DOCSLIB.ORG

New York Genome Center at a Glance

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
New York Genome Center at a Glance NEW YORK GENOME CENTER AT A GLANCE OVERVIEW The New York Genome Center (NYGC) is at the forefront of transforming biomedical research and clinical care with the mission of saving lives. Founded in 2011 and officially opened in September 2013 as a consortium of renowned academic, medical and industry leaders across the globe, NYGC is a 501(c)(3) charity that focuses on translating genomic research into clinical solutions for serious disease. Our member organizations are united in this unprecedented collaboration of technology, science and medicine. OUR MISSION We implement advanced genomic research and integrate our findings with world-class technologies and physician-scientists in order to help solve diseases. We harness the diversity of New York’s institutions and people to drive scientific discoveries that will vastly improve clinical care – ethically, equitably and urgently. We advocate and educate, sharing our findings with the global scientific, medical and thought leadership communities to broaden the reach of the New York Genome Center to help patients in every corner of the world. We create synergies through collaboration to continually innovate and advance our vision. CORE ACTIVITIES Our capacities and expertise reflect our commitment to being a vital resource – and driver – for the advancement of translational genomics. Our current core activity areas are: Sequencing and Bioinformatics Services We work with both our Member Institutions and the genomics research community at large to provide best-in-class technology and expertise to advance scientific breakthroughs. NYGC’s services include experimental design assistance, sample library preparation and sequencing (whole genome, exome, RNA, and lane sequencing), extensive data quality control, bioinformatics, and data storage. NYGC is the only institution in the Tri-State Area to acquire the Illumina HiSeq X Ten, the fastest and most advanced sequencing technology available. Through a Services Access Agreement, we also offer genomic sequencing and informatics services to Investigators and Scientists affiliated with the Howard Hughes Medical Institute (HHMI). Clinical Laboratory NYGC has established a Clinical Laboratory, which is offering Next Generation Sequencing (NGS)-based exome testing for constitutional disorders and is in the process of getting NY State approval to offer cancer testing and whole genome clinical sequencing. NYGC’s diagnostic services are accessible to physicians on behalf of their patients. WINTER 2016 Research As well as providing services and analysis, NYGC moves the clinical genomics needle forward through innovative research and methods development and improvement. Our Faculty Members include one Nobel Laureate and four members of the National Academy of Sciences, and each hold joint academic appointments at one of our Institutional Founding Members (IFMs). They lead clinically-focused genomic studies in a variety of areas, including cancer, neurologic disease (including autism, schizophrenia and neurodegenerative disease), inflammatory disease, epigenetics, population genomics, evolutionary mechanisms and disease risk, single cell genomics. NYGC also has an Innovation Lab dedicated to protocol development, technologic innovation, informatics tool development and integration. NYGC has spearheaded several collaborative clinical studies. We launched a multi-institutional trial in which we are partnering with IBM to explore whether their Watson artificial intelligence technology can help create personalized treatments for patients with glioblastoma, a deadly form of brain cancer. We are currently expanding this effort to include other cancers, in part by pursuing additional pharmaceutical, technology and related industry partnerships in addition to our relationship with IBM, our Founding Technology Member. NYGC has also begun a range of other clinical genomic studies, including those focused on pediatric cancers (leukemia and neuroblastoma), inflammatory diseases (rheumatoid arthritis, Crohn’s disease and asthma), and neurologic disease. Our Center for Genomics of Neurodegenerative Disease (CGND) is dedicated to studying neurodegenerative diseases such as ALS and Alzheimer’s. The CGND’s collaborating partners include our own IFMs, the Perelman School of Medicine at the University of Pennsylvania, the Northeast ALS Consortium, Mass