Search
Search
Thermo Fisher Scientific offers complete, end-to-end next-generation sequencing (NGS) research solutions on the Ion GeneStudio S5 systems to detect relevant biomarkers in oncology with exceptional speed and accuracy.
The breadth of ready-to-use Ion Torrent Oncomine NGS assays spans from targeted to comprehensive panels for solid tumors and hematological malignancies. Oncomine tumor-specific panels provide additional customizable assays created from a curated inventory of pretested genes, including RNA fusions as optional targets.
These NGS assays are sensitive and easy to implement for laboratory use, and come with automation, bioinformatics, and reporting capabilities to enable sample-to-report results in a matter of days.
Advancements in precision medicine are driving the need for NGS, as oncology research continues to explore the utility of targeted therapies and immunotherapies. NGS facilitates the simultaneous analysis of a broad range of biomarkers in one test to help maximize insights into the underlying oncogenic drivers in a timely manner.
Oncomine NGS assays for formalin-fixed, paraffin-embedded (FFPE) tissue samples span from focused to comprehensive panels to meet your laboratory research needs, even at varying levels of NGS experience. Regardless of panel size, they offer an end-to-end solution for broad genomic profiling of solid tumors with easy and automated workflows, fast results, and high success rates, even for challenging samples.
* One hour of hands-on time needed for the Oncomine Comprehensive Assay Plus for library preparation and sequencing compared to competitor literature stating that 10.5 hours are needed for a manual workflow, current as of September 2026.
| Ion Torrent Oncomine Comprehensive Assay Plus | Ion Torrent Oncomine Comprehensive Assay v3 | Ion Torrent Oncomine Focus Assay | |
| Description | Comprehensive genomic profiling from 517 genes plus genomic signatures | Comprehensive genomic profiling from 161 genes | Broad genomic profiling from 52 genes |
| Sample types | Tissue | Tissue | Tissue |
| Number of genes | 517 | 161 | 52 |
| Alteration types | Single-nucleotide variants (SNVs), insertions and/or deletions (indels), copy number variations (CNVs), fusions | SNVs, indels, CNVs, fusions | SNVs, indels, CNVs, fusions |
| Genomic signatures | Homologous recombination deficiency (HRD), tumor mutational burden (TMB), microsatellite instability (MSI) | – | – |
| Recommended nucleic acid input amount | 20 ng DNA/RNA | 20 ng DNA/RNA | 10 ng DNA/RNA |
| Turnaround time** | 3 days | 3 days | 3 days |
**Timing varies by the number of samples, sample type, and instrument used.
While tissue NGS is the standard for gaining insights into the biology of a tumor, liquid biopsy–based NGS is emerging as a highly sensitive method to understand resistance mechanisms as a tumor evolves. Liquid biopsies are minimally invasive and may be used as an alternative when tissue samples are not available. Moreover, liquid biopsy testing may complement tissue testing to better understand inter- and intra-tumor heterogeneity. Ion Torrent Oncomine cell-free assays can help lead to important insights from liquid samples, including blood, bile, cerebrospinal fluid, and urine.
| Ion Torrent Oncomine Pan-Cancer Cell-Free Assay |
Ion Torrent Oncomine Lung Cell-Free Total Nucleic Acid Research Assay |
Ion Torrent Oncomine Breast cfDNA Research Assay v2 |
Ion Torrent Oncomine Colon cfDNA Assay |
|
| Description | Broad, multibiomarker NGS assay for pan-cancer analysis |
Tumor-specific NGS assay focused on key genes in lung cancer | Tumor-specific NGS assay focused on key genes in breast cancer | Tumor-specific NGS assay focused on key genes in colon cancer |
| Number of genes | 52 | 12 | 12 | 14 |
| Alteration types | SNVs, indels, CNVs, fusions |
SNVs, indels, CNVs, fusions |
SNVs, indels, CNVs | SNVs, indels |
| Recommended nucleic acid input amount |
20 ng cell-free total nucleic acid (cfTNA)* |
20 ng cfTNA* | 20 ng cell-free DNA (cfDNA)* |
20 ng cfDNA* |
| Turnaround time** | 3 days | 3 days | 3 days | 3 days |
* Input recommended to achieve 0.1% limit of detection (LOD) for SNVs and indels. Lower amounts can be used.
** Timing varies by the number of samples, sample type, and instrument used.
Homologous recombination deficiency (HRD) is a phenotype that is characterized by the inability of a cell to effectively repair DNA double-stranded breaks using the homologous recombination repair (HRR) pathway. HRD is becoming more relevant in research applications, especially in ovarian, breast, prostate, and pancreatic cancers because of HRD-positive tumors are sensitive to platinum analogs and poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors, a class of anticancer agents that exhibit synthetic lethality when applied to cells defective in the HRR pathway.
Oncomine assays provide tools for identifying both causes and consequences of HRD.
| Oncomine Comprehensive Assay Plus | Ion Torrent Oncomine HRR Pathway Predesigned Panel | Ion Torrent Oncomine BRCA Research Assay | |
| Description | Comprehensive genomic profiling across 517 genes plus genomic signatures | HRR pathway panel relevant in ovarian, breast, prostate, and pancreatic cancers | Focused panel covering BRCA1/2 somatic and germline mutations |
| Sample types | Tissue | Tissue | Tissue, blood |
| Number of genes | 517 | 28 | 2 |
| Number of HRR genes | 47 | 26 | 2 |
| Alteration types | SNVs, indels, CNVs, fusions | SNVs, indels, CNVs | SNVs, indels, CNVs |
| Genomic signatures | HRD, TMB, MSI | – | – |
| Recommended nucleic acid input amount |
20 ng DNA/RNA | 20 ng DNA | 20 ng DNA |
| Turnaround time* | 3 days | 3 days | 3 days |
*Timing varies by the number of samples, sample type, and instrument used
Explore our comprehensive portfolio of NGS testing solutions designed to enhance your understanding of hematological malignancies. Our assays support multiple research applications for the analysis of myeloid and lymphoid malignancy samples.
