Cancer development is a multifactorial process. It begins with genetic changes that lead to abnormally proliferating cells, causing a tumor to grow. During tumor progression, additional mutations can promote rapid growth, enable replicative immortality, induce angiogenesis, enable immune and growth suppressor evasion, and even permit cell death resistance. Thus, tumors can accumulate a multitude of mutations in different genes during their development and progression, leading to the tumor cell’s increased capacity for proliferation, survival, invasion, and metastasis. Mutations in specific tumor-relevant genes can have crucial implications for targeted therapy approaches. Key immune-oncology biomarkers like tumor mutational burden (TMB) or microsatellite instability (MSI) can also provide valuable information for treatment choices. However, even if the optimal therapy is found, tumors can develop resistance mutations against the treatment.
With our Focused Tumor Profiling products, selected tumor-relevant genes in your tumor sample can be analyzed. Our products offer a focused, targeted, and efficient method to identify a patient’s best treatment choice, find patients eligible for clinical trials, and monitor a patient’s mutation status during therapeutic interventions.
CeGaT Is the Best Partner for Sequencing Your Project
Our Commitment to You
Fast Processing
Turnaround time
≤ 15 business days
High Quality
Highest accuracy for all processes
Secure Delivery
Secure provision of sequenced data via in-house servers
Safe Storage
Safe storage of samples and data after project completion
Our Service
We provide a comprehensive and first-class project support – from selecting the appropriate product to evaluating the data. Each project is supervised by a committed scientist. You will have a contact person throughout the whole project.
Our service includes:
- detailed project consulting
- product selection tailored to your project
- detailed bioinformatic evaluation of your data
- detailed project report with information about sample quality, sequencing parameters, bioinformatic analysis, and results
Benefit from our dedicated support and accredited workflows.
Explore Our Product Portfolio for Focused Tumor Profiling
We offer different Focused Tumor Profiling (FTP) products to address a variety of research questions.
Our most extensive tumor gene panel, FTP TUM, comprises more than 780 selected tumor-relevant genes. Furthermore, 39 therapy-relevant fusions are analyzed at a high sequencing depth. Additionally, selected tumor-relevant pathogens are detected. For FTP TUM TN, a tumor and a normal sample are used for a tumor-normal comparison. With FTP TUM T, a single tumor sample is analyzed.
Our FTP PAT T covers 55 genes highly relevant to tumor diseases. We also offer the FTP FUS T product. In contrast to the other two DNA panels, the FTP FUS T is an RNA panel focusing on fusions relevant to tumor diseases.
Each of our products can be supplemented with further services. We are happy to advise you.
FTP TUM TN | FTP TUM T | FTP PAT T | FTP FUS T |
Species | Species | Species | Species |
Sequencing panel Tumor panel (CeGaT GmbH) | Sequencing panel Tumor panel (CeGaT GmbH) | Sequencing panel Molecular pathology panel (CeGaT GmbH) | Sequencing panel |
Number of analyzed genes ~ 780 | Number of analyzed genes | Number of analyzed genes | Number of analyzed genes |
Analysis of tumor and normal tissue Yes | Analysis of tumor and normal tissue No | Analysis of tumor and normal tissue | Analysis of tumor and normal tissue |
Starting material | Starting material | Starting material | Starting material |
Sequencing platform | Sequencing platform | Sequencing platform | Sequencing platform |
Output 10 Gb normal tissue 10 Gb tumor tissue | Output 10 Gb tumor tissue | Output | Output |
Included deliverables Project report, files in FASTQ, BAM, CSV, VCF, JSON, GFF3, and TSV format | Included deliverables Project report, files in FASTQ, BAM, CSV, VCF, JSON, GFF3, and TSV format | Included deliverables Project report, files in FASTQ, BAM, CSV, VCF, JSON, and TSV format | Included deliverables Project report, files in FASTQ, BAM, and TSV format |
If you want to comprehensively profile your tumor sample, please look at our Comprehensive Tumor Profiling product portfolio.
Bioinformatics
Raw sequencing data are automatically processed. We analyze your FTP TUM and FTP PAT data with the DRAGEN Bio-IT Platform. We can perform the analyses based on the human reference hg19.
The analysis for FTP TUM TN, FTP TUM T, and FTP PAT T includes:
- demultiplexing and adapter trimming of the sequencing data (FASTQ format),
- mapping of the sequencing data (BAM format),
- calling of single nucleotide variants (SNVs) and small insertions and deletions (indels) of both germline and somatic variants (VCF format), and
- annotation of the SNVs and indels (JSON and TSV format).