General Hospital/Harvard Medical School and UMass Medical School. The CGND is also supported by an NYGC-organized group, the Northeast Neurologists Genomics Group, comprised of Chairs of Clinical Neurology across the tri-state area. Collaborative Infrastructure Development NYGC is committed to developing the systems and infrastructure to enable researchers from New York and beyond to carry out large-scale, collaborative genomics research. In January 2016 the NIH announced that NYGC was awarded a $40 million grant for support of a Center for Common Genetic Diseases. This highly competitive award serves as a benchmark for NYGC; the major US genome centers were all in the applicant pool. Due to its relative newness, NYGC underwent intense scrutiny during its review, including site visits at NYGC and at the NIH, as well as a personal tour of NYGC by Francis Collins, the NIH Director. The grant will support high quality and scalable genomics infrastructure, and efforts to identify all DNA variants associated with common diseases such as autism. NYGC also was awarded, along with a consortium of 10 medical institutions, a PCORI (Patient- Centered Outcomes Research Institute) contract. The contract supports building infrastructure to centralize clinical data across a number of hospitals and care providers, with the goal of enabling research and analysis that will provide evidence-based information that patients and providers can use to make better-informed care decisions. The New York City Clinical Data Research Network (NYC-CDRN) will bring together organizations across seven systems, and include comprehensive and longitudinal data for at least 2.5 million patients, and potentially as many as 6 million patients. WINTER 2016 2 Beyond PCORI, our bioinformaticians and engineers are engaged in a number of projects, including developing warehouses for genomics datasets and their analyses, with the goal of increasing efficiencies, scale and knowledge access for scientists, while reducing potential costs of and roadblocks to innovative research. Education and Outreach NYGC hosts two independent lecture series. Our Five Points Lectures are technically detailed weekly talks that bring together scientists from New York and beyond to discuss their work, in depth, with researchers, clinicians and students. Evening Talks is a monthly event that is open to the general public and is intended for a broader audience. Leading genomics researchers and theorists discuss recent discoveries, emerging techniques, bioethics, opportunities and challenges. Both series are free to participants. We also hold a number of scientific events and workshops in partnership with our Member Institutions and other organizations. Upcoming events can be viewed on our website. Funding Financial support from individuals and organizations who are committed to NYGC’s vision has been integral to the Center’s early success and growth. Since its inception, NYGC has raised over $200 million from a number of sources, including federal and private grants, corporate and philanthropic support, and other funding, including support from our member institutions, the New York City Economic Development Corporation, the Empire State Development Corporation, the Partnership Fund for New York City, and the State of New York. In spring 2014, the New York State Legislature approved $105 million in funding to advance genomic medicine through a partnership between the University at Buffalo and NYGC. As part of this initiative, NYGC is receiving $55.75 million from the State and has matched it dollar for dollar with funds raised separately. In December 2015, NYGC received a challenge grant of $100 million from the Simons Foundation and The Carson Family Charitable Trust. They will match every philanthropic dollar raised over the next three years up to $100 million; at the end of a successful challenge, dollars raised will total $200 million. LEADERSHIP Robert Darnell, MD, PhD, Founding Director and Chief Executive Officer Dr. Darnell’s career in neurology and genomics spans over 25 years and includes his roles as the Heilbrunn Professor at The Rockefeller University and a Howard Hughes Medical Institute Investigator. Dr. Darnell is a Senior Physician at The Rockefeller University Hospital as well as an Adjunct Attending Neuro-Oncologist at Memorial Sloan Kettering Cancer Center (MSKCC). He was elected a member of the National Academy of Sciences in 2014 and has been a member of the Institute of Medicine of the