NEW YORK
GENOME CENTER:
A YEAR I N REVI EW – 2 0 1 6 A Message from
Leadership
2016 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,
Tom Maniatis, PhD
Interim Scientific Director
Cheryl A. Moore
President and Chief Operating Officer
INSTITUTIONAL FOUNDING MEMBERS
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BOARD OF
DIRECTORS
Russell L. Carson
NYGC Board Co-Chair
Co-Founder and General Partner,
Welsh, Carson, Anderson & Stowe
Ivan G. Seidenberg
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
NYGC Board Co-Chair
Former Chair and CEO,
Verizon Communications
Herb Pardes, MD
Dafna Bar-Sagi, PhD
Frank E. Richardson, MA, JD
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)
Executive Vice Chairman of the Board of Trustees,
NewYork-Presbyterian Hospital
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 Foundation
President, Euclidean Capital, LLC
Board Chair, Renaissance Technologies
Steven D. Singer
Partner, WilmerHale
Allen M. Spiegel, MD
John B. Ehrenkranz
Chief Investment Officer, Ehrenkranz Partners
The Marilyn and Stanley M. Katz Dean,
Albert Einstein College of Medicine,
Executive Vice President and Chief
Academic Officer, Montefiore Medicine
Anthony B. Evnin, PhD
Samuel L. Stanley Jr., MD
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
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
Edison T. Liu, MD
President and CEO,
The Jackson Laboratory
INSTITUTIONAL ASSOCIATE MEMBERS
FOUNDING TECHNOLOGY MEMBER
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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
JLABS @ 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
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MIS S ION
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.
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“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
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20,000
NUMBER 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,
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.
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 adult
cancer, 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
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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.
1,000
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.
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.
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.
NUMBER OF PROJECTS
COMPLETED
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Faculty Update
NYGC 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.
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N U M B E R O F I N V E S T I G AT O R S
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.
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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.
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.
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
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
9 | A Ye a r I n R e v i e w
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.
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N U M B E R O F C O L L A B O R AT I N G
INSTITUTIONS
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“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
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Education & Outreach
As 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 Cell
Genomics 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.
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.
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.
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Looking Forward
Thanks 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
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NYGC DONORS
William Randolph Hearst Foundation
AE Family Foundation
Hereditary Disease Foundation
The ALS Association
Weslie R. Janeway
Bloomberg Philanthropies
Paul Tudor Jones
Bright Funds Foundation
JSRM Foundation
Megan and Bob Burbridge
Ruth Ellen Kaplan
The Carson Family Charitable Trust
Marie-Josée and Henry R. Kravis Foundation
Lisa and Dick Cashin
Elaine and Ken Langone
Robert and Jennifer Darnell
Christy and John Mack Foundation
Anthony J. and Christie B. de Nicola
Robert B. Millard
Bucky Dent/Embraced by Love
National Breast Cancer Coalition
Stanley and Fiona Druckenmiller
The New York Community Trust –
Pyewacket Fund
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.
Dorothy Oertel-Albright
Project ALS
Frank E. Richardson
David Rockefeller
The Sackler Trust
Arthur and Rebecca Samberg
Gleniss Schonholz
Eugene and Emily Grant Family Foundation
Phyllis and Ivan Seidenberg
Bill Harvey
The Honorable Colleen McMahon
and Frank V. Sica
John P. Havens
Peter H. and Louise Havens
Andria and Paul Heafy
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
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C O N TA C T U S
101 Avenue of the Americas
New York, NY 10013
646.977.7000
[email protected]
www.nygenome.org
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