638 DNA + 22 RNA
638 DNA genes and 22 RNA driver genes for detecting novel and clinically relevant fusions (ALK, ROS1, RET, MET-ex14).
Comprehensive Genomic Profiling
OncoDEEP® — comprehensive profiling of solid tumours
OncoDNA's most comprehensive biomarker test. A single multiplex assay covers 638 DNA genes and 22 RNA drivers: SNVs, indels, CNVs, fusions, TMB, MSI, HRD and LOH from a standard FFPE sample. The aim: to guide the oncologist to the right treatment for an advanced solid tumour.
- 638 DNA genes in the panel
- 22 RNA driver genes for fusions
- 1.8 Mb Targeted panel content
- 5 days From DNA to clinical report
About the test
End-to-end solution from sample to clinical report
OncoDEEP® is a CE-IVD certified test (IVDR certification in progress) for comprehensive genomic profiling of solid tumours. From a single FFPE sample, it detects all clinically relevant variants across solid tumour types: lung, breast, colorectal, ovarian and melanoma.
The test includes not only the library preparation kit, but also secondary and tertiary analysis in the proprietary OncoKDM database and a clinical report in the user-friendly OncoKDM® software, with recommended treatment, active clinical trials and bibliography.
Specifications
What OncoDEEP® delivers in one assay
TMB, MSI, HRD, LOH
A complete range of signatures: Tumour Mutational Burden, Microsatellite Instability, Homologous Recombination Deficiency and LOH in tumour-suppressor genes.
SNVs, indels, CNVs
Point mutations, small indels, copy-number variants and TERT promoter alterations in a single multiplex assay.
FFPE sample
Standard FFPE material, with no need for fresh-frozen tissue or a special sample collection. Compatible with the standard pathology pipeline.
CE-IVD certified
The kit is certified as a CE In Vitro Diagnostic. IVDR certification is in progress, in line with European regulation.
Multi-platform NGS
Compatible with Illumina NovaSeq 6000, NextSeq 2000, MGI DNBseq G400 and Element Aviti, depending on your laboratory's equipment.
Workflow
From extraction to report in 5 days
The complete pipeline runs in your own laboratory. OncoDNA provides the kit, clinical interpretation in the OncoKDM database and the final report in the OncoKDM® interface within 48 hours of the sequencing data being uploaded.
- 1
DNA/RNA extraction
Standard nucleic acid extraction from the FFPE sample as input for library prep.
- 2
Library preparation
Sequencing library preparation, fully automated on Opentrons Flex (see below).
- 3
Sequencing
Compatible with Illumina NovaSeq / NextSeq, MGI DNBseq G400 or Element Aviti, depending on your laboratory's equipment.
- 4
OncoKDM analysis
Patented algorithm with expert curation since 2012: daily specialist review and continuous updates based on new publications.
- 5
OncoKDM® report
Clinical report within 48 hours: variants, recommended treatment, active clinical trials, bibliography and QC metrics.
Automation
Library prep on Opentrons Flex
The OncoDEEP® library preparation kit is fully automation-ready on the Opentrons Flex platform. The robot takes over the entire library preparation workflow, from pipetting reaction mixes and SPRI magnetic bead clean-ups to equimolar pooling. The laboratory gets reproducible, scalable results without routine pipetting.
The automated workflow reduces hands-on time to a minimum, increases throughput and removes common sources of variability. Turnaround for the whole kit (extraction → sequencer) drops to as little as 48 hours, with consistent results across batches and operators.
Less hands-on time
Routine pipetting and clean-ups are handed over to the robot. The technician only handles sample loading and QC.
Higher reproducibility
The same protocol and the same results across operators and shifts, without human-error variance.
Scalable throughput
Multiple samples processed in parallel on the 96-channel head: dozens of samples a day without adding staff.
48-hour turnaround
Complete sample-to-sequencer workflow with libraries ready in under two days.
Opentrons Flex
An open liquid handler for NGS libraries
Opentrons Flex is a modular benchtop liquid-handling robot with an open Python API and swappable pipettes (1-, 8- or 96-channel, 1–1000 µL). 12 deck slots, an on-deck thermocycler, heater-shaker, temperature module and magnetic block, all controlled through a single touchscreen interface with no coding required.
- 1-, 8- and 96-channel swappable pipettes (1–1000 µL)
- 12 main deck slots + 4 staging positions
- On-deck modules: thermocycler, heater-shaker, temperature module, magnetic block
- Open-source Python API for your own and partner protocols
- Dimensions 87 × 69 × 84 cm, fits on half a lab bench
Video
Opentrons Flex in action
A short video from the manufacturer introduces the Flex platform: deck, modules and workflow for NGS library prep.
Let's start
Want OncoDEEP® in your lab?
We will be happy to go through the technical requirements and help with assay validation, integration with Opentrons Flex and connecting the OncoKDM® report to your clinic. Non-binding consultation in the Czech Republic and Slovakia.