• GENOMICS OVERVIEW

    Integrated Genomics

    NYGC advances health-relevant research by helping researchers and physicians generate, manage, and understand nucleic acid sequence data, through sequencing and bioinformatics services, interpretive collaboration and training.

     

    Such work has entailed sequencing and analyzing thousands of human exomes, hundreds of human whole genomes, and much other human and non-human RNA and DNA, via world-class infrastructure for sequencing, computation and collaboration.

     

    NYGC’s Integrated Genomics Solution includes experimental design assistance, sample quality control processes, library preparation, sequencing, extensive data quality control, bioinformatics, and data storage.

     

    Clinical

    NYGC is an independent, nonprofit research organization that is not approved by the FDA to interact directly with consumers or patients for the purposes of diagnosing conditions in the cure, mitigation, treatment or prevention of disease.

     

    However, NYGC is in the process of establishing a clinical lab, which will offer Next Generation Sequencing (NGS), based testing for rare diseases and cancer.

     

    NYGC’s clinical laboratory diagnostic services will be accessible to physicians on behalf of their patients.

     

    Research Sequencing Inquiries

     

    Email: service@nygenome.org

     

    Phone: 646-977-7222

     

     

     

    Clinical Sequencing Inquiries

     

    Email: clinical@nygenome.org

     

    Phone: 646-977-7171

     

    A clinical project manager can share information about our offerings and how to order them.

  • COLLABORATOR STORIES

    The collaboration with NYGC has been fantastic. They helped me prepare our initial grant application; once we secured the NIH funding, they moved quickly to accomplish a very large and high profile project to study asthma and drug response by performing whole genome sequencing of 1500 minority children. They hosted our two lead analysts for two weeks so that we could incorporate the new technical methods at UCSF. They even went the extra mile by providing additional computational power for our analyses. Finally, on my personal visit to NYGC, it was clear to me that they are a highly capable and professional operation with deep intellectual talent.

    Esteban Burchard, MD, MPH

    Professor, Departments of Bioengineering & Therapeutic Sciences and Medicine
    University of California, San Francisco
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    Bioinformatics Analysis

    Our team of bioinformaticians aims to develop, maintain and improve our analysis pipelines by leveraging the large amounts of sequencing data we produce. We work on estimating the sources of errors and variability in the data, defining methods to correct them, both computationally and on the lab side. We are also continually evaluating and benchmarking available tools, refining best practices to analyze and combine results, and are developing novel tools and methods.

    We are also supporting our CLIA lab by providing the expertise in clinical interpretation of constitutional and cancer genomics.

    Expertise
    Our diverse team of bioinformatics scientists has expertise in:

    • Statistical and population genetics
    • Cancer genomics
    • Expression analysis
    • Epigenomics and functional genomics
    • Metagenomics
    • Clinical interpretation

    Process
    A typical project is initiated with one of the sequencing project managers. Our bioinformatics scientists are consulted to further refine the experimental design, analytic plan, and project deliverables.
    The bioinformatics team performs standard and project-specific quality control, and analysis of sequencing data (e.g., differential expression and functional enrichment for RNA-Seq, variant annotation and interpretation for genome and exome sequencing, and somatic variant—both SNV and structural variant—for cancer). Results are delivered via our web interface or APIs and are stored and accessible for a period of time as part of NYGC’s Integrated Genomics.

    Clinical Interpretation
    As exome and genome sequencing data are processed and genomic variation between the sample and a reference are defined, annotated, and compared to existing databases, our bioinformatics scientists contribute to the last step of the analysis: clinical interpretation.

    This usually requires ranking and filtering of putative candidates, manual curation, and functional validation (when possible) of our findings. NYGC’s analysis alleviates the need for the investigator to perform the standard computationally intensive analysis steps, thus freeing up time to focus on the biology.

     

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    Consulting

    The New York Genome Center can provide researchers with the help and support to make even the most complex project successful. We’ve assembled a dedicated group of scientists to guide researchers at any project phase or from start to finish. At any point in the research process, a researcher may meet with our scientists to answer questions regarding experimental design, project status, and analysis options. After the data are delivered, our team will explain the analysis process and any applicable next steps. Please contact us to discuss the range of consulting options available.

     

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    Experimental Design

    NYGC’s Sequencing Program Managers are available to discuss all aspects of a project:

    • Sample quality control
    • Sample submission process
    • Cost of sequencing options
    • Turnaround time
    • Formats and options for data analysis and delivery

    Our scientific staff has extensive experience with a wide range of sequencing applications and protocols, and can help guide the experimental design process. Bioinformatics experts are brought into the discussion as needed to consult on data formats and analysis modalities.

     

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    High Performance Computing and Data Storage

    The job of NYGC’s research computing group is to use technology to bolster scientific research. We combine high performance computing, networking, and data storage to meet the dynamic needs of science at NYGC. NYGC has leveraged lessons learned from the first decade of high-throughput genomics to deploy infrastructure with unparalleled scalability and connectivity. 

    High Performance Computing

    The majority of computing at NYGC is performed on our research computing farm, or compute cluster. That cluster currently consists of 4400 cores. Our standard server contains 16 to 24 CPU cores, 256GB of RAM, and 5TB of local storage. .

