2017 Archived Content

Track 12: Cancer Informatics

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, May 23

7:00 am Workshop Registration and Morning Coffee

8:0011:30 Morning Pre-Conference Workshops*

12:304:00 pm Afternoon Pre-Conference Workshops*

* Separate registration required.

2:006:00 Main Conference Registration Open


GeneData logo5: 007:00 Welcome Reception in the Exhibit Hall with Poster Viewing

Wednesday, May 24

7:00 am Registration Open and Morning Coffee


9:50 Coffee Break in the Exhibit Hall with Poster Viewing


10:50 Chairperson’s Remarks
Bhanu Bahl, Ph.D., Director, Clinical and Translational Science Centre, Harvard Medical School

11:00 Deep Analytics of Cancer Genomics Data

Nicholas Camarda, Bioinformatics Analyst I, Carter Group, Dana-Farber Cancer Institute

The very large collection of cancer genomic data within Foundation Medicine allows us to see not only breadth of mutational variation, but re-occurring and significant patterns in many different cancers. These different mutational modes potentially have great relevance to more actionable diagnoses, as well as providing deeper insights for cancer research and drug development. We are exploring a new method to map each case into a statistically-defined multidimensional space along with functional and response associations.

11:30 Building a Harmonized Clinical Data Resource for Cancer Research and Translational Medicine: Challenges, Goals and Progress

John Methot, Director, Health Informatics Architecture, Dana-Farber Cancer Institute

Oncology’s pioneering role in precision medicine has led to routine tumor sequencing. However, the incompleteness and inconsistency of data from EMRs and other sources presents significant challenges to building the patient-specific diagnosis, treatment and outcome “stories” that are required as correlates to genomic data to inform outcomes and clinical quality research. At DFCI, we are striving to improve the quality and coverage of clinical data for research and translational medicine, including decision support in the clinic.

12:00 pm Graph Genome Tools Potential Impact on Precision Medicine

Jack DiGiovanna, Senior Scientist, Director, Program Management, Seven Bridges

Constructing a genome graph captures variations within a population as branches which diverge from the common reference but later rejoin it. This approach is fundamentally different than alignment and variant calling against a single linear reference, but does it matter for precision medicine? Here, we explore two key features of graph technology - improved variant calling and capturing distributions of variations in a population. We project these features onto the current state of precision medicine.

12:30 Session Break

12:40 Luncheon Presentation I: NGS in the Fast Lane: How a Collaborative Approach between the Mayo Clinic and Illumina Is Advancing Genetic Testing

Michael Ball, Vice President, EIBU Commercial, Illumina

Despite progress in sequencing technologies, obstacles still prevent a systematic method for deriving actionable information from an individual’s genome. The BaseSpace® Suite from Illumina was designed to eliminate obstacles and enable users to easily store, manage, and analyze genomic data. In this session, learn how the Mayo Clinic is using BaseSpace Suite to expedite the delivery of its genomic expertise, and how Illumina is applying feedback from the Mayo Clinic to make the BaseSpace Suite even more efficient.

WuXi Nextcode  1:10 Luncheon Presentation II: Making TCGA Tumor Datasets Accessible for Real-Time Multiomics Analysis and Visualization
Jim Lund, Ph.D., Director, Tumor Product Development, WuXi NextCODE 
The collection of cancer datasets in The Cancer Genome Atlas (TCGA) dataset has provided a wealth of insight into cancer biology; however, analyzing such a complex dataset is challenging for most investigators. This talk will demonstrate the Wuxi NextCODE approach using our proprietary genomically ordered relational (gor) database architecture to rapidly and simultaneously explore the diverse data types in TCGA. 

1:40 Session Break


1:50 Chairperson’s Remarks

Lance Smith, MBA, Associate Director, IT, Celgene

1:55 How BMS Uses cBioPortal for Cancer Genomics Research

Isaac Neuhaus, Ph.D., Director, Computational Genomics, Bristol-Myers Squibb
BMS has started using cBioPortal for visualizing cancer genomics datasets early 2016, supported by The Hyve, an open source bioinformatics company based in The Netherlands. The cBioPortal server runs on Amazon AWS and is tied to the company Active Directory for authentication. Currently loaded datasets are TCGA, CCLE and M2Gen and we will be loading clinical trial data later this year. Concurrently we are running a pilot for cBioPortal with mouse data.

2:25 Enabling Celgene's Innovation While Protecting the Enterprise in the Cloud

Lance Smith, MBA, Associate Director, IT, Celgene

Celgene uses Amazon Web Services (AWS) to run R&D workloads, enterprise systems, and collaboration environments securely and all controlled from a single pane. Topics covered include network design, HPC and job scheduling, workload isolation, storage, automated security, and environment auditing. We also discuss business use cases, challenges overcome (technical, legal, security, and organizational), and Turbot guardrails for management.

2:55 Automated High-Scale Computational Infrastructure

Jharrod LaFon, Chief Cloud Engineer, OpenEye Scientific

Large-scale computation is an important aspect of drug design, and increasingly is cloud-based. The true value of the cloud comes not just from computation but by enabling company-wide collaboration, the ability to build, modify, share, manage versions, and evaluate methods. OpenEye’s cloud-native platform, Orion, and its workflow engine, Floe, provide the tools to create innovative approaches for computation and collaboration.

3:10 Research Informatics: Get Ready for the Cloud!

