2018 Archived Content
Track 11: Clinical Genomics

As genomic testing becomes more routine, the data generated are more complete, but also more complex. Applications for analyzing, storing, processing, exploring, and sharing these dynamic data must keep pace with a variant landscape that is constantly being refined by new information and new classifications. Track 11 continues its tradition of exploring ways we are analyzing genome variant data to improve researchers’ understanding of human health and disease leading to medically actionable results.

Tuesday, May 15

7:00 am Workshop Registration Open (Commonwealth Hall) and Morning Coffee (Foyer)

8:0011:30 Recommended Morning Pre-Conference Workshops*

W6. An Intro to Blockchain in Life Sciences

12:304:00 pm Recommended Afternoon Pre-Conference Workshops*

W10. Digital Biomarkers in Pharma R&D: Technical Challenges and Strategies for Advancing Personalized Medicine

* Separate registration required.

2:006:30 Main Conference Registration Open (Commonwealth Hall)

4:00 PLENARY KEYNOTE SESSION (Amphitheater & Harborview 2)

5:007:00 Welcome Reception in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

Wednesday, May 16

7:00 am Registration Open (Commonwealth Hall) and Morning Coffee (Foyer)

8:00 PLENARY KEYNOTE SESSION (Amphitheater & Harborview 2)

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

Back Bay

10:50 Chairperson’s Remarks

11:00 Accelerating and Securing Mendelian Patient Diagnosis

Gill Bejerano, PhD, Associate Professor, Computer Science, Developmental Biology & Pediatrics (Medical Genetics), Stanford University

The talk consists of two main parts: I present our efforts to accelerate genetic diagnosis from whole genome data, including our portal at amelie.stanford.edu. I also discuss our recent seminal results (Jagadeesh, et al, Science) in protecting patient genomes, and their potential implications for the future of genome data-sharing.

11:30 Building a Digital Biobank for Military Precision Medicine

Michael Holmes, Lt Col, USAF, MSC, PMP, CPHIMS, Chief, Innovations and Information Technology, Air Force Medical Support Agency, United States Air Force

Ezekiel Maier, PhD, Genomic Data Scientist, Strategic Innovation Group, Booz Allen Hamilton

The Air Force Medical Service is developing a precision medicine platform named the Digital Biobank. The DB will enable scalable and secure storage, and analysis of massive volumes of high-throughput heterogeneous data. The integration and analysis of genomic data, electronic health records, and other health data holds immense potential for optimizing health and wellness of service members and their beneficiaries.

12:00 pm Genomics-Guided Pathogen Surveillance and Outbreak Response

Hayden Metsky, Graduate Research Assistant, Sabeti Lab, Broad Institute, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology

Deep sequencing of viral genomes has offered key insights into the evolution and spread of human viral pathogens. I talk in particular about how genome sequencing has informed our understanding of the 2015-2016 Zika virus epidemic on a global scale, and of a recent mumps outbreak in Massachusetts at a high resolution. But there are many difficulties to overcome in order to realize more effective pathogen surveillance and outbreak response, and I discuss emerging genomic technologies that offer promising solutions to these challenges.

12:30 Session Break

12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Enjoy Lunch on Your Own

1:40 Session Break

Back Bay

1:50 Chairperson’s Remarks

Catherine Brownstein, MPH, PhD, Scientific Director, Gene Discovery, Manton Center for Orphan Disease Research, Boston Children’s Hospital & Harvard Medical School

1:55 Accelerating Rare Disease Diagnosis Using Computer-Aided Differential Diagnosis

Paul McDonagh, PhD, Senior Director, Data Sciences, Alexion Pharmaceuticals

Rare diseases often have confusing combinations of symptoms and variants of unknown significance. Diagnosing this type of patient is difficult and creates unnecessary delays in management. Several analysis algorithms were created and compared for their ability to use real patients’ symptoms to provide a prioritized shortlist of genes, diseases and treatment options. Successes, problems and lessons learnt will be discussed.

2:25 A Global Platform for Rare Disease

Catherine Brownstein, MPH, PhD, Scientific Director, Gene Discovery, Manton Center for Orphan Disease Research, Boston Children’s Hospital & Harvard Medical School

In our research on very early onset psychosis and other rare conditions, we are making discoveries at a rapid pace. With the discovery of additional cases (globally) and functional work, we often need to go back and revise earlier conclusions. Here we give case studies and examples of how we partner with clinicians to provide the best possible care.

