The future of genomic medicine is here. Gene editing, gene therapy, clinical whole genome sequencing (WGS), and WGS-based diagnoses are already transforming the lives of patients and will soon become widely available—thanks in part to the people, partners, platforms, and programs of the New York Genome Center (NYGC).
Since 2011, we have been driving a new era of genomic science and medicine in New York City and beyond, laying the groundwork for a deeper understanding of the genetics, biology, and disease mechanisms necessary to advance healthcare around the world. Our multidisciplinary team of scientists, engineers, and faculty are accelerating the journey from the laboratory bench to patient bedside with:
Groundbreaking technological innovations, inventions, and scientific findings, which have been published in the most prestigious life science journals.
Leading-edge research in genomic science, which has attracted significant competitive sponsored research support from the National Institutes of Health, the National Cancer Institute, the National Institute of Mental Health, the National Human Genome Research Institute, the National Science Foundation, and the Chan Zuckerberg Initiative.
Exceptional Core Faculty Members, each of whom leads an independent research lab, holds a joint tenured or tenure-track appointment at one of our NYGC Institutional Founding Members, and is among the most world’s most cited experts on genomics.
Our expertise in convening top-tier talent across disciplines and institutions, empowering the acceleration of inter-institutional technological and scientific collaborations, biomedical discoveries, and advances in clinical genomics.
A state-of-the-art sequence production lab capable of processing and analyzing over 50,000 whole human genomes a year, and supporting large-scale single cell multiomics.
A best-in-class CLIA/CLEPaccredited clinical diagnostic laboratory focused on the application of whole genome sequencing in clinical genetic testing and oncology.
An outstanding Computational Biology group focused on the assembly and analysis of genomic data and the development and optimization of sequencing pipelines and tools for production sequencing services and novel genome technologies.
Our drive to advance genomic research and clinical genomic testing, laying the groundwork for precision medical treatments for cancer and neuropsychiatric and neurodevelopmental diseases.
An Outsized Impact on Genomic Science and Medicine in New York and Around the World
12 Member Institutions
More than 200 employees and staff, including:
10 Core Faculty Members
Nearly
500 publications
12 Associate Faculty Members
4 senior scientists
138 students, 50 postdocs, consultants, and visiting scientists
1st clinical laboratory to offer New York State-approved clinical whole genome and transcriptome CLIA tests for genetics and oncology
6 National Academy of Sciences members
4 NIH Director's New Innovator Award winners
2 Core Faculty Members named among the top 1 percent of the world’s most cited researchers
1 Nobel Laureate
3 Lasker Award winners
1 NIH Director’s Transformative Research Award
NYGC’s Collaborative Structure
Neuropsychiatric Disease Research
Faculty & Scientists
Cancer Research
Neurodegenerative Disease Research
Technology Innovation
Research Sequencing
Institutional Founding Members
Cold Spring Harbor Laboratory
Columbia University
Memorial Sloan Kettering Cancer Center
NewYork-Presbyterian Hospital
New York University
Northwell Health
Clinical Lab
Data Science
Rockefeller University
Stony Brook University
Weill Cornell Medicine
Associate Member Institutions
American Museum of Natural History
Hackensack Meridian Health
Hospital for Special Surgery
Thanks to NYGC's strategic investment in our people and genome sequencing technology, we are well-positioned for this moment. We have a high-throughput, next-generation sequencing lab and a robust analytics team capable of processing and analyzing over 50,000 whole human genomes every year.
In addition to running highly streamlined pipelines for the analysis of whole genome data, the research team has developed a diverse set of innovative methods for analyzing and integrating various types of genomic data, including exome, transcriptome, and single-cell sequencing data.
The National Institutes of Health has selected the NYGC as a multi-grant recipient under their Somatic Mosaicism across Human Tissues Network. The Network will:
• Create a comprehensive catalog of somatic variation in multiple tissue types from human donors with diverse ancestries at a variety of life stages.
• Build innovative tools to optimize variant detection across tissues and enable broad data sharing within the scientific community.
Clinical Genomic Testing
The NYGC is also at the forefront of clinical whole genome-based testing.