For FTP TUM TN and FTP TUM T, the analysis additionally includes
- calling of copy number variations (CNVs) (VCF and GFF3 format),
- detection of selected pathogen genomes (TSV format), and
- determination of the biomarkers tumor mutational burden (TMB) and microsatellite instability (MSI) (TSV format).
The HRD score is furthermore calculated (CSV format) for FTP TUM TN.
Supplementing the data, a project report (PDF format), metrics files (CSV format), and a MultiQC report (HTML format) are provided.
The analysis for our FTP FUS T product is performed based on the human reference hg19. It comprises:
- demultiplexing and adapter trimming of the sequencing data (FASTQ format),
- mapping of the sequencing data (BAM format), and
- delivery of detected fusion events (TSV format).
In addition to the data, a project report (PDF format) is provided.
Technical Information
At CeGaT, paired-end sequencing (2 x 100 bp) is performed using the Illumina sequencing platforms. If you require other sequencing parameters, please let us know! We can provide further solutions.
Gene Directory for FTP TUM TN/T, FTP PAT T, and FTP FUS T
Further Information About Focused Tumor Profiling
Cancer development is mainly a result of genetic mutations. On average, it takes 1 to 10 mutations for cancer to emerge, depending on the type of cancer. These mutations often occur in so-called cancer driver genes. The three main types of cancer driver genes are proto-oncogenes, tumor suppressor genes, and DNA repair genes.
Proto-oncogenes normally play a pivotal role in cell growth and division, helping cells to make new cells or stay alive. Mutations in proto-oncogenes can lead to unwanted activation of these genes, resulting in permanent initiation of cell growth and division processes. When mutations in the proto-oncogenes occur, these genes become oncogenes. Oncogenes can lead to uncontrollable growth of tumors, potentially leading to cancer. However, not only mutations can turn proto-oncogenes into oncogenes: epigenetic changes, chromosomal rearrangements, and gene duplications can also lead to permanent activation of oncogenes.
Tumor suppressor genes normally slow down cell division or induce programmed cell death, also known as apoptosis. Thus, they are the counterparts of the proto-oncogenes by stopping cells from dividing too fast. Mutations in tumor suppressor genes can interfere with their regulating role, potentially leading to uncontrolled cell division. One of the most mutated genes in human tumors is the tumor suppressor gene TP53.
During cell division, the DNA needs to be replicated. This process is error-prone, why cells have DNA repair genes. These genes help to repair the accrued replication errors. However, when the DNA repair genes are impaired due to mutations, they might not be able to repair replication errors properly, potentially resulting in an increasing number of mutations. Two prominent examples of DNA repair genes are BRCA1 and BRCA2.
Mutations in tumor-relevant genes, like proto-oncogenes, tumor suppressor genes, or DNA repair genes, can have crucial implications for targeted therapy approaches. Tumor-gene panels facilitate fast, efficient, and focused molecular profiling of tumors as only selected genes are sequenced and analyzed. Together with the determination of relevant biomarkers such as the tumor mutational burden (TMB), which measures the number of somatic mutations present in a tumor, the microsatellite instability (MSI) that is caused by the failure of the DNA repair system, and the homologous recombination deficiency (HRD) status that gives information about the cells ability to repair double-strand breaks, the detection of mutations in relevant genes can give valuable insights.
Our tumor gene panels cover known genes relevant to tumor emergence and cancer development. We offer a targeted molecular pathology panel. This FTP PAT T is our most focused tumor product, targeting 55 genes relevant to tumor disease. For a broader view of tumor-relevant genes, we developed our FTP TUM products, available as FTP TUM TN product, enabling a tumor-normal comparison, and FTP TUM T product, facilitating the focused analysis of a single tumor sample. As some pathogens are known to contribute to oncogenesis, our FTP TUM products additionally target selected cancer-relevant pathogens.
Cells with impaired DNA repair systems, especially cells with a homologous recombination deficiency, can accumulate double-strand breaks that are not properly repaired, leading to the emergence of chromosomal rearrangements. These chromosomal rearrangements can enable the fusion of genes. The emergence of such gene fusions can further promote the development of cancer as the fusion can deregulate genes, especially when oncogenes are involved in the gene fusions. To address the relevance of gene fusions, we have developed FTP FUS T, focusing on tumor-relevant fusions.
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Do you have a question or are you interested in our service? Feel free to contact us. We will take care of your request as soon as possible.
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We are happy to discuss sequencing options and to find a solution specifically tailored to your clinical study or research project.
When getting in contact, please specify sample information including starting material, number of samples, preferred library preparation option, preferred sequencing depth and required bioinformatic analysis level, if possible.
