Cancer Informatics

The Cancer Informatics track explores the important technology, 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 benchside or care at the bedside. Most clinical diagnoses involve the use of clinical testing, much of which is not standardized locally/nationally/internationally. How do your approaches address this reality?

Tuesday, October 6

PLENARY KEYNOTE PROGRAM

10:00 am

Welcome Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute
Scott Parker, Director of Product Marketing, Marketing, Sinequa
10:15 am

NIH’s Strategic Vision for Data Science

Susan K. Gregurick, PhD, Associate Director, Data Science (ADDS) and Director, Office of Data Science Strategy (ODSS), National Institutes of Health
Rebecca Baker, PhD, Director, HEAL (Helping to End Addiction Long-term) Initiative, Office of the Director, National Institutes of Health
11:05 am

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Ari E Berman, PhD, CEO, BioTeam Inc
11:25 am Lunch Break - View Our Virtual Exhibit Hall
11:55 am Recommended Pre-Conference Workshops*
W1: Data Management for Biologics: Registration and Beyond
W2: A Crash Course in AI: 0-60 in Three
W3: Data Science Driving Better Informed Decisions

*Separate registration required. See workshop page for details.

1:55 pm Refresh Break - View Our Virtual Exhibit Hall
2:15 pm Recommended Pre-Conference Workshops*
W4: Digital Biomarkers and Wearables in Pharma R&D and Clinical Trials
W5: AI-Celerating R&D: Foundational Approaches to How Emerging Technologies Can Create Value
W6: Dealing with Instrument Data at Scale: Challenges and Solutions

*Separate registration required. See workshop page for details.

4:15 pm Close of Day

Wednesday, October 7

PRECISION CANCER MEDICINE METHODS

9:00 am

The Human Intelligence Revolution – How Collaboration, Data Sharing, and Human Intelligence Will Create a Healthier Future

Jeffrey G. Reid, PhD, Vice President & Head, Genome Informatics & Data Engineering, Regeneron Pharmaceuticals Inc.

The future of medicine will be enabled by our understanding of genetic disease drivers. As the architects of the world’s largest database of genomic data paired with de-identified health records, the Regeneron Genetics Center (RGC) is aiming to improve human health through data innovation and collaborative knowledge sharing. Dr. Reid discusses initiatives like Project Glow and the RGC-UK Biobank exome consortium, which enable the global scientific community to tap key datasets and identify new, better ways of preventing and treating human disease.

9:20 am

Using Networks to Understand Genetic and Genomic Drivers of Disease

John Quackenbush, PhD, Chair, Biostatistics & Henry Pickering Walcott Professor, Computational Biology & Bioinformatics, Harvard T.H. Chan School of Public Health

This presentation will address the problem of biological complexity in which many factors, each of small effect size, collectively influence disease risk, development, complexity, and response to therapy in cancer and other complex diseases. By using innovative computational methods built around network representations of biological interactions, we can gain insight into the disease process, develop predictive biomarkers, and identify possible avenues of therapeutic intervention.

9:40 am

Precision Cancer Medicine

Jeffrey Rosenfeld, PhD, Manager, Biomedical Informatics Shared Resource and Assistant Professor of Pathology and Laboratory Medicine, Rutgers Cancer Institute of New Jersey; President, Rosenfeld Consulting LLC

This presentation will illustrate the current methods that are used for determining the precise treatment of cancer rather than the standard chemotherapy methods.

10:00 am Coffee Break - View Our Virtual Exhibit Hall

SYSTEMS-LEVEL DATA APPROACHES AND MODELS FOR PRECISION ONCOLOGY

10:20 am

mTOR System: A Database for Systems-Level Biomarker Discovery in Cancer

Iman Tavassoly, PhD, Physician Scientist, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai

mTOR system is a database I have designed for exploring biomarkers and systems-level data related to mTOR pathway in cancer. This database consists of different layers of molecular markers and quantitative parameters assigned to them through a current mathematical model. This database is an example of merging systems-level data with mathematical models for precision oncology.

