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Center for Cancer Genomics Services

Technologies for Both Research and Clinical Use

The Center for Cancer Genomics offers a variety of bulk RNA/DNA and single-cell/nucleus sequencing and data analysis solutions. Please email the Associate Director, Dr. Aaron Thorner, if you have any questions or if you’d like to begin a project.

    CCG performs a variety of genomics assays, from targeted hybrid capture to whole-genome DNA sequencing, RNA sequencing, and single-cell/nucleus 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. As part of this process, we work with investigators in forging a research and development proposal and can assist in all aspects of research, including procurement of funding (e.g., grant submissions).

    Sample Types Accepted

    • FFPE
    • Fresh tumor
    • Frozen tumor
    • Blood
    • Cell-free DNA (cfDNA)
    • Cultured Cell-line

    DNA Sequencing and Library Preparation (Illumina Platform)

    • Custom hybrid capture bait set design
    • Whole Exome sequencing (WES)
    • Whole Genome sequencing (WGS)
    • Pre-designed hybrid capture bait panels (e.g., OncoPanel) 

      CCG has extensive experience with various single cell technologies. CCG performs both single-cell RNAseq (scRNAseq) and single-nucleus RNAseq (snRNAseq) on fresh and frozen tissue samples, respectively. Our workflows include:

      • Fresh tissue dissociation for scRNAseq, including optimization and validation of new tissue dissociation protocols
      • Nuclei isolation from frozen tissue for snRNAseq
      • Single-cell and single-nucleus RNA-Seq using 10x Genomics platform, including:
        • 5' gene expression (GEx)
        • Multiome (3' GEx + ATACseq)
        • TCR/BCR sequencing  
        • Fixed RNA Profiling: FLEX probe-based GEx for fixed (e.g., FFPE) samples 

        CCG offers both poly-A enrichment and ribodepletion workflows, which are fully automated.  

          Liquid biopsies represent a readily accessible sample type upon which molecular profiling with NGS can be performed. CCG has worked with several investigators to develop library construction and hybrid capture assays tailored to the needs of cfDNA. All of our library adapters consist of unique, dual-matched barcodes containing a unique molecular identifier (UMI) which allow us to:

          • Reduce barcode cross-talk
          • Form UMI read families to identify PCR errors
          • Discriminate between unique molecules of identical sequence and true PCR duplicates 

            Our team of Biospecimen Coordinators and Project Managers can help optimize sample collection and project management for your study.

            • Project management: The Project Management Team can help create a streamlined infrastructure for sample acquisition, data collection, and overseeing tissue samples from biopsy to research assay.
            • Sample collection and triaging: CCG's experienced Biospecimen Acquisition Team can collect and triage tissue samples to allow for the maximum number of samples going to research, while ensuring high-quality samples are sent for clinical testing. The Biospecimen Coordinators are experienced at preserving and transporting tissue for many research assays, including scRNAseq, snRNAseq, bulk RNAseq, WES, and WGS as well as following sponsor or protocol-specific requirements.

              CCG's Biospecimen Acquisition Team is also responsible for research biopsy collections for all Dana-Farber research biopsies performed at Brigham and Women's Hospital Cross-Sectional Interventional Radiology (BWH CSIR). This initiative is called the Dana-Farber CSIR Biopsy Collection Initiative, or DCBC.

              DCBC was created to streamline research collections in CSIR by having a dedicated team to manage all research biopsy collections. Our team of Biospecimen Coordinators is trained to effectively communicate the specific research study needs to the clinical team in CSIR and to allocate research samples according to the unique priority lists and requirements for each study. DCBC has created a consistent, organized, and responsive process for procuring research samples on behalf of all Dana-Farber research protocols.

              If you have any questions about Dana-Farber CSIR Biopsy Collections, please email DFCI_Bx_CollectionsOPS@dfci.harvard.edu.

              If you are a Dana-Farber researcher who wishes to access DCBC resources, visit the BWH CSIR Research Biopsies website.

                Our bioinformatics team is well-equipped to go beyond the standard quality control (QC) analyses typically performed for our genomic research offerings. While these core QC steps ensure high-quality data, most research projects require more advanced, customized analyses tailored to specific scientific questions and project goals. By offering more focused analyses, we can address the unique requirements of each study. This may include refining variant detection, identifying rare or complex structural rearrangements, enhancing cell-type or gene expression profiling, or integrating multi-modal datasets. Custom analyses allow researchers to derive deeper insights from their data and optimize results for publication or downstream applications.

                Our team can engage in an iterative process, working closely with researchers to refine and adapt the analyses as new data or preliminary findings become available. This approach ensures that the computational strategies evolve in line with project needs, potentially uncovering novel biological insights that would be missed in a standard pipeline. These bespoke services are offered on a fee-for-service basis, allowing us to allocate the necessary resources and expertise to deliver high-quality, customized results.  Please inquire if you are interested in learning more. 

                  The clinical genomics analysis team collaborates with oncologists and scientists at Dana-Farber on projects that utilize next-generation DNA and RNA sequencing data, both from internal sources and external datasets. Together with our collaborators, we help acquire data and develop analysis plans. We create custom code tailored to each project and offer support with manuscript writing. Additionally, as part of our projects, we provide training for researchers interested in learning how to code their own analyses.

                  Contact the Center for Cancer Genomics

                  CCG Associate Director: Aaron Thorner
                  DCBC Biopsy Collections: Karla Helvie
                  Bioinformatics: Tony Anselmo

                  For general questions: 
                  617-582-7253 or aaron_thorner@dfci.harvard.edu