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

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