Revolutionizing laboratory operations with OncoDEEP® Kit

Biomarker testing is critical to learning more about each patient’s tumor type and can be used to help determine treatment options. Based on the test results, patients may be matched with targeted therapies aimed at specific biomarkers present in their genetic profile. That’s why CGP is critical for patient tratment management. The booming of new treatment options for cancer patients has led to a constant evolution of biomarker testing. Targeted therapies are commonly approved for treatment based on the presence of biomarkers found on the tumor and it is driving the development of new molecular test so as to detect these biomarkers. One of the latest newcomer is the PARP inhibitor that can be prescribed for ovarian cancer patients based on the presence of biomarkers pathogenic or likely pathogenic mutations or genomic instability (GI) : BRCA1/2 aberration or Homologous Recombination Deficiency (HRD).

The critical role of biomarker testing in cancer treatment

Hospital Lab XXX  is specialized in oncology molecular diagnostic by performing in-house comprehensive genomic profiling (CGP) by using commercial Next Generation Sequencing (NGS) oncology kit. NGS oncology kit allows them to detect genetic changes in 500 genes at the DNA level and also enabled them to detect additional genomic signatures such as Tumor Mutational Burden (TMB) and Microsatellite Instability (MSI). However, with the new biomarker HRD coming into the market, they were seeking for an improved NGS oncology kit to include the new biomarker into their routine test, as it had shown promising potential in predicting response to certain cancer treatments. They understood that incorporating this biomarker into their routine testing would enable them to provide more accurate and personalized treatment options for their patients. Furthermore, they were also considering making other improvements in their workflow to address their pain points; such as: • Improvement of turnaround time (TAT) • Addition of RNAseq to their workflow for the detection of fusion variants without affecting TAT • Incorporation of automation to reduce labor intensity/human error • Reduction of costs (optimized for ~8 samples/week) • Easy data to report analysis (integrated biological and clinical interpretation)

Rigorous selection process for the optimal NGS oncology kit

To ensure they selected the best NGS oncology kit for their needs, the lab team embarked on an extensive evaluation process. They reached out to various biotechnology companies and reviewed the latest advancements in NGS technology. After careful consideration, they shortlisted a few vendors who specialized in comprehensive genomic profiling and HRD testing. Over a few months of evaluation, the validation data together with the improvements they can achieve with OncoDEEP® CGP NGS Kit from OncoDNA (as summarized in the Table below), have led them to decide and chose OncoDEEP® Kit for their future oncology CGP routine test.
Initial situation Current situation
Detection of HRD
Not covered
Identification of patients who can benefit from PARP inhibitor treatment
Most of the time TAT is 10 days
5-6 days (8 DNA and 8 RNA)

Shorter TAT means patient can get treatment sooner
Not covered
Identification of patients who can benefit from treatments approved for fusion & splicing biomarkers
Not included
Decrease manual work preventing potential human error. Less laborious.
"Less expensive"
Data interpretation
Report generated is an excel sheet, manual review should be done
Integration biological and clinical interpretation for report generation on 1 platform

Enhancing lab efficiency with OncoDEEP® Kit and OncoKDM® analysis tool

With OncoDEEP® Kit in place, the lab team began implementing the necessary changes to their workflow. They focused on optimizing their sample preparation and sequencing processes to increase efficiency and reduce turnaround time. The new kit streamlined their workflow by providing automated and standardized protocols, allowing for faster and more consistent results. The clinical and biological interpretation tool OncoKDM® facilitated the analysis of complex genomic signatures generated, enabled the identification of actionable genetic alterations and the interpretation of HRD results.

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