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Center for Cancer Genomics

  • The Center for Cancer Genomics (CCG) is part of the Precision Cancer Medicine effort at Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Boston Children's Hospital. CCG's mission is to facilitate the design, execution, and analysis of cancer research projects through collaborations with investigators. We continually develop and adapt new technologies to accelerate discoveries in cancer genomics and apply these discoveries to improve personalized patient care.

    The three main components of our mission are:

    • Technology development: To develop new technologies for the analysis of cancer genomes.
    • Collaborative research: To provide access to these genomic technologies to basic, translational, and clinical investigators at Dana-Farber and beyond.
    • Translation: To translate technologies to the clinical setting.

  • CCG process illustration

  • We focus on the discovery of genomic alterations in human cancer and evaluation of their clinical significance for the informing diagnosis and treatment. We use Illumina next-generation sequencing platforms to perform bulk DNA and RNA sequencing. We also perform a variety of single-cell transcriptomic workflows using 10x Genomics and Illumina sequencing technologies. Using our workflows and expertise, we are able to detect a range of genomic alterations, including:

    • Single nucleotide variants
    • Insertions and deletions
    • Chromosomal rearrangements: translocations, inversions, duplications
    • Copy number changes
    • Expression changes
    • Allele-specific expression
    • Detection and quantification of gene fusion
    • Differential gene expression analysis
    • Single-cell transcriptomics

    An integral aspect of the Center's mission is working toward more effective clinical trial designs, in which patients with similar genetically defined cancers will receive drugs designed to target specific genetic aberrations. In addition to the principal areas indicated above, CCG is available to assist collaborators with funding (e.g., grant submissions), experimental design, and coordination of each project through the appropriate channels.

    Collaborations Welcome

    Our research and development group continuously evaluates and develops genomic technologies for both research and clinical use. From our inception, we have collaborated with research investigators to develop new genome discovery tools, and we welcome investigators and clinicians to contact us about new avenues of research that we can help facilitate. We provide a host of services that include project design, sequencing library construction, custom design and validation of hybrid capture gene panels for targeted sequencing, single-cell workflows, bioinformatic analysis, and more.

  • Our Research Focus

    researchers at computers in a lab

    Our Services

    CCG performs a variety of genomics assays, from targeted hybrid capture to whole-genome DNA sequencing, RNA sequencing, and single-cell sequencing on a multitude of sample types (e.g., fresh-, frozen-, and FFPE-derived nucleic acids). In addition to our standard suite of services, CCG often takes part in collaborations to develop and evaluate new NGS assays and techniques.
    lab equipment

    Bioinformatics

    The group consists of data analysts, software engineers, and computational biologists and has developed analytical pipelines to manage, store, annotate, and report on data produced by the Illumina sequencing platforms. We employ vendor, third-party, and in-house tools and databases to provide data-quality metrics, integrated candidate reports, and relevant biological and clinical context for experimental platform data.
    test tubes

    CSIR Biopsy Collections

    In addition to sample collection for Center for Cancer Genomics (CCG) collaborations, CCG's Pathology Team is integrated into the research biopsy collection process for all Dana-Farber research biopsies performed at Brigham and Women's Hospital Cross-Sectional Interventional Radiology (BWH CSIR). This initiative is called the DFCI CSIR Biopsy Collection Initiative, or DCBC.
    researcher looking at slide

    Profile

    CCG is the research and development group within the Precision Cancer Medicine effort at Dana-Farber and its partner hospitals. Working with Profile, CCG evaluates and develops new techniques and assays designed to increase our ability to detect genomic alterations which will better inform clinicians about which therapeutic avenues are most likely to positively impact cancer patients.
    researcher behind glass in lab

    Research & Development

    CCG's current research and development areas include improvements to single-nucleus RNA-Seq workflow; piloting single-nucleus epigenome and transcriptome profiling; cell-free DNA; RNA-seq from FFPE material; and Oxford nanopore sequencing.