10:40 am

Building an Artificial Intelligence-Based Vaccine Discovery System: Applications in Infectious Diseases & Personalized Neoantigen-Related Immunotherapy for Treatment of Cancers

Kamal Rawal, PhD, Associate Professor, Bioinformatics & Computational Biology, Amity University

Infectious disease affects several million individuals all over the world, particularly from developing countries. We have built a bioinformatics pipeline, which combines reverse vaccinology tools, network biology system, and text mining algorithms to analyze proteomes of pathogens, and ranks proteins based upon their propensity to be an optimal vaccine candidate. Our system compares various machine learning approaches, such as support vector machines, neural networks, ensemble learning, and decision trees.

Ritu Kamal, Staff Product Manager, Clinical Software, Illumina

Learn how TruSight™ Software Suite offers ready-made infrastructure to analyze and interpret rare disease variants.  Powered by DRAGEN variant-calling, this software platform can evaluate all rare disease variant types within a single interface. Intuitive variant filtering, visualization and curation enable laboratories to perform streamlined interpretation and generate customizable reports.

George Vacek, Sequencing Strategic Development, NVIDIA
Sasha Paegle, Senior Business Development Manager, Dell Technologies

Multiple somatic variant callers have been created to identify variants that tumor cells acquire during their evolution. It is still unclear which variant caller, or combination of callers, is best suited to analyze tumor sequencing data.  Dell Technologies and NVIDIA highlight tools/technologies to maximize opportunities for new methods development.

11:30 am LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Jeffrey Rosenfeld, PhD, Manager, Biomedical Informatics Shared Resource and Assistant Professor of Pathology and Laboratory Medicine, Rutgers Cancer Institute of New Jersey; President, Rosenfeld Consulting LLC
Panelists:
Kamal Rawal, PhD, Associate Professor, Bioinformatics & Computational Biology, Amity University
Jeffrey G. Reid, PhD, Vice President & Head, Genome Informatics & Data Engineering, Regeneron Pharmaceuticals Inc.
John Quackenbush, PhD, Chair, Biostatistics & Henry Pickering Walcott Professor, Computational Biology & Bioinformatics, Harvard T.H. Chan School of Public Health
Iman Tavassoly, PhD, Physician Scientist, Institute for Systems Biomedicine, Icahn School of Medicine at Mount Sinai
Ritu Kamal, Staff Product Manager, Clinical Software, Illumina
Sasha Paegle, Sr. Business Development Manager, Dell Technologies
George Vacek, Sequencing Strategic Development, NVIDIA
11:50 am Lunch Break - View Our Virtual Exhibit Hall
11:55 am Interactive Breakout Discussions

Consider joining a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Michael Riener, President, RCH Solutions

Join us for a lively discussion among prominent pharma leaders, and learn:

Why, when & how to implement a public Cloud for your computing needs

Challenges and opportunities when setting and managing stakeholder expectations

Critical keys to success to realize the best outcomes

To learn more about RCH Solutions, visit our Virtual Booth

Joe Donahue, Managing Director, Life Sciences, Accenture

Hosted by Joe Donahue, Managing Director, Life Sciences, Accenture

 

Participants include: 

Andreas Matern, Head of Digital Translational Medicine, Sanofi

John Quackenbush, Professor of Computational Biology and Bioinformatics; Harvard T.H. Chan School of Public Health

Seungtaek Lee, VP, Strategic Partnerships and AI RWE Head of CoE; ConcertAI

Preston Keller, PhD, MBA, President & CCO, PercayAI

Philip Payne, PhD, Becker Professor and Chief Data Scientist, Washington University in St. Louis

 

Jeff Evernham, VP of Customer Solutions, Consulting, Sinequa

Most large scale analysis of clinical trial data only leverages part of the picture, ignoring unstructured data and limiting findability across all the information collected throughout multiple disparate data sources.  This roundtable will discuss leveraging a cognitive platform to combine all data from multiple sources into one unified view using a single entry point to the data.

