Comprehensive Pan-tumor Solution
Comprehensive pan-tumor profiling of solid tumor is made possible with OncoDEEP® DNA and RNA Kit solutions. Designed for use with the powerful Next Generation Sequencing (NGS) technology, OncoDEEP® Kits can easily and quickly identify a vast number of relevant biomarkers in a patient’s tumor that could be associated with potential therapeutic recommendations. OncoDEEP® DNA and RNA kits are strategically designed based on biological and therapeutic relevance, with the panel probes targeting 638 genes and 22 driver genes, respectively.
The OncoDEEP® DNA Kit is the most comprehensive solution available to laboratories, capable of detecting biomarkers in 638 genes (SNV, indels, CNV) and 3 FDA-approved companion diagnostic (CDx) genomic signatures in parallel : tumor mutational burden (TMB), microsatellite instability (MSI) & homologous recombination deficiency (HRD). In addition to exonic fusion detection, introns tilling designed for genes ALK/ROS1/RET and Met-ex14. In addition the OncoDEEP® DNA Kit also allows detection of CDx rearrangement biomarkers derived from intronic breakpoints; which has been proven especially beneficial for non-small cell lung cancer patients whom biopsy quantity could be limiting for both DNA and RNA analysis.
In summary the OncoDEEP® RNA Kit is a compact panel carefully designed with all key relevant driver genes, tactically created to reduce the cost of sequencing yet fulfilling the requirements to identify all relevant CDx biomarkers related to cancer treatment.
| DNA (638 genes) | |||||
|---|---|---|---|---|---|
|
Genes alteration |
SNV |
CNV |
INSERTION |
DELETION |
LOH |
|
Complex signatures |
HRD |
MSI |
TMB |
||
|
Translocation (intronic) |
ALK |
ROS1 |
RET |
MET-EX14 |
|
| RNA (22 driver genes) | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Genes fusions |
ALK |
ROS1 |
RET |
FGFR1 |
FGFR2 |
FGFR3 |
NTRK1 |
NTRK2 |
NTRK3 |
BRAF |
NRG1 |
EWSR1 |
TMPRSS2 |
|
Unusual Splicing |
BRCA1 |
BRCA2 |
PTEN |
AR |
EGFR |
ERBB2 |
MET |
PALB2 |
RB1 |
||||
Table 1. OncoDEEP product detail : list of DNA/RNA genes (read more)
The OncoDEEP kit has been compared with Illumina TSO500 by a group of independent users in a multicenter study. Known samples were tested using OncoDEEP reagents and interpretation software. The data presented below is based on the results of this study, which were showcased at the AACR and AMP conferences.
Exceptional Coverage Uniformity
OncoDEEP® DNA and RNA Kits are built based on TWIST Bioscience chemistry, enabling OncoDNA to achieve superior enrichment and sequencing efficiency, resulting in improved coverage uniformity. Coverage uniformity indicates how evenly distributed individual reads are across the region of interest. Improved uniformity increases the percentage of bases covered at the desired depth for all intended targets; resulting in higher confidence in variant detection and also aiding a reduction in the amount of over sequencing.
OncoDEEP® Kits have proven to provide exceptional coverage uniformity for the intended targets, and as a result shown vast improvement as compared to TSO500 (Figure 1).
Figure 1. Distribution of the median coverage obtained with
TSO500 (blue) and OncoDEEP (red) (SD 217 vs 145)
illustrating the higher uniformity of the OncoDEEP capture (1).
Cost Reduction, up to 3X More Samples per Flow Cell
One of the great benefits of achieving exceptional coverage uniformity with OncoDEEP® Kits is the ability to sequence more samples with the same budget without sacrificing the quality of the result. Having eliminated the need to over sequence, OncoDEEP® Kits provide users with the ability to pool more samples on the sequencing platform, ultimately leading to cost reduction. It has been reported that OncoDEEP® DNA Kit supports pooling of at least 3X more samples when compared to TSO500.
Quality Assured
Quality assurance based on result concordancy between OncoDEEP® Kits and TSO500 was validated using 234 diagnostic DNA and RNA samples (various tumor types), together with 12 DNA and 8 RNA references, on either Illumina NextSeq500/550 or NovaSeq sequencers. Good alignment between both assays has been reported, evidenced by the high concordance.
