End-to-End Oncology Research Workflows
Oncology research takes the form of multiple applications including digital PCR (dPCR), library prep, next generation sequencing (NGS), and more. All applications must include sample preparation. Thermo Fisher Scientific provides end-to-end oncology research solutions for both liquid biopsy and solid tumor cell research. Both automated and manual workflows are available depending on your lab's requirements.
Liquid biopsies workflows examine biomarkers shed by tumors, such as circulating tumor cells, pieces of tumor DNA, or exosomes. Often, whole blood or plasma are utilized as less-invasive liquid biopsy samples compared to traditional surgical biopsies and can be used in place of or alongside them. Liquid biopsies are important because they can detect cancer at an early stage when it is most treatable. They can also be used to monitor treatment response and identify resistance to therapy.
Thermo Fisher Scientific offers complete sample preparation solutions for the liquid biopsy research workflow.
MagMAX chemistry workflows on KingFisher purification instruments provide highly accurate and reproducible results for liquid biopsy research, enabling researchers to confidently detect rare mutations and variations in circulating tumor DNA and RNA. Additionally, the scalability and versatility of these products make them ideal for processing a range of sample types and volumes, from plasma to cerebrospinal fluid.
Dynabeads magnetic beads provide an automation-friendly tool for isolation of intact exosomes and circulating tumor cells. Because of the low number of CTCs in circulation, highly sensitive methods are necessary to capture and detect down to single cells. Dynabeads magnetic beads provide researchers with a gentle, tube-based magnetic separation, enabling isolation of CTCs with high specificity and sensitivity for both positive and negative isolation techniques.
Overall, MagMAX, Dynabeads and KingFisher products are essential tools for liquid biopsy research, helping to advance our understanding of cancer biology and improve translational patient outcomes.
Sensitive cfDNA purification—MagMAX Cell-Free DNA Isolation Kit design allows for high-quality cfDNA yield and enrichment from plasma, serum, and urine.
Sensitive cfTNA purification—MagMAX Cell-Free Total Nucleic Acid Kit is designed for the purification of DNA, RNA, and miRNA from plasma, serum, and urine.
CTC isolation – Dynabeads Epithelial Enrich is designed for positive isolation of circulating tumor cells from PBMC’s and whole blood. Dynabeads CD45 is designed for negative isolation of circulating tumor cells from PBMC’s and lysed whole blood through depletion of CD45+ leukocytes.
Intact Exosome enrichment—Dynabeads Intact virus enrichment kit is designed for isolation of intact exosomes from plasma, serum, urine and cell culture.
Accurate and reproducible results—MagMAX and PureLink liquid biopsy kits as well as Dynabeads magnetic beads are designed with optimized protocols and reagents for maximum yield and purity, helping ensure high-quality results for downstream applications.
Click through workflow steps for more information.
Sample preparation for liquid biopsies
Nucleic acids, Exosomes and circulating tumor cells (CTCs) must be extracted from liquid biopsy samples for downstream oncology research applications. This sample preparation step can be automated using the KingFisher Apex System or be performed manually. We offer comprehensive solutions for your liquid biopsy samples. Explore our options for nucleic acid extraction, exosome isolation and CTC isolation, and find the product that best fits your research needs.
| Biomarker | Cell free nucleic acids | Exosmes | Circulating tumor cells | |||
|---|---|---|---|---|---|---|
| Product Click on the product names or images to learn more | KingFisher Apex | MagMAX Cell-Free Total Nucleic Acid Isolation Kit | MagMAX Cell-Free DNA Isolation Kit | Dynabeads Intact Virus Enrichment | Dynabeads Epithelial Enrich | Dynabeads CD45 |
| Sample type | RNA, DNA, protein, cells | Plasma, serum, urine | Plasma, serum, urine | Plasma, serum, urine, cell culture | PBMC, blood | PBMC, blood |
| Isolation technology | Automated magnetic beads | Magnetic beads | Magnetic beads | Magnetic beads | Magnetic beads—positive cell isolation | Magnetic beads—negative cell isolation |
| Downstream applications | RT-PCR, RT-qPCR, NGS, CE, Western | RT-PCR, RT-qPCR, NGS, CE, Western | RT-PCR, RT-qPCR, NGS | RT-PCR, RT-qPCR, NGS, Western, Immunoprecipitation, mass spectrometry | RT-PCR, RT-qPCR, NGS, Western, Immunoprecipitation, mass spectrometry | RT-PCR, RT-qPCR, NGS, Western, Immunoprecipitation, mass spectrometry |
| Automation compatible | Yes | Yes | Yes | Yes | Yes | Yes |
| Request a quote | Order now | Order now | Order now | Order now | Order now | |
Sample quantification for liquid biopsies
Qubit Fluorometric Quantification
Qubit Fluorometers provide fast, accurate, and precise quantification of the DNA, RNA, or protein within a sample. The Qubit 4 and Qubit Flex Fluorometers use target-selective Qubit assays that fluoresce when bound specifically to the target molecules of interest. Learn how the quantification of these analytes is important for downstream applications like next generation sequencing (NGS), PCR, transfection, western blotting, and immunoassays.
