new york genome center€¦ · cancer genomics study with ibm’s watson was recognized and...

NEW YORK GENOME CENTER :A YEAR IN REVIEW – 2016

1 | A Year In Review

Tom Maniatis, PhD Interim Scientific Director

Cheryl A. Moore President and Chief Operating Officer

INSTITUTIONAL FOUNDING MEMBERS

A Message from Leadership2016 was an exciting year of progress and transition at the New York Genome Center. By strengthening our reputation as a convening center of academic, medical and industry leaders in the rapidly evolving field of genomic research, we made important strides to further our mission of translating genomics into clinical solutions for serious diseases.

This past year, we recruited distinguished faculty and staff, broadening our research focus and capabilities. Working collaboratively with member institutions, our scientists were the recipients of grants totaling more than $20 million. Our cancer genomics study with IBM’s Watson was recognized and featured at the 2016 White House Precision Medicine Initiative Summit. To meet the growing demand, we expanded our clinical laboratory services, receiving approval from New York State for constitutional whole genome sequencing.

As a young organization, we have relied on generous, forward-thinking individuals and foundations to help us make advances that will lead to treatments for patients. In 2016, philanthropic support of the New York Genome Center was catalyzed by the visionary and transformative $100 million challenge grant presented by the Simons Foundation and The Carson Family Charitable Trust. Thanks to our supporters, we are enhancing our core programs and fostering vibrant collaborations to advance the development of new treatments, therapies and therapeutics against human disease.

Thank you for your interest in and support of the New York Genome Center. We are pleased to share the important accomplishments highlighted in this report.

Sincerely,

A Year In Review | 2

FOUNDING TECHNOLOGY MEMBER

BOARD OF DIRECTORS

Russell L. Carson NYGC Board Co-ChairCo-Founder and General Partner,Welsh, Carson, Anderson & Stowe

Ivan G. Seidenberg NYGC Board Co-Chair Former Chair and CEO, Verizon Communications

Dafna Bar-Sagi, PhD Professor of Biochemistry and Molecular Pharmacology and Medicine, Senior Vice President and Vice Dean for Science, Chief Scientific Officer,NYU Langone Medical Center

Dennis S. Charney, MD Dean, Icahn School of Medicine at Mount Sinai; President for Academic Affairs, Mount Sinai Health System

Augustine M.K. Choi, MD Stephen and Suzanne Weiss Dean, Weill Cornell Medicine; Provost for Medical Affairs, Cornell University

Nicholas Donofrio IBM Fellow Emeritus and EVP Innovation and Technology, IBM (retired)

John B. Ehrenkranz Chief Investment Officer, Ehrenkranz Partners

Anthony B. Evnin, PhD Partner, Venrock

Lee Goldman, MD, MPH Dean, Faculties of Health Sciences and Medicine, Chief Executive, Columbia University Medical Center

John Havens Partner and Non-Executive Chair, Napier Park Global Capital

Weslie R. Janeway President, Pyewacket Foundation

Richard P. Lifton, MD, PhD President, The Rockefeller University

Edison T. Liu, MD President and CEO, The Jackson Laboratory

Tom Maniatis, PhD NYGC Interim Scientific Director Director, Columbia Precision Medicine Initiative, Isidore S. Edelman Professor and Chair, Department of Biochemistry and Molecular Biophysics, Columbia University

Cheryl A. Moore NYGC President and Chief Operating Officer

Herb Pardes, MD Executive Vice Chairman of the Board of Trustees,NewYork-Presbyterian Hospital

Frank E. Richardson, MA, JD Co-founder and Senior Advisory Partner,Sentinel Capital Partners

Arthur J. Samberg Manager, Hawkes Financial LLC Frank V. Sica Partner, Tailwind Capital

Jim Simons, PhD Chair, Simons FoundationPresident, Euclidean Capital, LLC Board Chair, Renaissance Technologies

Steven D. Singer Partner, WilmerHale

Allen M. Spiegel, MD The Marilyn and Stanley M. Katz Dean,Albert Einstein College of Medicine, Executive Vice President and Chief Academic Officer, Montefiore Medicine

