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

Track 10: Clinical Omics 

Track 10 explores the shift from discovery research into clinical implementation. The ability to integrate and interrogate multiple 'omic data sets is critical for the understanding of disease and will only be accomplished through stringent data management, analysis, interpretation, and quantification. Ultimately, placing verified analytical tools in the hands of biomedical experts, and translating insights found between diverse datasets, will ensure that patients receive the correct diagnosis and individualized treatment.

Final Agenda

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7:00 am Workshop Registration and Morning Coffee

8:00 Pre-Conference Workshops*

Software for Clinical Genomics

*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

Positioning IT to Support Clinical Laboratories 

10:50 Chairperson's Remarks

Malcolm Tutor, Bio Specimen Tracking (itBioPath) Project Manager, Data Specialist, Research Informatics, Huntsman Cancer Institute, University of Utah


11:00 Preparing Laboratories for the Tidal Wave - Prepositioning Information Technology Needed to Support Deeper Use of Genetics in the Clinical Laboratory

Sandy Aronson, Executive Director, IT, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM)

Clinical genetic tests covering large numbers of genes are becoming increasingly common and the first whole genome sequencing tests have begun to enter clinical care. These tests create new and growing challenges for laboratories which need to interpret rapidly increasing numbers of variants identified in each test. Information technology can help. This talk will describe and provide an example of an infrastructure for managing the process of interpreting complex genetic tests and reporting results. Initiatives will be discussed that could be undertaken now to ensure that laboratories are prepared to deliver maximum clinical value through their reports. 

11:30 Dealing with the Data Deluge: IT and Informatics Infrastructure Supporting WGS Based Molecular Diagnostics

Elizabeth Worthey, Ph.D., Assistant Professor, Pediatrics & Bioinformatics Program, Human & Molecular Genetics Center, Medical College of Wisconsin

At MCW/CHW whole genome sequencing is already being used for clinical diagnostic purposes as part of a Genomic Medicine clinic. Supporting this endeavor and planning for the wider expansion of these technologies across clinical departments has required significant investment in IT. This talk will highlight the current structure at our midsized regional medical center and discuss IT challenges faced during development of our WGS based MDx program.

Oracle Health Sciences 12:00 pm Integrating Cross-platform ‘Omics’ and Clinical Data to Accelerate Personalized Medicine 

Jonathan Sheldon, Ph.D., Global Senior Director, Translational Medicine, Oracle Health Sciences

This presentation will focus on our work to provide a scalable, secure platform for personalized medicine that accelerates biomarker discovery, validation and delivery to the point of care. We will discuss our methodology to integrate cross platform ‘omics’ data with high quality clinical data in a manner that is agnostic to the scientific approach. This approach provides an integrated view across genotype and phenotype whilst ensuring scalability at hundreds of thousands of whole genome sequences.

Biofortis smaller12:30 Luncheon Presentation: Mind the Gap: Is Your Informatics Infrastructure Ready for the Demands of Biomarker-Based Clinical and Translational Research?

Matt Clark, Ph.D., Director, Professional Services, BioFortis

From biobanking, through clinical studies to translational research, biomarker-based discovery is challenging traditional informatics.We will present softwaresolutions for bridging the information gap between research and the clinic to provide a unified holistic view of data, which can then be explored by researchers using deep collaboration tools to generate scientific insights.

Software Spotlights 

1:40 Chairperson's Remarks

Dana L. Abramovitz, Ph.D., Senior Director, Scientific & Corporate Strategy, Strand Life Sciences

1:45 "Software Spotlight" (Sponsorship Opportunity Available)

Obtaining clinical 'omic data is relatively easy; it's the making sense and interpreting the data that's hard. While there are many commercial software solutions and pipelines for managing raw genome sequence data, providing the medical interpretation and delivering a clinical diagnosis will be the critical step in making good on the promise of genomic medicine. This session will showcase how genomic data analysis companies are streamlining the genomic diagnostic process through:

  • Transferring raw sequencing data
  • Interpreting genetic variations
  • Building new software and cloud-based analysis pipelines
  • Investigating the 'omic basis of disease
  • Integrating with other clinical data systems
  • Creating new medical-grade databases
  • Reporting relevant clinical information in a physician-friendly manner
  • Creating a continuous learning feedback

NextBio1:45 NextBio Clinical - A Patient-Centered Platform for Biomarker Discovery, Patient Selection and Target Epidemiology 

Ilya Kupershmidt, Cofounder, Vice President, Products, NextBio

In this talk I will discuss how NextBio Clinical platform is enabling our pharma clients to explore integrated sets of public and internal patient data with extensive molecular and clinical characteristcs in their translational and clinical development programs. These include biomarker discovery, target epidemiology and patient selection in an adaptive clinical trial setting.