We are leading the way as the first clinical laboratory to offer a New York State-approved clinical whole genome and transcriptome test for cancer.
Our best-in-class CLIA/CLEP-accredited clinical diagnostic laboratory uses next-generation sequencing technology to perform tests in genetics and oncology and is licensed to perform clinical testing in all 50 states.
Thanks in large part to the NYGC’s leadership, clinical whole genome sequencing is already becoming a reality at academic medical centers like NewYork-Presbyterian and Columbia University Irving Medical Center (see facing page), replacing a wide variety of expensive and less informative diagnostic tests.
• This will allow physicians, patients, and families to make better-informed diagnoses and treatment decisions, thereby improving patient outcomes and quality of life.
• The results will become part of each patient’s permanent clinical record, so the data can be continually evaluated as we learn more about the genomic basis for disease and as new therapeutics are considered.
WGS: POWERING MOLECULAR DIAGNOSTICS
The NYGC is partnering with NewYork-Presbyterian Hospital and Columbia University Irving Medical Center on a new Women’s Genetics Center focused on developing and implementing WGS-based tests at scale to provide the highest-quality healthcare for women. The Center will:
• Draw on the diversity of New York’s population to provide leadership in the delivery and expansion of clinical genomic testing among women of diverse races and ethnicities.
• Leverage novel technologies and analytical methods to reduce costs, advance clinical knowledge, and improve outcomes.
The Women’s Genetics Center currently relies on the genetic and clinical infrastructure, respectively, of both NYGC and the Columbia Department of Obstetrics and Gynecology.
Technology Innovation Lab
A dedicated incubator within the NYGC, the Technology Innovation Lab—led by Core Faculty Member Sanja Vicković, PhD—serves as a creative hub for advancing the development and deployment of novel genomic methods, including molecular diagnostic testing, single-cell analysis, CRISPR gene editing, and spatial methods along with informatics tool development and integration. Under the aegis of this lab, numerous programs and cross-disciplinary collaborations are expanding the boundaries of genomic science, including:
• The NIH Human BioMolecular Atlas Program, a large multiinstitutional collaboration developing an open global platform for mapping healthy cells in the human body, including tissue mapping, technology development, and data analysis.
• The recent development of the PySeq2500, a repurposing of Illumina’s HiSeq 2500 System that uses readily available, conventionally formulated antibodies and can map dozens of proteins for visualization of pathological features and cell types from a single sample.
These powerful tools have been widely disseminated and deployed.
The NYGC leads the Center for Integrated Cellular Analysis, which was established in 2020 through a prestigious Centers of Excellence in Genomic Science grant from the NIH’s National Human Genome Research Institute. Directed by Core Faculty Member Rahul Satija, PhD, the center is a collaborative program of six top New York institutions. It comprises technology developers, computational biologists, neuroscientists, and cancer biologists who are developing technologies to measure, analyze, and integrate multiple molecular characteristics of single cells within various biological contexts and systems.
Development of Statistical and Computational Methods
The NYGC Computational Biology group is renowned for developing and optimizing tools and novel technologies to generate and analyze genomic data.
Their work improves our ability to understand and treat a wide array of diseases, as exemplified by:
• The collaboration of NYGC’s Scientific Director of Computational Biology, Michael Zody, PhD, and his team with groups at Massachusetts General Hospital, Yale University, and the Human Genome Structural Variation Consortium. The resultant study, published in Cell, presents a comprehensive analysis of the high-coverage whole genome sequencing data on the expanded 1000 Genomes Project cohort, which now consists of 3,202 samples, including 602 parent-child trios.
• NYGC Core Faculty Members Rahul Satija and Dan Landau being among two of the 14 recipients of a $140 million NIH technology development grant that seeks to address the challenges of finding genetic variation between cells of the same individual and determine what those changes mean for health and disease.
Core Faculty
Gamze Gürsoy, PhD
Joint Appointment: Herbert Irving Assistant Professor of Biomedical Informatics, Columbia University
Research Interests: Increasing access to biomedical data for a larger group of scientists while preserving the privacy of research participants and uncovering the molecular underpinnings of gene dysregulation via knowledge gained from functional genomics data.
