The right answers to frequently asked questions
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What kind of samples can be processed with GATCLiquid Oncopanel All-In-One?
For GATCLiquid Oncopanel All-In-One, we accept fresh blood (must be provided in BCT with a stabilising buffer intended for the isolation of cfDNA) or plasma samples or retained plasma samples as well as already isolated cell-free DNA. Please refer to our sample preparation sheet. The extraction of cfDNA is performed from the blood plasma fraction.
For starting material like DNA isolated from FFPE and fresh-frozen tissue samples, please refer to our product aimed at solid tumour profiling, Inview Oncopanel All-In-One.
How much starting material is required?
We recommend the delivery of two 10 ml blood samples. The first 10 ml blood sample is used for testing, whereas the second sample can be stored as reserve material. For plasma samples the optimal amount is 4 ml. Please note, that with smaller plasma volumes the performance and sensitivity can decrease. Alternatively we accept 15 ng already isolated cell-free DNA (up to 30 µl / concentration > 0,5 ng/µl).
How is the target enrichment performed?
The genes of interests are enriched via proprietary Eurofins protocols using the latest Agilent SureSelect hybridisation technology. The target enrichment system captures genomic targets using long 120 nt RNA baits. The hybridisation-based strategy facilitates the deduction of PCR duplications in the assay. The Eurofins proprietary protocol enables the generation of highly complex libraries, deep coverage of regions of interest and improved sequence uniformity. Following target enrichment, next-generation sequencing of the library is performed.
What kind of mutations can be detected with GATCLiquid Oncopanel All-In-One?
The product interrogates the exons of about 600 genomic regions that are implicated in cancer development. Thereby, an extremely high number of possible mutations are covered and analysed. The detected genomic aberrations include SNPs, InDels, CNVs and gene fusion events.
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.
How should I choose between GATCLiquid Oncoexome, Oncopanel All-In-One and Oncotarget?
All three tests can be used with liquid biopsy samples (cfDNA). The three products serve as powerful non-invasive tools for cancer profiling.
GATCLiquid Oncoexome is the first commercially available service for whole exome sequencing (WES) of cfDNA. With this service, a comprehensive profile of all mutations present in the protein coding regions of the exome is obtained. This product is suitable for a comprehensive look at the exome of a cancer patient, in cases where limited information regarding clinically relevant mutations is available.
GATCLiquid Oncopanel All-In-One is a comprehensive NGS cancer panel for profiling important tumour-specific mutations implicated in nearly all cancer types. The service uses Agilent SureSelect with an optimized protocol to target about 600 known cancer genes including tumour suppressors, mutation hotspots and drug resistance markers. The panel is optimised for sequence coverage and uniformity with sensitivity down to 1%.
GATCLiquid Oncotarget facilitates ultra-sensitive detection of clinically relevant cancer-specific point mutations, insertions, deletions and gene fusions in circulating cell-free DNA down to an allele frequency of 0.1%. This approach is suitable for treatment monitoring as it has the appropriate sensitivity to detect a relapse at a very early stage.
Can I use GATCLiquid Oncopanel All-In-One for diagnostic purposes?
The product is available for research use only (RUO). All samples are processed compliant to ISO 17025:2005 accreditation.
What are the limitations of the CNV analysis?
Even when control samples (plasma samples from at least seven other patients/individuals) are submitted, the CNV analysis approach could be subjected to limitations. The sensitivity and specificity of the assay will depend on the level of CNVs present and the tumour fraction.
Will all copy number variations in my sample be detected?
Tumour heterogeneity could make it difficult to correctly identify all relevant copy number variations in a given plasma sample. In addition, excessive contamination with DNA from normal cells could lead to coverage differences that are too small to be detected even with Eurofins Genomics highly sensitive methods.
Where do I get my results?
All deliverables can be downloaded via your secure Ecom online account.
How soon after the blood draw should I ship the sample?
We recommend that the blood sample be shipped to Eurofins Genomics within 24 hours after blood drawing. The sample must be stored in BCT Streck tubes. Storage and delivery of blood samples must be at room temperature. Plasma samples have to be shipped on dry ice.
Where should I send my samples?
Eurofins Genomics Europe Sequencing GmbH