Ton van Daelen, ScienceCloud, Product Director, Dassault Systemes, BIOVIA

The life sciences industry is looking to the cloud to support outsourcing and external collaboration initiatives. At the same time the cloud can give research IT the ‘agility’ to innovate more rapidly and significantly reduce their IT footprint. BIOVIA is helping research organizations implement ‘hybrid cloud’ solutions with its ScienceCloud platform to facilitate this critical transition.

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


4:00 Computational Approaches to Cancer: Cooperation between India and the United States

Kenneth Buetow, Ph.D., Director, Computational Sciences and Informatics, Complex Adaptive Systems Initiative (CASI), Arizona State University 
Timothy Lance, Distinguished Service Professor Emeritus, University at Albany; President Emeritus and Chief Research Officer, NYSERNet

Amit Saxena, Senior Technical Officer, Bioinformatics Group, C-DAC

Anil Srivastava, President, Open Health Systems Laboratory (OHSL)

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. 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. ICTBioMed is a group of life sciences supercomputing centers brought together by OSHL. ICTBioMed members have been working together for almost four years to create a shared global cyberinfrastructure as a seamless and friction-free platform for the researchers worldwide for their collaborative research in consistent with the tenets of team science. The backbone research and education network in India and the United States are now connected by a direct 5+5 gig optical fiber links between Mumbai and New York making it possible for cooperation in biomedical research leveraging computational biology in a big way. OHSL and its IUCKA and ICTBioMed initiatives are playing a big role in this area. This panel session will discuss the biomedical applications and hardware engineering components, as well as the status, plans and prospects for US-India collaboration.

5:30 – 6:30 15th Anniversary Celebration in the Exhibit Hall with Poster Viewing and Best of Show Awards

Thursday, May 25

7:00 am Registration Open and Morning Coffee


8:05 Benjamin Franklin Awards and Laureate Presentation

8:35 Best Practices Awards Program

8:50 Plenary Keynote

9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced


10:30 Chairperson’s Remarks

Honey Reddi, Ph.D., FACMG, Clinical Laboratory Director, The Jackson Laboratory

10:40 Fusion RNAs and Their Implications in Cancer Diagnosis

Hui Li, Ph.D., Associate Professor, Pathology, University of Virginia

Gene fusions and fusion products have been thought to be cancer-unique features. However, our recent work on intergenic splicing challenged this prevailing view. These findings complicate the usage of fusion RNAs as a whole for cancer diagnosis and treatment. On the other hand, the novel mechanism represents a new repertoire for the discovery of new biomarkers and drug targets.

11:10 Somatic Variants – Approaches to Predicting Actionability

Honey Reddi, Ph.D., FACMG, Clinical Laboratory Director, The Jackson Laboratory

There are currently no defined algorithms in place for the interpretation and classification of somatic variants, unlike the ACMG guidelines for germline variants. We are currently evaluating a series of steps that can be implemented for the interpretation and classification of somatic cancer variants keeping in mind the factors that define actionability.

11:40 Unlock Asian Giant’s Precision Medicine Computing Potential – Intel’s Bio-IT Know-How and Footprints in China

Jian Li, Ph.D., Life Science Business Lead, Intel Health & Life Science, Greater Asia

Chang Yu, Life Science Solution Architect, Intel Health & Life Science, Greater Asia

China has become a new battlefield for global precision medicine, which could be largely attributed to it having the largest patient population in the world, the government’s endorsement and huge funding support, the booming market needs on NIPT and cancers, and also the emerging genomics giant players, e.g., Beijing Genomics Institute and Novogene.

12:10 pm Session Break

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

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


1:55 Chairperson’s Remarks

Michael N. Liebman, Ph.D., Managing Director, IPQ Analytics, LLC and Strategic Medicine, Inc.

2:00 Distinguishing between Precision Medicine and Accurate Medicine: Application to Heart Failure Patients and Clinical Practice

Michael N. Liebman, Ph.D., IPQ Analytics, LLC and Strategic Medicine, Inc.

Increasingly, patient stratification based on genomic analysis is being considered in disease management. Critically, the need to understand real world medical practice and real world patient complexities extends far beyond the genome of the patient. We have shown examples of this complexity in heart disease and how this impacts both development of clinical guidelines, trial design, and development of new patient management approaches.

2:30 CARPEDIEM - Comorbidity and Risk Profiles Evaluation in Diabetes and Heart Morbidities

Sabrina Molinaro, Psy.D., Ph.D., Head, Department of Epidemiology and Health Services, Institute of Clinical Physiology, National Research Council of Italy

Our project uniquely develops a patient record that includes clinical and individual factors (EHR-driven phenotyping) that will be validated through the comparison of existing standards for building new risk algorithms. An understanding of the current limitations and biases of risk profiling in heart disease and diabetes and how an extended, integrated database and automatic rule-based classification system can be used to improve patient management.

3:00 PANEL DISCUSSION: Precision Medicine vs. Accurate Medicine: The Need to Understand Real World Medicine and Real World Patients

Michael N. Liebman, Ph.D., IPQ Analytics, LLC and Strategic Medicine, Inc. (Moderator)

Charles Barr, M.D., MPH, Group Medical Director and Head, Evidence Science and Innovation, Genentech
Jonathan Morris, M.D., Vice President, Provider Solutions and Chief Medical Informatics Officer, Real World Insights, QuintilesIMS

Krishnan Nandabalan, Ph.D., President, CSO and Co-Founder, BioXcel
Hal Wolf, Director, National Leader of Information and Digital Health Strategy, The Chartis Group

4:00 Conference Adjourns

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