NanoDrop Microvolume Spectrophotometers
Quickly quantify DNA, RNA, and protein using only 1–2 µL of sample with Thermo Scientific NanoDrop Spectrophotometers. Our pioneering sample-retention technology has evolved across the full spectrum to bring you more knowledge about your sample, so that you can save days of troubleshooting and accelerate your research.
Digital PCR for liquid biopsies
Absolute Q DNA Digital PCR Master Mix
Accurate, sensitive, and precise dPCR data with a master mix specifically formulated to enable analysis of higher sample volumes. Delivers accurate quantification of DNA targets without using a standard curve.
Absolute Q Liquid Biopsy dPCR Assays
Enables 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
Sensitive and precise digital PCR data can be collected in as little as 90 minutes with a simple one-step workflow.
Library preparation for liquid biopsies
Ion Chef Instrument for Automated Library Preparation
Fully automates library preparation, template preparation, and produces sequencing-ready Ion Torrent semiconductor chips.
Dynabeads Streptavidin for Target Enrichment
Efficiently capture DNA sequences of interest through specific hybridization via immobilization of target-specific biotinylated probes to streptavidin coated beads.
Next generation sequencing for liquid biopsies
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.
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. Also simultaneously detect DNA and RNA variants across multiple cancer types.
Oncomine Precision Assay
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 a simple sample-to-data NGS workflow.
Sample preparation for liquid biopsies
Nucleic acids, Exosomes and circulating tumor cells (CTCs) must be extracted from liquid biopsy samples for downstream oncology research applications. This sample preparation step can be automated using the KingFisher Apex System or be performed manually. We offer comprehensive solutions for your liquid biopsy samples. Explore our options for nucleic acid extraction, exosome isolation and CTC isolation, and find the product that best fits your research needs.
| Biomarker | Cell free nucleic acids | Exosmes | Circulating tumor cells | |||
|---|---|---|---|---|---|---|
| Product Click on the product names or images to learn more | KingFisher Apex | MagMAX Cell-Free Total Nucleic Acid Isolation Kit | MagMAX Cell-Free DNA Isolation Kit | Dynabeads Intact Virus Enrichment | Dynabeads Epithelial Enrich | Dynabeads CD45 |
| Sample type | RNA, DNA, protein, cells | Plasma, serum, urine | Plasma, serum, urine | Plasma, serum, urine, cell culture | PBMC, blood | PBMC, blood |
| Isolation technology | Automated magnetic beads | Magnetic beads | Magnetic beads | Magnetic beads | Magnetic beads—positive cell isolation | Magnetic beads—negative cell isolation |
| Downstream applications | RT-PCR, RT-qPCR, NGS, CE, Western | RT-PCR, RT-qPCR, NGS, CE, Western | RT-PCR, RT-qPCR, NGS | RT-PCR, RT-qPCR, NGS, Western, Immunoprecipitation, mass spectrometry | RT-PCR, RT-qPCR, NGS, Western, Immunoprecipitation, mass spectrometry | RT-PCR, RT-qPCR, NGS, Western, Immunoprecipitation, mass spectrometry |
| Automation compatible | Yes | Yes | Yes | Yes | Yes | Yes |
| Request a quote | Order now | Order now | Order now | Order now | Order now | |
Sample quantification for liquid biopsies
Qubit Fluorometric Quantification
Qubit Fluorometers provide fast, accurate, and precise quantification of the DNA, RNA, or protein within a sample. The Qubit 4 and Qubit Flex Fluorometers use target-selective Qubit assays that fluoresce when bound specifically to the target molecules of interest. Learn how the quantification of these analytes is important for downstream applications like next generation sequencing (NGS), PCR, transfection, western blotting, and immunoassays.
NanoDrop Microvolume Spectrophotometers
Quickly quantify DNA, RNA, and protein using only 1–2 µL of sample with Thermo Scientific NanoDrop Spectrophotometers. Our pioneering sample-retention technology has evolved across the full spectrum to bring you more knowledge about your sample, so that you can save days of troubleshooting and accelerate your research.
