Measurement of the biomarker TMB
Tumor mutational burden (TMB) is a biomarker that measures the number of somatic mutations present in a cancer patient’s tumor and is quantified as mutations per megabase (mut/Mb). This metric can be used in order to stratify patients for the best treatment choice and support the thriving development of new immunotherapy combinations. Another key immunotherapy biomarker is the microsatellite instability (MSI), which is caused by failure of the DNA mismatch repair system.
With German DAkkS ISO 15189 and American CAP/CLIA accreditation, CeGaT can offer quality assured TMB and MSI evaluation for your clinical and research study. Different options are available, depending on your needs and the availability of patient material.
Turnaround time
Sequencing data are delivered within 10 – 20 working days.
A fast track option is available upon request.
The turnaround time (TAT) highly depends on the quality of the provided DNA and the requested bioinformatics level.
Delivery
Your sequencing data will be available for download from our server.
Upon request, as well as for large sample batches, data can also be delivered via external hard drive, or upload to your own server.
Storage
The original samples and, if applicable, the isolated nucleic acids will be stored at CeGaT for a period of 3 months after data delivery.
Your data will be stored for 5 months.
Explore our TMB product portfolio
TIO Panel
Sequencing panel
Somatic Tumor Panel (CeGaT GmbH)
Gene panel size (Mb)
2.2
Number of analyzed genes
>700
Analysis of tumor and normal tissue
yes
Selection of our bioinformatic options
TMB, MSI, alignment, variant calling (SNVs/InDels), annotation and filtering
Based on the CeGaT bioinformatic pipeline
TIO Exome
Sequencing panel
Whole exome sequencing (Twist Bioscience)
Gene panel size (Mb)
37
Number of analyzed genes
~ 20,000
Analysis of tumor and normal tissue
yes
Selection of our bioinformatic options
TMB, MSI, alignment, variant calling (SNVs/InDels), annotation and filtering
Based on the CeGaT bioinformatic pipeline
TSO500
Sequencing panel
TruSight Oncology 500 (Illumina)
Gene panel size (Mb)
1.94
Number of analyzed genes
523
Analysis of tumor and normal tissue
no
Selection of our bioinformatic options*
TMB, MSI, alignment, variant calling (SNVs/InDels), annotation and filtering
Based on the TSO500 (Illumina) bioinformatic pipeline
TIO: Tumor Immuno-Oncology
*additional analysis of fusion and splice variants available using the TruSight Tumor 170 (Illumina) – RNA panel
Starting material: high-molecular weight DNA, or fragmented DNA (FFPE)
Bioinformatics
Raw sequencing data are automatically processed in order to facilitate immediate genetic evaluation. Included in delivery are demultiplexed, and adapter trimmed FastQ files, as well as the Tumor Mutational Burden (TMB) and the Microsatellite Instability (MSI) status.
Further options for bioinformatic analyses are available depending on the selected product:
- Alignment of trimmed sequencing data (BAM format)
- Calling of SNVs and InDels
- Annotation of SNVs and InDels (variant frequency and consequence, population frequency, dbSNP ID, position in protein, GNOMAD)
- Copy number variant and large homozygous deletions calling
- Cancer somatic mutation analysis (tumor and normal samples required)
- HLA class I typing based on exome sequencing data
- Fusion and splice variants*
*based on TSO500 RNA analysis
Technical Information
At CeGaT, paired-end sequencing (2 x 100 bp) is performed using state-of-the-art Illumina NovaSeq6000 Sequencing Systems.
If you require sequencing parameters other than those presented in our product portfolio, please let us know! We can provide further solutions.
Contact Us
Start Your Project Now
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 prep option, preferred sequencing depth and required bioinformatics, if possible.
Further Reading
Case Study: Automating NGS Library Preparation for TMB and MSI Analysis
Tumor Mutational Burden and Other Biomarkers Help to Assess the Efficacy of Immunotherapies
