Bio IT World Expo 2016  
Bio IT World Expo 2016

Track 12 - April 5 – 7, 2016

Cancer Informatics

Applying Computational Biology to Cancer Research & Care

Track 12 explores the important technology and informatics trends and challenges of applying computational biology to cancer research and care. Themes that will be covered in expert-led presentations include collaboration and network models, data access/management/integration strategies, and applications of biological interpretation to aid in research at the bench side or care at the bedside.

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Tuesday, April 5

7:00 am Workshop Registration and Morning Coffee

8:00 – 11:30 Recommended Morning Pre-Conference Workshops*
Innovation and Patient-Centricity

12:30 – 4:00 pm Recommended Afternoon Pre-Conference Workshops*
iConquerMS™: A Patient-Centered Research Model

* Separate registration required

2:00 – 6:00 Main Conference Registration


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5:00 – 7:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Wednesday, April 6

7:00 am Registration Open and Morning Coffee


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9:00 Benjamin Franklin Awards and Laureate Presentation

9:30 Best Practices Awards Program

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



10:50 Chairperson’s Opening Remarks

Anil Srivastava, President, Open Health Systems Laboratory

Panel Discussion: IUCKA: Indo-US Cancer Knowledge Alliance

Moderator: Anil Srivastava, President, Open Health Systems Laboratory

Kenneth Buetow, Ph.D., Director of Computational Sciences and Informatics, Complex Adaptive Systems Initiative (CASI), Arizona State University

Rajendra Joshi, Ph.D., Associate Director and Head, Bioinformatics Group, Centre for Development of Advanced Computing, Pune University Campus

Sharmila Bapat, Ph.D., FNASc, FASc, Independent Project Investigator and Group Head, National Centre for Cell Science (NCCS), Pune India

IUCKA: Indo-US Cancer Knowledge Alliance is being designed as an integrated biomedical informatics cyberinfrastructure for cancer treatment and research in India. It will be a true translational research platform from bench to bedside connecting cancer treatment and research centers across the country with access and connection to global centers of research, especially in the United States. The promoters of the IUCKA are Arizona State University, Open Health Systems Laboratory and Varian Medical Systems. IUCKA is being implemented as a PPP (public private partnership) and is bringing together technology products and service providers and cancer treatment and research centers in an ecosystem to directly benefit cancer patients in India and contribute to global research collaboration, especially between cancer centers in India.

12:00 pm Managing Data Across the Research Life-Cycle for Life Sciences

George Vacek, Global Director, Life Sciences, DDN

Dr. Vacek will deliver several in-depth case studies of leading life sciences organizations leveraging high performance & high scale data solutions for genomics, imaging & simulation workflows. Cases will focus on implemented solutions: capturing & effectively exploiting large scale data at speed, regulated & non-regulated stewardship considerations, transitioning from non-scaling architectures & bringing the benefits of high-end HPC technologies & techniques into smaller deployments & collaborative scenarios.

Computational and Storage Solutions for Researchers

12:15 Computational Solutions for Genomics Analysis

Kirill Malkin, Director, Storage Engineering, SGI

A historical perspective of computational solutions for genomics analysis, with an eye towards how the generation and manipulation of genomics data has enabled and constrained the science. An overview of SGI customers and their workflows in the genomics research space is presented. With ever-expanding genomics workflows in mind, a converged infrastructure solution with the SGI UV platform and NVMe storage is also reviewed.

12:30 Session Break

12:40 Luncheon Presentation I: Enabling Technology. Leveraging Data. Transforming Precision Medicine.

Ketan Paranjape, General Manager, Life Sciences, Health and Life Sciences, Intel

Panelists to be Announced

Through collaborations, research and innovation, Intel is supporting the advancement of processing, storage, networking, data security,  sequencing efficiency, accelerated bioinformatics and advanced analytics – to push the boundaries of this new “precision medicine” and bring us closer than ever to truly making care personal. Listen to this panel discuss why Intel’s Collaborative Cancer Cloud is leading the way.