Digital PCR for liquid biopsies
Absolute Q DNA Digital PCR Master Mix
Accurate, sensitive, and precise dPCR data with a master mix specifically formulated to enable analysis of higher sample volumes. Delivers accurate quantification of DNA targets without using a standard curve.
Absolute Q Liquid Biopsy dPCR Assays
Enables 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
Sensitive and precise digital PCR data can be collected in as little as 90 minutes with a simple one-step workflow.
Library preparation for liquid biopsies
Ion Chef Instrument for Automated Library Preparation
Fully automates library preparation, template preparation, and produces sequencing-ready Ion Torrent semiconductor chips.
Dynabeads Streptavidin for Target Enrichment
Efficiently capture DNA sequences of interest through specific hybridization via immobilization of target-specific biotinylated probes to streptavidin coated beads.
Next generation sequencing for liquid biopsies
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.
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. Also simultaneously detect DNA and RNA variants across multiple cancer types.
Oncomine Precision Assay
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 a simple sample-to-data NGS workflow.
Automate your liquid biopsy sample preparation with KingFisher sample purification systems
Dynabeads magnetic beads enable higher-throughput applications for which samples can be processed in 24- or 96-well plates on the KingFisher family of instruments. Sample types include RNA, DNA, proteins, cells and exosomes.
Read about our liquid biopsy solutions in the following application notes:
Rapid bead-based isolation of exosomes for multiomic research
Isolation of circulating tumor cells using Dynabeads magnetic beads
Improved efficiency and reproducibility using the automated Multidrop Combi Reagent Dispenser
Solid tumors are heterotypic aggregates of many cell types, including cancer cells, cancer stem cells, connective-tissue cells, and immune cells. Common sample types used to begin cancer research and detection include fresh-frozen (FF) or formalin-fixed paraffin-embedded (FFPE) sample tissues. These are obtained through biopsy or excision of the malignant mass.
Sequential extraction—MagMAX FFPE DNA/RNA Ultra Kit allows sequential isolation of DNA and RNA from the same formalin-fixed, paraffin-embedded (FFPE) tissue sample.
Accurate and reproducible downstream results—MagMAX and Purelink kits for solid tumor nucleic acid purification are designed with optimized protocols and reagents for maximum yield and purity, helping ensure high-quality input for downstream applications.
Click through workflow steps for more information.
Sample processing for solid tumors
Process formalin-fixed paraffin-embedded (FFPE) tissue samples for high-quality nucleic acid isolation and simplify deparaffinization. AutoLys M Tubes eliminate the need for solvent based deparaffinization and extensive hands on time for sample preprocessing.
AutoLys M | AutoLys M | AutoLys M | AutoLys M | AutoLys M | |
| Description | AutoLys M Tubes are for the preparation of FFPE samples for nucleic acid extraction. They feature a novel tube-in-tube design that creates cleared lysates from FFPE tissue samples, without the need for deparaffinization or wash steps, while increasing DNA and RNA yields. | The AutoLys M TubeLifter enables a rack of 24 AutoLys M Tubes to be simultaneously “lifted” and readied for centrifugation. Once centrifugation is complete, the rack of tubes is returned to the TubeLifter and the inner tube of each AutoLys M Tube is separated from the outer tube. | This is an extra locking lid for use with the AutoLys M Tube system. Note that two locking lids are included with the purchase of the AutoLys M TubeLifter. The locking lid is required to prevent the inner tube of the AutoLys M Tube from sliding into the outer tube during centrifugation. | These AutoLys M Tube Racks hold 24 AutoLys M Tubes per rack. The racks are locked and unlocked using the AutoLys M TubeLifter. | AutoLys M Tube Pliers can be used to separate the inner-tube from the outer-tube of AutoLys M Tubes. Centrifugation of the tubes in an AutoLys M Tube Rack is required when processing FFPE samples using the MagMAX FFPE DNA/RNA Ultra Kit. The outer-tube will contain the lysate that is processed further to recover the nucleic acids. |
| Sample types | FFPE curls, FFPE blocks | ||||
| Order now | Order now | Order now | Order now | Order now | |
Nucleic acid purification for solid tumors
We offer multiple solutions for extracting nucleic acid from solid tumor samples. Our kits are designed to provide maximum yield, purity, and integrity so that your purified nucleic acid can be used in a variety of downstream applications.
