Comprehensive genomic profiling based on the analysis of tumor tissue
The changing paradigm – away from a one-size-fits-all approach toward precision medicine – raises the importance of comprehensive genomic profiling (CGP) of tumor samples. Comprehensive genomic profiling refers to the simultaneous evaluation of several biomarkers within one analysis. This approach not only enables detecting the most relevant predictive markers for current targeted therapies but also key immuno-oncology biomarkers, such as TMB and MSI. 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). Another key immunotherapy biomarker is microsatellite instability (MSI), which is caused by the failure of the DNA mismatch repair system.
The application areas of CGP are manifold, with a focus on:
- Stratifying patients for the best treatment choice
- Identifying patients eligible for clinical trials
- Driving clinical research, especially in the area of immune therapy
Turnaround time
Sequencing data are delivered within 20 – 30 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
We offer three different approaches depending on your needs and the availability of patient material:
- TIO Panel: CeGaT’s “Somatic Tumor Panel” covers the analysis of more than 760 cancer-associated genes, as well as 31 selected, therapy-relevant fusions at a high sequencing coverage of 500 – 1.000 x.
- TIO Exome: the analysis of the whole exome offers maximal insights into more than 20.000 genes.
- TSO500: this product from Illumina covers the accurate analysis of 523 tumor-associated genes. In addition, TMB and MSI evaluation can be performed without the need for tumor/normal comparison.
TIO Panel
Sequencing panel
Somatic Tumor Panel (CeGaT GmbH)
Gene panel size (Mb)
2.2
Number of analyzed genes
>760
Analysis of tumor and normal tissue
Yes
Starting material
Fresh frozen tissue, FFPE tissue, high-molecular weight DNA, or fragmented DNA (FFPE)**
Deliverables
TMB, MSI, alignment, variant calling and annotation (SNVs/InDels), copy number variants (CNVs), project report
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
Starting material
Fresh frozen tissue, FFPE tissue, high-molecular weight DNA, or fragmented DNA (FFPE) **
Deliverables
TMB, MSI, alignment, variant calling and annotation (SNVs/InDels), copy number variants (CNVs), project report
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
Not required
Starting material
Fresh frozen tissue, FFPE tissue, high-molecular weight DNA, or fragmented DNA (FFPE) **
Deliverables
TMB, MSI, alignment, variant calling and annotation (SNVs/InDels), copy number variants (CNVs), project report
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)
** for comprehensive genomic profiling based on the analysis of liquid biopsies (ctDNA), please check our liquid biopsy product portfolio.
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 indel
- Annotation of SNVs and indels (variant frequency and consequence, population frequency, dbSNP ID, position in protein, GNOMAD)
- Copy number variant (CNV) 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 TruSight Tumor 170 RNA panel
Technical Information
At CeGaT, paired-end sequencing (2 x 100 bp) is performed using state-of-the-art Illumina NovaSeq 6000 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