1:10 Luncheon Presentation II: High-Performance Server and Storage Solutions for Life Sciences

Dan Chow, COO & CTO, Silicon Mechanics

Hear from Silicon Mechanics COO/CTO, Daniel Chow, as he describes current challenges and trends that are impacting computational and storage needs for researchers. To learn more about Silicon Mechanics, please visit  

1:40 Session Break


1:50 Chairperson’s Remarks

John E. Mattison, M.D., Chief Medical Information Officer, Assistant Medical Director, Southern California Medical Group, Kaiser Permanente; Co-Chair, eHealth Workgroup, Global Alliance for Genomics and Health GA4GH

1:55 Update of the Department of Veterans Affairs Precision Oncology (POP) Program

Louis Fiore, M.D., MPH, Executive Director, MAVERIC, Research, Veterans Affairs Boston Healthcare System

This presentation reviews the progress made to date on the VA Precision Oncology Program. The review includes progress on the informatics infrastructure and clinical success of the clinical trial matching, patient engagement, clinical prediction engine and sharing of genomic data components.

2:25 Connecting Rare Disease Patient Databases with the Matchmaker Exchange API

Orion Buske, Research Scientist, Department of Computer Science, University of Toronto; Genetics and Genome Biology Program, Hospital for Sick Children

Over 350 million people are affected by rare diseases, but many remain unsolved due to the challenge of finding additional families with the same disease. Using structured phenotype and genotype data, we are able to discover similar patients within patient databases such as PhenomeCentral. The Matchmaker Exchange API then enables patient matchmaking between such organizations, lowering the barrier for clinicians to finding similar patients.

2:55 An Ensemble Approach with Machine Learning to Detect Cancer Variants

Li Tai Fang, Senior Scientist, Bioinformatics, Research & Development, Bina Technologies

Accurately detecting somatic mutations in cancer is a challenging task due to tumor heterogeneity and sample contamination. To address this problem, Bina has developed SomaticSeq, a somatic mutation detection pipeline that integrates multiple cutting edge tools and machine learning. It has recently placed No. 1 and No. 2 in INDEL and SNV, respectively, during the last stage of the ICGC-TCGA DREAM Somatic Mutation Calling Challenge.

3:10 Beyond the Cancer Genome - Computational Enablement of Holistic, Evidence-Driven Patient Care in Clinical Oncology

David Jackson, Ph.D., Chief Innovations Officer, Innovations Management, Molecular Health, Inc.

In oncology, the molecular characterization of tumor genes as part of patient care is now synonymous with the concept of precision medicine. In this talk, I describe a computational platform that enables holistic clinical interpretation of multiple clinico-molecular parameters.

3:25 Refreshment Break in the Exhibit Hall with Poster Viewing


4:00 Custom Applications of Cloud-Based Analytics with Processed NGS Data (or, “My Pipelines are Finished, Now What?”)

Jacob Feala, Ph.D., Founder, Outlier Bio

Cloud-based platforms allow us to scale out next-generation sequencing analysis pipelines. The explosion of NGS data, however, will require scalable storage and computing even for the reduced, preprocessed outputs downstream of these pipelines. I demonstrate oncology-focused applications of big data technology on downstream NGS outputs, such as alignments, variant calls and expression, using Amazon Redshift, Spark/ADAM and Amazon S3.

4:30 The ISB Cancer Genomics Cloud

Sheila Reynolds, Ph.D., Senior Research Scientist, Ilya Shmulevich Laboratory, Institute for Systems Biology

The ISB-CGC is a cloud-based platform that will serve as a large-scale data repository for TCGA data, while also providing the computational infrastructure and interactive exploratory tools necessary to carry out cancer genomics research at unprecedented scales. The ISB-CGC will provide both interactive and programmatic access to the TCGA data, leveraging many aspects of Google Cloud Platform including BigQuery and Compute Engine.