Product Click on the product names or images to learn more | KingFisher Apex | MagMAX FFPE DNA/RNA Ultra Kit | MagMAX DNA Multi-Sample Ultra Kit | MagMAX mirVana Total RNA Isolation Kit | PureLink FFPE RNA Isolation Kit |
| Sample type | RNA, DNA, protein, cells | FFPE tissue samples | Multiple, including whole blood, swabs, tissue, and more | Blood, cells, liquid samples (e.g., serum), RNA, tissue | FFPE tissue samples |
| Isolation technology | Automated magnetic beads | Magnetic beads | Magnetic beads | Magnetic beads | Silica spin column |
| Downstream applications | RT-PCR, RT-qPCR, NGS, western workflow | RT-PCR, RT-qPCR, NGS, microRNA analysis | RT-PCR, RT-qPCR, NGS, microarray analysis | RT-PCR, RT-qPCR, NGS, microRNA analysis | Microarray analysis, RT-qPCR, RT-PCR, northern blotting, cDNA library construction |
| Automation compatible | Yes | Yes | Yes | Yes | No |
| Request a quote | Order now | Order now | Order now | Order now |
Sample Quantification for solid tumors
Qubit Fluorometric Quantification
Qubit Fluorometers provide fast, accurate, and precise quantification of the DNA, RNA, or protein within a sample. The Qubit 4 and Qubit Flex Fluorometers use target-selective Qubit assays that fluoresce when bound specifically to the target molecules of interest. Learn how the quantification of these analytes is important for downstream applications like next generation sequencing (NGS), PCR, transfection, western blotting, and immunoassays.
NanoDrop Microvolume Spectrophotometers
Quickly quantify DNA, RNA, and protein using only 1–2 µL of sample with Thermo Scientific NanoDrop Spectrophotometers. Our pioneering sample-retention technology has evolved across the full spectrum to bring you more knowledge about your sample, so that you can save days of troubleshooting and accelerate your research.
Digital PCR for solid tumors
Absolute Q DNA Digital PCR Master Mix
Accurate, sensitive, and precise dPCR data with a master mix specifically formulated to enable analysis of higher sample volumes. Delivers accurate quantification of DNA targets without using a standard curve.
QuantStudio Absolute Q Digital PCR System
Sensitive and precise digital PCR data can be collected in as little as 90 minutes with a simple one-step workflow.
Library preparation for solid tumors
Ion Chef Instrument for Automated Library Preparation
Fully automates library preparation, template preparation, and produces sequencing-ready Ion Torrent semiconductor chips.
Dynabeads Streptavidin for Target Enrichment
Efficiently capture DNA sequences of interest through specific hybridization via immobilization of target-specific biotinylated probes to streptavidin coated beads.
Next generation sequencing for solid tumors
Thermo Fisher Scientific offers a wide range of solutions for solid tumor research and detection. Browse our Oncomine Assays and tumor-specific panels and find the right products to meet your specific tumor research needs.
Oncomine Colorectal and Pancreatic Panel
Oncomine Gynecological Panel
Oncomine Kidney Panel
Oncomine Lymphoma Panel
Oncomine Prostate Panel
Oncomine BRCA Expanded Panel
Oncomine Gastric and Esophageal Panel
Oncomine Tumor Specific RNA Panel
Oncomine Liver Panel
Oncomine Melanoma Panel
Oncomine HRR Pathway Predesigned Panel
Data analysis & reporting for solid tumors
Ion Reporter Software
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.
Sample processing for solid tumors
Process formalin-fixed paraffin-embedded (FFPE) tissue samples for high-quality nucleic acid isolation and simplify deparaffinization. AutoLys M Tubes eliminate the need for solvent based deparaffinization and extensive hands on time for sample preprocessing.
AutoLys M | AutoLys M | AutoLys M | AutoLys M | AutoLys M | |
| Description | AutoLys M Tubes are for the preparation of FFPE samples for nucleic acid extraction. They feature a novel tube-in-tube design that creates cleared lysates from FFPE tissue samples, without the need for deparaffinization or wash steps, while increasing DNA and RNA yields. | The AutoLys M TubeLifter enables a rack of 24 AutoLys M Tubes to be simultaneously “lifted” and readied for centrifugation. Once centrifugation is complete, the rack of tubes is returned to the TubeLifter and the inner tube of each AutoLys M Tube is separated from the outer tube. | This is an extra locking lid for use with the AutoLys M Tube system. Note that two locking lids are included with the purchase of the AutoLys M TubeLifter. The locking lid is required to prevent the inner tube of the AutoLys M Tube from sliding into the outer tube during centrifugation. | These AutoLys M Tube Racks hold 24 AutoLys M Tubes per rack. The racks are locked and unlocked using the AutoLys M TubeLifter. | AutoLys M Tube Pliers can be used to separate the inner-tube from the outer-tube of AutoLys M Tubes. Centrifugation of the tubes in an AutoLys M Tube Rack is required when processing FFPE samples using the MagMAX FFPE DNA/RNA Ultra Kit. The outer-tube will contain the lysate that is processed further to recover the nucleic acids. |
| Sample types | FFPE curls, FFPE blocks | ||||
| Order now | Order now | Order now | Order now | Order now | |
Nucleic acid purification for solid tumors
We offer multiple solutions for extracting nucleic acid from solid tumor samples. Our kits are designed to provide maximum yield, purity, and integrity so that your purified nucleic acid can be used in a variety of downstream applications.
