Genomics and Patient Privacy Conference 2016

Genomics and Patient Privacy: Research and Practice

Stanford University

Purpose of this conference is to gather experts in genomics and privacy and investigate the role of privacy-preserving technologies in genomics data collaboration.

Research using genomics data is fraught with concerns around patient re-identification using de-identified sequence data. This has resulted in complex data sharing agreements and patient consent process. We believe that the current genomics research bottleneck is no longer within a data silo but being able to share insights across silos. 

At this conference, we will focus on the technological approaches to genomics privacy protection. Are there classes of relevant genomics algorithms or queries that can benefit from privacy protecting analytical methods, and be applied to real world data sharing scenarios? 

Even if these methods have limited genomic applications in the beginning, over time these methods will be able to deliver more. With availability of flexible Cloud computing resources, it has now become possible to harness computationally intensive methods at a reasonable cost e.g. boot up 1000 machines simultaneously for a brief instance. 

Our ultimate goal is to develop a set of genomics research and collaboration tools, in coordination with our industry partners, that will not only allow patients and institutes to feel more confident about privacy protection, but will also bring sophisticated risk assessment and risk management approaches to genomics.

@Bechtel Conference Center

Encina Hall, 616 Serra Street Stanford, CA 94305

 


Speakers: Researchers

Cynthia Dwork, PhD, Distinguished Scientist, Microsoft Research

Cynthia Dwork, Distinguished Scientist at Microsoft Research, is renowned for placing privacy-preserving data analysis on a mathematically rigorous foundation. A cornerstone of this work is differential privacy, a strong privacy guarantee frequently permitting highly accurate data analysis. Dr. Dwork has also made seminal contributions in cryptography and distributed computing, and is a recipient of the Edsger W. Dijkstra Prize, recognizing some of her earliest work establishing the pillars on which every fault-tolerant system has been built for decades.


Carl Gunter, PhD, Professor of Computer Science, University of Illinois

Carl Gunter's current projects relate to security and privacy in the healthcare and electric power sectors and for networking. Carl has made research contributions in the semantics of programming languages, formal methods, security, and privacy. His contributions to the semantics of programming languages include the interpretation of subtypes using implicit coercions, type inference for continuations and prompts, the use of Grothendieck fibrations as a model of parametric polymorphism, the mixed powerdomain, and the use of Petri nets as a model of linear logic.


Jean-Pierre Hubaux, Dr.-Eng., Professor at School of Information and Communication Sciences of EPFL

Jean-Pierre Hubaux is a full professor at the School of Information and Communication Sciences of École polytechnique fédérale de Lausanne (EPFL). Through his research, he contributes to laying the foundations and developing the tools to protect privacy in tomorrow’s hyper-connected world. He is focusing notably on network privacy and security, with an emphasis on mobile/wireless networks and on data protection, with an emphasis on health-related data and especially genomic data. He has worked on the topic of genome privacy since 2011 and has designed related cryptographic solutions, notably in collaboration with the Lausanne University Hospital (CHUV) and the EPFL School of Life Sciences.

He has co-chaired the first workshop devoted to the topic (in Dagstuhl, Germany, in 2013) and is a co-founder and chair of the steering committee of the International Workshop on Genome Privacy and Security (GenoPri). He was recently appointed to the “Information Security Task Force”, set up by the Swiss federal government. He is also a member of the “Genomics” task force set up by the Cantonal Ministry of Health. He is a Fellow of both IEEE (2008) and ACM (2010). 


Kristin Lauter, PhD, Principal Researcher, Microsoft Research

Kristin Lauter is a Principal Researcher and Research Manager for the Cryptography group at Microsoft Research. She directs the group's research activities in theoretical and applied cryptography and in the related math fields of number theory and algebraic geometry. Her research interests include algorithmic number theory, elliptic curve, pairing-based,  and lattice-based cryptography, homomorphic encryption, and cloud security and privacy, including privacy for healthcare and genomics. Her group is releasing a homomorphic encryption library to be used in bioinformatics applications to allow outsourcing of computation on encrypted data. 

She is a Fellow of the American Mathematical Society and President of the Association for Women in Mathematics.