Samuel L. Stanley Jr., MD President, Stony Brook University

Bruce Stillman, PhD President and CEO, Cold Spring Harbor Laboratory

Craig B. Thompson, MD President and CEO, Memorial Sloan Kettering Cancer Center

Kevin J. Tracey, MD President and CEO, Feinstein Institute for Medical Research, Professor of Neurosurgery and Molecular Medicine, Hofstra Northwell School of Medicine

INSTITUTIONAL ASSOCIATE MEMBERS


T hroughout the past year, the New York Genome Center (NYGC) celebrated a number of important accomplishments.

We were pleased to welcome Princeton University as our newest Institutional Associate Member, bringing our member institutions to a total of 18. Our collaboration with Princeton, a world-renowned research university, and its Lewis-Sigler Institute for Integrative Genomics strengthens the NYGC’s focus on clinically actionable genomics and science. Princeton’s faculty have the opportunity to participate in the NYGC’s robust scientific culture, including scientific symposia, workshops, conferences and training programs. This new partnership paves the way for new collaborations and innovation between researchers at Princeton, the Lewis-Sigler Institute, the NYGC and our other member institutions.

Our CLEP-certified Clinical Lab received conditional approval from New York State to offer clinical constitutional whole genome sequencing testing for undiagnosed diseases and presymptomatic individuals. This is an expansion of our clinical genomic services, which includes constitutional exome sequencing for undiagnosed diseases, reference sequencing and Sanger validations. We are awaiting approval from New York State to conduct whole genome and transcriptome testing for cancer.

In fall 2016, Governor Cuomo appointed Cheryl A. Moore, President and Chief Operating Officer of the NYGC, as Co-Chair of the New York City Regional Economic Development Council (NYCREDC). She and Co-Chair Winston Fisher, Executive Vice Chair of Fisher House Foundation, are working to help bring new investments and growth into the New York City area economy.

Furthering our mission to enhance the life sciences in New York, the NYGC will launch a life science innovation incubator at our facility in partnership with Johnson & Johnson Innovation and New York State. Called JLABS @ NYC, the incubator will make use of our third-floor space to host up to 30 life science startup companies in biotechnology, pharmaceutics, medical devices and consumer health. This new partnership, announced in Governor Cuomo’s annual State of the State address in January 2017, generated wide print, broadcast and social media coverage. Governor Cuomo has proposed $17 million in funding for capital investments to support this initiative. JLABS @ NYC, scheduled to open in 2018, will offer an invaluable opportunity for the NYGC and our member institutions to establish new collaborations and partnerships with these emerging companies.

NYGC Research

In 2016, researchers at the NYGC helped contribute to advancements in the field of genomics through their translational research on a wide range of diseases. Their findings were published in more than 50 high-impact scientific journals.

Our Bioinformatics scientists conducted an array of investigations, including research on renal cell carcinoma, autism and breast cancer. The Bioinformatics team also developed and will shortly launch the MetroNome database, a web application that allows researchers to explore data visually, with the goal of correlating genotypes with phenotypes. The system accepts genomic sequencing and clinical data from any research project. Participating researchers can explore their data in an

J LABS @ NYC COMING TO THE NEW YORK GENOME CENTER

“ The new, vital incubator JLABS will be the catalyst that pushes our state into the forefront of this exciting field. I look forward to working with Johnson & Johnson and the New York Genome Center to build momentum in the life science industry and establish New York as the home of discoveries that will drive the economy and create a better future for all.”

— Andrew Cuomo Governor, New York State


MISSION The New York Genome Center is an independent, nonprofit academic research organization at the forefront of transforming biomedical research and clinical care with the mission of saving lives.

A collaboration of renowned academic, medical and industry leaders in New York and other partners throughout the country, the New York Genome Center focuses on translating genomic research into clinical solutions for serious diseases. New York Genome Center member institutions and partners are united in this unprecedented collaboration of technology, science and medicine.

