Comprehensive profile of all mutations present in the exome
GATCLIQUID ONCOEXOME is the first non-invasive service to provide researchers and clinicians an overview of all protein- coding regions in the genome of a suspected cancer patient. The cancer exome sequencing tool offers the opportunity to discover novel variants, recurrent or frequent somatic mutations in circulating tumour DNA (ctDNA) in cases where limited information on tumour-associated genome instability exists.
Highlights of GATCLIQUID ONCOEXOME
- Analysis of novel and known tumour mutations in ctDNA based on next-generation sequencing (NGS)
- Optimised protocols for low-input ctDNA extraction from plasma
- Proprietary workflows for obtaining libraries of high complexity
- Expert data processing with QIAGEN Ingenuity Variant Analysis
Full-service package offered by GATCLIQUID ONCOEXOME includes the following:
- Cancer exome sequencing of circulating tumour DNA (ctDNA)
- Optimised protocols for library preparation with low duplicate rates
- Exome enrichment of more than 23,000 genes with the Agilent SureSelect V6 platform
- Mutation detection with sensitivity as low as 5% depending on gene loci
- NGS data analysis performed with industry-leading QIAGEN Ingenuity Variant Analysis application
- Entire process carried out according to ISO 17025
Accepted starting material for GATCLIQUID ONCOEXOME
- 4 mL plasma sample
- 15 ng already isolated cell-free DNA (up to 30 µl / concentration > 0,5 ng/µl)
Sequencing technology used for GATCLIQUID ONCOEXOME
- Illumina 150 bp paired-end sequencing
Bioinformatics analysis using Ingenuity® Variant Analysis
- Faster identification of relevant variants based on curated biological content from the Ingenuity Knowledge Base
- Prioritisation of most promising variants for further analysis
Deliverables of GATCLIQUID ONCOEXOME
- Alignment file (bam)
- SNP and InDel tables including annotated variants and effects (vcf, tsv, bed)
- Comprehensive Data Analysis Report (pdf)
The product is available for research use only (RUO).
Our one-stop Diagnostic Solution for tumour exome sequencing of ctDNA isolated from liquid biopsies offers clinicians and researchers stringent quality assurance throughout the entire process. The product includes a range of pre-sequencing services, starting from ctDNA isolation from low-input samples, to library preparation with reduced duplicate rates, as well as superior exon enrichment and uniform coverage with Agilent’s SureSelect latest chemistry.
The next-generation sequencing is carried out under diagnostic conditions and the bioinformatics analysis is performed with the industry’s leading tool, QIAGEN Ingenuity Variant Analysis.
Figure 1. Workflow GATCLIQUID ONCOEXOME
Typical applications for GATCLIQUID ONCOEXOME include the following:
- Tumour exome analysis of plasma ctDNA from a non-invasive blood test, where tissue biopsy is not feasible or recommended
- Examination of all mutations in the coding regions of a suspected cancer patient
- Cancer profiling in cases where limited information on tumour-associated mutations is available
- Discovery of structural variants, novel and common genomic alterations
- Comparison of exomes from tissue biopsy and liquid biopsy samples
- Selection of mutations for further analysis
GATCLIQUID ONCOEXOME can be used for clinical applications such as the following:
- Basic molecular profiling of carcinomatosis
- Confirmation of conventional diagnosis
The product is available for research use only (RUO).
1. What kind of samples can be processed with GATCLIQUID ONCOEXOME?
For ONCOEXOME, we accept fresh or retained plasma samples as well as already isolated cell-free DNA. Please refer to our GATCLIQUID sample preparation sheet (see "Files"). The ctDNA is extracted from the blood plasma fraction.
For starting material such as DNA isolated from FFPE and tissue samples, please refer to our product INVIEW HUMAN EXOME.
2. How much starting material is required?
In general we require either 4 mL of plasma or 15 ng already isolated cell-free DNA (up to 30 µl / concentration > 0,5 ng/µl).
3. What pre-sequencing services are available?
Several pre-sequencing services are included in the ONCOEXOME product. These include ctDNA extraction from plasma and high- complexity library preparation with low duplicate rates. Exon targeting is accomplished with Agilent’s SureSelect platform, which offers superior exon enrichment and coverage uniformity.
4. What sequencing coverage should I use?
The required coverage depends on the required sensitivity of variant detection. You may choose the sequencing coverage you need for your individual project study objective.
We typically recommend 100x coverage based on experience gained from analysing cell-free DNA from more than 40,000 samples to date.
5. What kind of quality controls do you perform?
The quality and quantity of each sample will be determined upon receiving the sample. Further quality controls are performed at various steps of the process.
6. How should I choose between ONCOEXOME, ONCOPANEL and ONCOTARGET?
All three tests are based on liquid biopsy. The three products serve as powerful non-invasive tools for real-time cancer profiling with the ability to capture the entire heterogeneity of the disease.
GATCLIQUID ONCOEXOME is the first commercially available service for whole exome sequencing (WES) of ctDNA. With this service, you can obtain a comprehensive profile of all mutations present in the protein-coding regions of the genome. This product is suitable for a preliminary look at the genome of a suspected cancer patient, in cases where limited information regarding clinically relevant mutations is available.
GATCLIQUID ONCOPANEL is a comprehensive NGS panel for profiling important cancer mutations. It uses single-molecule PCR to target 50 known cancer genes including tumour suppressors, mutation hotspots and drug-resistance markers. The panel sets a new industry standard in terms of sequence coverage and uniformity with a sensitivity of about 1%.
GATCLIQUID ONCOTARGET facilitates ultra-sensitive detection of clinically relevant cancer-specific point mutations, insertions, deletions and gene fusions in circulating tumour DNA down to an allele frequency of 0.1%. This approach is suitable for treatment monitoring as it is sensitive enough to detect a relapse at a very early stage.
7. How do I obtain my results and what form will they be in when delivered?
All deliverables can be downloaded via your secure myGATC online account.
8. How soon after the blood draw should I ship the sample?
Blood samples have to be shipped to GATC Biotech within 24 hours after drawing blood. The sample must be stored in BCT Streck tubes. Samples may be stored and delivered at room temperature. Plasma samples have to be shipped on dry ice.
9. How many samples can I submit?
GATC Biotech accepts any number of samples in multiples of four.
10. Where should I send my samples?
Please mail your samples to:
GATC Biotech AG
European Genome and Diagnostics Centre
Please do not use GATC Collection Points for shipping NextGen samples, because this will delay sample arrival at the appropriate destination.