2:55 Target Discovery at UCB Pharma Using Genetics of Rare Mendelian Diseases

Ioana Cutcutache, Principal Scientist, Translational Bioinformatics, UCB Pharma

Studying rare Mendelian diseases, through next-generation sequencing, is a powerful tool to causally link mutations in a gene to phenotypic outcomes in humans by highlighting fundamental molecular mechanisms that can serve as a gateway to treating or understanding more common illnesses. UCB Pharma shares our genetic strategy for target discovery through identification of novel rare disease causing genes and progress we've made in this area, including high-level outputs from trio whole genome sequencing for ~50 patients with rare genetic epilepsies. Emphasis will be given to analysis and interpretation of patient-derived genetic data.

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

4:00 Discovering Mobile Element Insertions in Human Genomes: Population Genetics, Human Diseases, and Clinical Genomics

Scott E. Devine, PhD, Associate Professor, Institute for Genome Sciences, University of Maryland School of Medicine

4:30 Using Clinical WGS to Detect Small Sequence Changes, Structural Variants, Short Tandem Repeats and Mitochondrial Variants

Alexander Kaplun, PhD, Director, Product Management, Variantyx, Inc.

PCR-free whole genome sequencing provides unique opportunities for detection of structural variants, trinucleotide repeat expansions and mitochondrial heteroplasmy. This talk describes the pipeline that we have built to detect, analyze, interpret and report on these classes of variants for rare disease patient samples, resulting in improved diagnostic yield.

5:00 “Perfect Storm” Components, Including Infectious Disease and Stem Cell Pathologies, Omics and Their Contributions to Degenerative and Neoplastic Disease

Dennis A. Steindler, PhD, Senior Investigator and Director, Neuroscience and Aging Lab, Jean Mayer USDA Human Nutrition Research Center on Aging; Professor, Nutrition, The Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy; Senior Scientist, CTSI, Tufts University

There are common elements and mechanisms involved in degenerative and neoplastic diseases. Within a “perfect storm” of components that contribute to neurodegenerative diseases and brain cancer, there are genetics, stem cell pathologies, infectious disease and chronic inflammation. Infectious disease elements include chronic infections from pathogens like T. gondii, and involve transcellular spread of disease mediated by prion-like extracellular vesicles.

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


7:0010:00 Bio-IT World After Hours @Lawn on D
 **Conference Registration Required. Please bring your conference badge, wristband, and photo ID for entry.   

Thursday, May 17

7:30 am Registration Open (Commonwealth Hall) and Morning Coffee (Foyer)

8:00 PLENARY KEYNOTE SESSION & AWARDS PROGRAM (Amphitheater & Harborview 2)

9:45 Coffee Break in the Exhibit Hall and Poster Competition Winners Announced (Commonwealth Hall)

Cityview 1

10:30 Chairperson’s Remarks

Duncan R. MacCannell, PhD, CSO, Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention

10:40 A Cloud-Based Bioinformatics Solution for Infectious Disease Diagnostics     

Manoj Dadlani, MEng, CEO, CosmosID

Currently many pathogens escape detection in samples when traditional assays, such as culture and PCR, are employed. It is critical to develop unbiased, timely methods of pathogen detection. This presentation describes our success utilizing such facile methods for infectious disease research with various pilot studies including necrotizing fasciitis, infective endocarditis, urinary tract infections, and wound infections. Methods of metagenomic identification and antimicrobial resistance profiling will be presented.

11:10 Cloud-Based Asynchronous Virtual Tumor Board (VTB) to Operationalize and Scale the Democratization of Precision Oncology

Edik Blais, PhD, Computational Biologist, Perthera, Inc.

Since 95% of cancer patients are treated in the community, the ability to provide a leading-edge, scalable precision medicine workflow is of critical importance. We have developed a scalable, asynchronous Virtual Tumor Board (VTB) that can bring together patients’ clinical and molecular data along with clinical evidence to the fingertips of the clinician for precision treatment planning.

11:40 Pathogen Genomics in Public Health

Duncan R. MacCannell, PhD, CSO, Office of Advanced Molecular Detection, National Center for Emerging & Zoonotic Infectious Diseases, Centers for Disease Control and Prevention

Microbial genomics is playing a rapidly increasing role in public health, from detecting and responding to outbreaks, to providing better data for disease surveillance, to monitoring the impact of vaccines, to developing a new generation of diagnostics. This presentation provides an overview of how next-generation sequencing is transforming infectious disease public health in the United States.

