Bio IT World Expo 2016  
Bio IT World Expo 2016

Track 9 - April 21 – 23, 2015

Clinical Genomics 

Tools for Investigation, Integration and Implementation

The ability to integrate and interrogate multiple -omic datasets is critical for understanding disease. This can 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 ensures that patients receive the correct diagnosis and treatment. Track 9 examines the shift from genomic discovery research into clinical implementation.

Final Agenda

Tuesday, April 21

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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

2:00 – 6:30 Main Conference Registration



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

Wednesday, April 22


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

Internet 2

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


10:50 Chairperson’s Opening Remarks
Scott Kahn, Ph.D., Vice President, Commercial Enterprise Informatics, Illumina, Inc. 



Robert C. Green, M.D., MPH, Director, G2P Research Program; Associate Director, Research, Partners Personalized Medicine, Division of Genetics, Department of Medicine, Brigham & Women’s Hospital and Harvard Medical School

Much of the controversy surrounding the implementation of incidental findings in clinical sequencing is due to uncertainty about the penetrance of such findings in persons unselected for clinical features or family history. This uncertainty also influences the question of genomic population screening, i.e., whether actionable sequence variants should be sought and reported in ostensibly healthy individuals. In this talk, new data will be presented estimating the penetrance of actionable incidental findings.



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

Continuously updated knowledge bases will be required to enable a true continuous learning healthcare environment. However, modern healthcare pressures make their maintenance difficult. The clinical genomic IT community has been wrestling with this issue for some time. We present lessons learned from supporting clinical genomic IT processes that may be generalizable to broader development of IT support for continuous learning healthcare processes.

Elsevier12:00 pm Census of the Apoptosis Pathway

Philip L. Lorenzi, Ph.D., Department of Bioinformatics and Computational Biology & the Proteomics and Metabolomics Core Facility, MD Anderson Cancer Center

We recently compared several different “omic” approaches to constructing the autophagy pathway de novo, including siRNA screening, mass spectrometry-based proteomics, and three different pathway analysis software packages. Unexpectedly, although merging all of the validated data sets yielded 739 autophagy-modulating genes, each individual approach alone yielded sparse coverage of the autophagy pathway. The best individual siRNA screen, for example, yielded only 169 of the 739 (23%) genes. Nevertheless, text mining-based pathway analysis with Pathway Studio in conjunction with manual curation provided the most comprehensive coverage, yielding 417 targets (56% of the pathway). Here, we explored the generalizability of those findings by examining a more well-characterized pathway—apoptosis. We compiled apoptosis-modulating genes from 12 published siRNA screens and two pathway analysis software packages—Ingenuity Pathway Analysis (IPA) and Pathway Studio. The resulting inventory of 6,882 proteins consisted of 215 targets identified by siRNA screening, 3,378 targets by IPA, and 6,381 targets by Pathway Studio. The extensive coverage (93%) of the apoptosis pathway provided by text mining with Pathway Studio can likely be attributed to recent upgrades in the software, including an expanded database and collection of full-text articles. Together with our previous autophagy pathway analysis, the new apoptosis results support the generalizable conclusions that: 1) siRNA screening has a large false negative rate (i.e., fails to identify many true “hits”), and 2) text mining-based pathway analysis using Pathway Studio provides the most comprehensive pathway coverage.

12:30 Session Break

Molecular Health12:40 Luncheon Presentation I: Computational Enablement of the Hippocratic Oath in a Clinical Oncology Setting

David B. Jackson, Ph.D., Chief Innovation Officer, Molecular Health, Gmbh

The clinical response of cancer patients to oncolytic agents is influenced by three major classes of molecular determinant; tumor intrinsic factors (e.g. tumor biomarkers); patient intrinsic factors (e.g. polymorphisms) and patient extrinsic factors (e.g. co-medications). In my talk, I will present a novel computational technology and associated treatment decision support process that was designed to provide this knowledge-driven approach to clinical care in oncology.

illumina NEW1:10 Luncheon Presentation II: A High Performance Application Development Platform for Collaborative Genomics Research

Paul Flook, Ph.D., Senior Director, Enterprise Informatics, Illumina Inc.