National Academy of Sciences since 2010. Cheryl A. Moore, President and Chief Operating Officer A highly esteemed and nationally recognized research executive, Cheryl Moore joined NYGC in January 2016. Ms. Moore spent over ten years with the Howard Hughes Medical Institute (HHMI) where she was most recently the Executive Vice President and Chief Operating Officer for five years, and previously Chief Operating Officer of HHMI’s Janelia Research Campus. Prior to joining HHMI, she served as Senior Vice President and Chief Operating Officer of the Sanford Burnham Prebys Medical Discovery Institute in La Jolla, California. WINTER 2016 3 BOARD OF DIRECTORS Russell L. Carson NYGC Board
Load more

Recommended publications
  • Biolegend® and New York Genome Center® Enter Into Exclusive Global
    BioLegend® and New York Genome Center® Enter into Exclusive Global License and Research Agreement for CITE-seq™, a Novel Technique for Multidimensional Single Cell Analysis New Partnership to Help Accelerate Translational Genomic Science Research NEW YORK, NY (January 11, 2018) – BioLegend, Inc. (“BioLegend”) and the New York Genome Center (“NYGC”) announced today that they have entered into an exclusive worldwide license and collaborative research agreement for CITE-seq™ technology for use in the research field. CITE-seq™, Cellular Indexing of Transcriptomes and Epitopes by sequencing, developed in the NYGC’s Technology Innovation Lab by a team led by Dr. Marlon Stoeckius, complements BioLegend’s extensive portfolio of antibodies and biomedical reagents. The new CITE-seq™ technology enables scientists to simultaneously measure protein and RNA expression at the single-cell level, allowing researchers to distinguish different cell types and cell states, and study disease mechanisms at the level of individual cells. The partnership with the NYGC expands the reach of BioLegend’s antibody and protein portfolio of reagents into the rapidly advancing space of genomic and transcriptomic profiling. In an effort to facilitate standardization of the technology and allow comparison of data across many studies, BioLegend and the NYGC have established a large set of static barcodes, each of which are assigned to unique antibodies/proteins. In advance of the official release of CITE-seq™ catalog products, and related products for sample multiplexing and doublet identification, BioLegend is now providing specific custom CITE-seq™ antibody conjugates to interested customers. Whether provided by catalog or in custom form, BioLegend’s oligo-barcoded CITE-seq™ antibodies establish high-quality reagent standards for this new profiling technology.
    [Show full text]
  • E-Newsletter
    Spring 2014 Center for Clinical and Translational Science e-Newsletter Center News Rockefeller Leads Largest Survey of Clinical Research Participants: New England Journal of Medicine Report Documents Mostly Positive Experiences By Zach Veilleux Propel Center for Population Health, A multi-center survey of close to data we can use to improve those included responses from participants 5,000 volunteers who enrolled in experiences for every participant.” clinical research studies, the largest at 15 clinical research centers including of its kind, shows that by and large 13 funded by Clinical and Translational The researchers distributed their participants feel valued and respected Science Awards from the NIH. It was 77-question survey — similar to by investigators. But although many published in the New England Journal those used by physicians’ groups gave high marks to the research teams’ of Medicine. (http://www.nejm.org/ and hospitals to incorporate patient trustworthiness and ability to explain doi/full/10.1056/NEJMp1311461) feedback into quality improvement their protocols, the survey also revealed efforts — to a total of 18,890 clinical “We depend on research participants that a sizable minority did not feel trial participants. Overall, 73 percent as our partners to advance science and completely prepared for the study, and of those who returned the surveys rated medicine,” says study author Rhonda that participants wanted researchers to their overall experience very highly Kost, clinical research officer at The inform them of the results of the studies. (marking 9 or 10 on a 10-point scale), Rockefeller University Hospital. “But and 66 percent said they would either their experiences have never been The study, which was led by probably or definitely recommend widely measured in a scientific way.
