INVIEW ONCOPANEL ALL-IN-ONE
Validated cancer panel for analysis of 597 key cancer-specific genes from tissue biopsy samples
INVIEW ONCOPANEL ALL-IN-ONE is the most comprehensive gene panel available for optimised detection of tumour-specific genomic alterations. The oncology panel is optimised for formalin-fixed paraffin embedded (FFPE) or fresh-frozen tissue samples to deliver accurate genomic information on the status of clinically relevant driver mutations. This solid tumour panel uniformly and reproducibly covers the entire exons of about 600 characterised cancer genes, including tumour activators, tumour suppressors and biomarkers for drug resistance.
Highlights INVIEW ONCOPANEL ALL-IN-ONE
- Highly uniform coverage of all exons in 597 cancer-associated genes
- Detection of relevant structural rearrangements and copy number variations (see “Product Details”)
- Ultra-sensitive detection levels down to 1% allele frequency
- Proprietary protocols for DNA library preparation from challenging tissue and FFPE samples
Full service package offered by INVIEW ONCOPANEL ALL-IN-ONE including
- Validated next-generation sequencing (NGS) cancer gene panel for analysis of key tumour-associated mutations in 597 protein-coding genes and select promoter regions
- Reproducible detection of single nucleotide polymorphisms (SNPs), insertions and deletions (InDels)
- Accurate detection of gene fusions between all covered genes, as well as 20 additional cancer-associated gene fusions
- Highly efficient target enrichment with latest Agilent SureSelect technology
- Reduced PCR-bias thanks to hybridisation-based target capture approach
- Industry-leading sequence coverage and uniformity
- Detection of variants with sensitivity levels down to 1%
- Optimised protocols for DNA library preparation from FFPE or fresh-frozen tissue samples
- Professional bioinformatical analysis with optional use of QIAGEN’s Ingenuity Variant Analysis software
- Analysis of copy number variations (CNVs) possible*
*CNV analysis has to be performed in paired analysis of tumour versus matched normal tissue which is used as reference. In the case of tumour FFPE samples, either send a healthy tissue FFPE sample from the same patient, or tumour FFPE samples from at least seven other patients. For fresh frozen tissue, either send blood or healthy tissue from the same patient or fresh frozen tissue from at least seven other patients or controls.
Accepted starting material for INVIEW ONCOPANEL ALL-IN-ONE
- FFPE tissue
- Fresh-frozen tissue
Technology used for INVIEW ONCOPANEL ALL-IN-ONE
- Hybridisation-based target capture using GATC optimised protocols and latest Agilent SureSelect technology
- Next-generation sequencing on Illumina platform
Deliverables of INVIEW ONCOPANEL ALL-IN-ONE
- FastQ Files (sequences and quality scores)
- Alignment file (bam)
- SNP and InDel tables including annotated variants and effects (vcf, tsv)
- Tables of copy gain and copy loss events (tsv)
- Table of gene fusion events (tsv)
- Comprehensive Data Analysis Report (pdf)
The product is available for research use only (RUO).
INVIEW ONCOPANEL ALL-IN-ONE, as the most comprehensive cancer panel in the world, offers the unique opportunity to explore hundreds of well-known cancer genes with a single panel. Clinical researchers can now confidently use a single test to detect multiple driver mutations in any type of solid tumour. Thanks to a proven target enrichment strategy and proprietary protocols, the targeted gene panel enables the sensitive analysis of actionable mutations in about 600 cancer-associated genes. The service is the first of its kind to investigate structural variants and CNVs, in addition to SNPs and InDels from FFPE and tissue biopsy samples. The oncology panel can be used to derive meaningful information on key driver mutations in order to provide fast, cost-efficient and reliable cancer screening.
Figure 1. Workflow INVIEW ONCOPANEL ALL-IN-ONE
Typical applications for INVIEW ONCOPANEL ALL-IN-ONE include:
- Comparative analysis of data from tissue biopsy and liquid biopsy (GATCLIQUID ONCOPANEL ALL-IN-ONE)
- Cancer screening by detection of well-known tumour-associated mutations such as driver mutations
- Determination of most important mutations for further studies
INVIEW ONCOPANEL is suitable for clinical applications like:
- Molecular stratification
- Detection of resistance genes
- Guidance for treatment decisions
- Assignment of patients to clinical trials
- Post-treatment follow-up, especially for monitoring of multiple mutations
1. What kind of samples can be processed with INVIEW ONCOPANEL ALL-IN-ONE?
For INVIEW ONCOPANEL, we accept fresh-frozen and FFPE tissue and blood samples.
For liquid biopsy analysis of cell-free DNA (cfDNA) isolated from blood plasma, please refer to our GATCLIQUID ONCOPANEL ALL-IN-ONE product.
2. How is the target enrichment performed?
The genes of interests are enriched via a proprietary GATC protocols using Agilent SureSelect chemistry. The hybridisation-based strategy eliminates PCR-bias and reduces the number of PCR duplications. The proven target enrichment method has been optimised by GATC Biotech 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.
3. 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 and select fusion gene events. In addition to SNPs and InDels, the product can also detect CNVs.
4. What is the sensitivity of the product?
SNP and InDel detection has a technical sensitivity down to 1%.
5. 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.
6. 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.
7. 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.
8. 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.
9. 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 GATC Biotech’s highly sensitive methods.
10. 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.
11. Where do I get my results and in which form are they delivered?
All deliverables can be downloaded via your secure myGATC online account.
12. Where should I send my samples
Please post your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Please do not use GATC Collection Points for shipment of NextGen samples, because this will cause delay in sample arrival at the appropriate destination!