David A. Knowles, PhD
Joint Appointment: Assistant Professor in the Departments of Computer Science and Systems Biology, Columbia University
Research Interest: Developing novel machine learning methods and applying them to data analysis challenges in genomics with the aim of better understanding the role of transcriptomic dysregulation across the spectrum from rare to common genetic diseases.
Neville Sanjana, PhD
Joint Appointments: Associate Professor in the Department of Biology, New York University, and the Department of Neuroscience and Physiology, NYU Grossman School of Medicine
Research Interest: Expanding the genome engineering toolbox to gain further scientific understanding of the non-coding genome and its vital role in human health and disease.
Rahul Satija, PhD
Joint Appointment: Professor, Center for Genomics and Systems Biology, New York University
Research Interest: Developing computational and experimental methods to sequence and interpret the molecular contents of a single cell.
Sanja Vicković, PhD
Joint Appointments: Assistant Professor, the Fu Foundation School of Engineering and Applied Science and the Herbert and Florence Irving Institute for Cancer Dynamics, Columbia University; and Wallenberg Academy Fellow of the Royal Swedish Academy of Sciences and the Royal Swedish Academy of Engineering Sciences, Uppsala University
Research Interest: As Director of the NYGC Technology Innovation Lab, Dr. Vicković develops breakthrough genomic tools and technologies with the potential to advance research for the wider scientific community.
Chenxu Zhu, PhD
Joint Appointment: Assistant Professor, Department of Physiology and Biophysics and the Institute for Computational Biomedicine, Weill Cornell Medicine
Research Interest: Applying and developing genomics tools and methods, including single-cell technologies, to gain a greater understanding of the molecular mechanisms of gene regulation in human development and disease, particularly in cancer.
NYGC's Genomics Programs
Are at the Forefront of the
Fight Against Disease
The scientists of the New York Genome Center—in partnership with extraordinary NYGC-convened cross-disciplinary teams at the best hospitals, medical schools, and labs in New York City and beyond—are:
• Making advances in the quest to understand the genomic and biological mechanisms underlying cancer, neuropsychiatric diseases, and neurodegenerative diseases, and working to identify effective methods of diagnosing and treating these diseases.
• Leading the way in democratizing genomic science and understanding the contribution of genetic diversity to disease.
Arc of Discovery
A comprehensive understanding of diseases requires integration of data across levels of analysis
Clinical Implementation
Computational Models
Animal Models
Circuits
Cells
Molecules
Genes
Cancer Program
Exemplifying the high caliber and outsized impact of NYGC’s work in the fight against disease, the recently launched MacMillan Center for the Study of the Non-Coding Cancer Genome is:
• A multidisciplinary collaboration of 23 investigators across nine institutions.
• Dedicated to understanding the “dark genome” and epigenome and their impact on cancer progression and treatment.
The MacMillan Center: Shining Light on the Dark Genome
98% of the human genome— the non-coding genome—plays an essential regulatory role in normal human physiology Human Genome
2% 20,000 Protein-Coding Genes
The Center will advance four directions of inquiry:
• Developing technologies and undertaking studies aimed at understanding the structure and function of the non-coding genome and epigenome in cancer evolution, progression, and treatment response.
• Advancing large-scale mapping of cancer genomes.
• Developing new methods to advance the understanding of the organization of non-coding DNA and chromatin structure.
• Partnering with NYGC’s Polyethnic-1000 initiative to study the cancer genomes of underrepresented minority populations, ensuring that the MacMillan Center’s work will expand the application of precision medicine and help reverse generations of racial and ethnic disparities in health outcomes.
The MacMillan Center will convene the New York scientific research community around the shared goal of understanding the role of the non-coding genome and epigenome in cancer, with a commitment to open science and collaboration.
NYGC RESEARCHERS AIM TO ADDRESS CANCER INEQUITIES IN THE AFRICAN DIASPORA
A world-class research team led by Melissa B. Davis, PhD, NYGC Associate Faculty and Polyethnic-1000 (P-1000) Cancer Ethnicity Scholar and the Director of the Institute of Translational Genomic Medicine at Morehouse School of Medicine, was recently selected as one of five international research teams to receive up to $25M in funding from Cancer Grand Challenges.