    [Show full text]
  • A Year in Review 2018 Board of Directors
    A Year in Review 2018 Board of Directors Russell L. Carson Anthony B. Evnin, PhD Frank V. Sica NYGC Board Co-Chair Partner, Venrock Partner, Tailwind Capital Chairman, The Carson Family Charitable Trust, Co-Founder and Lee Goldman, MD, MPH Jim Simons, PhD General Partner, Welsh, Carson, Dean, Faculties of Health Sciences Chair, Simons Foundation, Chair, Anderson & Stowe and Medicine, Chief Executive, Euclidean Capital, LLC, Board Chair, Columbia University Irving Medical Center Renaissance Technologies Ivan G. Seidenberg NYGC Board Co-Chair Weslie R. Janeway Steven D. Singer Former Chair and Chief Executive Director, Finistere Charitable Foundation Partner, WilmerHale Officer, Verizon Communications Richard P. Lifton, MD, PhD Samuel L. Stanley Jr., MD Dafna Bar-Sagi, PhD President, The Rockefeller University President, Stony Brook University Professor of Biochemistry and Molecular Pharmacology and Edison T. Liu, MD Bruce Stillman, PhD Medicine, Senior Vice President and President and Chief Executive Officer, President and Chief Executive Officer, Vice Dean for Science, Chief Scientific The Jackson Laboratory Cold Spring Harbor Laboratory Officer, NYU Langone Health Tom Maniatis, PhD Craig B. Thompson, MD Dennis S. Charney, MD NYGC Scientific Director and President and Chief Executive Officer, Anne and Joel Ehrenkranz Dean, Chief Executive Officer Memorial Sloan Kettering Cancer Center Icahn School of Medicine at Mount Isidore S. Edelman Professor and Chair, Sinai, President for Academic Affairs, Department of Biochemistry and Mount Sinai Health System Gordon F. Tomaselli, MD, FAHA, Molecular Biophysics, Columbia University FACC, FHRS Founding Director, Columbia The Marilyn and Stanley M. Katz Dean, Augustine M.K. Choi, MD Precision Medicine Initiative Stephen and Suzanne Weiss Dean, Albert Einstein College of Medicine, Executive Vice President and Weill Cornell Medicine, Provost for Cheryl A.
    [Show full text]
  • P1000 Poster AACR2019 02
    Polyethnic-1000 Advancing cancer genomics by studying ethnically diverse patient populations in New York Fieke Froeling1,2, Nicolas Robine1, Benjamin Hubert1, Michael Zody1, Dayna Oschwald1, Harold Varmus1,3, Charles Sawyers1,4, David Tuveson1,2, On behalf of the NYGC P1000 Consortium 1 New York Genome Center, 2 Cold Spring Harbor Laboratory, 3 Weill Cornell Medicine, 4 Memorial Sloan Kettering Cancer Center Background Stage I: retrospective, feasibility study • Known ethnic differences in cancer incidence and mortality. • Central IRB approval (BRANY) with waiver of informed consent • In most cases, the causes for these variations are multi-factorial, however little • Sample requirements: remains known about the molecular attributes. - Self-identified non-white cancer patient > 18 years old • Advances in sequencing technologies have revolutionized approaches to the - Tumor sample no older than 2016 prevention, risk assessment, early detection, diagnosis, and treatment of cancers. - Estimated tumor percentage at least 50% • However, many ethnic groups, especially non-European populations, continue to be - Size of the tumor needs to be at least 0.5 cm x 0.5 cm significantly under-represented in cancer research, including clinical trials, and have - All samples will be de-identified before submission to NYGC not received equal benefits in clinical practice. • Central pathology review at NYGC by P1000 pathologist: - 30 samples reviewed, ~70 in pipeline for shipment to NYGC from total of 14 different sites Our current knowledge about cancer
    [Show full text]
  • 2014 FACT SHEET Overview: the New York Genome Center (NYGC
    2014 FACT SHEET Overview: The New York Genome Center (NYGC) is at the forefront of transforming biomedical research and clinical care with the mission of saving lives. As a consortium of renowned academic, medical and industry leaders across the globe, NYGC focuses on translating genomic research into clinical solutions for serious disease. Our member organizations are united in this unprecedented collaboration of technology, science, and medicine. Our Vision: To save lives by creating an unprecedented collaboration of technology, science and medicine. Our Mission: We implement advanced genomic research and integrate our findings with world-class technologies and physician-scientists in order to help solve diseases. We harness the diversity of New York’s institutions and people to drive scientific discoveries that will vastly improve clinical care – ethically, equitably and urgently. We advocate and educate, sharing our findings with the global scientific, medical and thought leadership communities to broaden the reach of the New York Genome Center to help patients in every corner of the world. We create synergies through collaboration to continually innovate and advance our vision. Our Values: • We Are Patient Driven • We “Break the Mold” Through Innovation • We Are Focused on the Greater Good • We Create Synergies Through Collaboration • We Translate Research Urgently to Help People Genomics: NYGC’s Integrated Genomics include experimental design assistance, sample quality control processes, library preparation, sequencing, extensive data quality control, bioinformatics, and data storage. 101 Avenue of the Americas 7th Floor | New York, NY 10013 | www.nygenome.org | 888.415.NYGC (6942) Clinical Initiatives: Glioblastoma Outcomes Trial: Glioblastoma (GBM) is a complex and confounding disease that works quickly and whose prognosis has not seen much improvement in 30 years; patients with aggressive glioblastoma, and who respond to treatment, have a median survival rate of about 14 months.