Cypher Genomics 2:00 Rapid Identification of Disease Causative Mutations 

Ali Torkamani, Ph.D., Co-Founder & CSO, Cypher Genomics

Recent successes in clinical genome sequencing have highlighted the potential for sequencing to greatly improve molecular diagnosis and clinical decision-making. However, these successes have relied upon large bioinformatics teams and in-depth literature surveys. We will demonstrate how the Cypher Genomics software service can quickly return a small set of well-annotated genetic variants most likely to contribute to a patient's disease.

Genophen2:15 Comprehensive Web-Based Platform, Integrating Genomics in Primary Care to Prevent Chronic Disease

Hossein Fakhrai-Rad, Ph.D., CEO, President, and Co-founder, Genophen

Complex chronic diseases are caused by the interactions of genetic, medical, environmental & behavioral factors, but there is no single source today looking at the problem comprehensively.  Genophen has developed a healthcare software platform that assesses an individual's disease risks comprehensively and provides a personalized and actionable set of recommendations to keep individuals healthy, for longer.

2:30 Clinical Research: An Integrated Data Approach

Malcolm Tutor, Bio Specimen Tracking (itBioPath) Project Manager, Data Specialist, Research Informatics, Huntsman Cancer Institute, University of Utah

Finding a cure for cancer is a monumental undertaking and the researchers at Huntsman Cancer Institute at the University of Utah have embraced the concept that data collaboration is one of the key elements in solving this puzzle. By bringing together disparate data sources (bio-specimen data, genomic data, familial history data, clinical data and pathology data), the researchers at HCI are able to find new ways to cure, predict and prevent cancer.

3:00 (Sponsorship Opportunity Available) 

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

Clinical Data Storage and Management 

EMC3:45 Sequencing in the Private Cloud

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

With the ENCODE project spotlighting the complexity of the human genome, the case for whole genome sequencing has been made. As the regulatory industry readies the implementation guidelines, the four tenets of Big Data are becoming obvious: Volume, Variability and Veracity. We will showcase the components of a Private Cloud infrastructure for the genomics pipeline.

4:15 A Comprehensive Map of Microsatellite Repeat Variation in Human Genomes

David Mittelman, Ph.D., Associate Professor, Virginia Bioinformatics Institute, Virginia Tech; Associate Professor, Department of Basic Science, Virginia Tech Carilion School of Medicine

The utility of accurately and globally measuring tandem repeats spans medicine, genetics and biotechnology; repeats influence clinical and subclinical phenotypes, are signatures for genomic instability and cancer and are important markers for forensics and genealogy. We present an integrated germline and somatic variant caller for microsatellite repeats that can be applied to whole genome and exome datasets. Further we present a public database resource in which we have cataloged repeat variation across worldwide human populations.

4:45 DMuDB, A Database of Clinical Quality Genetic Variants

Andrew Devereau, Director, National Genetics Reference Laboratory Manchester, Genetic Medicine, Central Manchester University Hospitals NHS Foundation Trust

DMuDB, the Diagnostic Mutation Database, was funded by the UK Government to provide confidential sharing of clinical-quality variant data between National Health Service diagnostic genetic laboratories to support variant interpretation in patients. It has now grown to contain nearly 44,000 variants in 73 genes, and is available to diagnostic laboratories worldwide as a subscription service. I will describe the challenges of the project, the future of the service, and the role of data sharing for clinical use.