| Ion Torrent Oncomine Myeloid Research Assay |
Ion Torrent Oncomine Myeloid MRD (RUO) Assay |
Ion Torrent Oncomine Lymphoma Panel |
Ion AmpliSeq Liverpool Lymphoid Network Panel |
Ion Torrent Oncomine Childhood Cancer Research Assay |
|
| Description | Genomic profiling of myeloid malignancy samples |
Measurable residual disease (MRD) detection for myeloid malignancy samples |
Genomic profiling of lymphoma samples |
Genomic profiling of lymphoid malignancy samples |
CGP of cancers associated with children and young adults |
| Sample types | Blood, bone marrow | Blood, bone marrow | Tissue, blood, bone marrow | Tissue, blood, bone marrow | Tissue, blood, bone marrow |
| Number of genes | 40 genes (DNA), 29 fusion drivers (RNA), and 5 expression control genes |
33 gene (DNA), 42 fusion drivers (RNA) |
25 genes (DNA) | 60 genes (DNA) | 138 genes (DNA), 28 CNVs (DNA), 91 fusion drivers (RNA), 9 expression genes (RNA) |
| Alteration types | SNVs, indels, fusions, gene expression |
SNVs, indels, fusions |
SNVs, indels | SNVs, indels | SNVs, indels, fusions, CNVs, gene expression |
| Recommended nucleic acid input amount |
10 ng DNA or RNA | 10 ng RNA, 120 ng DNA |
20 ng DNA | 10 ng DNA | 10 ng DNA or RNA |
| Turnaround time* | 3 days | 3 days | 3 days | 3 days | 3 days |
*Timing varies by the number of samples, sample type, and instrument used.
Ion Torrent Oncomine immune repertoire research assays offer a robust suite of solutions for profiling the immune repertoire. They offer highly sensitive NGS capabilities to accurately assess clonality and detect biomarkers associated with MRD across various lymphoid malignancy sample types.
| Assay | Target(s) | Nucleic acid input | Sample types | Application(s) |
| Ion Torrent Oncomine BCR Pan-Clonality Assay |
BCR, IGH, IGK, IGL, KDE/C-int, (FR3-J) |
gDNA | Whole blood; bone marrow; PBLs*; PBMCs;** FFPE sorted cells; fresh, frozen, and FFPE-preserved tissue samples | Clonality, MRD research |
| Ion Torrent Oncomine BCR IGH SR Assay |
BCR IGH (FR3-J) | gDNA, RNA | ||
| Ion Torrent Oncomine IGH FR3(d)-J Assay |
BCR IGH (FR3(d)-J) | gDNA | ||
| Ion Torrent Oncomine IGH FR2-J Assay |
BCR IGH (FR2-J) | gDNA | ||
| Ion Torrent Oncomine TCR Pan-Clonality Assay |
TCRB, TCRG (FR3-J) | gDNA | ||
| Ion Torrent Oncomine BCR IGHV Leader-J Assay |
BCR IGH (Leader-J) | gDNA | Whole blood, bone marrow, PBLs, PBMCs, sorted cells |
SHM |
| Ion Torrent Oncomine BCR IGH LR Assay |
BCR IGHV (FR1-C) | Non-FFPE RNA | Whole blood, bone marrow, PBLs, PBMCs, fresh and frozen specimens | |
| Ion Torrent Oncomine IGH FR1-J Assay |
BCR IGH (FR1-J) | Non-FFPE DNA |
* PBLs: peripheral blood leukocytes.
* * PBMCs: peripheral blood mononuclear cells.
Ion Torrent Oncomine tumor-specific panels (TSPs) are small, curated panels with verified performance complementing the portfolio of Oncomine assays. They are part of an end-to-end solution for clinical cancer research on specific tumors, such as bladder, prostate, melanoma, and others, from FFPE tissue samples.
Oncomine TSPs are predesigned, web-lab tested, and verified to work with Ion GeneStudio S5 systems. Select from the following panels or create your own.
Need something else? If there is not an Oncomine assay or panel available that is right for you, our custom menu services can help. Whether you are interested in just a few regions or hundreds of targets, custom Ion AmpliSeq panels can be designed to meet your NGS testing needs.
You can get help selecting the custom panel type and design strategy that best fit your needs by using the Ion AmpliSeq Designer online tool at ampliseq.com or by talking to one of our knowledgeable representatives.
Thermo Fisher Scientific is dedicated to providing exceptional products and services to our customers. As an Oncomine Solutions user, you have access to a worldwide team committed to enabling NGS testing to a broad spectrum of oncology research labs.
Our service and support teams enable our users across the customer support continuum. Whether you are a new customer in need of instrument set-up assistance or an established user looking to troubleshoot, add a new assay to your workflow, or perform an analytical validation, we are with you every step of the way.
For Research Use Only. Not for use in diagnostic procedures.
References
1. Jantus-Lewintre E, Rappa A, Ruano D et al. (2025) Multicenter in-house evaluation of an amplicon-based next-generation sequencing panel for comprehensive molecular profiling. Mol Diagn Ther 29(2):249–261.
2. Campbell, A (2025) Reliable results, rapid delivery: Performance evaluation of Oncomine Comprehensive Assay Plus and the Ion Torrent Genexus System. AMP Workshop.
PMR-009310