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Contact Us

GENOMIC RESEARCH SERVICES

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    NYGC Project Management Team
    The NYGC Project Management team is the direct point of contact for investigators from initial project inquiry through data delivery. Each project is assigned a dedicated project manager that tracks and communicates updates on project progress and timelines. Our team of trained scientists can expertly answer your questions on a wide range of sequencing technologies, protocols, applications, analyses, and guide your project to meet expectations. We are experienced in project designs under fee-for-service, collaborative, grant funding, and sub-contract models and will work with investigators to find the model that best fits the project.
    Contact us at service@nygenome.org for more details. PROJECTREVIEW DATA DELIVERY PROJECT PROGRESS SAMPLE QC SAMPLESUBMISSION QUOTE PROJECTINQUIRY
    Project inquiry: through website, email, or phone call. The project manager will arrange an initial phone call to review study background, design, methodology, deliverables, and pricing.
    Quote: The project manager will issue a quote specifying the services to be provided, including: pricing, sample requirements, analysis, and deliverables. Once accepted by investigator, the project manager will initiate sample submission.
    Sample Submission: through website, email, or phone call. The project manager will arrange an initial phone call to review study background, design, methodology, deliverables, and pricing.
    Sample QC: Once samples are received by NYGC sequencing laboratory, the investigator will receive automated notification by email. When sample QC is complete, the project manager will communicate results to the investigator and any next steps required.
    Project Progress: The project manager will communicate updates on project progress and timelines via email.
    Data Delivery: Data will be delivered through the NYGC collaborator’s portal for download by investigator. Several download options are available to best fit the investigator’s need.
    Project Review: The project manager will coordinate any project discussions and address any questions once data is delivered. At the investigator’s request, the project manager will schedule a meeting to review data and analysis jointly with the bioinformaticians working on the project.
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    Whole Genome Sequencing

    Human – Germline

    • NYGC’s whole genome service provides investigators with high quality whole genome data and analysis at the most competitive rate at a variety of coverages.
    • NYGC has completed thousands of whole genomes on Illumina’s HiSeq X sequencing platform.

    WGS Germline Specifications
    Human – Somatic

    • NYGC’s whole genome cancer service is designed to deliver the highest quality, complete profile to understand the molecular drivers of the cancer.
    • Cancer WGS services include tumor only, tumor-normal and integration with RNA data options at a variety of coverages.

    WGS Somatic Specifications
    Non-Human WGS

    1. NYGC’s non-human whole genome service can be customized to your organism of interest. Past projects have included mouse, rat, bacteria, viral strains, and many other non-model organisms.
    2. De novo assembly is available as an additional service for genomes without a reference.

    Contact us at service@nygenome.org for more details.

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    Whole Exome Sequencing

    Human – Germline

    • NYGC uses Agilent SureSelect capture kits to provides optimal coverage by targeting ~21,000 genes at a variety of coverages.
    • Whole exome sequencing plus 5’ and 3’ untranslated regions is also available and allows interrogation of regulatory genome regions.

    WES Germline Specifications
    Human – Somatic

    • NYGC’s whole exome cancer service applies our state-of-the-art somatic analysis pipeline to either whole exome capture or exome plus untranslated regions to create an in-depth profile of the tumor.
    • Cancer WES services include tumor only, tumor-normal and integration with RNA data options at a variety of coverages.

    WES Somatic Specifications
    Mouse – Germline or Somatic

    • NYGC has workflows to perform mouse specific alignment, variant calling, and annotation, employing either our germline or somatic pipeline.

    Contact us at service@nygenome.org for more details.

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    RNA Sequencing

    Total RNA

    • Total RNA library preparation allows the study of protein coding RNA as well as long ncRNAs, NYGC uses an upfront ribosomal depletion to minimize the presence of rRNA in the sequencing results.
    • NYGC’s high caliber analysis includes gene and transcript quantification, normalization, differential expression, and differential isoform expression with the addition of fusion gene discovery for somatic studies.

    Total RNA Specifications
    mRNA

    • mRNA library preparations uses oligo-dT beads to enrich the polyadenylated RNA molecules in the sample, while preserving strand information.
    • NYGC’s high caliber analysis includes gene and transcript quantification, normalization, differential expression, and differential isoform expression with the addition of fusion gene discovery for somatic studies.

    mRNA Specifications

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    Patient-derived Tumor Xenograph (PDX) Sequencing
    • NYGC has designed analysis pipelines to deliver the highest quality human data from patient derived xenographs. PDX samples can be submitted for any of our Whole Genome, Whole Exome, or RNA sequencing services.

    Contact us at service@nygenome.org for more details.

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    Lane Sequencing

    Overview: NYGC Lane Sequencing Services refers to sequencing of investigator-prepared libraries. NYGC has designed its Lane Sequencing offering to be flexible and support the diverse application needs of the community while maintaining high quality results. We will provide provide lane levele FASTQ files as the deliverable.

    Example Uses of Lane Sequencing

    • Custom Target enrichment panels
    • Single Cell Sequencing
    • Metagenomics
    • ChIP-seq
    • HITS-CLIP
    • ddRAD-seq
    • shRNA screen libraries
    • 16S Libraries

    Lane Sequencing Specifications

     

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    Bioinformatics Analysis

    Overview: NYGC currently runs 11 application-specific fully automated analysis pipelines that process data from instrument through automated annotation. Importantly, these pipeline components have been geared toward reducing compute time for generated data.
    Germline Whole Genome and Whole Exome Analysis

    1. Alignment
    2. SNV and Indel Calling
    3. Structural variant calling
    4. Extended familial analysis

    Cancer Whole Genome and Whole Exome Analysis

    1. SNV and Indel calling
    2. Structural variant calling – includes copy number variants, translocations and other complex variants

    RNA Sequencing Analysis

    1. Differential expression analysis
    2. Functional annotation
    3. Fusion gene discovery

    Additional Analysis

    1. Mitochondrial and Functional analysis
    2. Viral Integration Analysis
    3. Epigenetics analysis pipelines
    4. De novo genome assembly
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    Services in Development

    Overview: NYGC recognizes that one-size doesn’t fit all projects and are constantly in the process of adding additional services to our customers. For other services not listed here, please contact us directly at service@nygenome.org or 646-977-7222.

    Current Services in Development

    1. 10x
    2. Single Cell RNA sequencing
    3. Whole Genome Bisulfite Sequencing
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    Contact Us

    Contact us at service@nygenome.org for more details.