Solid Biopsy (OncoDEEP®)
Initiated for patients by oncology experts
10 years of knowledge that matters
Since 2013, OncoDNA has performed more than 100,000 tests, enabling us to build a comprehensive database (OncoKDO®) comprising 4,6 million variants across 22,000 genes, along with information on 1,600 drugs and 10,000 clinical trials. This vast repository of information allows OncoDNA to provide our clients with the most accurate and up-to-date molecular profiling for personalized cancer treatment.
An all-in-one solution with the largest panel in the market
OncoDEEP® Kit DNA & RNA panel is the largest and the most complete of the market. This panel is composed of probes targeting 638 genes for a final content of 1.8 Mb. It supports identification of all relevant variants involved in various solid tumor types with genes carefully selected based on their biological and therapeutical relevance.
In addition, specific sequences have been added to cover key regions associated with phenotypes of interest such as Tumor Mutational Burden (TMB), Microsatellite Instability (MSI), Loss Of Heterozygosity (LOH) in Tumor Suppressor Genes (TSGs), introns tilling for genes ALK/ROS1/RET and MET-ex14, sub-telomeric Single Nucleotide Polymorphisms (SNPs) for Homologous Recombination Deficiency (HRD) calculation and promoter of TERT.
A unique capture method for high quality data with less sequencing
OncoDEEP® Kit uses a unique Twist Biosciences’ capture method allowing high coverage and uniformity with less DNA/RNA input and less sequencing needed.
An easy process automatization
Thanks to the compatibility with Illumina’s technology, the easy automation process simplifies tasks by continuing using the current tools without disturbing the automate routine activities and losing time in extra training and manipulations.
Compatible with Illumina Technology
OncoDEEP® Kit has been meticulously designed to seamlessly integrate Illumina’s cutting-edge sequencing platforms, ensuring a streamlined and efficient workflow. This singular compatibility empowers researchers to concentrate on their scientific goals, free from the burden of technical obstacles. By optimizing the compatibility of
OncoDEEP® Kit, we strike the perfect balance between cost efficiency and constand precision, guaranteeing reliable results without compromising accuracy.
| Sequencer | NextSeq 500/550 2x75 cycles | NextSeq 2000 2x100 cycles | NovaSeq 6000 | |||
|---|---|---|---|---|---|---|
|
Flow-cell type |
Mid
Output |
High
Output |
P2 |
P3 |
SP |
S1 |
|
# of samples |
8 |
24 |
32 |
96 |
64 |
128 |
Achieving high-performance sequencing is now more accessible than ever, thanks to the OncoDEEP® Kit and Illumina sequencers. By utilizing these cutting-edge technologies, laboratories can process multiple samples per flow cell, as outlined in the Table above. This streamlined process allows faster and more efficient sequencing, resulting in more accurate data and better outcomes.
From sample preparation to clinical insights in just 5 days
OncoDEEP® Kit revolutionizes the diagnostic process by significantly reducing the timeline from DNA extraction to clinical and biological interpretation to just 5 days. This accelerated timeframe enables healthcare professionals to make faster decisions, resulting in enhanced patient care and improved outcomes.
Day 1: Extraction
- Extracted DNA and/or RNA from FFPE tumor tissue or unstained slides
Day 2: Library preparation
- DNA fragmentation, end repair & dA tailing
- Ligation Twist universal adapters and purification
- PCR amplification using Twist UDI Primers, purification and QC
Day 3: Target Enrichment
- Libraries preparation for hybridization
- Binding hybridized targets to streptavidin beads
- Post-capture PCR amplification, purification and QC
Day 4: Sequencing
- DNA concentration adjustment according to sequencer specifications
- Flow-cell loading
Day 5: Analyse and interpretation
- Upload FASTQ files
- Secondary and tertiary analysis via OncoDEEP pipeline
- Clinical and biological interpretation through OncoKDM
- QC visualization via Mercury
Clinically-relevant oncology targets and biomarkers
Designed by oncology experts, the OncoDEEP® panel contains the most relevant and complete cancer gene panel. Over the time this panel was optimized to include all clinically-relevant oncology targets. The panel is composed of 638 genes, reporting genomic alterations (SNV, insertion, deletion, CNV) and complex genetic signature (HRD, MSI and TMB).
Clear data insight and clinical interpretation
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
We use our proprietary knowledge base to perform tertiary analysis
Clinical validation by scientific team
Our team of oncology experts reviews each report
OncoKDM® ’s comprehensive interpretation reports provide labs with eight essential assets to enhance the understanding of NGS data, including detailed annotations, a list of actionable variants, a list of therapies recommendation and a summary of relevant clinical trials.
Extensive QC data visualization
Besides providing labs with QC data on sample quality such as read length and read quality, OncoKDM also offers genomic information at both the sample and gene levels.
Frequently Asked Questions
Which types of cancer is the OncoDEEP® Kit recommended for?
The OncoDEEP® Kit is recommended for a wide range of cancer types. Its comprehensive gene panel and ability to detect various genomic alterations make it applicable to solid tumors across different cancer types. It can help in identifying relevant variants and genetic signatures in cancers such as lung cancer, breast cancer, colorectal cancer, ovarian cancer, melanoma, and many others.
How long does it take to get my reports available in OncoKDM®?
How often do we update our annotation database / information?
We regularly update our annotation database and information to ensure that it reflects the most relevant and accurate information for clinical interpretation and decision-making. The frequency of updates may vary, but it is done on a regular basis to incorporate new scientific discoveries, clinical findings, and emerging genomic data.
Can I edit the analysis report after it has been published in OncoKDM®?
Depending on your workspace configuration, you can edit almost every part of the report until you validate it. Every change is recorded and can be reviewed in the report’s history of changes.
How many genes are covered by OncoDEEP® Kit panel?
