Comprehensive Genomic Profiling of Solid Tumor Patients for Broad Analysis in clinical diagnostics – A Comparative Analysis of OncoDEEP® Kit and Illumina TSO500

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)

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).

exceptional coverage uniformity

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 inputDNA : 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
2 overnight
Yes (8 samples)
1 overnight
 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
ICI software required
OncoKDM
OncoKDM
 Wet lab
Overall duration including sequencing3 days1,5 – 2,5 days

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

Easy sequencing files upload

After the sequencing, output files (Fastq + medata files) are uploaded to secured storage to automatically launch a batch of samples.

Variants identification & annotation

Our BioIT pipeline performs the secondary analysis of genomic data

Variants identification & annotation

The BioIT pipeline performs the secondary analysis of genomic data by aligning the data, identifying, annotating and classifying the variants, and eliminating bias.

Data cross-referencing with our proprietary knowledge base

Use of the proprietary knowledge base OncoKDO enables tertiary analysis

Data cross-referencing with our proprietary knowledge base

Use of the proprietary knowledge base OncoKDO enables tertiary analysis by cross-referencing molecular data, resulting in the clinical interpretation of the data.

Clinical validation by scientific team

Finally OncoDNA's team of oncology experts reviews each report

Clinical validation by scientific team

Finally OncoDNA’s team of oncology experts reviews every report before making it available in OncoKDM® meaning there is a ‘human touch’in the technology process.

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

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