including the development of an NGS assay to support the chimeric antigen
receptor T-cell directed therapy (CAR T) for EGFRvIII to identify appropriate
patients with glioblastoma multiforma for inclusion.
12:00 pm Enjoy Lunch on Your Own
NGS Assay Development and Platforms

1:35 Development of Clinical Sequencing Assays: Analytical

Validation Approaches
Saumya Pant, Ph.D., Senior Research Investigator and Head,
Sequencing Technologies, Bristol-Myers Squibb
2:00 Detection of Variants in Cardiomyopathies and Arrhythmias:

Validation and Case Studies
We detect genetic variants underlying nine myocardial phenotypes with often
overlapping and/or subtle presentations. Testing is executed from a validated
clinical exome (Agilent Clinical Research Exome). Data analysis and visualization
are performed using a WashU developed computational suite, Clinical Genomics
Workstation. I will review the design, validation and experience with this
new assay.
2:25 Different Next-Generation Sequencing Platforms and Their

Clinical Utility
David Smith, Ph.D., Professor, Laboratory Medicine & Pathology, Mayo
Clinic
Next-generation sequencing (NGS) is a powerful technology that utilizes
massively parallel sequencing to analyze many millions of DNA molecules
simultaneously. The first NGS platform was developed by 454 in 2005, but this
was quickly eclipsed by the Illumina sequencing platform. Today there are a
number of different NGS platforms including Illumina, Ion Torrent and Pacific
Biosciences. There are also numerous new NGS technologies being developed.
In this presentation I will talk about the various NGS platforms and discuss their
strengths and weaknesses. Then, I will discuss the clinical applications of these
platforms and how these powerful technologies will totally transform the way we
clinically manage cancer patients.
P R E S E N T
P O S T E R
Cambridge Healthtech Institute encourages attendees to gain further

exposure by sharing their work in the poster sessions.
Reasons you should present your research poster at this conference:
Your poster will be seen by our international delegation, representing leaders from top
pharmaceutical, biotech, academic and government institutions
Receive $50 off your registration
Your poster abstract will be published in our conference materials
To secure a poster board and inclusion in the conference materials, your abstract must be submitted, approved and your registration paid in full by March 27, 2015.
BIOMARKERS & DIAGNOSTICS
W O R LD
CO N G R E S S
20 1 5
PRICING AND REGISTRATION INFORMATION

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BEST VALUE Main Conference Pricing: Includes access to entire 3-days of Congress programs. (Does not include access to short courses).
Late Registration after March 27, 2015
$2399
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Single Conference Pricing: Includes access to 1 program. (Does not include access to short courses).
Late Registration after March 27, 2015
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ClinicalInformaticsNews.com
May 5-6, 2015

T1: Biomarkers for Patient Selection
May 6-7, 2015

T5: Companion Diagnostics
T2: Big Data for Personalized Medicine and Biomarker Discovery
T6: Clinical and Translational Biomarkers in Drug Discovery
T3: Cell-Free Biomarkers and Diagnostics
T7: Clinical NGS Testing
T4: Predictive Cancer Biomarkers
SHORT COURSES
Single Short Course Pricing
Double Short Course Pricing
$595
$295
$895
$495
May 5, 2015
May 6, 2015
A series of diverse reports designed to

keep life science professionals informed
of the salient trends in pharmaceutical
technology, business, clinical development,
and therapeutic disease markets.
For a detailed list of reports, visit
InsightPharmaReports.com, or contact
Adriana Randall, arandall@healthtech.com,
+1-781-972-5402.
CONFERENCE DISCOUNTS
Alumni Discount: (20% off) We appreciate your past participation at the Biomarkers & Diagnostics World Congress. Through loyalty
like yours, this event has become a must-attend for senior level decision makers. As a result of your great loyalty, we are pleased to
extend this exclusive opportunity to save an additional 20% off the registration rate. Simply select the Alumni Discount option on
the online registration form to take advantage of this special offer. Please note: In order to qualify, our records must indicate you are
a past attendee of this event. Discounts not applicable on Short Courses and cannot be combined with any other offer or discount
(Conference registrations only.)
Poster Submission - Discount ($50 off): Poster abstracts are due by March 27, 2015. Once your registration has been fully processed,
we will send an email containing a unique link allowing you to submit your poster abstract. If you do not receive your link within 5
business days, please contact jring@healthtech.com. * CHI reserves the right to publish your poster title and abstract in various
marketing materials and products.
REGISTER 3 - 4th IS FREE: Individuals must register for the same conference or conference combination and submit completed registration forms
together for discount to apply. Please reproduce this registration form as needed.
Group Discounts are Available! Special rates are available for multiple attendees from the same organization. For more information on group
discounts contact Cheryle Rosenberg at 781-972-5489
Barnett is a recognized leader in clinical