We advocate and educate, sharing our findings and discoveries with the scientific, medical and thought leadership communities. We integrate our genomic research with cutting-edge technologies and leading physician-scientists so that patients around the world can benefit from more effective clinical treatments.


“ Our collaborative work with the NYGC is on the frontier of molecular medicine. We hope our research can advance knowledge of how non-coding as well as protein-coding regions of the genome can contribute to neurological disease. We really like the opportunity the NYGC offers to interact with other genomic scientists throughout the city and the world, and it certainly accelerated our progress. The collaboration stimulated better work and created a synergistic environment that enhanced our research and made the whole process a lot more fun.”

— M. Elizabeth Ross, MD, PhD Nathan Cummings Professor of Neurology and Head, Laboratory of Neurogenetics and Development Director, Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine


or determining which alleles of genetic variants lie in the same chromosome and may act together. This study, which was published in Nature Communications, is part of her lab’s ongoing work to uncover general rules of the genomic sources of human traits and diseases.

Collaborative Projects

Working together with researchers from our member institutions, as well as renowned scientists worldwide, the NYGC participated in many collaborative research projects on a wide range of diseases, including pediatric and adultcancer, autism, Alzheimer’s disease, ALS, arthritis, glaucoma, brain injury, schizophrenia and hemophilia.

The NYGC’s Center for Common Disease Genomics received funding from the National Human Genome Research Institute to help us expand our research on autism, asthma and Alzheimer’s disease.

The Cancer Genomics Alliance study, a joint initiative between the NYGC and IBM, was recognized and highlighted at the 2016 White House Precision Medicine

We strengthened collaborative research

projects with our Institutional Founding

Members and were jointly awarded a National

Cancer Institute grant with Weill Cornell

Medicine for a specialized genomic data

center, with Michael Zody, PhD, Senior

Director, Computational Biology, as the

co-principal investigator at the NYGC.

20,000NUMBER OF WHOLE GENOME SAMPLES SEQUENCED

interactive, visual interface and organize data along many dimensions. MetroNome enables investigators to search for genomic differences across large populations, investigate the effects of genomic variants and relate them to phenotypic conditions. The Bioinformatics team’s research in 2016 has resulted in more than a dozen publications in journals such as Nature, The American Journal of Human Genetics and The Journal of Clinical Investigation.

Marcin Imielinski, MD, PhD, discovered a new class of mutations in cancer that may represent a novel class of driver in liver, lung, thyroid and stomach cancer, and his findings were subsequently published in Cell. Neville Sanjana, PhD, utilized CRISPR, an advanced gene-editing technique, to analyze non-coding regions of the human genome that drive drug-resistant cancer. His study, which may offer new treatment options for patients with melanoma and other cancers, was published in Science and featured in an article in TIME.

Joseph Pickrell, PhD, and Yaniv Erlich, PhD, completed several breakthrough genome-wide association studies in 2016. One study discovered multi-tasking genes that influence a wide variety of human traits and conditions, identifying some unexpected connections between diseases. This research could provide a powerful new tool for scientists to identify shared causal relationships between diseases and better understand how diseases interrelate. In another study, Drs. Pickrell and Erlich deployed advanced data analytics and genome-wide association by proxy, using the DNA of patients’ families to map risk factors. They uncovered 17 new disease-causing mutations for Alzheimer’s disease, cardiac disease and diabetes. Both studies were published in Nature Genetics.

Research done by Tuuli Lappalainen, PhD, and her team resulted in the development of phASER, a novel method and software tool that substantially improves haplotype phasing,


1,000NUMBER OF PROJECTS COMPLETED

As part of our efforts to advance the field of epigenomics, our scientists collaborated on a whole genome bisulfite sequencing pilot study with researchers at Albert Einstein College of Medicine. We developed a whole genome bisulfite sequencing library prep compatible with the HiSeq X, reducing the cost of whole genome bisulfite sequencing by two-thirds and cutting the turnaround time in half, making it accessible to more researchers worldwide.

