Bio IT World Expo 2016  
Bio IT World Expo 2016
Archived Content

Track 12: Cancer Informatics 

Track 12 explores the trends and challenges in cancer research/care. Topics will cover data access, analysis, integration, management, and application for biological interpretation to aid in research at the benchside or care at the bedside.

Final Agenda

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7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*

*Separate Registration Required

2:00 - 7:00 pm Main Conference Registration

4:00 Event Chairperson’s Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute

4:05 Keynote Introduction

Kevin Brode, Senior Director, Health & Life Sciences, Americas Hitachi Data Systems


Do Network Pharmacologists Need Robot Chemists?

Andrew HopkinsAndrew L. Hopkins, DPhil, FRSC, FSB, Division of Biological Chemistry and Drug Design, College of Life Sciences, University of Dundee



OKTA10 Minute Welcome to the Reception!

Mike Nolte, Regional Sales Manager – East, Okta 

Cycle Computing logo
5:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Drop off a business card at the CHI Sales booth for a chance to win 1 of 2 iPads® or 1 of 2 Kindle Fires®!*

*Apple® is not a sponsor or participant in this program


7:00 am Registration and Morning Coffee

8:00 Chairperson’s Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute

8:05 Keynote Introduction

Sanjay Joshi, CTO, Life Sciences, EMC Isilon


Atul ButteAtul Butte, M.D., Ph.D., Division Chief and Associate Professor, Stanford University School of Medicine; Director, Center for Pediatric Bioinformatics, Lucile Packard Children's Hospital; Co-founder, Personalis and Numedii


8:55 Benjamin Franklin Award & Laureate Presentation

9:15 Best Practices Award Program

9:45 Coffee Break in the Exhibit Hall with Poster Viewing

10:50 Chairperson’s Remarks

Michael Liebman, Ph.D., Managing Director, Strategic Medicine, Inc. 



PerkinElmer NEW 2009 11:00 Tools for Revolutionizing Translational Cancer Medicine

Kevin Hrusovsky, President, Life Sciences & Technology, PerkinElmer, Inc.

While breakthroughs abound in cancer research, there is a profound disconnect in translating these discoveries to clinical medicine. This talk will discuss how combining the “in vitro-to-in vivo-to human” continuum of research tools with a powerful in silico infrastructure has successfully bridged the chasm from lab to clinic, particularly in the field of cancer medicine and personalized health.

Bioinformatics across Multiple Research Initiatives 

11:30 Biological Research through Omic-Data Integration Using the “Programmable Web”

Matt Roth, Ph.D., Assistant Professor, Human Genetics, Baylor College of Medicine

This talk presents results from a human breast cancer study that utilized “programmable web” technology via Genboree to drive “virtual data integration” by bringing together only relevant “omic” data from multiple physical locations just in time for analysis. The results presented will illustrate how virtual data integration across multiple research initiatives (large and small) can be applied to any disease.

12:00 pm CECARDIS, An International Consortium to Evaluate Comparative Effectiveness in Cardiovascular Disease Risk Assessment: Algorithms, Biomarkers and Diagnostics

Michael Liebman, Ph.D., Managing Director, Strategic Medicine, Inc.

Sabrina Molinaro, Ph.D., Institute for Clinical Physiology, National Research Council, Italy

CECARDIS is an international consortium of hospitals, ministries of health, and government agencies that compare clinical approaches, procedures/devices and guidelines in large populations exhibiting symptoms of coronary artery disease and the impact of biomarkers in diagnosis/treatment. CECARDIS is developing a platform to support ongoing evaluation of new patient records and to compare effectiveness of existing technologies for prevention, diagnosis and treatment of CVD.

12:30 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

High Content Analysis: Cancer Cell Lines 

1:40 Chairperson’s Remarks

1:45 Systems Pharmacology Using CellMiner and the NCI-60 Cancerous Cell Lines

William Reinhold, Manager, Genomics and Bioinformatics Group, Laboratory of Molecular Pharmacology (LMP), National Cancer Institute (NCI)

CellMiner is a web-based application that allows rapid access to and comparison between 20,503 compound activities and the expression levels of 26,065 genes and 360 microRNAs. Included are 102 FDA-approved drugs as well as 53 in clinical trials. The tool is designed for the non-informatisist, and allows the user wide latitude in defining the question of interest.

