GATCLIQUID ONCOPANEL ALL-IN-ONE
Reliable detection of cancer-associated mutations in 597 genes from liquid biopsy samples
GATCLIQUID ONCOPANEL ALL-IN-ONE offers the most comprehensive cancer gene panel testing of liquid biopsy samples in the world. The service fully covers the exons of about 600 cancer-relevant genomic regions, including protein-coding genes, selected promoter regions and fusion gene events. The service is the first of its kind to enable the detection of structural variants, including copy number variations and fusion events from circulating tumour DNA (ctDNA). The broad coverage of oncogenic alterations enables the non-invasive investigation for nearly any kind of tumour type.
Highlights GATCLIQUID ONCOPANEL ALL-IN-ONE
- Screening of ctDNA isolated from blood plasma for 597 key cancer-associated genes
- Efficient capture of all exons of the targeted genes
- Analysis of structural and copy number variants (see “Product Details”)
- Industry leading sequence coverage and uniformity
- Limit of quantification (LOQ) down to an allele frequency of 1%
Full service package offered by GATCLIQUID ONCOPANEL ALL-IN-ONE including
- Reproducible cell-free DNA (cfDNA) analysis of whole exons of 597 protein-coding genes and selected promoter regions
- Accurate characterisation of single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels)
- Reliable detection of gene fusions between the covered genes plus 20 additional cancer-specific gene fusions
- Proprietary protocols for cfDNA extraction and library preparation from plasma samples
- Superior target enrichment efficiency using optimised hybridisation techniques with latest Agilent SureSelect chemistry
- Highly sensitive assay with a lower detection limit down to 1% tumor allele frequency
- Professional bioinformatical analysis complemented with QIAGEN’s Ingenuity Variant Analysis platform
- Analysis of copy number variations (CNV)s possible*
*CNV analysis using GATCLIQUID ONCOPANEL ALL-IN-ONE has to be performed with the appropriate control group. Please send us plasma samples from at least seven other patients/individuals in order to correctly identify somatic CNVs in a given sample.
Accepted starting material for GATCLIQUID ONCOPANEL ALL-IN-ONE
- 10 ml blood
- 4 ml plasma*
- 15 ng already isolated cell-free DNA (up to 30 µl / concentration > 0,5 ng/µl)
* If possible, please provide an additional aliquot. Prepare plasma according to provided protocol (See Files). Ship plasma on dry ice. Thawing of the plasma will lead to degradation of the cell-free DNA (cfDNA).
Technology used for GATCLIQUID ONCOPANEL ALL-IN-ONE
- Hybridisation-based target capture using proprietary protocols and latest Agilent SureSelect technology
- Next-generation sequencing on Illumina platform
Deliverables of GATCLIQUID 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).
GATCLIQUID ONCOPANEL ALL-IN-ONE offers the most in-depth approach for tumour mutation profiling from plasma cell-free (cfDNA) via a targeted cancer gene panel. As a powerful non-invasive tool, this tumour panel enables monitoring of cancer specific mutations with high fidelity and sensitivity. The analysed material, ctDNA, is described as a specific and sensitive biomarker in multiple human cancers, which allows for comprehensive molecular profiling of the tumour. This cancer panel enables the detection of about 600 clinically actionable genomic regions, including frequently mutated genes, such as BRAF, KRAS, EGFR, PIK3CA, HER2 and TP53. The scope of this mutation panel makes the product perfectly suitable for the investigation of nearly any type of cancer, including melanoma, bladder cancer, ovarian cancer, breast cancer, colorectal cancer, prostate cancer, thyroid cancer, kidney cancer, liver cancer and lung cancer.
Figure 1. Workflow GATCLIQUID ONCOPANEL ALL-IN-ONE
Typical applications for GATCLIQUID ONCOPANEL ALL-IN-ONE include:
- Non-invasive screening for clinically relevant tumour-associated mutations
- Comparison of matched samples from tumour biopsies and liquid biopsies
- Research on mechanisms of cancer progression
- Selection of the most-relevant mutation for follow-up studies with GATCLIQUID ONCOTARGET
1. 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.
2. 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).
3. How is the target enrichment performed?
The genes of interests are enriched via proprietary GATC 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 GATC 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.
4. 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.
5. What is the sensitivity of the product?
SNP and InDel detection has a technical sensitivity down to 1%.
6. 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.
7. 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 GATC 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.
8. 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.
9. 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.
10. 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 GATC Biotech’s highly sensitive methods.
11. Where do I get my results?
All deliverables can be downloaded via your secure myGATC online account.
12. How soon after the blood draw should I ship the sample?
We recommend that the blood sample be shipped to GATC Biotech 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.
13. 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!