With support from the Sohn Conference Foundation, our scientists are working closely with researchers at Columbia University, Memorial Sloan Kettering Cancer Center and New York University on a collaborative project that involves whole genome and RNA sequencing to find potential new clinical treatments for children with acute lymphoblastic leukemia and neuroblastomas. With a grant from the Hereditary Disease Foundation and the W.M. Keck Foundation, we are collaborating with researchers at Columbia University and the Massachusetts Institute of Technology on a study to find modifiers of Huntington’s disease. These research findings may also be relevant in other neurological diseases, including autism and schizophrenia.

The New York Genome Center participated

in many collaborative research projects on a

wide range of diseases, including pediatric and

adult cancer, autism, Alzheimer’s disease, ALS,

arthritis, glaucoma, brain injury, schizophrenia

and hemophilia.

Initiative Summit. In collaboration with IBM, our Founding Technology Member, we are working to build a comprehensive and open repository of genetic data to accelerate cancer research. NYGC scientists sequenced the DNA and RNA from 200 cancer patients being treated at our member institutions. We are housing the contributed data and training Watson’s cognitive computing capacities for genomic analysis. The genetic information and clinical data from the patients were fed into Watson to review massive amounts of medical evidence to help identify existing drugs that may be candidates to potentially target patients’ cancer-causing mutations. All clinically actionable results were shared with treating physicians.


To advance collaborative efforts on cancer genomics, Nobel Laureate Harold Varmus, MD, Senior Associate Core Member, NYGC, and Lewis Thomas University Professor of Medicine, Weill Cornell Medicine, established the New York Cancer Genomics Research Network. Dr. Varmus convenes monthly meetings at the NYGC with leading cancer researchers and clinicians from our Institutional Founding Members and other key academic institutions around the world. The objective of this multidisciplinary approach is to help set critical priorities in translating genomic science into more effective treatment options for all cancer patients in New York and beyond.

Since its inception, the NYGC has attracted world-class scientists whose genomic expertise – including single cell genomics, genome engineering, population and evolutionary genomics, technology and methods development, statistics, computational biology and bioengineering – bring a multidisciplinary and in-depth approach to the evolving field of genomics. In 2016, we recruited two distinguished researchers, Drs. Neville Sanjana and Simon Tavaré, to our faculty.

Faculty UpdateNYGC scientists were awarded several prestigious grants. Rahul Satija, PhD, received a New Innovator Award from the National Institutes of Health to fund research focusing on how the interaction between molecular and environmental factors governs cell behavior. Yaniv Erlich, PhD, and Joseph Pickrell, PhD, were awarded a grant from the National Breast Cancer Coalition to expand the services of DNA.Land, the nonprofit web-based platform they created that houses genomes from 40,000 people, for a targeted collection of data of breast cancer patients. Dan Landau, MD, PhD, was the recipient of a Stand Up to Cancer Innovative Research Grant for a project with Weill Cornell Medicine, focused on a new mathematical approach to design combination therapies for chronic lymphocytic leukemia.

Our Center for Genomics of Neurodegenerative Disease’s ALS Consortium, led by Hemali Phatnani, PhD, was joined by two new members, The Jackson Laboratory and the University of California, Irvine. The Consortium now includes 15 leading institutions in the United States and abroad. Scientists and clinicians work collaboratively to apply state-of-the-art clinical and functional genomics together with bioinformatics to study ALS disease mechanisms and better understand how mutations underlying ALS cause disease. The target of this global multidisciplinary effort is whole genome sequencing and analysis of 3,200 clinically well-annotated ALS samples within the next three years to enhance early diagnosis and effective drug discovery.

260NUMBER OF INVESTIGATORS


Cognitive Sciences and completed his undergraduate education at Stanford University. In his postdoctoral research, Dr. Sanjana helped develop two classes of targeted nucleases for genome engineering: TALEs (transcription activator-like effectors) and the microbial immune system-derived CRISPR (clustered regularly-interspaced short palindromic repeats) enzymes. He uses these genome-engineering tools in a variety of contexts to understand how genetic variants affect human health and disease.