With these funds, the SAMBAI (Societal, Ancestry, Molecular, and Biological Analyses of Inequalities) team will address the issue of inequities in cancer prevention, screening, and treatment by:
• Focusing on prostate, breast, and pancreatic cancers in diverse cohorts of African descent from regions within Africa, the United Kingdom, and the United States.
• Building an unprecedented resource comprised of comprehensive measurements of social, environmental, genetic, and biological factors used to help define the causes of disparate outcomes in the selected populations.
“Together, we've built a foundation strong enough to embark on this ambitious journey, largely through our Polyethnic-1000 project efforts at the New York Genome Center,” said Dr. Melissa Davis. “With this monumental award, we will continue to push the boundaries of what's possible in cancer research, inspired by the collaborative philosophies of my NYGC colleagues that have brought us this far.”
The team unites clinicians, advocates, and scientists across fifteen institutions and seven countries with broad expertise in epidemiology, exposomics, genomics, immunology, and computational biology.
Dr. Nicolas Robine, Director of Computational Biology at NYGC, and Dr. Marcin Imieliński, Core Faculty Member at NYGC and Director of Cancer Genomics at NYU Langone Health's Perlmutter Cancer Center, are working alongside other genomics collaborators to process and contextualize large and complex data using novel algorithms, cloud computing, and graph representations of reference sequences, which are well-suited to analyze genomic data of participants from diverse ancestries.
Cancer Grand Challenges is a global funding platform, co-founded by Cancer Research UK and the National Cancer Institute (NCI), that supports a community of diverse, global teams in their effort to innovatively tackle cancer’s biggest challenges.
The People Accelerating Cancer Genomics
Core Faculty Members
Marcin Imieliński, MD, PhD
Joint Appointment: Director of Cancer Genomics, NYU Langone Health’s Perlmutter Cancer Center
Research Interest: Applying high-throughput sequencing technology and genomic data science to study patterns of complex and non-coding somatic DNA variations in cancer.
Dan A. Landau, MD, PhD
Joint Appointment: Associate Professor in the Division of Hematology and Medical Oncology and the Department of Physiology and Biophysics, Weill Cornell Medicine
Research Interest: Charting a roadmap of the basic dimensions that determine the course of cancer evolution to devise therapies that directly anticipate and address tumor evolution.
Senior Associate Core Members and Associate Members
Samuel Aparicio, BM, BCh, PhD, FRCPath, FRSC
Senior Scientific Director of Cancer Genomics
Dr. Aparicio is the Nan & Lorraine Robertson Chair in Breast Cancer Research at the University of British Columbia (UBC) in Vancouver, Canada. He is also Head of the Department of Breast and Molecular Oncology at BC Cancer Research, part of the Provincial Health Services Authority, and a Professor in the Department of Pathology and Laboratory Medicine at UBC.
Research Interests: Studying the evolution of human cancers using next-generation sequencing approaches and single-cell sequencing methods.
Onyinye Balogun, MD, MSc
Associate Member
Joint Appointment: Assistant Professor, Radiation Oncology, Weill Cornell Medicine
Research Interests: As a Cancer and Ethnicity Scholar at the New York Genome Center, Dr. Balogun oversees the Polyethnic-1000 project, an initiative to study the genome's contribution to cancer disparities, and serves as the co-Principal Investigator of the Polyethnic-1000 endometrial cancer project.
Melissa B. Davis, PhD
Associate Member
Director of the Institute of Translational Genomic Medicine at Morehouse School of Medicine and Distinguished Investigator with the Georgia Research Alliance
Research Interests: Uncovering the biological determinants of health disparities in cancer and how they intersect with the marginalization of minoritized populations. Dr. Davis is an Ethnicity and Cancer Scholar for NYGC’s Polyethnic-1000 initiative.
Simon Tavaré, PhD
Senior Associate Core Member
Director of the Irving Institute for Cancer Dynamics and Professor of Biological Sciences and Statistics, Columbia University
Research Interests: Statistical and population genetics, statistical inference and stochastic computation, cancer evolution, bioinformatics, and computational biology.