Collaborative research among groups working with genomic data presents major logistical challenges. Transferring huge volumes of data can be prohibitively expensive for projects utilizing WGS data sets. Illumina has addressed this challenge by building a platform that enables collaborators to not only share data in a secure multitenant environment, but to develop and deploy their own applications close to the data.

1:40 Session Break


1:50 Chairperson’s Remarks

Nora Manstein, Ph.D., IT Project Manager, Bayer Business Services GmbH

1:55 Security vs. Freedom – It‘s Not a Matter of Philosophy

Nora Manstein, Ph.D., IT Project Manager, Bayer Business Services GmbH

We contribute to the debate on how patient’s rights and wishes are respected and meaningful research with patient data can be done. In order to support this, we have developed an organizational process and a technical tool by which patients’ informed consents are an integral part of the authorization process, allowing compliant access to and scientific analysis of patient data.

2:25 Privacy, Access Control and Security in Clinical Genomics Environments

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

The integration of clinical and genomic data introduces new, complex problems in privacy and security. These include protecting the anonymity of clinical data when it is linked to “self-identifying” genomic data; managing the fine-granularity access control required to share data from multiple projects; and overcoming the regulatory and legal hurdles associated with clinical genomic data. We discuss these and other access issues.

2:55 Blocking the Cyber Barbarians

Betsy Fallen, Global Head, Program and Business Development, SAFE-BioPharma Association

Identity trust is necessary for secure and regulated Internet communications. The presentation explains the issues associated with establishing online trust and the role of the industry-driven SAFE-BioPharma global identity management/digital signature standard in assuring that only authorized identities have access to protected information. Participants will learn about types and levels of identity credentials, government and industry organizations involved in establishing identity trust infrastructures, applicable standards, governance models and approaches to cloud-based identity management.

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

4:00 Data Integration, Privacy and Openness at PatientsLikeMe, a Social Network for Patients with Life-Altering Conditions

Marcia M. Nizzari, MS, Vice President, Engineering, PatientsLikeMe, Inc.

PatientsLikeMe provides a social network and research platform for capturing, curating and analyzing patient-reported data. With 300,000+ users, 2,300+ conditions represented and over 25 million health datapoints collected, it provides a new, rich source of data to integrate with EHR and genomic data to drive new insights about disease. We discuss trade-offs in privacy and openness when combining EHR and other sources of clinical and research data – such as -omics – with patient-reported data.

4:30 Differential Privacy: Future-Proof Protection for Sensitive Data

Ishaan Nerurkar, CEO & Founder, Shroudbase, Inc.

In the analysis of sensitive data, current methods of privacy protection severely compromise utility, access and opportunities for collaboration. Shroudbase is a cloud software that creates and manages permanently de-identified copies of high-dimensional data with strong, mathematically proven guarantees of statistical accuracy. Our patent-pending technology enables previously untouchable information to be open-sourced and analyzed while maintaining differential privacy, the gold standard of data privacy. This presentation discusses an instance of the Shroudbase platform optimized to handle the unique privacy challenges posed by genomics data.

5:00 PANEL DISCUSSION: Genomic Research: Utility vs. Patient Rights


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


Betsy Fallen, Global Head, Program and Business Development, SAFE-BioPharma Association

Nora Manstein, Ph.D., IT Project Manager, Bayer Business Services GmbH

Ishaan Nerurkar, CEO & Founder, Shroudbase, Inc.

Marcia M. Nizzari, MS, Vice President, Engineering, PatientsLikeMe, Inc.

Juhapekka Piiroinen, Head, Personalized Medicine Development, MediSapiens, Ltd.

What software tools, organizational processes and regulatory minefields must researchers and clinicians understand to not only improve drug development and personalized therapies, but also preserve the privacy of patient data? Experts share their perspectives on informed consent, security access, technical infrastructures, genomic and clinical data integration and more.