Product Click on the product names or images to learn more | KingFisher Apex | MagMAX FFPE DNA/RNA Ultra Kit | MagMAX DNA Multi-Sample Ultra Kit | MagMAX mirVana Total RNA Isolation Kit | PureLink FFPE RNA Isolation Kit |
| Sample type | RNA, DNA, protein, cells | FFPE tissue samples | Multiple, including whole blood, swabs, tissue, and more | Blood, cells, liquid samples (e.g., serum), RNA, tissue | FFPE tissue samples |
| Isolation technology | Automated magnetic beads | Magnetic beads | Magnetic beads | Magnetic beads | Silica spin column |
| Downstream applications | RT-PCR, RT-qPCR, NGS, western workflow | RT-PCR, RT-qPCR, NGS, microRNA analysis | RT-PCR, RT-qPCR, NGS, microarray analysis | RT-PCR, RT-qPCR, NGS, microRNA analysis | Microarray analysis, RT-qPCR, RT-PCR, northern blotting, cDNA library construction |
| Automation compatible | Yes | Yes | Yes | Yes | No |
| Request a quote | Order now | Order now | Order now | Order now |
Sample Quantification for solid tumors
Qubit Fluorometric Quantification
Qubit Fluorometers provide fast, accurate, and precise quantification of the DNA, RNA, or protein within a sample. The Qubit 4 and Qubit Flex Fluorometers use target-selective Qubit assays that fluoresce when bound specifically to the target molecules of interest. Learn how the quantification of these analytes is important for downstream applications like next generation sequencing (NGS), PCR, transfection, western blotting, and immunoassays.
NanoDrop Microvolume Spectrophotometers
Quickly quantify DNA, RNA, and protein using only 1–2 µL of sample with Thermo Scientific NanoDrop Spectrophotometers. Our pioneering sample-retention technology has evolved across the full spectrum to bring you more knowledge about your sample, so that you can save days of troubleshooting and accelerate your research.
Digital PCR for solid tumors
Absolute Q DNA Digital PCR Master Mix
Accurate, sensitive, and precise dPCR data with a master mix specifically formulated to enable analysis of higher sample volumes. Delivers accurate quantification of DNA targets without using a standard curve.
QuantStudio Absolute Q Digital PCR System
Sensitive and precise digital PCR data can be collected in as little as 90 minutes with a simple one-step workflow.
Library preparation for solid tumors
Ion Chef Instrument for Automated Library Preparation
Fully automates library preparation, template preparation, and produces sequencing-ready Ion Torrent semiconductor chips.
Dynabeads Streptavidin for Target Enrichment
Efficiently capture DNA sequences of interest through specific hybridization via immobilization of target-specific biotinylated probes to streptavidin coated beads.
Next generation sequencing for solid tumors
Thermo Fisher Scientific offers a wide range of solutions for solid tumor research and detection. Browse our Oncomine Assays and tumor-specific panels and find the right products to meet your specific tumor research needs.
Oncomine Bladder Panel
Oncomine Colorectal and Pancreatic Panel
Oncomine Gynecological Panel
Oncomine Kidney Panel
Oncomine Lymphoma Panel
Oncomine Prostate Panel
Oncomine BRCA Expanded Panel
Oncomine Gastric and Esophageal Panel
Oncomine Tumor Specific RNA Panel
Oncomine Liver Panel
Oncomine Melanoma Panel
Oncomine HRR Pathway Predesigned Panel
Data analysis & reporting for solid tumors
Ion Reporter Software
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.
Read about our solid tumor solutions in the following application notes:
Comparison of DNA and RNA from fresh-frozen vs. FFPE tissue samples
Mutation detection sensitivity in matched FFPE tissue and liquid biopsy samples
A convenient, solvent-free deparaffinization method for FFPE sample preparation
For Research Use Only. Not for use in diagnostic procedures.
Style Sheet for Global Design System