    [Show full text]
  • Research Highlights 2020
    systemsbiology.columbia.edu Department of Systems Biology Columbia University Irving Medical Center Research Highlights Addressing the Global Pandemic New Tumor-Specific Molecular Interaction Maps 2019-2020 Capture Complexity of Cancer Networks Dynamics of Gut Bacteria Follow Ecological Laws Ancient Part of Immune System May Underpin Severe COVID COLUMBIA UNIVERSITY DEPARTMENT OF SYSTEMS BIOLOGY Table of Contents Inside this issue, learn about the latest research, noteworthy grants and milestones from the Department of Systems Biology. Systems Biology Faculty Address the Global Pandemic Q+A: Raul Rabadan, PhD Find out how several faculty in the department are rapidly As the author of Understanding Coronavirus, Dr. Rabadan has set out to provide readers an accessible overview that quells addressing the novel SARS-CoV-2 virus. ............................Page 3 misinformation about the novel virus, its origin, causes, and spread. Page 10 Systems Biology COVID Volunteers .................................................................................................... During the spring COVID-19 outbreak in New York City, four New Faculty: Mohammed AlQuraishi, PhD members of the systems biology department were especially active in a volunteer effort called Columbia Researchers A warm welcome to Dr. Mohammed AlQuraishi, who Against Coronavirus. ........................................................................Page 4 joined the department as an assistant professor and as a member of Columbia’s Program for Mathematical Genomics. Page
    [Show full text]
  • New York Genome Center Officially Launches in Manhattan
    New York Genome Center Officially Launches in Manhattan By Matt Jones NEW YORK (GenomeWeb News) – The New York Genome Center officially launched at its new facility in downtown Manhattan today with a ribbon-cutting ceremony that featured statements by NYGC President and Scientific Director Robert Darnell and New York City Mayor Michael Bloomberg. Nearly two years after the plan for the center was unveiled, NYGC has effectively completed the build-out of its seven-floor, 170,000-square-foot facility, and it is currently working to hire the bioinformatics, genome sequencing, and lab specialists who will fill the space. The center is actually a consortium of 16 institutional members, mostly academic research institutions and hospitals from the New York region, as well as Jackson Laboratory, and each of the faculty members on its staff will hold joint appointments with both NYGC and their home institution. The ceremony this morning kicked off a two-day scientific symposium at the center that will feature talks by luminaries in the genomics world, including National Cancer Institute Director Harold Varmus and Rockefeller University President Marc Tessier-Lavigne, among others. The center so far has reeled in $140 million from its members, philanthropic organizations, and funding agencies, including the Simons Foundation, the Alfred P. Sloan Foundation, and Bloomberg Philanthropies, as well as the New York City Economic Development Corporation, the Partnership for New York City, and the Empire State Development Corporation. Mayor Bloomberg, who noted that his administration provided $5 million in support to help build the NYGC, said he sees the center as part of an effort to help build up the city's bioeconomy and tech sector.