Bradley Malin, PhD, Vice Chair for Research and Associate Professor of Biomedical Informatics, Vanderbilt University

 

Bradley Malin has made contributions to a number of health-related areas, including distributed data processing methods for medical record linkage and predictive modeling, intelligent auditing technologies to protect electronic medical records from misuse in the context of primary care, and algorithms to formally anonymize patient information disseminated for secondary research purposes. 

Additionally, he is the founder and current director of the Health Information Privacy Laboratory (HIPLab), which was established to address the growing need for data privacy research and development for the health information technology sector.


Suyash Shringapure, PhD, Post-doctoral scholar, Stanford University

Suyash is a postdoctoral scholar in the Bustamante lab in the Genetics Department at Stanford University. Prior to joining Stanford, Suyash was a graduate student in the Machine Learning Department at Carnegie Mellon University.

Suyash and Prof Bustamante have demonstrated a technique for hacking a network of global genomic databases, Beacon, and how to prevent it. They are working with investigators from the Global Alliance for Genomics and Health on implementing preventive measures.


Michael Snyder, PhD, Professor and Chair of Genetics, Stanford University 

Michael Snyder is the Stanford Ascherman Professor and Chair of Genetics and the Director of the Center of Genomics and Personalized Medicine. Dr. Snyder received his Ph.D. training at the California Institute of Technology and carried out postdoctoral training at Stanford University.

He is a leader in the field of functional genomics and proteomics, and one of the major participants of the ENCODE project. His laboratory study was the first to perform a large-scale functional genomics project in any organism, and has developed many technologies in genomics and proteomics. These including the development of proteome chips, high resolution tiling arrays for the entire human genome, methods for global mapping of transcription factor binding sites (ChIP-chip now replaced by ChIP-seq), paired end sequencing for mapping of structural variation in eukaryotes, de novo genome sequencing of genomes using high throughput technologies and RNA-Seq. These technologies have been used for characterizing genomes, proteomes and regulatory networks. Seminal findings from the Snyder laboratory include the discovery that much more of the human genome is transcribed and contains regulatory information than was previously appreciated, and a high diversity of transcription factor binding occurs both between and within species. He has also combined different state-of–the-art “omics” technologies to perform the first longitudinal detailed integrative personal omics profile (iPOP) of person and used this to assess disease risk and monitor disease states for personalized medicine. He is a cofounder of several biotechnology companies, including Protometrix (now part of Life Tehcnologies), Affomix (now part of Illumina), Excelix, and Personalis, and he presently serves on the board of a number of companies.

Mike provided expert briefing to the JASON task force and JASON report includes the various omics data types as integral part of future EHRs. 


Philip Tsao, PhD, Co-Director of Epidemiological Research and Information Center for Genomics, VA Palo Alto

Dr. Philip Tsao is a Professor (Research) of Cardiovascular Medicine in the Stanford School of Medicine, Associate Chief of Staff of R&D  and Co-Director of Epidemiological Research and Information Center for Genomics at VA Palo Alto.

In his current research, the primary interests are in understanding the molecular underpinnings of vascular disease as well as assessing disease risk, using a wide range of biochemical, molecular and physiological techniques to make primary observations in cell systems as well as preclinical models. Furthermore, continuing to extend the findings to human subjects in order to confirm their clinical applicability. 

Phil is one of the key drivers of genomics research for VA's Million Veteran Program(MVP). The aim of the MVP is to produce a resource for better understanding of the inter-relation of genetics, behaviors and environmental factors, and veteran health. Participants provide a blood sample, response to lifestyle questionnaires, and consent to allow access to clinical data from VA electronic medical records. 


XiaoFeng Wang, PhD, Professor at School of Informatics and Computing at Indiana University, Bloomington 

XiaoFeng Wang is a professor in the School of Informatics and Computing at Indiana University, Bloomington. He received his Ph.D. in Electrical and Computer Engineering from Carnegie Mellon University in 2004, and has since been a faculty member at IU.  Dr. Wang is a well-recognized active researcher on system and network security and data privacy.  His group is known for their research on cloud and mobile security, and genomic data privacy. He is a recipient of 2011 Award for Outstanding Research in Privacy Enhancing Technologies (the PET Award) and the Best Practical Paper Award at the 32nd IEEE Symposium on Security and Privacy.  His work has been regularly reported by the media, including CNN, MSNBC, Slashdot, CNet, PC World, etc.  He is the director of IU’s Center for Security Informatics.


