Bio IT World Expo 2016  
Bio IT World Expo 2016
2014 Archived Content

Clinical Genomics 

Track 10 explores the shift from discovery research into clinical implementation. The ability to integrate and interrogate multiple -omic datasets is critical for understanding 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 from diverse datasets, will ensure that patients receive the correct diagnoses and individualized treatments.

Final Agenda

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7:00 am Workshop Registration and Morning Coffee

8:00 - 11:30 Recommended Morning Pre-Conference Workshops*

Genome Assembly and Annotation

12:30 - 4:00 pm Recommended Afternoon Pre-Conference Workshops*

Determining Genome Variation and Clinical Utility

*Separate Registration Required. Click here for detailed information.

2:00 - 7:00 pm Main Conference Registration

4:00 Event Chairperson's Opening Remarks

Cindy Crowninshield, RD, LDN, Conference Director, Cambridge Healthtech Institute


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




7:00 am Registration Open and Morning Coffee

8:00 Chairperson's Opening Remarks

Phillips Kuhl, Co-Founder and President, Cambridge Healthtech Institute


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9:00 Benjamin Franklin Award & Laureate Presentation

9:30 Best Practices Awards Program

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

Implementing NGS in the Clinic 

10:50 Chairperson's Remarks

Fred Lee, M.D., MPH, Director, Healthcare Strategy and Business Development, Oracle Health Sciences

11:00 Projected Clinical Utility of NGS Screening in the General Population

Joseph V. Thakuria, M.D., Medical Geneticist, Massachusetts General Hospital

Clinical utility of NGS in patients suspected of rare Mendelian disorders is now generally accepted, but mounting evidence also supports medical utility of NGS screening in the general populace. We explore opportunities and challenges in NGS’s transition from research and clinical use in subsets of genetic patients to genomic health screening strategies on asymptomatic individuals.


11:30 Rapid Tumor Evolution Propagating across the Genome, Epigenome, Transcriptome and Epitranscriptome

Christopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell Medical College

We have identified the evolution of molecular changes in tumors at diagnosis and relapse stages in acute myeloid leukemia patients spanning the genome, epigenome, transcriptome and epitranscriptome, with NGS revealing 1000s of relapse-specific molecular changes driving chemo-resistance. Integrating these data can validate mutations, reveal regulatory dynamics and build predictive models.

12:00 pm Clinical Genomics 2013: Lesson Learned – A Summary

Sanjay Joshi, CTO, Life Sciences, EMC Isilon

A lot has happened in the past year: clinically, ethically, infrastructurally, methodologically and regulatorily. We will look at a summary of the happenings in 2013 and their effects on scalable infrastructures moving forward.

12:40 Luncheon Presentation I: Harnessing the Power of Patient Cohort Data with NextBio

Ilya Kupershmidt, Head, Products, Enterprise Informatics, Illumina Inc.

Advances in genomic and other molecular technologies have vastly expanded the richness of the information available to investigators in drug development, cancer, and other biomedical research. Until recently the myriad opportunities to use this data for patient stratification, to understand differential patient response, to predict adverse events, and to drive a better mechanistic understanding were limited by a number of factors. In this talk we will show how NexBio removes many of these barriers by standardizing, normalizing and integrating patient molecular and phenotype information. More importantly, we will focus on how simple interfaces make these data useful to a broader set of participants in both medical and pharmaceutical settings.

1:10 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own

From Genome Variation to Clinical Utility 

1:50 Chairperson's Remarks

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

1:55 Mapping Disease Risk to the Human Variome

Yana Bromberg, Ph.D., Assistant Professor, Biochemistry and Microbiology, School of Environmental and Biological Sciences, Rutgers University

The drop in sequencing cost and its increased speed and accuracy are bringing genome-based evaluation of individual disease risk to the bedside. Personalized medicine research today is tasked with developing techniques to connect human phenotypes with individual variomes. We discuss building computational pipelines bridging these new tools for predicting “variome”-defined disease risk.

