Comprehensive genomic profiling in oncology: A revolutionary approach by Marcel Trautmann

OncoDNA has received a glowing testimonial from one of the largest German care providers that has selected and incorporated our OncoDEEP Kit in their routine clinical diagnostic oncology screening. We are more than honored to have played a role in their exceptional outcomes and look forward to continuing our collaboration in advancing cancer management strategies for the betterment of patients’ lives.

Could you please introduce yourself and your position at the University Hospital Munster?

As Head of the molecular diagnostics and translational cancer research lab (Assistant Professor, Gerhard- Domagk-Institute of Pathology, Division of Translational Pathology), I am dedicated to genetic/molecular testing based on e.g. DNA/RNA NGS technology to guide individualized clinical therapeutic selection based on molecularly matched precision oncology testing (focusing on solid-, lung-, sarcoma Dx). I am responsible for the validation, implementation & automation of laboratory developed (LDT) or in vitro diagnostics (IVD) tests/ services into our routine pan cancer Dx laboratory workflows and bioinformatic interpretation & reporting pipelines.

Could you briefly describe your lab situation before considering OncoDEEP® Kit solution?

Before we adopted OncoDNA’s OncoDEEP® Kit solution as our test of choice for in-house comprehensive genomic biomarker profiling in formalin-fixed, paraffin-embedded (FFPE) samples, we focused on separate, sequential testing with multiple targeted and tumor type specific NGS panels covering customized sets of up to 60 cancer-related genes. To detect novel and pan cancer related fusion genes, we apply a targeted RNA sequencing panel covering >500 genes in a single assay optimized for FFPE samples. We run all streamlined NGS library preparation workflows as semi automated applications on flexible and scalable MiniSeq, MiSeq and NextSeq systems based on Illumina’s NGS technology.

How did you hear about OncoDNA Group? What finally encouraged you to get in touch with us?

While discussing options for routine NGS library preparation automation with representatives of Twist Bioscience, we were first introduced to OncoDNA’s comprehensive genomic profiling solution as the OncoDEEP® in-house workflow is enabled by Twist Bioscience’s NGS technology. During the Annual Meeting of the German Society for Pathology (DGP), we got in touch with OncoDNA.

What other solutions have you considered? What comparison criteria did you consider when selecting our solution?

We considered multiple in-house comprehensive genomic profiling NGS options as single multiplex assay with >1Mb to simultaneously detect current and emerging clinically actionable alterations and biomarker for therapy guidance launched.

What were the key results you were able to generate during the test phase?

During the validation phase, our results demonstrated that OncoDNA’s OncoDEEP® single multiplex assay provides a consistent, time-efficient and simple sample-to-clinical report solution for accurate comprehensive genomic profiling in FFPE samples maximizing our ability to match cancer patients to more effective therapies according to clinical guidelines or innovative clinical trials, based on their individual tumor profile.

What were the major factors that made you adopt our solution in your daily routine? What do you value the most in our product?

As we are the first Department of Pathology in Germany and the first member within the German Network for Personalized Medicine (DNPM) to implement OncoDNA’s OncoDEEP® Kit solution in our routine pan cancer genomic/molecular Dx NGS workflow for in-house comprehensive genomic profiling – our main priorities and added benefits are:
  • most comprehensive pan-cancer genomic profiling test currently available on the market that uses a single NGS approach to simultaneously assess 638 DNA genes, 20 RNA genes, CNVs, and relevant cancer biomarkers as established in clinical guidelines and trials for therapy guidance such as homologous recombination deficiency (HRD), microsatellite instability (MSI), and tumor mutational burden (TMB) (in total 1.8 Mb).
  • compatible with nucleic acids extracted from challenging and low-input FFPE samples. Less likely to exhaust limited tumor tissue biopsy samples reducing the risk of repeat biopsies.
  • rapid turn-around time from nucleic acids extraction & quality control check, NGS library preparation and sequencing to clinical interpretation and reporting in 1 week.
  • integrated clinical decision support platform for secondary analysis, variant interpretation and the final intuitive report with clinical recommendations.
  • CE-IVD clearance.
  • compatibility with the flexible and scalable NextSeq systems based on Illumina’s NGS technology to maximize lab budgets.
  • automation-friendly NGS library preparation based on Twist Bioscience’s NGS technology enabling increased routine testing volumes.

Could you briefly explain the OncoDEEP® Kit integration stage?

Extensive validation of OncoDNA’s OncoDEEP® workflow was performed on >250 FFPE tissue specimens (neoplastic content down to 20%) comprising multiple tumor types in combination with commercially available reference materials with known genomic profiles (e.g. TMB, HRD, MSI status) to assess analytical accuracy, sensitivity, and precision. In 2023, we successfully completed the external proficiency testing of HRD (QuiP; Quality in Pathology QuIP GmbH).

What were the challenges you faced during this integration stage?

The merge and harmonization of OncoDNA’s integrated clinical decision support platforms OncoKDM® and MercuryTM, with OncoDNA’s BioIT team at hand to assist and manage the process.

What do you value most in your relationship with OncoDNA?

Generally speaking, we mostly appreciate the partnership based on the customer- and result orientated focus of OncoDNA’s team in providing rapid assistance and efficient troubleshooting which is crucial for our routine pan-cancer Dx laboratory practice.
We have thoroughly enjoyed working through the testing phase with one of the largest German care providers and are delighted to be a part of their expanding genomic profiling services. We look forward to our ongoing collaboration, with the shared goal of ultimately helping patients.
Jean-Pol Detiffe
Founder of OncoDNA

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