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

Delivering 'Omic Diagnosis to Patients and Physicians 

8:45 Chairperson's Opening Remarks

Jonathan Sheldon, Ph.D., Global Senior Director, Translational Medicine, Oracle Health Sciences



8:50 Delivering Genomic Medicine to Patients

Heidi L. Rehm, Ph.D., FACMG, Director, Laboratory for Molecular Medicine, Partners HealthCare Center for Personalized Medicine and Assistant Professor of Pathology, Harvard Medical School

Genomic approaches to diagnostics are transforming genetic laboratory testing. Laboratories and clinicians must become experts in all genes and diseases as genome analyses returns many unsuspected and unfamiliar results. This talk will address solutions for these challenges through software tools, data sharing efforts in variant interpretation and studying the return of genome results though the MedSeq study, a pilot clinical trial for returning whole genome sequencing results or ordinary physicians and their patients.

9:20 Improved Gene Test Reporting in the Modern 'Omics Era

David K. Crockett, Ph.D., Director, Research Informatics, ARUP Laboratories

Structured results annotation and detailed laboratory interpretation are critical elements to improve gene test reporting in this era of high throughput sequencing.  Clinical offerings of gene panels, exome or genome testing will necessitate parallel strategic advancements in test reporting.  This effort includes structured data capture, summarizing supporting evidence, building target audience templates and objective framework for evaluation of variants of uncertain significance.

Syapse9:50 Syapse and InVitae Use Case: How to Implement a Next Generation IT and Informatics Infrastructure for Omics Diagnostics and Clinical Reporting 

Jonathan Hirsch, M.Sc., Neuroscience, Founder & President, Syapse
John Major, M.Sc., Bioinformatics, InVitae

Implementing a clinical omics test requires a sophisticated, robust IT and informatics infrastructure. Historically, laboratories have been faced with the choice of rigid off-the-shelf software that does not fully solve their needs or building a custom system, both requiring large time and monetary investments. We will describe the implementation of Syapse’s software solution at InVitae, illustrating how Syapse’s configurable data models and programmatic interfaces enable rapid, cost-effective adoption. Syapse will announce a breakthrough solution for storing and working with omics data and reporting results to the clinic.

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 pm Luncheon in the Exhibit Hall with Poster Viewing

Clinical Implementation 

1:55 Chairperson's Remarks

Tim Lautenschlaeger, M.D., Assistant Professor, Radiation Oncology, The Ohio State University

2:00 Integrated Genome-Phenome Analysis

Michael Segal, M.D., Ph.D., Founder and Chief Scientist, SimulConsult

State-of-the-art diagnostic decision support does a computational analysis of a patient’s pertinent positive and pertinent negative clinical findings, and compares this to detailed phenotypes for thousands of diseases.  When such “phenome analysis” is analyzed together with an annotated genome variant table, in just a few minutes these two orthogonal types of data combine to give an integrated genome-phenome analysis.  The power of this approach is further enhanced by the ability of such software to advise not only about likely diagnoses, but about which genetic variants are most pertinent to the patient’s clinical picture.

2:30 Clinical Research in the Age of Integrated Personalized Omics Profiles (iPOP's)

Robin Haring, Ph.D., Epidemiologist, Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Ferdinand-Sauerbruch-Strasse

Recent advances of diverse high-throughput technologies enabled the application of 'Omics' (genomics, metabolomics, transcriptomics) to epidemiological and clinical research. Integrating multi-omic molecular biomarker promises to not only improve the diagnosis, treatment, and monitoring of specific clinical endpoints, but also to unravel insights into the complexities of human pathophysiology at a population-level.

3:00 Methods for the Interpretation of Next-Generation Sequencing Data for Clinical Phenotypes

Benjamin M. Neale, Ph.D, Medical and Population Genetics, Broad Institute of MIT and Harvard

3:30 Clinical 'Omics in Radiation Oncology

Tim Lautenschlaeger, M.D., Assistant Professor, Radiation Oncology, The Ohio State University

We will share some of our experiences of bringing omics into clinical radiation oncology to improve patient care. We will present examples of how the integration of omics research with traditional radiation therapy details could improve the ability to predict treatment side effects. Further we will discuss some of the technical difficulties that remain to be overcome to optimize and automate maintenance and update of a clinical radiation oncology omics data resource.

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4:00 Conference Adjourns

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  • Making the World's Knowledge Computable
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