 

Sasha Paegle, Life Science Business Development, Dell Technologies

Evaluating, optimizing and benchmarking of next generation sequencing (NGS) methods are essential for clinical, commercial and academic NGS pipelines. Optimizations for speed and accuracy often require making trade-offs relative to other constraints. Join this roundtable to discuss benchmarking strategies, trade-offs, and the value of benchmarking genomics tools and applications. 

PLENARY KEYNOTE PROGRAM

Michael Schwartz, Head, Product Marketing, Marketing, Benchling

The life science industry has forged ahead with a new generation of therapeutics. A new R&D paradigm is required to develop scientific platforms, manage data complexity, and orchestrate progress across specialized teams. Digital solutions and data ecosystems are at the heart of this, but require both structure and adaptability to thrive in the modern life science R&D environment.

12:30 pm KEYNOTE PRESENTATION & PANEL DISCUSSION:

Game On: How AI, Citizen Science, and Human Computation Are Facilitating the Next Leap Forward

Allison Proffitt, Editorial Director, Bio-IT World

While the precision medicine movement augurs for better outcomes through targeted prevention and intervention, those ambitions entail a bold new set of data challenges. Various panomic and traditional data streams must be integrated if we are to develop a comprehensive basis for individualized care. However, deriving actionable information requires complex predictive models that depend on the acquisition and integration of patient data on a massive scale. This picture is further complicated by new data streams emerging from quantified self-tracking and health social networks, both of which are driven by experimentation-feedback loops. Tackling these issues may seem insurmountable, but recent advancements in human/AI partnerships and crowdsourcing science adds a new set of capabilities to our analytic toolkit. This session describes recent work in online collective systems that combine human and machine-based information processing to solve biomedical data problems that have been otherwise intractable, and an information processing ecosystem emerging from this work that could transform the landscape of precision medicine for all stakeholders. Pietro will open with a framing talk, followed by short presentations from each panelist, ending with a moderated Q&A discussion by Allison with speakers and attendees. 

Panelists:
Seth Cooper, PhD, Assistant Professor, Khoury College of Computer Sciences, Northeastern University
Lee Lancashire, PhD, CIO, Cohen Veterans Bioscience
Pietro Michelucci, PhD, Director, Human Computation Institute
Jérôme Waldispühl, PhD, Associate Professor, School of Computer Science, McGill University
1:55 pm Refresh Break - View Our Virtual Exhibit Hall

GENOMIC DATA PROCESSING AND APPLICATION: TOOLS AND PIPELINES

2:10 pm

Rapid RNA Sequencing Data Analysis Using Serverless Computing

Ka Yee Yeung, Professor, School of Engineering and Technology, University of Washington Tacoma; Adjunct Professor, Microbiology, University of Washington Seattle

We reduced the alignment time for a 640 million read human RNA-sequencing dataset from 19 hours to 1 minute using serverless cloud computing. We make the methodology accessible to researchers who are not cloud experts by providing a graphical interface for the accelerated workflow.  We illustrate how this 1100-fold computational speedup allows biomedical scientists to experiment with alignment parameters which impact the final analytical results.

UNDERSTANDING HETEROGENEITY AND HUMAN DISEASE

2:30 pm

Estimating Genotypic Heterogeneity Underlying Human Disease

Yuval Itan, PhD, Assistant Professor, Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai

Whole exome and whole genome sequencing provide hundreds of thousands of genetic variants per patient, however, of them only very few are pathogenic. Current computational methods are inefficient in differentiating pathogenic mutations from neutral genetic variants that are predicted to be damaging and cannot predict the functional outcome of mutations. We will present deep learning approaches and machine learning methods in the role of detecting pathogenic mutations. Visualization tools for better utilizing NGS data will be presented to understand human disease genomics.