    Massively Parallel Storage

    We currently have 11PB of EMC Isilon massively parallel storage. That disk farm can handle thousands of processes concurrently, without affecting performance. Data remains in this “tier 1”storage for a period of time commensurate with the duration and complexity of the project. Typically, 3 months of storage is included in the price of sequencing.

    Our permanent archival storage is a combination of disk and tape. The tape system is automated and will retrieve files to disk automatically if access to those files occurs. We are currently building out a second tier of active storage to precede archival, to move rarely-used data to object storage, keeping it available online, before moving to tape.

     

     

    Networking:

    Network connectivity between the storage cluster and the compute cluster is 160Gb, providing throughput capacity far above our current needs to ensure fast I/O for all computation. Our systems are architected to scale easily.

    We currently provide 10Gb connectivity to each of Internet2, commodity Internet, and Nysernet, allowing our users to move data quickly, or distribute their computational and storage needs among our data centers and theirs.

    Data Availability and Durability

    Our archive site is currently in the state of Washington, on the Columbia River. We are planning a second archival site, and possibly an additional computational site at the University of Buffalo (on Niagara Falls, for cheaper power).

    We currently produce 8-10 terabytes of raw data per data, and use thousands of hours of compute per terabyte.

    BioInformatics Commons:

    To allow our collaborators to make use of this scalable, high-performance resource, we are building a “BioInformatics Commons” that will allow users to perform their analysis on our compute farm, integrate with other data, make use of our available analysis tools, and store data here long-term, should they desire. The Commons is currently in beta test, with limited functionality available for users requesting it. We expect a more complete version by year-end. Pricing is per core-hour and per terabyte-month.

     

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    Sequencing

    At the New York Genome Center, sequencing is much more than processing samples.

    NYGC’s scientists have developed protocols and procedures designed to ensure that projects are completed in accordance with rigorous quality standards. Whether this is a researcher’s first project or an ongoing multi-year study, our team will work to ensure that every step in the process is accomplished smoothly and efficiently.

    Sample QC and Library Prep
    Upon receipt of the samples, NYGC performs an initial DNA/RNA quality control (QC) assessment to evaluate the concentration and quality for each sample. This is an interactive process with an open dialogue between the researcher and NYGC to ensure that all samples pass the initial stringent QC step prior to library prep and sequencing.

    Throughout the library preparation process, quality control steps monitor each sample to ensure high quality sequencing libraries.

    Project Initiation
    NYGC’s Sequencing Project Managers guide researchers through the experimental design phase. The team can discuss the design of the project and how best to utilize technology in research. The team can also assist the grant
    writing process with text about the particulars of an assay and the NYGC facility and team, and supply letters of support.

    Fee-for-Service Terms and Conditions
    Sample Submission
    Once a purchase order has been submitted, NYGC will ship barcoded sample submission tubes and appropriate packaging for samples to be delivered to the NYGC laboratory.

    During the sample submission process, and throughout the life of the project, we are available to answer questions.

    Sequencing
    NYGC supports the following core offerings:

    • Human Whole Genome Sequencing, including access to the HiSeq X sequencing system
    • Exome Sequencing
    • RNA Sequencing

    In addition, we can support customized options, including:

    • ChIP seq
    • Small RNA seq
    • Non-human genome
    • Others by request

     

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    COLLABORATOR STORIES
    • The collaboration with NYGC has been fantastic. They helped me prepare our initial grant application; once we secured the NIH funding, they moved quickly to accomplish a very large and high profile project to study asthma and drug response by performing whole genome sequencing of 1500 minority children. They hosted our two lead analysts for two weeks so that we could incorporate the new technical methods at UCSF. They even went the extra mile by providing additional computational power for our analyses. Finally, on my personal visit to NYGC, it was clear to me that they are a highly capable and professional operation with deep intellectual talent.

      Esteban Burchard, MD, MPH

      Professor, Departments of Bioengineering & Therapeutic Sciences and Medicine
      University of California, San Francisco
    • The service NYGC has provided has just been outstanding. Speaking from the people who use the data on the backside, the end product is exceptional as well. NYGC has been very responsive to our needs and better than most. There has been great communication and open discussions, and it’s easy to contact the right people.

      Keri Zabokrtsky and Leonard Sender

      Hyundai Cancer Institute at Children’s Hospital Orange County
    • Collaboration is the key to advancing science and improving lives. Through a generous $1,000,000 grant from the W.M. Keck Foundation, we are working with the New York Genome Center to better understand why Huntington’s disease strikes some people when they are very young and others when they are old. We're hunting for modifier genes, genes that can push Huntington's out of the normal lifespan.

      Nancy Wexler, PhD

      Higgins Professor of Neuropsychology, Departments of Neurology and Psychiatry, Columbia University Medical College President, The Hereditary Disease Foundation
    • The New York Genome Center works as side-by-side collaborators from the beginning to the end of the project! No problem is too large or insolvable.

      Richard Mayeux, MD, MSc

      Sergievsky Professor of Neurology, Psychiatry & Epidemiology
      Chair, Department of Neurology
      Columbia University Medical College