2:15 Oncology Drug Combinations at Novartis

Joseph Lehár, Ph.D., Director of Bioinformatics OTR, Oncology Translational Medicine, Novartis Institutes for Biomedical Research

In collaboration with academic and industrial partners, we have generated mutation status, gene copy number, and gene expression data for a library of 1,000 cancer cell lines, representing most cancer lineages and common genetic backgrounds. We expect this large-scale campaign to enable efficient patient selection for clinical trials on existing cancer drugs, reveal many therapeutically promising drug synergies or anti-resistance combinations, and provide unprecedented detail on functional interactions between cancer signaling pathways.

2:45 Selected Oral Poster Presentation: Genotype-Based Analysis for Cancer Therapy Using Large-Scale Data Modeling

Nayoung Kim, Ph.D. Candidate, Biological Sciences, Sookmyung Women’s University

An integrative approach of large-scale omics and drug response data on various cell lines enables us to identify the cellular signaling and drug sensitivity in cancer. Signatures in different levels of biological process such as gene expression, protein expression and protein activation have applications in finding novel diagnostic or prognostic biomarkers. They are also key components in accelerating mechanism-based drug discovery or genotype-specific repositioning. Here we present a system-level analysis of cell line data for predicting the sensitivity and mechanisms of targeted drug response based on major genotypes of cancers. Association study with the genotypic classification was performed on drug data and omics data such as transcriptome, proteome and phosphateome on human cancer cell lines. This approach reproduced the known patterns of mechanism-based drug response in cancers. Also, gene and protein signatures significantly associated with genotype were identified and integrated into a drug-oriented network. Furthermore, we process the optimization of public gene sets to draw an advanced pathway-based interpretation using omics data and develop RNAi screening systems for analysis of cancer-regulation markers and anticancer effects perturbed by mutation. This study provides an integrated approach for omics, drug response data and cancer mutation types in cancers.

3:15 Refreshment Break in the Exhibit Hall with Poster Viewing


Pharmacodynamic Models for Oncology 

3:45 Systems Biology in Cancer Immunotherapy: Applications in the Understanding of Mechanism of Action and Therapeutic Response

Debraj GuhaThakurta, Ph.D., Associate Director, Systems Biology, Dendreon Corporation

We are using high-content platforms (DNA and protein microarrays, RNA-seq) in various stages of the development of cellular immunotherapies for cancer. We will provide examples of genomic applications that can aid in the mechanistic understanding and the discovery of molecular markers associated with the efficacy of a cancer immunotherapy.

4:15 Talk Title to be Announced

Anna Georgieva Kondic, Ph.D., Senior Principal Scientist, Modeling and Simulation, Merck Research Labs

The last few years have seen an increased use of physiologically-based pharmacokinetics and pharmacodynamics models in Oncology drug development. This is partially due to an improved mechanistic understanding of disease drivers and the collection of better patient-level quantitative data that lends itself to modeling. In this talk, a suite of studies where systems modeling was successfully used to inform either preclinical to clinical transition or clinical study design will be presented. The talk will complete with a potential systems pharmacology framework that can be used systematically in drug development. 

4:45 Two-Edged Sword Role of the Mammalian DNA Methyltransferases: New Implication to Cancer Therapy Targeting the Epigenetic Pathway  

C.-K. James Shen, Ph.D., Distinguished Research Fellow, Institute of Molecular Biology, Academia Sinica

Methylation at the 5-position of cytosine (C) to generate 5-methylcytosine (5-mC) on the vertebrate genomes is an essential epigenetic modification that regulates different biological processes including carcinogenesis. This modification has been known to be accomplished by the combined catalytic actions of three DNA methyltransferases (DNMTs), the de novo enzymes DNMT3A/ DNMT3B and the maintenance enzyme DNMT1. This property of DNMTs and the imbalance of CpG methylation in cancer cells have led to the development of cancer therapeutic drugs/ chemicals targeting the DNA methylation activities of DNMTs. However, we have recently discovered that the mammalian DNMTs could also act as active DNA 5-mC demethylases in a Ca++ion-and redox state-dependent manner. This suggests new directions for re-investigation of the structures of DNMTs and their functions in the genome wide and/or local DNA methylation in the mammalian cells. In particular, the concept and strategies for drug therapy targeting the DNMTs may need to be re-evaluated.

