TEST:

OncoDEEP

OncoDEEP kit is an end-to-end solution allowing the detection of variants in 638 genes and the calculation of genomic signatures such as tumor mutation burden , microsatellite instability , and HRD. OncoDEEP HRD analysis showed a concordance of 89.1% with a sensitivity and specificity of 90% and 88%, respectively, compared to the gold standard and is therefore applicable to the identification of ovarian cancer patients eligible for PARPi therapy.

The tool using the Li et al., 2021, method works properly and gives an overview of the contamination level of samples. Nevertheless, this method is only a qualitative tool due to the exponential nature of the formula. The threshold set at 4.5% provided a sensitivity of 100% on the clinical samples' cohort.

The OncoDEEP CGP assay provides highly similar data as compared to the validated TSO500 assay but includes a workflow from library preparation to report. Validation demonstrated it can reliably be used for diagnostic profiling of solid tumors, but currently extensive fusion analysis requires an additional screening method.

The OncoDEEP® is a cost-effective, end-to-end solution, based on Twist Bioscience technology and Illumina sequencing, offering a full characterization of the tumour. MGI platform was shown to be an alternative to Illumina by generating high quality data. All variants and fusion detected, as well as the calculation of genomic signatures were comparable to those using an Illumina platform.

The use of CSFctDNA as a surrogate for tumor tissue DNA in CNS metastases appears to be a feasible and safe approach. Clinically actionable alterations have been identified in CSFctDNA of pts with BC. Further results will be presented at a later stage.Table 1: Pathogenic molecular alterations in matched tumor, plasma and CSF from pts with detectable CSFctDNA

All performance metrics passed the validation criteria. In conclusion, the OncoDEEP kit can be used for reliable diagnostic comprehensive profiling of solid tumors, but currently, extensive fusion analysis requires an additional screening method.

Our real-world findings highlight the significant impact of complex molecular profiling on the treatment decisions made by oncologists for a substantial portion of patients with advanced solid tumours. Regrettably, no significant advantage was detected in terms of treatment response or disease control rates.

Conclusions Our results demonstrate that OncoDNA's OncoDEEP® kit provides an efficient pan-cancer solution for accurate comprehensive genomic profiling for biomarker-matched therapy selection, including HRD, TMB and MSI. The integrated software suite allows for clinical interpretation and reporting with robust analytical performance.

"...this is an important first step in a collaboration that will make it much easier for public and privately practising oncologists to access biopsy tissue and request ONCODEEP for the purpose of routine next generation sequencing."

"ONCODNA...ANNOUNCED THE OFFICIAL LAUNCH OF THE ONCODEEP KIT DURING THE ESMO (EUROPEAN SOCIETY FOR MEDICAL ONCOLOGY) CONGRESS IN PARIS, FRANCE. THE KIT OFFERS A COMPLETE WORKFLOW SOLUTION TO ENABLE LABORATORIES WITH NGS CAPABILITIES TO SUPPORT ONCOLOGISTS IN FINDING THE MOST EFFECTIVE AND PERSONALIZED TREATMENTS FOR THEIR CANCER PATIENTS."

"OncoDNA...announced today a partnership with Synlab...integrating OncoDEEP in their portfolio, Synlab laboratories in Germany will perform comprehensive testing of solid tumors and deliver decision support for oncologists. The technology transfer is ongoing, with the objective of processing the first patient samples early Q2."

"OncoDNA...announced today the launch of the OncoDEEP kit. The kit offers a complete workflow solution which enables laboratories with NGS capabilities to perform comprehensive biomarker testing, provide powerful data analysis and support oncologists in the most effective and personalized treatments for their cancer patients. The OncoDEEP kit integrates both reagents and quality control standards for the sequencing of over 600 cancer biomarkers. the offer will come in combination with OncoDNA’s data analysis and clinical interpretation tools for the rapid analysis and reporting of a patient’s tumor molecular profile. OncoDEEP kit is available for early access and will be commercially available by the end of Q2 2022."

"OncoDNA...and Bergonié Institute...announced a new clinical trial to evaluate the use of comprehensive biomarker testing and liquid biopsy in 700 patients diagnosed with an advanced metastatic cancer. The Appolo study will recruit patients from 6 participating sites across the French Aquitaine region to be offered OncoDEEP® and OncoFOLLOW™ biomarker tests."

The samples were analyzed by NGS with the OncoDEEP (OncoDNA) panel covering 313 genes.ResultsOnly one of the cases was not evaluable due to the low cellularity of the tumor block. Of the 12 evaluable cases, molecular alterations were identified in 6 of them, as detailed below: in case number 1 (lung cancer) variant of TP53 cDNA c.595G> T-AA p. G199, in case number 2 (lung cancer) mutation in TP53 cDNA c.488a> G-AAp.Y163C and mutation in FANCA cDNA: c.3263C> T-AA: p.S1088F, in case number 3 (lung cancer) variant de TP53 c.DNA: c.455del-Aap.P152Rfs * 18, alteration in MRE11A cDNA: c.1688C> G-AA: p.S563 * and alteration KEAP1 cDNAc.224dup-Aap.L76Afs * 3, in case number 4 (lung cancer) AKT amplification and alteration in BRCA2 cDNA c.2701del-Aap.A902Lfs * 2, in case number 5 (lung cancer) mutation in PI3KCA E545 K, amplification in MDM2 and mutation in TP53 cDNA c.871AA> T-AA p.K291 *, in case number 6 (bladder cancer) amplification of JAK1 and in case number 7 (head and neck cancer) mutation of PI3KCA E545, mutation of TPMT Y240C and mutation in TPMT A154 T.Conclusions This review presents as its objective the analysis of these molecular alterations and their impact on the prognosis, and therapeutic evolution of patients with the aim of integrating clinical and molecular information in a translational oncology study

"In this particular case, we show that ARID1A gene mutations with sporadic MSI due to somatic MLH1 gene promoter methylation and MLH1 gene mutation could change the prognosis and define the response to immunotherapy in a patient with lung adenocarcinoma. Comprehensive solid and liquid biopsy tests are useful to find out resistance mechanisms to immune checkpoint inhibitors. Our data encourages the development of new therapies against ARID1A mutations and epigenomic methylation when involved in MSI neoplasms."