FAQs Next Generation Sequencing

• General FAQs for Next Generation Sequencing >>

For the INVIEW Oncoprofiling, we accept fresh-frozen and FFPE tissue and genomic DNA.

For liquid biopsy analysis of cell-free DNA (cfDNA) isolated from blood plasma, please refer to our INVIEW Liquid Biopsy Oncoprofiling product.

Genes of interest are enriched using Eurofins’ proprietary protocols built on Agilent SureSelect technology. This target enrichment approach outperforms traditional PCR-based methods by providing highly uniform coverage and complete exon representation. Optimized by Eurofins, the method enables the creation of complex libraries from low-input DNA, ensuring deep and consistent sequencing coverage. After target capture, the enriched libraries undergo next-generation sequencing to deliver accurate and comprehensive genomic data.

The service provides complete coverage of all exons from approximately 728 cancer-relevant genes, along with:

• Selected promoter regions
• 81 microRNAs (miRNAs)
• 5 additional promoter regions
• 281 extra-exonic variants, including introns, regulatory elements, untranslated regions (UTRs), and intergenic regions

For a detailed list of all genes and targeted regions, please contact us.

• TMB is defined as the number of somatic, coding, base substitution, and InDel mutations per megabase of genome examined. All base substitutions and InDels in the coding region of targeted genes, including synonymous mutations, are initially counted before filtering as outlined below.
• The following mutations are excluded in silico from the TMB computation: Known somatic mutations in COSMIC and ClinVar, low-confident mutations, known germline variants in the ExAC (gnomAD) database, mutations predicted to be germline by the somatic-germline-zygosity algorithm, and mutations in tumor suppressor genes due to the focus of the Oncopanel All-In-One on actionable cancer mutations and potential panel design bias.
• To calculate the TMB per megabase, the total number of mutations counted is normalized by the size of the coding region of the targeted region in megabase (mutations per megabase, mut/MB). Due to the lack of standardization in TMB quantification we provide three TMB values:
  • Non-synonymous mutations
  • Non-synonymous mutations and plus indels and iii) including all mutations.

Although the gold standard for TMB determination is whole-exome sequencing (WES), focused panels, like the INVIEW Oncoprofiling, have been evaluated extensively for TMB estimation because of their lower sequencing cost and higher sensitivity. Recent research shows, that panels with a size > 1.5 Mbp are sufficiently suited to determine TMB with a high concordance to WES (Buchhalter et al. 2019, Int J Cancer 144:848–858). Thus, INVIEW Oncoprofiling's size of 3 Mbp provides more precise TMB estimates than other smaller panels.

Depending on the input DNA quality and genomic region, the limit of detection (LOD) for SNP and InDel variants is a minor allele frequency as low as 1%. 

Upon receipt or following DNA extraction, we assess the quality and quantity of each sample. Additional quality control checks are conducted throughout multiple stages of the workflow to ensure accuracy and reliability of the results.

Choosing between Clinical Research Exome - CRE V4 and INVIEW Oncoprofiling depends on your research or clinical goals:

• Clinical Research Exome - CRE V4 offers broad coverage of the entire exome, allowing comprehensive detection of variants across all coding regions. It’s ideal if you want to explore a wide range of genes beyond a specific set or discover novel mutations.
• INVIEW Oncoprofiling targets a focused panel of cancer-relevant genes and regions, providing deep coverage optimized for known clinically actionable mutations. It’s best suited for targeted cancer diagnostics or when you need high sensitivity in specific genes.

If you require wide discovery and broader variant detection, go with CRE V4. For a targeted, high-depth analysis of established cancer markers, Oncoprofiling is the better choice.

Yes, the two services are ideally suited for studies aimed at comparing the performance of traditional biopsies versus liquid biopsies.

Even with control samples (plasma from at least seven different individuals) included, the CNV analysis may face certain limitations. The assay’s sensitivity and specificity are influenced by the abundance of CNVs and the tumor fraction present in the sample.

Tumor heterogeneity can complicate the accurate detection of all relevant copy number variations in a plasma sample. Additionally, high levels of contamination from normal cell DNA may reduce coverage differences below the detection threshold, even when using Eurofins Genomics’ highly sensitive methods.

The product is available for research use only (RUO). All samples are processed compliant to ISO 17025:2005 accreditation.