Center for Cancer Genomics Services

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


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

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.