The concordant study was also performed for the pan-cancer biomarkers, TMB and MSI. Threshold calling between the two assays tends to differ slightly, nevertheless, they are reported to be in line and in general there is good alignment between both assays. The TSO500 HRD assay is an supplementary panel that needs to be added separately to the TSO500 assay. Therefore, for this study, only samples with available HRD results were partially analyzed for concordance with HRD. The analysis demonstrated concordance in these cases.
Due to the unavailability of loss of heterozygosity (LOH) and HRD analysis on the TSO500 assay, concordance studies as such were not feasible with the OncoDEEP® DNA Kit.
Additionally, 82 of the diagnostic samples and 8 reference samples were tested in a validation setup and shown to be successful based on assay precision, sensitivity, specificity, accuracy and limit-of-detection.
Ease of Use & Reduced Chance of Human Error
In addition to developing OncoDEEP® DNA and RNA Kits capable of achieving high quality assurance, OncoDNA also explored the possibility to improve the kits’ ease of use to ensure high levels of customer satisfaction. Both the OncoDEEP® DNA and RNA Kits have been reported to reduce manual effort from 5 hours to 4 hours when compared with TSO500. The reduction in manual effort is made possible as a result of (1) OncoDEEP® single hybridization step compared to TSO500 2-step hybridization & (2) OncoDEEP® feasibility for sample pooling before hybridization (up to 8 samples), a feature not possible with TSO500. Furthermore, with a more simplified protocol supporting easier management of samples, the use of OncoDEEP can also greatly reduce the possibility of human error and/or contamination.
| TSO500 (Illumina) | OncoDEEP (OncoDNA) | |
| Pre-analytics | ||
| Recommended input | DNA : 40 ng RNA : 40 ng |
DNA : 30-100 ng RNA : 50-200 ng (dried) |
| Library Prep | ||
| DNA Fragmentation method Normalisation |
Shearing With Bead |
Enzymatic (no need for additional instrument) Quantification and dilution |
| Hybridization capture | ||
| Pooling before hyb # Hybridization steps |
No |
Yes (8 samples) 1 |
| Sequencing on a NextSeq550 | ||
| Read length # Samples per run Flowcell NextSeq550Dx |
101 bp 8 (DNA + RNA) High output Kit v2.5 (300 cycle) |
74 bp 24 (DNA + RNA) High output Kit v2.5 (150 cycle) |
| Data analysis | ||
| Secondary analysis Tertiary analysis |
TSO500 local app (*) or any other tertiary analysis tool |
OncoKDM OncoKDM |
| Wet lab |
||
| Hands-on-time Cost/sample |
5 h $$$ |
4 h $$ |
* At the time of the study, TSO500 users utilized the local application. Since then, alternative software solutions have been released. For the latest updates, please refer to the Illumina website.
Table 2. Comparison of TSO500 and OncoDEEP assay features (1).
All in One Data Analysis
OncoDEEP® DNA and RNA Kits are underpinned by an all-in-one data analysis solution. OncoKDM®, a BioIT analytical tool developed by OncoDNA, is interactive and user friendly; with the capability to process primary, secondary, tertiary analysis and ultimately generate actionable patient reports in less than 48 hours via this single platform.
OncoKDM® draws knowledge from OncoKDO™, OncoDNA’s proprietary database proprietary database counting no less than 4,500,000 genetic variants, 1,400 cancer drugs, and data from 9,000 clinical trials; seamlessly facilitating clinical interpretation (tertiary analysis) and generating actionable reports with therapeutic recommendations, a feature currently lacking alongside TSO500.
Easy sequencing files upload
After the sequencing, output files (FASTQ + Medata files) are uploaded
Variants identification & annotation
Our BioIT pipeline performs the secondary analysis of genomic data
Data cross-referencing with our proprietary knowledge base
Use of the proprietary knowledge base OncoKDO enables tertiary analysis
Clinical validation by scientific team
Finally OncoDNA's team of oncology experts reviews each report
Authors : Hendrikus Jan Dubbink, Pieter-Jan Volders, Joni Van der Meulen, Aaron De Cock, Stefanie Vermeire, Jacques Van Huysse, Marie De Barsy, Gabriela Beniuga, Zeliha Ozgur, Wendy de Leng, Anne Jansen, Ernst-Jan Speel, Imke Demers, Wilfred van Ijcken, Brigitte Maes and Guy Froyen