    [Show full text]
  • ! ! Jennifer Baldwin Joins New York Genome Center As
    ! JENNIFER BALDWIN JOINS NEW YORK GENOME CENTER AS CHIEF OPERATING OFFICER New York, NY (March 3, 2014) – The New York Genome Center (NYGC) announced that Jennifer Baldwin has joined the organization as Chief Operating Officer. Baldwin brings extensive management experience in the field of genomics, having previously served as a senior leader of the Broad Institute, overseeing high-throughput DNA sequencing and other related activities. “As COO, Jen’s expertise in the industry will strengthen NYGC’s strategic growth as a leading academic institution focused on advancing genomic research,” said Robert B. Darnell, President, CEO and Scientific Director of NYGC. “The NYGC team looks forward to working with Jen as she implements her genomic expertise to benefit our consortium.” “I am delighted to be joining such a unique organization in Manhattan where philanthropy, technology and science are converging,” said Baldwin. “NYGC is harnessing the power of clinical genomics in a transformative model to drive discoveries and improve patient care.” Baldwin originally joined the field of genomics as an early contributor to the Human Genome Project. She went on to lead the Broad Institute’s Genome Sequencing Platform and served in a variety of additional organization development and management roles during the foundational years of the Broad Institute. She received an MBA from Yale School of Management and a Bachelor of Science in Biology from James Madison University. # # # About the New York Genome Center The New York Genome Center (NYGC) is an independent, nonprofit at the forefront of transforming biomedical research and clinical care with the mission of saving lives. As a consortium of renowned academic, medical and industry leaders across the globe, NYGC focuses on translating genomic research into clinical solutions for serious disease.
    [Show full text]
  • Whole-Genome Bisulfite Sequencing with Improved Accuracy and Cost
    Downloaded from genome.cshlp.org on August 15, 2018 - Published by Cold Spring Harbor Laboratory Press Method Whole-genome bisulfite sequencing with improved accuracy and cost Masako Suzuki,1,3 Will Liao,2,3 Frank Wos,2,3 Andrew D. Johnston,1 Justin DeGrazia,2 Jennifer Ishii,2 Toby Bloom,2 Michael C. Zody,2 Soren Germer,2 and John M. Greally1 1Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA; 2New York Genome Center, New York, New York 10013, USA DNA methylation patterns in the genome both reflect and help to mediate transcriptional regulatory processes. The digital nature of DNA methylation, present or absent on each allele, makes this assay capable of quantifying events in subpopu- lations of cells, whereas genome-wide chromatin studies lack the same quantitative capacity. Testing DNA methylation throughout the genome is possible using whole-genome bisulfite sequencing (WGBS), but the high costs associated with the assay have made it impractical for studies involving more than limited numbers of samples. We have optimized a new transposase-based library preparation assay for the Illumina HiSeq X platform suitable for limited amounts of DNA and providing a major cost reduction for WGBS. By incorporating methylated cytosines during fragment end repair, we reveal an end-repair artifact affecting 1%–2% of reads that we can remove analytically. We show that the use of a high (G + C) content spike-in performs better than PhiX in terms of bisulfite sequencing quality. As expected, the loci with trans- posase-accessible chromatin are DNA hypomethylated and enriched in flanking regions by post-translational modifications of histones usually associated with positive effects on gene expression.
