The right answers to frequently asked questions
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What kind of samples can be processed with Inview Oncopanel All-In-One?
For the INVIEW Oncopanel, 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 GATCLiquid Oncopanel All-In-One product.
How is the target enrichment performed?
The genes of interests are enriched via a proprietary Eurofins protocols. Target enrichment approach outcompetes common PCR-based enrichment with very uniform coverage and all exons of the genes covered. The proven target enrichment method has been optimised by Eurofins to develop highly complex libraries from low DNA and to deliver deep and uniform sequence coverage. Following target capture, next-generation sequencing of the library is performed.
What kind of mutations can be detected with Inview Oncopanel All-In-One?
The service fully covers the entire exons of about 600 cancer-relevant genomic regions, including protein-coding genes, select promoter regions, miRNAs, extra-exonic variants and select fusion gene events. In addition to SNPs and InDels, the product can also detect CNVs.
How is the tumor mutational burden (TMB) calculated?
- 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.
Is a focused gene panel, like Oncopanel All-In-One, suitable for TMB determination in comparison to whole-exome sequencing (WES)?
Although the gold standard for TMB determination is whole-exome sequencing (WES), focused panels, like the Oncopanel All-In-One v2.0, 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, Oncopanel All-In-One 2.0’s size of 3 Mbp provides more precise TMB estimates than other smaller panels.
What is the sensitivity of the product?
SNP and InDel detection has a technical sensitivity down to 1%.
What kind of quality controls do you perform?
The quality and quantity of each sample will be determined at sample receipt or after DNA extraction. Further quality controls are performed at various steps of the process.
What is the difference between Inview Oncopanel All-In-One and GATCLiquid Oncopanel All-In-One?
Both tests offer cancer variant detection services based on a validated oncology panel. The interrogated genes and genomic alterations of the panel are the same. Similarly, the techniques used for both products are based on hybridisation for target enrichment and next-generation sequencing.
The two products differ in their starting material. Inview Oncopanel All-In-One can accept conventional source material like fresh-frozen and FFPE tissues, whereas GATCLiquid Oncopanel All-In-One analyses cfDNA extracted from blood plasma samples.
Can I directly compare results between Inview Oncopanel All-In-One and GATCLiquid Oncopanel All-In-One?
Yes, the two services are ideally suited for studies aimed at comparing the performance of traditional biopsies versus liquid biopsies.
What are the limitations of the CNV analysis?
Even when matched samples (tumour tissue and normal tissue or blood from the same patient) are submitted, the paired analysis approach could be subjected to limitations. The measurement variance on this single matched reference sample will be higher than that for a reference consisting of multiple reference samples. This could cause a modest number of (false-positive) CNV calls even in cases where the two paired samples are truly copy number identical.
Will all variants in my sample be detected?
Tumour heterogeneity could make it difficult to correctly identify all relevant copy number variations in a given sample. Even when the tumour itself is homogeneous, excessive contamination of normal cells within a tumour sample could lead to coverage differences that are too small to be detected even with Eurofins Genomics highly sensitive methods.
Can I use Inview Oncopanel All-In-One for diagnostic purposes?
The product is available for research use only (RUO). The service is performed in an ISO17025:2005 –accredited and ISO13485:2016-certified laboratory.
Where do I get my results and in which form are they delivered?
All deliverables (FAST-Q files and analyzed data) can be downloaded via your secure online account.
Where should I send my samples?
Eurofins Genomics Europe Sequencing GmbH