12:10 pm Session Break

IDBS12:20 Luncheon Presentation I to be Announced

Scott Weiss, PhD, Vice President, Product Strategy, IDBS



Amazon Web Services12:50 Luncheon Presentation II: Biotech-in-a-Box: Turn-Key Cloud Infrastructure for Enterprise-Grade Research 

Elliot Menschik, MD, PhD, Healthcare and Life Science Ventures, Amazon Web Services

This talk introduces the AWS Biotech Blueprint, a toolset enabling biotechs to rapidly establish enterprise-grade research environments in the cloud, supporting both wet and computational labs. Optimized out-of-the-box for security, resilience and regulatory compliance, it further automates the installation and integration of leading scientific applications under the customer’s direct control. The talks will include illustrations drawn from successful customer deployments.

1:20 Dessert Refreshment Break in the Exhibit Hall with Poster Viewing (Commonwealth Hall)

Back Bay

1:55 Chairperson’s Remarks

Eric Klee, PhD, Associate Director of Bioinformatics, Mayo Center for Individualized Medicine, Department of Health Sciences Research, Mayo Clinic

2:00 Investigating Heterogeneity of Innate Lymphoid Cells (ILCs) in Inflammatory Bowel Disease Using Single-Cell RNA Seq Analysis

Ramya Gamini, PhD, Postdoctoral Research Fellow, Precision Medicine, Early Clinical Development, Pfizer, Inc.

Innate lymphoid cells (ILCs) have been shown to mediate immune and metabolic homeostasis and play an essential role in the pathogenesis of certain inflammatory diseases, predominantly through cytokine-activated cytokine production. We explore the heterogeneity of ILCs to further investigate their role in IBD. Through using single-cell transcriptomics approaches we define the different ILC subtypes and disease-relevant ILCs and discover novel and key marker genes and pathways that impact ILC biology to further evaluate IBD disease-causing biomarkers.

2:30 Disambiguating Variants of Uncertain Significance in Clinical Sequencing

Eric Klee, PhD, Associate Director of Bioinformatics, Mayo Center for Individualized Medicine, Department of Health Sciences Research, Mayo Clinic

Clinical next-generation sequencing has transformed molecular testing and dramatically impacted our ability to provide patients with genetic diagnoses. However, a significant challenge exists in interpreting variants where the impact on a disease is unclear. Here we describe how complementary -omics, protein modeling, and in vitro and in vivo testing are used to clarify the pathogenicity of variants of uncertain significance.

3:00 PANEL DISCUSSION: Can We Improve Breast Cancer Patient Outcomes through Artificial Intelligence?

John Methot, Director, Health Informatics Architecture, Dana-Farber Cancer Institute (Chairperson)


Maya Said, ScD, President & CEO, Outcomes4me, Inc. (Moderator)


Regina Barzilay, PhD, MacArthur Fellow and Delta Electronics Professor, Massachusetts Institute of Technology (MIT) Department of Electrical Engineering and Computer Science; Member, Computer Science and Artificial Intelligence Laboratory, MIT

Kevin Hughes, MD, Co-Director, Avon Breast Evaluation Program, Massachusetts General Hospital; Associate Professor of Surgery, Harvard Medical School; Medical Director, Bermuda Cancer Genetics Risk Assessment Clinics 


Osama Rahma, MD, Assistant Professor of Medicine, Center For Immuno-Oncology, Dana-Farber Cancer Institute

Newly diagnosed cancer patients attempting to understand their treatment options face the overwhelming task of filtering an information deluge, much of which is irrelevant, outdated and occasionally inaccurate. Additionally, matching their diagnosis to best-in-class treatments or potential clinical trials, while simultaneously learning to navigate an extremely complex healthcare system is daunting, even for the most highly trained physicians. We will explore various platforms aimed at improving patient outcomes by leveraging technology to help educate, track, and connect patients with personalized resources while simultaneously working to improve the care continuum and the development of new treatments. We will explore the nexus of healthcare networks and their IT systems, clinical decision-making and delivery, R&D, and patients, for whom we all create our innovation solutions. Attendees will be interested to understand how various groups are working to increase value across the entire system by bringing laboratory, clinical and pharmaceutical science, real-world evidence and patient-reported data together with technology and artificial intelligence to solve health challenges. These approaches offer the opportunity to generate deeper insights into how therapies perform in the real world and harness that understanding to improve efficiency, effectiveness, value, and ultimately, patient care.

4:00 Conference Adjourns

Exhibit Hall and Keynote Pass

Data Platforms and Storage Infrastructure