5:00 Sponsored Presentation (Opportunity Available)

5:30 – 6:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

Thursday, April 7

7:00 am Registration and Morning Coffee


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10:00 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced


10:30 Chairperson’s Opening Remarks

10:40 Application of Targeted NGS Sequencing in Personalized Clinical Cancer Therapies

Qichao Zhu, Ph.D., Associate Professor, Genetics & Genomics Sciences, Icahn School of Medicine at Mount Sinai

Our current clinical cancer genome research project is focused on the three key components, sequence analysis for patient genetic profiling, biomarker (genetic variation) collection for cancer precision medicine, and the data processing and integration platform application for clinical report. The goal of the project is developing a comprehensive platform that can totally support precision medicine approach in cancer treatment. The approach is based on the approved concepts that tumor biomarkers are associated with patient prognosis and tumor response to therapy and patient genetic profile can be associated with drug metabolism, drug response and toxicity. Personalized tumor genetic profiles, combining with tumor site and other relevant information are then used for determining optimum individualized therapy options. This presentation concentrates on the following major components for our project: 1) Accurately detecting the tumor genetic and molecular variants in terms of both coverage and precision by developing the new algorithms to improve our variant calling; 2) Matching patients with treatments that are more likely to be effective and cause fewer side effects by collecting, curating and associating biomarkers (genetic and molecular variations) with diseases, drugs and treatment plans; and, 3) Handling the cases in a high-throughput manner by developing a web-based pipeline platform for cancer data processing, sequence analysis, data integration and report generation.

11:10 Comparative Analysis of RNA-Seq Techniques to Study Prostate Cancer

Carlos P. Sosa, Ph.D., Biomarker Discovery Group, Mayo Clinic and Adjunct Assistant Professor, Biomedical Informatics and Computational Biology (BICB), University of Minnesota, Rochester, MN

Co-authors: Carlos P. Sosa, Ph.D., Ling Cen, Ph.D., and George Vasmatzis, Ph.D.


11:40 Presentation to be Announced

12:10 pm Session Break

12:20 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing


1:55 Chairperson’s Remarks

William Loging, Ph.D., Associate Professor of Genomics & Head, Production Bioinformatics, Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai

2:00 A Discussion of the Three Types of Cancer Informatics Tools: Statistical, Dimensional, and Semantic, and a Commentary on Cancer Viewed as a Complex System

William Rice, M.D., Senior Vice President, Clinical Innovation, Central and West Texas Division, Hospital Corporation of America

For non-specialists, we'd like to present the 3 types of informatics tools that are used in cancer research. Statistical tools use correlative mathematics to infer relationships, dimensional tools use structural models of shapes and interactions to define physiology, and semantic approaches attempt to associate word position and context to define meaning. Parsing the topic of cancer informatics into these 3 general categories may help non-informaticists be better collaborators with computational modeling colleagues. Finally, an introduction to the topic of cancer as a complex system may highlight new kinds of opportunities to accelerate cancer research.

2:30 Talk Title to be Announced

Prahlad T. Ram, Ph.D., Associate Professor, Department of Systems Biology; Co-Director, Biostatistics, Bioinformatics and Systems Biology Program, The University of Texas MD Anderson Cancer Center

3:00 Molecular Impacts of Immune Modulating Drugs on Cancer Patients

William Loging, Ph.D., Associate Professor of Genomics & Head, Production Bioinformatics, Genetics and Genomics Sciences, Icahn School of Medicine at Mount Sinai

The area of Immuno-Oncology provides a novel strategy for cancer treatment by utilizing the patient’s Immune system to combat tumor growth. We investigated the impact of specific immune modulating drugs on patients with diagnosed tumors in order to understand the molecular changes that take place at the pathway level. These data are correlated to phenotypic effect and provide insights into the mechanism of immune system directed therapies for cancer.

3:30 Biosimilar Structural Comparability Assessment by NMR: From Small Proteins to Monoclonal Antibodies

Bostjan Japelj, Ph.D., Senior Scientist, Protein Biophysics and Bioinformatics, Sandoz Biopharmaceuticals

This talk will discuss 1) the insight on how to use NMR as a method to evaluate high order similarity between biosimilar and reference product on the market; 2) methods to evaluate degree of similarity between two NMR spectra of proteins shown by examples from three case studies; and 3) an update on the current state of the art NMR spectroscopy in biosimilar drug product formulations and associated challenges.

4:00 Conference Adjourns

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  • Making the World's Knowledge Computable
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