Software Spotlights (Sponsorship Opportunities Available)

Next-generation sequencing has made obtaining A, C, T, Gs relatively easy; making sense of and interpreting them is hard. There are commercial software solutions and pipelines for managing raw genome sequence data. However, providing the medical interpretation and delivering a clinical diagnosis is critical in making good on the promise of personalized medicine. This session showcases how genomic data analysis companies are streamlining the genomic diagnostic process through:

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

2:25 Topological Data Analysis for Translational Research and Development
Pek Lum, Vice President of Solutions & Chief Data Scientist, Ayasdi
There is an urgent need for modern analytical techniques to couple myriad data sources such as molecular, genetic and phenotypic to drive discoveries related to clinical outcomes of interest. In this session, we generalize methods of Topological Data Analysis (TDA) past the basic research phase and discuss how this approach permits rapid exploration of multi-modal clinical data. 

2:40 Pertinence Metric Enables Hypothesis-Independent Genome-Phenome Analysis in Seconds
 Michael M. Segal, M.D., Ph.D., Chief Scientist, SimulConsultGenome-phenome analysis uses a genomic variant table and compares patient’s findings to those of known diseases (“phenome”).  Accuracy was 100% with trios with family-aware calling, and close to that with only probands.  The gene pertinence metric calculated in the analysis was 99.9% for the causal genes, and the analysis took seconds and was hypothesis-independent. 

2:55 Clinician-Friendly Diagnostic Tools for Using Whole-Genome Sequence Data in Real Time

Jeffrey R. Gulcher, M.D., Ph.D., President and CSO, NextCODE Health

NextCODE offers informatics solutions we first developed at deCODE genetics to store, query and analyze whole-genome sequence data on 300,000 individuals. These are built on the genomic ordered relational (GOR) data architecture that allows for real-time queries of massive variant and raw sequence datasets for clinical diagnosis and quality control. Our clinically-intuitive, web-based tools can be used for the analysis of individual patients, families or cohorts.

3:15 Selected Oral Poster Presentation: A Robust and Versatile MiSeq Data Analysis Pipeline to Support Translational Projects

Aleksandra Markovets, Ph.D., Senior Scientist, Oncology, AstraZeneca, Inc.

Next-generation sequencing (NGS) is increasingly important in oncology drug development. The MiSeqDX is becoming a commonly adopted platform for next-generation sequencing of targeted gene panels in patient samples, achieving FDA approval for in vitro diagnostic use. To overcome the challenges associated with processing, analysis and interpretation of vast amounts of data returned by a sequencing platform, we have developed an effective and versatile analytical pipeline. This pipeline enables quality assessment of sequencing runs, disambiguation of sequencing data from animal models and precise identification of various DNA aberrations. The application of this pipeline to accurately measure genetic biomarkers in patients and preclinical samples has provided impactful data to a number of drug projects.

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

4:00 Returning Genomic Results to Physicians and Patients: Where the Rubber Meets the Road

Elissa Levin, MS, CGC, Head, Genomics and Integrative Health Innovations; Assistant Professor, Genetics and Genomic Sciences, Icahn Institute for Genomics and Multiscale Biology, Mount Sinai School of Medicine

There is much discussion on how to responsibly deliver complex, probabilistic genomic information into clinical practice in our current system. We review innovative approaches being applied in research, clinical and consumer settings that strive to further enable access and personalization of genomic information, with the goal of making it useful and relevant for patients and providers.

4:30 Integrating Genomics into Medicine

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

We will discuss the integration of genomic sequencing into medical practice for both diagnostic purposes and screening of healthy adults and newborns. Systems to enable patients, physicians, clinical laboratories and researchers to all interact and support data sharing and genomic knowledge curation will be discussed as they relate to the new NIH-funded Clinical Genome Resource Program.