Speakers: Practioners

Narges Bani Asadi, CEO and Founder, Bina Technologies (Roche)

After many years of multidisciplinary research in systems biology and high performance computing, at both Stanford University and UC Berkeley, Narges founded Bina to begin applying those results to the world of genomics. She holds multiple patents, and has several publications, as well as a Masters and a PhD in Electrical Engineering from Stanford University. 


Scott Burke, Co-founder & CTO, Helix

Scott Burke is Co-founder and CTO for Helix, a consumer genomics company backed by Illumina, Warburg Pincus, and Sutter Hill Ventures. Helix's mission is to empower every individual to gain insights into his or her DNA. Before Helix, Scott was SVP of Advertising and Data Platforms at Yahoo. Prior to Yahoo, Scott held engineering leadership positions at PacketHop, Seven Networks, and WebMD. Scott started his career as a computational physicist at Hewlett-Packard. He holds a bachelor’s degree in physics from Harvey Mudd College in Claremont, California.


Ramon Felciano, Co-founder, CTO, VP Research, Ingenuity (Qiagen)

Ramon co-founded Ingenuity Systems, a global leader in systems biology and knowledge management solutions for life science researchers and the scientific enterprise. Ramon leads Ingenuity's R&D efforts, advanced product development, strategic business development and scientific collaborations. He has a PhD in biomedical informatics from Stanford University.


Todd Ferris, MD, CTO, Stanford School of Medicine

Todd is the Chief Technology Officer at Stanford University School of Medicine. He is a graduate of Stanford's Biomedical Informatics Training Program; his research interests include the security of health information and data repository architectures. He is the security architect and access granting authority for the STRIDE system.


Andro Hsu, PhD, Director of Product Marketing, Syapse

Andro Hsu is a former molecular biologist who has played a variety of product development and marketing roles at companies whose technologies bridge genomics and information technology. Andro holds a BS in Biology from Yale University and earned a PhD in Molecular & Cell Biology from the University of California at Berkeley. An early employee at the personal genomics company 23andMe, Andro led pre-launch development of customer content, scientific curation pipelines, and IRB-approved procedures for obtaining customer research consent. At NextBio (acquired by Illumina), Andro was product manager for its web-based tools for mining curated public genomic data. Taking a step into the biomedical device field, Andro joined GigaGen as VP of Product to identify research and diagnostic applications for GigaGen's massively parallel single-cell genomics microfluidics technology. Returning to the software world, Andro now leads product marketing at Syapse, helping healthcare systems realize the value of Syapse’s precision medicine clinical decision support tools and its underlying centralized clinical and molecular data store.


Sanjay Joshi, CTO Health Care and Lifesciences, EMC, Emerging Technologies Division

Sanjay Joshi is the Isilon CTO of Healthcare and Life Sciences at the EMC Emerging Technologies Division. Based in Seattle, Sanjay's 28+ year career has spanned the entire gamut of life-sciences and healthcare from clinical and biotechnology research to healthcare informatics to medical devices; he defines himself as a “non-reductionist systems guy.”

His current focus is a systems view of Genomics, Proteomics and Healthcare for infrastructures and informatics. Recent experience has included data management and instruments for Electronic Medical Records; Proteomics and Flow Cytometry; FDA and HIPAA validations; Lab Information Management Systems (LIMS); Translational Genomics research and Imaging. Sanjay holds a patent in multi-dimensional flow cytometry analytics. He began his career developing and building X-Ray machines.

Sanjay was the recipient of a National Institutes of Health (NIH) Small Business Innovation Research (SBIR) grant and has been a consultant or co-Principal-Investigator on several NIH grants. He is actively involved in non-profit biotech networking and educational organizations in the Seattle area and beyond.

Sanjay holds a Master of Biomedical Engineering from the University of New South Wales, Sydney and a Bachelor of Instrumentation Technology from Bangalore University. He has completed several medical school and PhD level courses.


