TEST:

OncoDEEP

Tertiary data analysis, including reporting, is integrated in the OncoDEEP solution, whereas this is an add-on for TSO500. Finally, we showed that, analytically, the OncoDEEP panel performs well, thereby advocating its use for CGP of solid tumors in diagnostic laboratories, providing an all-in-one solution for optimal patient management.

"MGI...today announced the collaboration with OncoDNA, a genomic and theranostic company specializing in precision medicine for the treatment of cancer and genetic diseases. The OncoDEEP® Kit’s comprehensive workflow— encompassing sequencing, secondary analysis, and final interpretation of NGS data (OncoKDMTM) —is now fully compatible with MGI sequencers."

"MGI Tech Co., Ltd....announced the collaboration with OncoDNA, a genomic and theranostic company specializing in precision medicine for the treatment of cancer and genetic diseases. The OncoDEEP® Kit’s comprehensive workflow—encompassing sequencing, secondary analysis, and final interpretation of NGS data (OncoKDM™) —is now fully compatible with MGI sequencers."

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.

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 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."