Harold Varmus, MD
Senior Associate Core Member
Lewis Thomas University Professor of Medicine, Weill Cornell Medicine.
Research Interests: Dr. Varmus is a co-recipient of the Nobel Prize in Physiology or Medicine for discovering the cellular origin of retroviral oncogenes. He leads the Genome Center Cancer Group with Charles Sawyers, MD, chair of the Human Oncology and Pathogenesis program at Memorial Sloan Kettering.
Michael Wigler, PhD
Senior Associate Core Member
Russell and Janet Doubleday Professor of Cancer Research and Cancer Center Member, Cold Spring Harbor Laboratory
Research Interests: Understanding the genomics of cancer and the genetics of autism and related disorders.
Neuropsychiatric Disease Genomics
In 2015, only three years after our founding, the NYGC was awarded a five-year $50 million NIH grant to support the work of the highly competitive and prestigious Centers for Common Disease Genomics to determine the whole genome DNA sequences of nearly 50,000 individuals— 38,000 of whom were from families with autism. NYGC produced the high-quality genome sequences, which are now available on the NIH Data Commons, a platform that is broadly accessible to the research community internationally. This data is already leading to important new insights into the genetics of autism.
We are leveraging our research on the genetic architecture of autism to advance the understanding of autism and neuropsychiatric disorders, including bipolar disorder and schizophrenia:
• Launching a new BD2-funded study to address the gaps in our knowledge of the mechanisms underlying genetic risk for bipolar disorder and advance our ability to translate genetic findings into treatment strategies.
• The New York Genome Center, the Broad Institute of MIT and Harvard, and the University of California, Los Angeles, will collaborate to create the BD2 Genetics Platform. This platform will be used to perform genomic profiling of one of the most diverse populations of people with bipolar disorder, including more than 30,000 study subjects from Africa, Central America, South America, and Asia.
• Under the auspices of GeMMA, researchers from the NYGC, working with Columbia University, the New York State Office of Mental Health, and a group of Institutional Founding Members and scientists, are pursuing the goal of building a vast clinical-genomic database focused on severe mental illnesses. This unparalleled resource, which will contain longitudinal data of biospecimens and associated genomic and clinical records of consenting patients, will:
– Advance genomic discovery and functional studies.
– Facilitate data-driven clinical trial recruitment and drug development.
– Expand access to state-of-the-art genomic diagnostics and clinical interpretation services for underserved patient populations.
The People Driving Our Neuropsychiatric Disease Program
Core Faculty Member
Ivan Iossifov, PhD
Joint Appointment: Associate Professor, Cold Spring Harbor Laboratory
Research Interest: Applying genomics and systems biology to the study of the etiologies of common diseases including autism, schizophrenia, and cancer.
Senior Associate Faculty Member
Tom Maniatis, PhD
Joint Appointment: Isidore S. Edelman Professor of Biochemistry and Molecular Biophysics, Columbia University
Investigator: The Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University
Research Interest: Molecular mechanisms that underlie neurodegenerative and neurodevelopmental disorders.
Senior Associate Core Members and Associate Members
Mary-Claire King, PhD
Senior Associate Core Member
American Cancer Society
Professor in the Departments of Genome Sciences and Medicine, University of Washington
Research Interest: The genetics of complex common human conditions, with a primary focus on the influence of genetics on major mental illnesses, especially schizophrenia.
Stephan Sanders, BMBS, PhD
Associate Member
Dr. Sanders is a Professor of Pediatric Neurogenetics in the Department of Pediatrics at the University of Oxford and an Associate Professor of Psychiatry at the University of California, San Francisco.
Research Interests: Using gene discovery, functional genomics, and bioinformatics to understand the etiology of neurodevelopmental disorders.
Tarjinder Singh, PhD
Associate Member
Dr. Singh is an Assistant Professor of Computational and Statistical Genomics in the Department of Psychiatry at Columbia University, with joint appointments at the Mortimer B. Zuckerman Mind Brain Behavior Institute at Columbia University and the New York State Psychiatric Institute.
Research Interests: Generating, analyzing, and integrating genetic and functional data to understand the causes of mental illness.