Devin Locke, Principal Scientist, Seven Bridges Genomics

Devin Locke studied human and evolutionary structural variation in Dr. Evan Eichler’s lab, followed by postdoctoral studies in several NGS application areas under Dr. Elaine Mardis at the McDonnell Genome Institute.  He led the Orangutan Genome Project, and was part of the first team to perform whole genome tumor/normal sequencing using NGS techniques.  At Seven Bridges, he works in all three major areas of the company, including Product Development, Research and Development and Strategic Partnerships.


David Maher, Executive VP and CTO, Intertrust

David Maher has over 30 years of experience in secure computing and is responsible for Research and Development at Intertrust. Before joining Intertrust in 1999, he was chief scientist for AT&T Secure Communications Systems, Head of the Secure Systems Research Department, and security architect for AT&T's Internet services platform. After joining Bell Labs in 1981, Maher developed secure communications, information vending, and e-commerce systems. He was Chief Architect for AT&T's STU-III secure voice, data, and video products used by the White House and Department of Defense for top-secret communications. In 1992, Maher became a Bell Labs Fellow in recognition of his accomplishments in communications security. Maher holds multiple patents in secure computing; has published papers in the fields of mathematics and computer science; and has consulted with the National Science Foundation, National Security Agency, National Institute of Standards and Technology, and the Congressional Office of Technology Assessment. Maher holds a Ph.D. in mathematics from Lehigh University. He has taught electrical engineering, mathematics, and computer science at several institutions.


Ursheet Parikh, Partner, Mayfield Fund

Ursheet Parikh is a partner at the Mayfield Fund. Founded in 1969, Mayfield is a leading venture capital firm has partnered with exceptional entrepreneurs who have founded over 500 companies including Genetech, Amgen and Intuitive Surgical. Recent investments in digital health include Basis Science (acquired by Intel), HealthTap, Lantern and Brighter.

Ursheet brings 15 years of enterprise product and leadership experience to Mayfield, as a repeat entrepreneur, and former executive at Microsoft and Cisco. Prior to joining Mayfield, he was a co-founder and the Chief Executive Officer of StorSimple, the leading cloud-integrated storage company that was acquired by Microsoft. StorSimple was the largest IaaS/PaaS infrastructure acquisition (as of Q4 2013) and has been highlighted by Microsoft as one of its most successful acquisitions. StorSimple’s made it easy for businesses with large volumes of data including regulated data stores use public cloud services at scale.  At Cisco, Ursheet grew the WAN optimization business from concept to $100M/quarter and market leadership.

He focuses on innovation that is redefining the application and infrastructure stacks in cloud, mobile, enterprise technologies, genomics and digital health. He is passionate about helping entrepreneurs find product/market fit, the San Francisco 49ers and health and fitness.

Ursheet holds an MBA from the Wharton School of the University of Pennsylvania and is a computer science and engineering graduate of IIT Bombay.


Nathan Pearson, PhD, Sr Director of Scientific Engagement and Public Outreach

After training at Stanford, the University of Chicago, and the University of Michigan, he served as Senior Director of Science and Research at Knome, and as Principal Genome Scientist at QIAGEN, where he teamed with colleagues to build and use software for interpreting human genomes, in order to better understand health, drug response, and other traits. Nathan has also worked with genome-curious individuals, including historian Henry Louis Gates, Jr. and singer Ozzy Osbourne. In this spirit, he founded the Empowered Genome Community, which helps citizen-scientists make their genomes scientifically useful; and Genomena.com, where he writes on the promise and challenges of the coming era of genomically informed living.


Jonathan Sheffi, Co-founder and VP, Customer & Business Development, Curoverse 

Jonathan is cofounder and leads customer & business development at Curoverse, a federated data service for genomics & health. Before cofounding Curoverse, he spent several years in the biotechnology industry, including roles with Novartis Diagnostics, Amgen, and Accenture. Jonathan holds an MBA from Harvard Business School, an MEng focused in computational molecular biology from MIT, and undergraduate degrees in mathematics & computer science, also from MIT.


Robert Shelton, CEO and Founder, Private Access

Robert Shelton is CEO of Private Access, Inc., which he founded in late-2006 to develop an enterprise grade technology to simultaneously improve personal privacy while also making it possible for each individual (and others with a right to discover, view and use their information) to access sensitive and otherwise confidential information such as personal medical records and genomic data significantly faster and more easily. Robert work integrates a great number of his experiences in addition to his role as CEO of Private Access, including as the father of a child who was prenatally diagnosed with a rare chromosomal variation; having served for 7 years as chairman of a national non-profit disease advocacy organization serving several genetics-based conditions; and in health care information systems, as an inventor, entrepreneur; and developer of public-private projects.

