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.

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


Click here for detailed information.

Precision for Medicine5:00 – 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

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 Data Management in Large Scale Sequencing and Analysis

Kirill Malkin, Director, Storage Engineering, SGI

Next Generation Sequencing and its accompanying analyses are driving exponential growth in sequence data that needs to be stored, analyzed, and made accessible for future interrogations. This session presents a converged storage-and-analytics infrastructure framework based on SGI’s experience in enabling data-intensive supercomputing solutions – along with genomics customer case examples and best practices for simplifying the management of data sets that can contain billions of files/objects.

12:30 Session Break

12:40 Luncheon Presentation I: Accelerating the Analysis of High-Throughput Sequencing

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

Panelists: Paolo Narvaez, Ph.D., Principal Engineer & Director, Personalized Care Platform, Intel Corporation

Adam Kiezun, Ph.D., Senior Group Leader, Computational Methods Development, Broad Institute of MIT and Harvard

Jeff Gentry, Principal Software Engineer, Broad Institute

Accelerating the analysis of high-throughput sequencing data enables all of us to push the boundaries of precision medicine. The BROAD’s Genome Analysis Toolkit (GATK) is the industry standard software package for variant discovery and genotyping. In this luncheon, experts from the BROAD and Intel will discuss the exciting new capabilities that are coming to GATK, and the impact that this could have on the industry.

1:10 Luncheon Presentation II: Cloud Bursting HPC Workloads: Challenges and Opportunities

Dan Chow, COO/CTO, Silicon Mechanics

Feeling constrained by your HPC cluster? Are there times that you need more capacity or to offload some storage? Bursting to the public cloud offers you an alternative to grow with added flexibility. Dan will share about the benefits our customers have experienced and cover some of the pitfalls to be wary of when evaluating how to implement cloud bursting.

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

PodcastLouis 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

Laura Housman, Global Head, Therapeutics Business, SVP Corporate Development, 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.

Microsoft Way3:25 Refreshment Break in the Exhibit Hall with Poster Viewing


4:00 Building Cloud-Enabled Cancer Genomics Workflows with Luigi and Docker

Jacob Feala, Ph.D., Principal Scientist, Bioinformatics, Caperna, an affiliate of Moderna Therapeutics

As bioinformatics scientists, we tend to write custom tools for managing our workflows, even when viable, open-source alternatives are available from the tech community. Our field has, however, begun to adopt Docker containers to stabilize compute environments. I introduce Luigi, a workflow system built by engineers at Spotify to manage long-running big data processing jobs with complex dependencies. Focusing on a case study of next-generation sequencing analysis in cancer genomics research, I show how Luigi can connect simple, containerized applications into complex bioinformatics pipelines that can be easily integrated with compute, storage, and data warehousing on the cloud.

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. February 2016 Speaker Interview

5:00 GATK4 - The Next Generation of Broad Institute's Genomics Tools, on the Cloud

Adam Kiezun, Ph.D., Senior Group Leader, Computational Methods Development, Broad Institute of MIT and Harvard

The breathtaking pace of genomics growth requires tools and pipelines that can support cutting-edge analyses, at petabyte scales, with optimized speed and cost. With this in mind, we have launched GATK4, a complete reimagining of Broad’s Genome Analysis Toolkit. GATK4 now supports both germline and somatic mutation analysis, CNV and SV detection, tumor heterogeneity analysis, and more. Designed with cloud infrastructure in mind, GATK4 is implemented with support for Apache Spark and is hundreds of times faster than previous generations of GATK.

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

Brandi Davis Dusenbury, Senior Scientist, Seven Bridges

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 Integration of Whole Genome and RNA Sequencing to Inform Clinical Treatment of Cancer

Michael Zody, Ph.D., Research Director, Computational Biology, New York Genome Center


11:40 Building National-Scale Genomics Projects with Collaborative, Portable, Reproducible Analysis

Deniz Kural, CEO, Seven Bridges

The number of large genomics projects worldwide is rapidly growing. Such projects involve analysis of hundreds of thousands of whole genomes to accelerate discovery in basic and clinical research. National-scale genomics projects make intensive demands on computation and storage, and test the limits of existing infrastructure. They present severe challenges that require novel approaches to overcome.

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 Bioinformatics Pipeline for Detection of Fusions and Gene Expression in Clinical Oncology Samples using RNA-Seq

Keith Callenberg, Ph.D., Lead Bioinformatics Scientist, Molecular & Genomic Pathology, University of Pittsburgh Medical Center

2:30 Talk Title to be Announced
Andreas Matern, GeneDx

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

**Book signing in the Exhibit Hall (preceding talk) Thurs April 7 10:15am Booths 122 & 124 “Bioinformatics and Computational Biology in Drug Discovery and Development"

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