2:50 pm Refresh Break - View Our Virtual Exhibit Hall
3:10 pm

M2A: DNA Methylome Reveals Genome-wide Promoter Activities in Individual Tumors and Captures Tumor-Type-Specific Promoter Usages

Xiang Chen, PhD, Assistant Member, Computational Biology, St. Jude Children's Research Hospital

Tumors use alternative promoters to increase isoform diversity, to activate oncogenes, and to evade host immune attacks. ChIP-seq has been the gold standard to measure promoter activities, but scarcity of fresh starting materials restricts interrogation of individual patient tumors. We present MethylToActivity (M2A), a deep-learning framework for inference of H3K4me3 and H3K27ac levels from DNA methylomes. M2A accurately reveals promoter activities in individual tumors, captures tumor-type specific promoter usages, and is generalizable to various pediatric and adult cancers.

3:30 pm

The CRISPR Revolution and the Future of Genome Editing

Kevin Davies, PhD, Executive Editor, The CRISPR Journal; Founding Editor, Bio-IT World

In less than a decade, CRISPR has evolved from a bacterial immune system to the foundation of a powerful, flexible genome editing technology that has already transformed biomedical research, spawned a $10-billion biotech industry, and is poised to make major strides in the clinic. Kevin Davies, the founding editor of Bio-IT World, has spent the past few years working closely with the CRISPR community as the Executive Editor of The CRISPR Journal. In this talk, he shares highlights of his new book, EDITING HUMANITY, published this week, which explores the genesis of the CRISPR revolution, its impact on the gene therapy field, and the recent scandal involving the birth of CRISPR babies in China.

4:00 pm LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Yuval Itan, PhD, Assistant Professor, Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai
Panelists:
Xiang Chen, PhD, Assistant Member, Computational Biology, St. Jude Children's Research Hospital
Kevin Davies, PhD, Executive Editor, The CRISPR Journal; Founding Editor, Bio-IT World
Ka Yee Yeung, Professor, School of Engineering and Technology, University of Washington Tacoma; Adjunct Professor, Microbiology, University of Washington Seattle
4:20 pm Bio-IT Connects - View Our Virtual Exhibit Hall
5:00 pm Close of Day

Thursday, October 8

APPLICATION OF TOOLS IN CLINICAL, POPULATION, AND COLLABORATIVE HEALTH SETTINGS

9:00 am

Open Science with OHDSI: From Question to Evidence in 4 Days

Kees Van Bochove, Founder, The Hyve

The OHDSI (Observational Health Data Sciences and Informatics) COVID-19 studyathon in March 2020 produced a number of high profile studies, such as the study of the safety profile of hydroxychloroquine in real world data from nearly 1 million prevalent users of the drug across the globe, which went on to inform public health guidance from a.o. the European Medicines Agency (EMA). The volume and speed of the studies is interesting, since these studies typically take many months to prepare and execute. In this talk, we will illustrate how the OHDSI community leverages the OMOP common data model, standardized analytics as well as a powerful global open science network to make this a reality without compromising statistical rigor or scientific standards. We will also cover the role of the IMI EHDEN project which is building a European network of health data sources to strengthen the OHDSI community and further observational research in real world health data.

9:20 am

Development of Risk Prediction Models for Cardiovascular Diseases and Prostate Cancer Using Deep Learning: Case Studies from Ongoing Collaboration between the Department of Veterans Affairs (VA) and the Department of Energy (DOE)

Ravi K. Madduri, Scientist, Computation Institute, University of Chicago
9:40 am Coffee Break - View Our Virtual Exhibit Hall
10:00 am

Extending the Cancer Data Ecosystem

Ian M Fore, PhD, Sr Biomedical Informatics Program Mgr, Cancer Informatics, NIH NCI

This talk will explore the National Cancer Institute’s engagement in the Global Alliance for Genomics and Health (GA4GH) as a way of extending the ability of cancer researchers and physicians beyond the Cancer Research Data Commons to access a broader range of data and tools, potentially increasing the power of analyses of rare cancers.