Robert is the recipient of five U.S. patents as well as a number of other currently pending applications addressing improved access controls, clinical trials recruitment, redaction and dynamic consent tools, and oversees a team that has built and deployed these technologies in service of support organizations, patients and researchers.


John Shon, MD, MS, VP of Bioinformatics and Data Sciences, Illumina

John Shon is VP of Bioinformatics and Data Sciences at Illumina.  In this role he leads a global team of bioinformatics scientists in developing algorithms and methods for Illumina NGS instruments and assays.  As part of the Enterprise Informatics business unit, he also leads bioinformatics for clinical interpretation and translational informatics software.  Prior to Illumina, Dr. Shon has over a decade of experience in large pharmaceutical companies, most recently as VP of Informatics, Research IT and External Innovation at Janssen Pharmaceuticals (a division of J&J) where he supported R&D, clinical development and Janssen Diagnostics teams. At Roche, Dr. Shon led informatics groups in translational research for target discovery, biomarker selection, drug safety and personalized healthcare.

John earned his AB in Biochemistry from Harvard, an MD from Stanford, and completed his internship and residency in Internal Medicine at the University of Chicago, and an MS and postdoc in Medical Information Sciences at Stanford.


James Williams, Software Engineer, Google

James Williams is a software engineer at Google Inc. Prior to joining Google he worked as a privacy lawyer in Toronto, focusing on privacy issues in health care. He has published numerous peer reviewed articles on software engineering and privacy law. He is a member of the MIT CSAIL Big Data privacy working group, and the Global Alliance for Genomics and Health security working group. In recent years he has also served as an adjunct professor of law at Osgoode Hall and Stanford law schools, teaching privacy law and legal information technology. In addition to his duties with Google, he is chipping away at a PhD thesis in computer science at the University of Toronto, investigating computational methods for analyzing the dynamics of complex infrastructure systems.


Sasha Zaranek, PhD, Co-founder and Chief Scientist, Curoverse

Alexander (Sasha) Wait Zaranek, PhD is co-founder and Chief Scientist at Curoverse, a venture-backed company focused on building a free and open-source platform for storing, analyzing and sharing biomedical data. Sasha works on open technologies that are part of the revolution that reduced human DNA sequencing costs by a million-fold since the completion of the Human Genome Project. A current research focus is the development of clinical-quality applications for processing massive data sets spanning millions of individuals across collaborating organizations, eventually encompassing exabytes of data.

His contributions have led to highly cited publications in Science, Nature, the Lancet and other leading scientific journals. Sasha is also a co-founder and Director of Informatics at the Harvard Personal Genome Project.

 

Organizers

Somalee Datta, PhD, Director of Bioinformatics, Stanford University

Somalee is Director of Bioinformatics at Stanford Center for Genomics and Personalized Medicine. She is currently developing Stanford's capabilities in genomics driven healthcare, both in research and clinical domains. She leads a bioinformatics team at Stanford responsible for informatics for large scale genomics projects such as ENCODE, Stanford Sequencing Center, CIRM Center for Excellence in Stem Cell Genomics, Stanford Clinical Genomics Service, and VA’s Million Veteran Program collaboration. Her team has established Stanford's Bioinformatics Service Center that supports 500+ researchers and over $100M in grants. 

She is seeing a shift in bioinformatics bottlenecks - from compute to data sharing. A primary problem in data sharing and collaborating on genomics data is how to protect patient’s privacy while allowing researchers and clinicians effective (and timely) access to the data. She also believes that it is possible to build privacy preserving tools as integral part of genomics research toolkit. 

 


Frank Austin Nothaft, PhD Student in CS at UC Berkeley

Frank Austin Nothaft is a MS/PhD student in Computer Science at UC Berkeley. His research uses large scale commodity computing systems to process scientific data. Frank works with Professor David Patterson in the AMPLab and the ASPIRE lab, and is one of the lead authors of ADAM genomics data analysis platform built using Apache Avro, Spark and Parquet.