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CCGD Services and Technology Platforms

  • researchers at computers in a lab
  • The Center for Cancer Genome Discovery (CCGD) can provide collaborators with comprehensive services that include personal consultation on the type of sequencing most suitable for project needs, preparation of sequencing libraries, and custom bait set design for targeted sequencing. Additionally, sequencing libraries prepared by CCGD are provided with bioinformatic analysis.

    Sample types accepted include collaborator prepared libraries or purified nucleic acid, including difficult samples such as cfDNA and FFPE nucleic acid.

    Over the years, many of our collaborators have brought us archived FFPE samples for next-generation sequencing. As a result, we have acquired a great deal of experience with sub-optimal FFPE samples and have developed and validated techniques that consistently allow us to obtain high-quality data.

    In addition to our standard suite of services, CCGD 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).

  • gene palette illustration

  • Sample Types Accepted (Purified Nucleic Acid)
    • Cell free DNA (cfDNA)
    • Cell-line
    • FFPE
    • Fresh Tumor
    DNA Sequencing and Library Preparation (Illumina Platform)
    • Amplicon Sequencing
    • Exome Sequencing
    • Genome Sequencing
    • Pre-designed Hybrid Capture Bait Panels (Oncopanel)
    • Custom Hybrid Capture Bait Set Design
    Cell Free DNA (cfDNA) Sequencing

    Liquid biopsies represent a readily accessible sample type upon which molecular profiling with NGS can be performed. CCGD has worked with several investigators to develop library construction methods tailored to the needs of cfDNA.

    We've recently replaced our library adapters with dual-matched barcode adapters 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

    Current efforts are directed towards development of custom cfDNA hybrid capture gene panels.

    RNA Sequencing and Library Preparation (Stranded RNA-Seq)

    We are currently refining our library prep protocol to use 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
    Contact us to start collaborating