5:30 Best of Show Awards Reception in the Exhibit Hall with Poster Viewing

6:30 Close of Day

Thursday, April 23


7:00 am Registration Open and Morning Coffee



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


10:30 Chairperson’s Remarks

Heidi L. Rehm, Ph.D., FACMG, Chief Laboratory Director, Laboratory for Molecular Medicine, Partners HealthCare; Associate Professor, Pathology, Brigham & Women’s Hospital and Harvard Medical School

10:30 ClinGen: The Clinical Genome Resource

Heidi L. Rehm, Ph.D., FACMG, Chief Laboratory Director, Laboratory for Molecular Medicine, Partners HealthCare; Associate Professor, Pathology, Brigham & Women’s Hospital and Harvard Medical School

ClinGen is an NIH-funded program developing resources to understand genomic variation and optimize its use in medicine. ClinGen interfaces research and clinical testing and includes the development of standards for variant and gene interpretation as well as broad data sharing. The ClinVar database serves as the primary site for deposition and retrieval of variant interpretations as well as aggregation for expert curation.

10:55 Human Genome Analysis

Mark Gerstein, Ph.D., Albert L. Williams Professor, Biomedical Informatics, Yale University

Identification of noncoding cancer “drivers” from thousands of somatic alterations is an unsolved problem. Here, we developed a computational framework to annotate cancer regulatory mutations. The framework combines an adjustable data context summarizing large-scale genomics and cancer-relevant datasets with an efficient variant prioritization pipeline. To prioritize high-impact variants, we developed a weighted scoring scheme to score each mutation’s impact.

11:20 Clinical Genomicist Workstation: Analyze, Interpret and Report Next-Gen-Based Molecular Diagnostic Studies

Rakesh Nagarajan, M.D., Ph.D., Associate Professor, Pathology & Immunology and Genetics, Washington University in St. Louis; Chief Biomedical Informatics Officer, PierianDx

Clinical NGS has been gaining traction over the past few years. The Clinical Genomicist Workstation was developed to address the informatics barriers that limit the more broad and rapid adoption of this technology broadly in the medical community. This presentation discusses adoption of the CGW by molecular diagnostic laboratories and approaches to data and information sharing.

Oracle Health Sciences11:40 Coordinated Care in the Age of Personalized Medicine

Ketan Patel, Ph.D., Healthcare Solutions Consultant, Oracle Health Sciences

Advances in genome diagnostics are starting to make an impact on patient care. A key challenge is how to enable a multidisciplinary care team to collaborate using genomic data from an individual patient. We describe an architecture which enables researchers, clinicians, molecular pathologists and genetic counselors to interact with the data using role-based interfaces which are tuned to their task in the clinical workflow. Such a system can speed up adoption of genomic data into routine clinical care scenarios.

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


2:25 Chairperson’s Remarks

Louis Fiore, M.D., MPH, Executive Director, MAVERIC, Research, Veterans Affairs Boston Healthcare System

2:30 Epigenetic Profiling of DNA Methylation to Identify Breast Tumor Aggressiveness

Adam Marsh, Ph.D., Professor, Center for Bioinformatics and Computational Biology, University of Delaware; CSO, Genome Profiling, LLC

Women with triple-negative genotypes (i.e., normal for the three common marker mutations for breast cancer) are still at risk for developing aggressive breast tumors. We identify a suite of differentially methylated CpG sites between normal and tumor breast tissues using NGS that indicate a high degree of epigenetic conservation among different triple-negative patients who have developed advanced-stage breast tumors. Subtle epigenetic shifts in methylation status may provide a key line of evidence for assessing tumor risk and informing therapy decisions between surgery or versus noninvasive treatments.

3:00 Establishing Clinical-Grade RNA Sequencing

Sheng Li, Ph.D., Instructor, Bioinformatics, Neurological Surgery, Weill Cornell Medical College

High-throughput sequencing drastically expands the potential for large-scale whole transcriptome profiling of clinical samples for disease monitoring and diagnosis. Here we established standard approach and analysis methods and benchmark datasets for evaluation of RNA-seq performance of different platforms, protocols and various qualities of input materials.

3:30 The Department of Veterans Affairs Precision Oncology Program: The Crossroads of Clinical Care and Research

Louis Fiore, M.D., MPH, Executive Director, MAVERIC, Research, Veterans Affairs Boston Healthcare System

This presentation describes a model for creation of “Learning Healthcare Systems” through integration of a clinical precision oncology program with a tailored research program that leverages and augments the clinical investment. Databases and applications that support clinical trial matching, capture of patient reported outcomes, clinician collaboration and patient outcome prediction will be discussed.

4:00 Conference Adjourns

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