Lea K. Davis, PhD
Associate Member
Dr. Davis is a Professor in the Departments of Medicine, Genetics and Genomic Sciences, and Psychiatry at Icahn School of Medicine at Mount Sinai.
Research Interests: The genetic basis of a wide range of complex health conditions, diseases, and common traits ranging from neurodevelopmental disorders to women’s health.
Neurodegenerative Disease Program
The NYGC’s Center for Genomics of Neurodegenerative Disease, led by Core Faculty Member
Hemali Phatnani, PhD, is transforming the way we understand and treat neurodegenerative diseases such as ALS, dementia, Alzheimer’s disease, frontotemporal dementia, Parkinson’s disease, and Huntington’s disease.
The Center is known for the international ALS Consortium it established, which now includes 46 institutions in seven countries. The consortium developed a framework to apply clinical and functional genomics together with bioinformatics to the study of ALS disease mechanisms and sequenced and collected nearly 5,000 whole genomes of ALS patients with the goals of:
• Investigating the genetic determinants of disease onset and progression.
• Improving and enabling earlier diagnoses.
• Identifying therapeutic targets to prevent and slow disease progression.
Powering Studies of Neurodegenerative Diseases
Core Faculty Member
Hemali Phatnani, PhD
Joint Appointment: Assistant Professor of Neurology, Columbia University Vagelos College of Physicians and Surgeons
Research Interest: Applying state-of-the-art genomics and bioinformatics to understand the role of cell-cell interactions in amyotrophic lateral sclerosis (ALS) pathophysiology.
Dr. Phatnani is the Director of NYGC’s Center for Genomics of Neurodegenerative Disease.
Senior Associate Faculty Member
Tom Maniatis, PhD
Joint Appointment: Isidore S. Edelman Professor of Biochemistry and Molecular Biophysics, Columbia University
Investigator: The Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University
Research Interest: Molecular mechanisms that underlie neurodegenerative and neurodevelopmental disorders.
Bing Ren, PhD
Scientific Director and Chief Executive Officer, New York Genome Center, Professor of Genetics and Development, Biochemistry and Molecular Biophysics, and Systems Biology, Associate Director in the Vagelos Institute for Basic Biomedical Science (Vagelos Institute) in VP&S, Columbia University
Dr. Ren leads the research and operational activities of the NYGC, which focus on the development of computational and experimental genomic methods and disease-focused research to better understand the genetic basis of cancer, neurodegenerative diseases, and neuropsychiatric diseases. He also directs NYGC’s faculty, who lead independent research labs based at the Center.
As a pioneer in the field of epigenomics, Dr. Bing Ren has devoted his career to unraveling the complexities of gene regulation and chromatin architecture. Dr. Ren’s research has led to fundamental discoveries in gene regulation, including the mapping of millions of regulatory elements within the human genome, elucidation of chromatin organization principles, and the functional interpretation of non-coding disease variants.
Dr. Ren has played a central role in multiple large-scale genomics initiatives, including the ENCODE Project, the NIH Roadmap Epigenomics Mapping Consortium, the International Human Epigenome Consortium, and the 4D Nucleome Consortium. His work has significantly advanced our understanding of how epigenetic modifications influence cellular identity and human disease, particularly in neurodegeneration and cancer.
Dr. Ren earned his Ph.D. in Biochemistry from Harvard University in 1998 and completed postdoctoral training at the Whitehead Institute before joining the UC San Diego faculty in 2001. He has received numerous accolades, including the Chen Award for Distinguished Academic Achievement in Human Genetic and Genomic Research, the Ray Wu Award for Outstanding Leadership and Accomplishment in Biomedical Sciences, and election as a Fellow of the American Association for the Advancement of Science.
Beyond academia, Dr. Ren has translated his scientific discoveries into real-world applications by founding two biotechnology companies, Arima Genomics and Epigenome Technologies. His work continues to drive innovation in epigenome profiling and its applications in precision medicine.
Since our founding in 2011, the New York Genome Center has served as New York’s nexus for collaborative genomic research. We harness the energy and intellectual firepower of New York City to fuel breakthroughs in genomics science and medicine.