    [Show full text]
  • New York Genome Center Is Honored by Columbia University Medical Center and New York-Presbyterian Health Sciences Advisory Council
    New York Genome Center is Honored by Columbia University Medical Center and New York-Presbyterian Health Sciences Advisory Council Robert Darnell, MD, PhD Lee Goldman, MD, Bob Darnell and Andria Castellanos The New York Genome Center received the Columbia University Medical Center and New York-Presbyterian Health Sciences Advisory Council (HSAC) Award for Distinguished Service at the HSAC annual meeting on October 22. The Award, the HSAC’s highest honor, is given to individuals who have shown a strong and committed interest in health sciences and whose influence and reputation have made a significant impact on the public concerning healthcare. Previous recipients, since 1990, have included Ms. Barbara Walters, Mr. and Mrs. Robert Wright, The Honorable Edward I. Koch, Dr. Sanjay Gupta, Dr. Michael DeBakey, Mr. Derek Jeter and Mrs. Katharine Graham. Robert Darnell, MD, PhD, President, Chief Executive Officer and Scientific Director of NYGC, accepted the award from Stuart J. Rabin, Chairman of the Council; Lee Goldman, MD, Harold and Margaret Hatch Professor of the University, Dean of the Faculties of Health Sciences and Medicine, Chief Executive, Columbia University Medical Center, Columbia University, and Andria L. Castellanos, MBA, Group Senior Vice President & Chief Operating Officer, NewYork-Presbyterian/Columbia University Medical Center. HSAC’s mission is to increase recognition and resources for NewYork- Presbyterian/Columbia and Columbia University Medical Center’s programs in healthcare, training, research and service. “The New
    [Show full text]
  • Mapping and Characterization of Structural Variation in 17,795 Human Genomes
    Article Mapping and characterization of structural variation in 17,795 human genomes https://doi.org/10.1038/s41586-020-2371-0 Haley J. Abel1,2,68, David E. Larson1,2,68, Allison A. Regier1,3, Colby Chiang1, Indraniel Das1, Krishna L. Kanchi1, Ryan M. Layer4,5, Benjamin M. Neale6,7,8, William J. Salerno9, Received: 29 December 2018 Catherine Reeves10, Steven Buyske11, NHGRI Centers for Common Disease Genomics*, Accepted: 18 May 2020 Tara C. Matise12, Donna M. Muzny9, Michael C. Zody10, Eric S. Lander6,13,14, Susan K. Dutcher1,2, Nathan O. Stitziel1,2,3 & Ira M. Hall1,2,3 ✉ Published online: 27 May 2020 Check for updates A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline1 to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants afect the dosage or structure of 4.2 genes and account for 4.0–11.2% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2% of rare alleles genome-wide, with predicted deleterious efects that are equivalent to loss-of-function coding alleles; approximately 90% of such structural variants are noncoding deletions (mean 19.1 per genome).
    [Show full text]
  • Frequently Asked Questions (FAQ)
    Frequently Asked TM Questions (FAQ) Q. What is the New York Genome Center (“NYGC”)? A. The New York Genome Center (“NYGC”) is an independent, nonprofit consortium of leading academic medical centers, research universities and commercial organizations that will transform biomedical research and clinical care in New York through the creation of what will become one of the largest bioinformatics and genomics facilities in North America. Equipped with the latest molecular scanning technologies, the NYGC will enable the most prestigious research institutions in the greater New York region to share data and resources on an unprecedented scale, helping to accelerate new discoveries, diagnostics, and treatments for human diseases. Through this national and international collaboration, NYGC can have an impact globally. Q. How is genomics impacting science and medicine? A. The technology that launched the biomedical revolution and made the Human Genome Project possible – DNA sequencing – is once again on the cusp of transforming biomedical research and healthcare. National thought leaders have forecast that the cost of sequencing an entire human genome will soon be reduced to $1,000 or less. This advance will pave the way for each person’s genome to be sequenced as part of the standard of care, leading to a revolution in the practice of medicine. This revolution is unfolding in a variety of ways. The cost and duration of genomic sequencing is rapidly falling, the federal government is making a strong commitment to support full implementation of electronic health records that are a requisite for genomic medicine, and the number of targeted drugs and companion diagnostics entering clinical practice continues to rise.
    [Show full text]