Skip Navigation

Visiting Dana-Farber? See our prescreening and mask requirements.

Center for Cancer Genomics Services

  • researchers at computers in a lab

  • Bulk and Single-Cell Genomics

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

    DNA Sequencing and Library Preparation (Illumina Platform)

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

    Cell-Free DNA (cfDNA) Sequencing

    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

    RNA Sequencing and Library Preparation (Stranded RNA-Seq)

    CCG offers both poly-A enrichment and ribodepletion workflows, which are fully automated. We are continuously improving our library construction techniques on FFPE samples and will be designing custom hybrid capture bait sets that will target both messenger RNA and fusion transcripts resulting from genomic rearrangements:

    • Expression analysis
    • Fusion transcript detection

    Single-cell Sequencing

    Our Innovation Lab 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 3' gene expression, 5' gene expression, and TCR/BRC sequencing

  • specimen collection to profiling and sequencing to analysis

  • Sample Collection and Project Management

    Our teams of Pathology Technicians 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 pathology technicians 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 PTs are experienced at preserving and transporting tissue for many research assays, including scRNAseq, snRNAseq, WES, and RNAseq.

  • sample collection diagram