Accelerating the future of liquid biopsies with digital PCR and next-generation sequencing

The term liquid biopsy in the context of oncology refers to the real-time monitoring of the dynamic alterations of a tumor through detection of cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), or exosomes in blood or other fluid samples.

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As a complementary, noninvasive option to traditional biopsies, liquid biopsies enable the discovery of highly specific and sensitive biomarkers and can be used for dynamic and timely monitoring of tumor progression. At Thermo Fisher Scientific we are committed to developing robust sample preparation solutions for cell-free nucleic acids and highly sensitive liquid biopsy assays utilizing both digital PCR (dPCR) and targeted next-generation sequencing (NGS) to enable cancer driver identification, serial monitoring, and recurrence detection. Through the powerful combination of customizable or pre-designed targeted NGS panels, which provide comprehensive detection of cancer-related mutations, and dPCR assays, which offer rapid monitoring of a targeted set of mutations, liquid biopsies may soon become the future standard in cancer management.

Poster: Orthogonal Verification of Oncomine cfDNA Data with Digital PCR Using TaqMan dPCR Liquid Biopsy Assays

The wide-angle view provided by NGS panels, combined with digital PCR’s zoomed-in precision detection of DNA provide a more complete picture of the cancer genome. Download our poster to see how Oncomine cell-free nucleic acid assays and TaqMan dPCR Liquid Biopsy assays can be used in a complementary manner for liquid biopsy analysis.

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Explore liquid biopsy solutions for discovery, monitoring, and recurrence

Discover cancer driver mutations

Analyze cell-free nucleic acid (cfNA) from cell-free DNA and RNA to identify primary cancer driver and resistance mutations using predesigned Oncomine cell-free nucleic acid assays or customizable Ion AmpliSeq HD panels.

Monitoring response and resistance

Orthogonally verify NGS results and/or monitor cancer-driver and therapy-resistant mutations using TaqMan Liquid Biopsy dPCR Assays.

Discover new driver mutations at recurrence

Identify new cancer driver and resistance mutations related to recurrence using Oncomine cell-free nucleic acid assays.

Liquid biopsy solutions and workflows

We offer complete liquid biopsy solutions from sample preparation through data analysis and interpretation. Learn more about our sample preparation kits and NGS, dPCR, and real-time PCR-based liquid biopsy solutions below.

Sample preparation

Cell-free nucleic acid extraction

Exosome isolation

  • Dynabeads products—enrich for intact exosomes from a variety of starting samples or further purify exosomes into specific subpopulations using our flexible and scalable reagents

Master mix for dPCR

  • QuantStudio 3D Digital PCR Master Mix v2—enables accurate, sensitive, and precise dPCR data from TaqMan dPCR assays on the QuantStudio 3D Digital PCR System with a master mix specifically formulated to help ensure robust PCR amplification of single copy templates

Mutation detection

NGS assays and instruments

  • Ion AmpliSeq HD panels for targeted NGS—amplicon-based library preparation technology that gives you the power to design your own panels and find variants with a low limit of detection (down to 0.1% for cfDNA). This revolutionary technology enables researchers to routinely get answers when ultra-high sensitivity is required, such as when detecting low-frequency alleles in ctDNA.
  • Oncomine Cell-Free assays for liquid biopsy clinical research—identify known somatic mutations, CNVs, and fusion genes with targeted NGS assays that are tumor-type specific for breast, colon, or lung cancer, in addition to a broad-coverage pan-cancer assay that simultaneously detects DNA and RNA variants across multiple cancer types
  • Ion GeneStudio S5 next-generation sequencing systems—rapidly and efficiently run small and large projects across multiple research applications, with the simplest sample-to-data NGS workflow

dPCR assays and instruments

  • TaqMan Liquid Biopsy dPCR assays—detect and quantify known cancer-related and therapy-resistant mutations with these highly sensitive, fully wet-lab verified TaqMan assays available in a single-tube format
  • QuantStudio 3D Digital PCR System—enables accurate, sensitive, and precise dPCR data on the QuantStudio 3D Digital PCR instrument

castPCR assays and instruments

Data analysis and reporting

NGS analysis and reporting software

  • Torrent Suite Software—get customizable, automated sequencing data analysis including seamless integration with Ion Reporter Software for downstream processing
  • Ion Reporter Software—obtain fast, simple variant calling and annotation of SNPs, indels, CNVs, and fusions
  • Oncomine Reporter—summarize relevant cancer drivers in a simple report that links sample-specific variants to labels, guidelines, and current global clinical trials

dPCR analysis software

castPCR analysis software

  • Mutation Detector Software—determine the mutation status of samples with automated mutation detection data analysis software