10:20 am

TREAT-AD: Diversifying the Alzheimer's Disease Target Pipeline

Lara M. Mangravite, PhD, President, Sage Bionetworks

Here we describe a radically open approach to diversify the AD drug portfolio. Using multi-omic and genetic models of disease built from human brain data, a suite of emerging therapeutic hypotheses are generated that complement the small set already in drug development. To catalyze rapid evaluation of these targets, target enabling packages – containing computational and experimental resources including prototype drug compounds – are developed and openly distributed for use across the research community.

11:10 am LIVE Q&A:

Session Wrap-Up Panel Discussion

Panel Moderator:
Chris Anderson, Editor in Chief, Clinical OMICs
Panelists:
Ian M Fore, PhD, Sr Biomedical Informatics Program Mgr, Cancer Informatics, NIH NCI
Ravi K. Madduri, Scientist, Computation Institute, University of Chicago
Lara M. Mangravite, PhD, President, Sage Bionetworks
Kees Van Bochove, Founder, The Hyve
11:30 am Lunch Break - View Our Virtual Exhibit Hall
11:35 am Interactive Breakout Discussions

Consider joining a breakout discussion group. These are informal, moderated discussions with brainstorming and interactive problem solving, allowing participants from diverse backgrounds to exchange ideas and experiences and develop future collaborations around a focused topic.

Timothy Gardner, CEO, Riffyn, Inc.

How do you use data / digitization today to drive scientific discovery / product development?

What are you greatest scientific pain points / gaps that are not being met by digitization?

What kinds of outcomes do you believe digital tools could help you achieve?

 

Scott Jeschonek, Principal Program Manager, Microsoft Azure

Welcome to this discussion group on the growth of demand for HPC in scientific research. We are looking forward to a lively forum. We'll start by looking at three related topics:

- What events trigger demand in your organization? How has the current pandemic impacted resources?

- What could make scale and collaboration more accessible to more researchers?

- Share a recent experience of shifting workloads to manage HPC capacity.

Greg DiFraia, General Manager, Americas, Executive Team, Scality
Shailesh Manjrekar, Head of AI and Strategic Alliances, Executive Team, WekaIO

In this session we’ll discuss how to provide researchers with performance and scale in genomics & research analytics, to drive results at a price point that’s economically viable on public & private cloud.

11:35 am

Breakout: NGS Pipeline Optimizations

Tristan J Lubinski, PhD, Sr Scientist, Next Generation Sequencing Informatics, AstraZeneca Pharmaceuticals; Co-organizer, Boston Computational Biology and Bioinformatics (BCBB)
Howard Marks, Technologist Extraordinary and Plenipotentiary, VAST Data

Storage solutions we’ve been using force bioinformaticists to make trade-offs between the capacity and low-cost of disk and the performance of flash. This results in complex tiering configurations that only deliver performance for a small slice of the data. In this session, we will review how advancements in technology enable VAST Data to revolutionize the cost of all-flash and allows bioinformatists faster analysis across larger datasets for deeper insights.

PLENARY KEYNOTE PROGRAM

12:00 pm

Welcome Remarks

Cindy Crowninshield, Executive Event Director, Cambridge Healthtech Institute
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
12:15 pm

Toward Preventive Genomics: Lessons from MedSeq and BabySeq

Robert C. Green, Professor & Director, G2P Research, Genetics & Medicine, Brigham & Womens Hospital
12:40 pm

AI in Pharma: Where We Are Today and How We Will Succeed in the Future

Natalija Z. Jovanovic, PhD, Chief Digital Officer, Sanofi
1:05 pm

LIVE Q&A: Session Wrap-Up Panel Discussion

Panel Moderator:
Vivien R. Bonazzi, PhD, Managing Director & Chief Biomedical Data Scientist, Deloitte Consulting LLP
Juergen A. Klenk, PhD, Principal, Deloitte Consulting LLP
1:25 pm Happy Hour - View Our Virtual Exhibit Hall
2:00 pm Close of Conference





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