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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

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


10:50 Chairperson’s Opening Remarks



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.



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.

12:00 pm Sponsored Presentation (Opportunity Available)

12:30 Session Break

Molecular Health12:40 Luncheon Presentation to be Announced

Speaker to be Announced


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

Scott Kahn, Ph.D., Vice President, Commercial 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 Speaker to be Announced

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 and Co-Founder, LeapYear Innovations

Sophisticated analytical techniques for cross-referencing and querying databases have demonstrated that de-identification does a poor job of protecting private information. LeapYear Privacy is a differential privacy software that guarantees complete concealment of sensitive information while ensuring that the aggregate results of analysis run on privatized data are almost indistinguishable from aggregate results from the original database.

5:00 Speaker to be Announced

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


1:55 Chairperson’s Remarks

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

2:00 Striking the Right Balance in Clinical Interpretation of Genomes

Elizabeth Worthey, Ph.D., Assistant Professor, Pediatrics; Director, Genomic Informatics, Human and Molecular Genetics Center, Medical College Wisconsin

I provide a review of the 2014 lessons learned in our molecular diagnostic lab and the challenges and opportunities for 2015. It focuses on the end-to-end solution for clinical genomics we have implemented, including platforms developed for genomic medicine clinical decision support. It also discusses how we integrate this data into the practice of medicine in our genomic medicine clinics, providing specific case examples.

2:30 Interpretation of Genetic Variation in Tens of Thousands of Humans

Daniel MacArthur, Ph.D., Assistant Professor, Harvard Medical School and Massachusetts General Hospital; Associate Member, Broad Institute of Harvard and MIT

New databases of human genetic variation promise to transform the interpretation of variants found in clinical samples. Here I describe the analysis of protein-coding genetic variation in over 90,000 humans, and efforts to link the full spectrum of genetic variation with gene function and clinical phenotype.

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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