5:00 Clinical Interpretation Tools

Matthew Lebo, Ph.D., Instructor, Pathology, Brigham & Women’s Hospital and Harvard Medical School; Assistant Laboratory Director, Senior IS Domain Specialist, Laboratory for Molecular Medicine

5:30 - 6:30 Best of Show Awards Reception in the Exhibit Hall


7:00 am Registration Open

7:00 Breakfast Presentation (Sponsorship Opportunity Available) or Morning Coffee

8:00 Chairperson’s Opening Remarks

Kevin Davies, Ph.D., Vice President Business Development & Publisher C&EN, American Chemical Society; Founding Editor, Bio-IT World


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

Ensuring Genomic Privacy and Security 

10:30 Chairperson's Opening Remarks

Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Institute

10:35 Featured Presentation

A Global Alliance for Interoperability of Genomic and Clinical Data

David Altshuler, M.D., Ph.D., Deputy Director and Chief Academic Officer, Broad Institute of Harvard and MIT; Professor, Genetics and Medicine, Harvard Medical School and Massachusetts General Hospital; Adjunct Professor, Biology, Massachusetts Institute of Technology

Analysis of large-scale data on genome sequence and clinical outcomes holds great promise for medicine. Learning requires access to datasets and to methods beyond the scope of any single institution. I will discuss a global alliance created to nurture a common framework of international standards for how genomic and clinical data are shared in a responsible and effective manner.

11:05 Featured Presentation

Incorporating Security Infrastructure from the Beginning at the New York Genome Center

Toby Bloom, Ph.D., Deputy Scientific Director, Informatics, New York Genome Center

As genomic data falls under more regulations governing personally identifiable information and more clinical genomics studies combine deep clinical data with genomic data, privacy and security requirements integrated into genome centers’ informatics infrastructures become increasingly complex. We discuss how NYGC is addressing these challenges.

11:35 Architecture of Omics-Aware Clinical Decision Support Systems

Ketan Patel, Principal Solutions Consultant, Oracle Health Sciences

While many EMR implementations include some form of configurable decision support, the demands of genome data – gene panels as well as whole-exome and whole-genome data – make molecular decision support in the EMR a significant challenge. We propose architectures for decision support systems external to but integrated with an EMR, along with analytical tools and scalability appropriate for genome-wide personalized medicine.

12:15 pm Luncheon Presentations (Sponsorship Opportunities Available) or Lunch on Your Own

1:15 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing

Integrating Genomics into the Clinic 

1:55 Chairperson's Remarks
John Quackenbush, CEO, Genospace; Professor, Dana-Farber Cancer Institute and Harvard School of Public Health 

2:00 Enterprise-Wide Support for Individualized Treatment at a Cancer Center: Dana-Farber’s Profile Project

Barrett J. Rollins, M.D., Ph.D., CSO, Dana-Farber Cancer Institute; Linde Family Professor of Medicine, Harvard Medical School

Bringing the promise of precision medicine to cancer patients requires overcoming scientific and operational impediments. Dana-Farber Cancer Institute’s Profile project attempts to address these problems. It seeks to obtain broad genetic profiles on every patient who visits our hospital, link the data to their clinical information and make it available for research and clinical care.

2:30 PANEL DISCUSSION: From Data to Knowledge, from Research to Care – Meeting the Challenges of Genomic Medicine

Moderator: John Quackenbush, CEO, Genospace; Professor, Dana-Farber Cancer Institute and Harvard School of Public Health

Walter M. Capone, President, Multiple Myeloma Research Foundation

Andy Corts, Chief Information Officer, Sarah Cannon Research Institute

Pranil Chandra, DO, FCAP, FASCP, Director, Molecular Pathology Services, PathGroup

Joe Donahue, Senior Vice President, Thomson Reuters

While delivering actionable personalized medicine reports to physicians seems, on the surface, like a relatively straight-forward exercise, there are many stakeholders who play a role in making the endeavor successful. Key elements in building a truly successful program include collecting and managing clinical and genomic data, integrating these in a decision support system, creating an appropriate knowledgebase to support data interpretation, and effectively delivering the data at the point of care. This panel brings together representatives from GenoSpace, Sarah Cannon Research Institute, Multiple Myeloma Research Foundation, PathGroup, and Thomson Reuters to discuss strategies to meet the challenges of genomic medicine.

4:00 Conference Adjourns


*IBM and the IBM logo are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. 

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  • Making the World's Knowledge Computable
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