education, training, and reference guides
for life science professionals involved in
the drug development process. For more
information, visit barnettinternational.com.
*Alumni and Register 3 - 4th is free. Discounts cannot be combined

If you are unable to attend but would like to purchase the Biomarkers & Diagnostics World Congress CD for $750.00 USD (plus shipping), please
visit www.BiomarkerWorldCongress.com Massachusetts delivery will include sales tax.
How to Register: BiomarkerWorldCongress.com

reg@healthtech.com P: 781.972.5400 or Toll-free in the U.S. 888.999.6288
Please use keycode
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Final Agenda

BIOMARKERS & DIAGNOSTICS

The Leading Annual Meeting Dedicated to Biomarkers

Register today and network with 400 of your colleagues

Chair, Cancer Biology

Chair, Molecular Oncology

Executive Director, Biomarkers

Chief, Hematology & Oncology

Biomarkers for Patient Selection

Clinical and Translational Biomarkers

Director, Companion Diagnostics

Chief Medical Officer

Clinical NGS Testing NEW

Director, Biomarker Laboratory

Precision Medicine Leader

Fit-for-Purpose Biomarker Assay Development and Validation

T2: Big Data for Personalized

T1: Biomarkers for Patient Selection

T3: Cell-Free Biomarkers and

T4: Predictive Cancer Biomarkers

Conference Registration and Morning Coffee

Implementing Precision Medicine

Coffee Break in the Exhibit Hall with Poster Viewing

Implementing Precision Medicine (contd)

Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

Big Data for Biomarker Discovery and Drug

Circulating Tumor DNA as Biomarkers and

Circulating Tumor DNA as Biomarkers and

Big Data for Biomarker Discovery and Drug

Circulating Tumor DNA as Biomarkers and

Circulating Tumor DNA as Biomarkers and

Exosomes and Microvesicles

NGS for Biomarker Discovery and Patient Selection

Circulating Biomarkers in Drug Discovery

NGS for Biomarker Discovery and Patient Selection

Genomic Data Analysis

microRNA and ncRNA

Predictive Cancer Biomarkers for Targeted

Genomic Data Analysis (contd)

microRNA and ncRNA (contd)

Predictive Cancer Biomarkers for Targeted

NGS for Biomarker Discovery and Patient Selection

Refreshment Break in the Exhibit Hall with Poster Viewing

Big Data to Advance Personalized Medicine

NGS for Biomarker Discovery and Patient Selection

Welcome Reception in the Exhibit Hall with Poster Viewing

Short Course Registration

Big Data to Advance Personalized Medicine (contd)

Breakfast Presentations (Sponsorship Opportunities Available) or Morning Coffee

Predictive Cancer Biomarkers for Targeted Therapy

Coffee Break in the Exhibit Hall with Poster Viewing

Predictive Cancer Biomarkers for Targeted Therapy

T6: Clinical and Translational

T5: Companion Diagnostics

T7: Clinical NGS Testing

Lunch on Your Own

Luncheon Presentation Sponsored by Quanterix

Luncheon Presentation Sponsored by NuGen

Companion Diagnostics Development and

Biomarkers in Drug Discovery Decision Making

NGS in the Clinic

Refreshment Break in the Exhibit Hall with Poster Viewing

Companion Diagnostics Development and

Short Course Registration

Dinner SC2: Next-Generation Sequencing as a Clinical Test (Separate registration required)