Simon Tavaré, PhD, joined the NYGC as a Senior Researcher while continuing his appointments as the Director of the Cancer Research UK Cambridge Institute and Professor in the Departments of Oncology and Applied Mathematics and Theoretical Physics at the University of Cambridge. Dr. Tavaré is widely recognized as one of the world’s leading experts in

Neville Sanjana, PhD, joined the NYGC as a Core Member and Assistant Investigator. Dr. Sanjana’s scientific expertise includes genome engineering, functional genomic screening using programmable nucleases, autism genetics and synaptic pathophysiology. He holds a joint appointment at New York University as an Assistant Professor in the Department of Biology and the Center for Genomics and Systems Biology and an associate faculty appointment with the Institute for Systems Genetics at New York University Langone Medical Center.

Previously at the Broad Institute of Harvard and the Massachusetts Institute of Technology and in the Departments of Brain and Cognitive Sciences and Bioengineering at the Massachusetts Institute of Technology, Dr. Sanjana was a postdoctoral scientist in the laboratory of Dr. Feng Zhang. Dr. Sanjana received his PhD from the Massachusetts Institute of Technology in Brain and


statistics and probability in computational biology. His research interests include statistical genetics, evolutionary approaches to cancer and stochastic computation.

Dr. Tavaré received his BSc degree, MSc degree and PhD in probability and statistics from the University of Sheffield, UK. He spent 25 years in academia in the United States before moving to Cambridge in 2004. He was elected a Fellow of the Academy of Medical Sciences in 2009 and named a Fellow of the Royal Society in 2011. Dr. Tavaré currently serves as President of the London Mathematical Society.

Dr. Tavaré is helping to forge connections and collaborations between the NYGC and other cancer research centers worldwide.

89NUMBER OF COLLABORATING INSTITUTIONS


“ We chose to work with the NYGC because of its high-quality sequencing services, coupled with its skilled bioinformatics team, which provided the flexibility to meet the unique needs of our study. We’ve had a tremendously positive experience collaborating with the NYGC faculty and staff. The project managers that we have worked with have been organized, cordial and highly responsive. Communication about questions, data transfers, meetings, budgets and timelines have been addressed promptly and thoroughly.”

— Brian J. Reid, MD, PhD Full Member, Divisions of Public Health Sciences and Human Biology, Fred Hutchinson Cancer Research Center; Professor of Medicine and Adjunct Professor of Genetics, University of Washington


Education & OutreachAs part of our educational mission, we hosted many scientific meetings, workshops, conferences and lectures in 2016. We held Evening Talks, our lecture series for the general public on advances in genomic science, sponsored by the New York Community Trust–Pyewacket Fund. We hosted Five Points lectures for the scientific community, featuring leading researchers from around the country and abroad. In addition, the NYGC held well-attended workshops for the medical community on single cell genomics, epigenomics, sequencing informatics and ancestry.

In October, the NYGC hosted its inaugural Single CellGenomics Day: A Practical Workshop to provide researchers a basic overview of single cell sequencing. The event, organized by the NYGC’s Rahul Satija, PhD, attracted 200 attendees from 30 academic and commercial institutions. The program focused on technology development, molecular protocols and computational analysis.

This past September, the NYGC hosted the first DNA.Land User Group Meeting. This unique “family reunion” was attended by more than 100 people and attracted media coverage on Fox 5 News. The panel featured best-selling author A.J. Jacobs and NYGC’s Yaniv Erlich, PhD, Joesph Pickrell, PhD, Dina Zielinski, Jie Yuan and Sophie Zaaijer.

Also in September, the NYGC hosted its first Sequencing Informatics Workshop, which was organized by Michael Zody, PhD, Senior Director, Computational Biology. Colleagues at our Institutional Founding Members, graduate students, postdocs, faculty and research laboratory staff learned the basics of sequence data alignment, data analysis and identifying somatic variations in cancer samples. Participants also learned how to read and understand common file formats and analyze RNA-seq data for expression and differential expression.