5:15 Best of Show Awards Reception in the Exhibit Hall

6:15 Exhibit Hall Closes

Thursday, April 11

7:00 am Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

Integrating Clinical Information into Drug Discovery 

8:45 Chairperson’s Opening Remarks

8:50 The Challenges in Integrating Information During the Discovery Of Biomarkers in Cancer Patients Treated with Chemotherapy: A Pharmacology and Oncology Perspective

Federico Innocenti, M.D., Ph.D., Associate Professor, University of North Carolina at Chapel Hill; Associate Director , Institute for Pharmacogenomics and Individualized Therapy

Genomic studies for discovering biomarkers of outcome of patients treated with chemotherapy are quite advanced. However, we face the interpretative difficulty in connecting the dots among clinical data, genomic information (both of the host and the tumor), and functional annotation of genomic regions. This presentation will provide an oncology and pharmacology perspective of the contemporary challenges of integrative analyses that could (and should) aid the discovery of clinically useful markers for enrichment of responsive populations during drug development, as well as for improving patient management at the bed side.

9:20 “Integrating Molecular and Clinical Data to Expedite Translation in Computational Drug Repurposing

Joel Dudley, Ph.D., Director of Biomedical Informatics, Mount Sinai School of Medicine

Although drug repurposing approaches that leverage approved therapies can potentially expedite the drug development process by leveraging existing drug safety data, establishing efficacy for alternative indications can remain just as challenging as in novel drug development. Because many patients are prescribed approved therapies for their primary indications, there is a wealth of clinical data captured in electronic medical record (EMR) systems that could potentially inform on the system-wide physiological and pathophysiological effects of the approved therapies in humans. In this talk I will discuss efforts to integrate public gene expression data with clinical data captured from EMR systems to expedite translation in computational drug repurposing.

Elsevier9:50 Managing Information Challenges with Elsevier Life Science Solutions

Shuhag Ghosh, Vice President, Global Marketing, Elsevier Life Science Solutions

From increasing discoverability to making sense of ever-growing data sets to leveraging new data sources, Life Sciences organizations face challenges in making more informed and effective decisions based on a changing landscape. Elsevier Life Science Solutions is a suite of interoperable domain-specific decision support tools built from our understanding of and commitment to Life Sciences. This suite is designed to enhance how organizations make decisions and to power information flows across discovery, pre-clinical, clinical and post-market domains, for end-to-end success. The potential to leverage customized taxonomies, newly mined content sources and internal data in the suite changes how organizations interact with information to conduct R&D.

10:20 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced

10:45 Plenary Keynote Panel Chairperson’s Remarks

Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

10:50 Plenary Keynote Panel Introduction

Yury Rozenman, Head of BT for Life Sciences, BT Global Services

Niven R. Narain, President & CTO, Berg Pharma


11:05 The Life Sciences CIO Panel

Remy Evard, CIO, Novartis Institutes for BioMedical Research
Martin Leach, Ph.D., Vice President, R&D IT, Biogen Idec
Andrea T. Norris, Director, Center for Information Technology (CIT) and Chief Information Officer, NIH
Gunaretnam (Guna) Rajagopal, Ph.D., VP & CIO - R&D IT, Research, Bioinformatics & External Innovation, Janssen Pharmaceuticals
Cris Ross, Chief Information Officer, Mayo Clinic
Matthew Trunnell, CIO, Broad Institute of MIT and Harvard

12:15 Luncheon in the Exhibit Hall with Poster Viewing

Panel Session: Building the IT Architecture of the New York Genome Center 

2:00 Closing Featured Panel Session Introduction

Wanmei Ou, Senior Product Strategist, Oracle Health Sciences

2:10 Panel Session: Building the IT Architecture of the New York Genome Center

Moderator: Kevin Davies, Ph.D., Editor-in-Chief, Bio-IT World

Chris Dwan, Acting Senior Vice President, Information Technology and Research Computing, New York Genome Center

Robert B. Darnell, M.D., Ph.D., President & Scientific Director, New York Genome Center

Jim Harding, CTO, Sabey Corporation

Sanjay Joshi, CTO, Life Sciences, EMC Isilon Storage Division

George Gosselin, CTO, Computer Design & Integration LLC

In 2011, a consortium of 11 major academic and medical organizations in and around New York announced the creation of the New York Genome Center (NYGC). Under the direction of Robert B. Darnell, the NYGC aspires to be a world-class genomics and medical research center, and is currently undergoing construction in the heart of Manhattan. NYGC management has the opportunity to design and create a state-of-the-art IT and data management infrastructure to handle, store and share the output from what will rapidly become one of the world’s foremost genome sequencing facilities. This series of talks will describe the thinking that went into the design, creation and construction of the NYGC’s IT infrastructure and entire data management strategy.

4:00 Conference Adjourns

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  • Making the World's Knowledge Computable
  • Bioinformatics in the Cloud
  • The Application of Text Analytics to Drug Safety Surveillance

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