Liquid Biopsy Analysis

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, that run on the GeneStudio, or the Oncomine Precision Assay that runs on the Genexus Integrated Sequencer 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.

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, customizable Ion AmpliSeq HD panels, or the predesigned Oncomine Precision Assay that runs on the Genexus Integrated Sequencer.

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, or the predesigned Oncomine Precision Assay that runs on the Genexus Integrated Sequencer.

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 MagMAX Cell-Free Total Nucleic Acid Isolation Kit—isolate and purify cfDNA and cfRNA from plasma, serum, or urine samples using magnetic bead-based technology MagMAX Cell-Free DNA Isolation Kit—isolate and purify cfDNA from plasma, serum, and urine using magnetic bead-based technology Genexus Cell-Free Total Nucleic Acid Purification Kit—enables automated extraction and quantitation of total nucleic acids from cell-free plasma isolated from whole blood when using the Genexus Purification System Genexus Purification System—automates the extraction of nucleic acids from various sample types, including plasma, whole blood, peripheral blood leukocytes (PBLs), formalin-fixed, paraffin-embedded (FFPE) lysate, fresh or frozen tissue, cultured cells, and bone marrow aspirate 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 Absolute Q DNA Digital PCR Master Mix (5X)—enables accurate, sensitive, and precise dPCR data from Applied Biosystems dPCR assays on the QuantStudio Absolute Q Digital PCR System with a master mix specifically formulated to enable analysis of higher sample volumes and delivers accurate quantification of DNA targets without using a standard curve
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 Oncomine Precision Assay—enables rapid simultaneous detection of biomarkers across 50 genes from liquid biopsy samples, as well as solid tissue samples 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 Ion Torrent Genexus System—automates sample and library preparation, sequencing, analysis, and reporting. The system, along with Genexus Software, works seamlessly, tracking sample information and results automatically. dPCR assays and instruments Absolute Q Liquid Biopsy dPCR Assays—enable reproducible, specific detection of known somatic mutations with wet-lab validated assays capable of detecting down to 0.1% variant allele frequency in genes relevant for cancer research QuantStudio Absolute Q Digital PCR System—enables accurate, sensitive and precise digital PCR data to be collected in as little as 90 minutes with a simple one-step workflow on the QuantStudio Absolute Q Digital PCR System castPCR assays and instruments TaqMan Mutation Detection assays—detect and measure rare amounts of mutated DNA in samples that contain large amounts of normal DNA using TaqMan PCR (castPCR Technology) QuantStudio real-time PCR systems—find the Real-Time PCR instrument that is right for you from our family of QuantStudio real-time PCR systems
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 QuantStudio Absolute Q Digital PCR Software—allows users to set up dPCR runs, control the thermal cycling process, and analyze experiment data such as absolute quantification of rare targets or measuring copy number variation castPCR analysis software Mutation Detector Software—determine the mutation status of samples with automated mutation detection data analysis software

Sample preparation

Cell-free nucleic acid extraction

MagMAX Cell-Free Total Nucleic Acid Isolation Kit—isolate and purify cfDNA and cfRNA from plasma, serum, or urine samples using magnetic bead-based technology
MagMAX Cell-Free DNA Isolation Kit—isolate and purify cfDNA from plasma, serum, and urine using magnetic bead-based technology
Genexus Cell-Free Total Nucleic Acid Purification Kit—enables automated extraction and quantitation of total nucleic acids from cell-free plasma isolated from whole blood when using the Genexus Purification System
Genexus Purification System—automates the extraction of nucleic acids from various sample types, including plasma, whole blood, peripheral blood leukocytes (PBLs), formalin-fixed, paraffin-embedded (FFPE) lysate, fresh or frozen tissue, cultured cells, and bone marrow aspirate

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

Absolute Q DNA Digital PCR Master Mix (5X)—enables accurate, sensitive, and precise dPCR data from Applied Biosystems dPCR assays on the QuantStudio Absolute Q Digital PCR System with a master mix specifically formulated to enable analysis of higher sample volumes and delivers accurate quantification of DNA targets without using a standard curve

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
Oncomine Precision Assay—enables rapid simultaneous detection of biomarkers across 50 genes from liquid biopsy samples, as well as solid tissue samples
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
Ion Torrent Genexus System—automates sample and library preparation, sequencing, analysis, and reporting. The system, along with Genexus Software, works seamlessly, tracking sample information and results automatically.

dPCR assays and instruments

Absolute Q Liquid Biopsy dPCR Assays—enable reproducible, specific detection of known somatic mutations with wet-lab validated assays capable of detecting down to 0.1% variant allele frequency in genes relevant for cancer research
QuantStudio Absolute Q Digital PCR System—enables accurate, sensitive and precise digital PCR data to be collected in as little as 90 minutes with a simple one-step workflow on the QuantStudio Absolute Q Digital PCR System

castPCR assays and instruments

TaqMan Mutation Detection assays—detect and measure rare amounts of mutated DNA in samples that contain large amounts of normal DNA using TaqMan PCR (castPCR Technology)
QuantStudio real-time PCR systems—find the Real-Time PCR instrument that is right for you from our family of QuantStudio real-time PCR systems

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

QuantStudio Absolute Q Digital PCR Software—allows users to set up dPCR runs, control the thermal cycling process, and analyze experiment data such as absolute quantification of rare targets or measuring copy number variation

castPCR analysis software