In May, the NYGC hosted our second annual New York Epigenomics Symposium. This day-long event, organized by NYGC’s Will Liao, PhD, was attended by more than 160 people. It included sessions that explored recent discoveries, ongoing work and novel methods in the field of epigenomics.

Using next-generation sequencing, the NYGC can sequence genomes more efficiently and cost effectively than previously possible — more than 500 whole genomes are sequenced each week.

We generated 9,000 terabytes of data — the

equivalent of 4.5 million Netflix movies.

We used more than 22.4 million core hours of compute, which would take 1,269 years on a typical computer.


Looking ForwardThanks to the continued support of our donors, the New York Genome Center has made important strides in contributing to the advancement of knowledge in the field of genomics.

The NYGC harnesses the diversity of New York’s leading academic and medical institutions to drive scientific discoveries that aim to improve medical treatment for patients. Our momentum is strong, and the upcoming year holds great promise for continued leaps forward.

Our progress is made possible by the incredible generosity of friends that allowed us to put in place the necessary personnel, faculty, technology and infrastructure to help us translate genomic research into actionable solutions to improve and save lives.

We continue to benefit from the Simons Carson challenge grant, wherein NYGC Directors Jim Simons and Russ Carson match each philanthropic gift made to the NYGC over the next two years. The generosity of our donors inspires others to invest in our work, and our donor base continues to expand. We are grateful for the confidence these gifts signify as we move toward our $100 million goal.

For more information on how to help further our progress, please contact:

Kathleen Kearns Vice President, Development and Communications Email: [email protected] Phone: 646.977.7026

New York Genome Center 101 Avenue of the Americas, 7th Floor New York, NY 10013


NYGC DONORS

AE Family Foundation

The ALS Association

Bloomberg Philanthropies

Bright Funds Foundation

Megan and Bob Burbridge

The Carson Family Charitable Trust

Lisa and Dick Cashin

Robert and Jennifer Darnell

Anthony J. and Christie B. de Nicola

Bucky Dent/Embraced by Love

Stanley and Fiona Druckenmiller

Andra and John B. Ehrenkranz

Roger W. and Carol B. Einiger Philanthropic Fund of the Jewish Communal Fund

Barbara and Burton Einspruch Philanthropic Fund of the Dallas Jewish Community Foundation

Empire State Development Corporation

Judith and Anthony Evnin

Gerald J. & Dorothy R. Friedman New York Foundation for Medical Research, Inc.

Eugene and Emily Grant Family Foundation

Bill Harvey

John P. Havens

Peter H. and Louise Havens

Andria and Paul Heafy

William Randolph Hearst Foundation

Hereditary Disease Foundation

Weslie R. Janeway

Paul Tudor Jones

JSRM Foundation

Ruth Ellen Kaplan

Marie-Josée and Henry R. Kravis Foundation

Elaine and Ken Langone

Christy and John Mack Foundation

Robert B. Millard

National Breast Cancer Coalition

The New York Community Trust – Pyewacket Fund

Dorothy Oertel-Albright

Project ALS

Frank E. Richardson

David Rockefeller

The Sackler Trust

Arthur and Rebecca Samberg

Gleniss Schonholz

Phyllis and Ivan Seidenberg

The Honorable Colleen McMahon and Frank V. Sica

Simons Foundation

The Alfred P. Sloan Foundation

The Sohn Conference Foundation

The Speyer Family Foundation, Inc.

The Starr Foundation

Mr. & Mrs. Anthony Tamer

Target ALS

Three Little Pigs Foundation (William E. Ford)

The Tow Foundation

Sue and Edgar Wachenheim III Foundation

Lulu C. Wang

Brian F. Wruble

Mortimer B. Zuckerman

CONTACT US

101 Avenue of the Americas New York, NY 10013

646.977.7000 [email protected] www.nygenome.org

CONNECT WITH US

new york genome center€¦ · cancer genomics study with ibm’s watson was recognized and...

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