TEST:

Oncomine Precision Assay

Since its initial proposal in December of 2022, discrete reporting at the University of California, San Diego genomic lab was an effort that took close to a year-and-a-half to accomplish. Although the process was not without its hardships, the decision to go with an in-house approach saved the lab both time and resources compared to an outside approach. By exploring the capabilities and functionalities of its current laboratory information systems and EHR systems, the lab built a discrete reporting system that is effective for its needs as well as a framework for converting other and future NGS assays to discrete reporting.

The OPA-GX fully automated NGS platform accurately and reproducibly detects actionable solid-tumor hotspot mutations. Low FFPE DNA and RNA input requirement (10ng) allows for profiling of small tissue specimens that resulted in 100% sequencing success rate. The OPA-GX completes the entire NGS workflow and delivers clinically significant genomic findings in 16 to 20 hours depending on number of tested samples.

Given the importance of timely, comprehensive molecular test results to inform appropriate treatment decisions in NSCLC and CRC, these results suggest that the rapid in-house GeneXus NGS system can reduce TAT with comparable failure rates and alteration detection rates compared to other testing methods. Further studies evaluating the impact of the rapid OPA compared to other methods on patient care, as well as the economics of different molecular tests, are ongoing.

This report offers a thorough characterization of expected prevalence and expression levels for CSFs and NDFs with an NGS study of a broad scope. We describe ESR1 fusions in a cohort of thousands of breast tumors and show lower median expression levels relative to NDFs such as ALK, ROS1, and RET fusions. Our findings suggest that some CSFs, like ESR1 fusions in breast cancer, may be the result of tandem duplication with upstream partners, and may be subclonal and acquired later in cancer progression.

Our results regarding the proportion of samples with actionable mutations demonstrate the value of NGS testing for NSCLC patients in a real-world clinical diagnostic setting.

We were able to successfully conduct NGS studies in paraffin-embedded material archived for 10 years using both middlesized (OPA) and large (OCA v3) NGS panels. The identified S3FB1 mutation helps to explain the onset of metastases, even though the patient had spindle cell predominant UM with BAP-1 preservation, which are normally associated with decreased metastases risk. Our case highlights the value of using large NGS panels to unravel the molecular landscape of UM and further understand this unique eye cancer.

KRAS is an attractive therapeutic strategy due to its high prevalence and its role in initiating and sustaining tumour growth. Approval of KRAS G12C inhibitors in locally advanced or metastatic NSCLC has brought hope to many patients. Studies show that non G12C KRAS mutation are found in 53% of adenocarcinomas.

Massive parallel sequencing and personalized therapeutic targets for personalized mutational status might allow patients with adenosquamous carcinomas to improve survival at the different levels of progression. Adapted criteria in the classification recognized by WHO 2021, which tumoural cellular level sub-classification might be a particular sub-typing with particular outcomes as exemplified in the present mutational exercise. This small series, defined after routine IHC classification correlated with tumoural heterogeneity/clonality previewed for adenosquamous carcinoma.

Oncogenic activation of genes-drivers are responsible for resistance mechanisms either understood has resistance to METtargeted therapies and as primary resistance. Recently it has been reported that PI3K pathway alteration is common in concomitancy with METex14 and believed that confers primary resistance to MET TKI. Early identification of alterations in MET kinase domain at diagnosis, is crucial for understanding progression and resistance mechanism, to develop novel therapies or to design treatment strategies in order to improve patient outcomes.

The sequenced adenocarcinomas presented predominant acinar pattern as well as solid, papillary/micropapillary and lepidic patterns, respectively, without relevance for the mutational status. Multiple parallel sequencing (MPS) allows accumulation of tumoural mutational knowledge overtaking concise standardized mutational equipment. Considering effective lab costs, clinical decisions for therapeutic available options and MPS is now the more advisable method.

Known under low incidence – mutations require research for 0.4% to 1.1 in pulmonary adenocarcinomas, IDH1/2 inhibitors prescription due to high prevalence of lung carcinoma worldwide. Mutations in IDH1/2 gene may be branching drivers leading to lower subclonality evolution with predictable benefit of IDH1/2 inhibitors.The accumulation of more known cases with IDH1/2 mutations is necessary to elucidate clinicopathological characteristics/clinical evolution after target therapy, in order to reforce the new interpretation of malignant tumours postponed survival through conversion of cell cycle.

According to our findings, US-guided lung biopsy is a safe, minimally invasive procedure in patients with suspected lung malignancies, providing an excellent diagnostic yield for both comprehensive molecular profiling and PD-L1 testing. In addition, our results suggest that US-guided biopsy may also be an effective diagnostic approach in patients with suspected lung lymphoma.

This study demonstrates that rapid in-house liquid biopsy using point of care methodology is feasible. The technique facilitates precision treatment and offers many additional advantages for cancer care.

Conclusions : In our cohort, KRAS -mutant patients appear to have a different metastatic pattern depending on their KRAS mutation subtype. In addition, KRAS G12C and KRAS G12V -mutant patients seem to have better prognosis and response to chemoimmunotherapy than KRAS G12D -mutant patients.

Only a few driver mutations were detected exclusively in plasma samples. Characteristics of detected driver genes by NGS analysis Tissue Plasma EGFR 63 37 ALK 11 2 ROS1 8 4 BRAF 5 3 MET 8 3 RET 4 3 KRAS-G12C 13 9 HER2 4 6

We also studied preclinical Ba/F3 models expressing EGFR -K745_E746insIPVAIK (Ba/F3-IPVAIK) and EGFR -delE746_A750 (Ba/F3-Del19) to investigate the sensitivity to 1st-generation (gen) (gefitinib and erlotinib), 2nd-gen (afatinib, dacomitinib, and poziotinib), 3rd-gen (osimertinib), and EGFR exon 20 insertion active TKIs (mobocertinib, sunvozertinib, and zipalertinib). The preclinical therapeutic window of Ba/F3-IPVAIK and Ba/F3-Del19 for all the 2nd generation TKIs were similarly favorable, whereas Ba/F3-IPVAIK had much unfavorable therapeutic windows to other EGFR-TKIs compared to Ba/F3-Del19. Conclusions : Our clinical and preclinical findings indicate 2nd-gen EGFR-TKIs are more effective than 1st and 3rd-gen EGFR-TKIs in patients with EGFR exon 19 insertions.

Despite the low number of cases, using blood from the tumor-draining vein during lung resection might improve the sensitivity of NGS-based detection of ctDNA when compared to peripheral blood.

Three patients presented with metastases as the initial manifestation of disease; 8 patients died of their tumors from 6 months to 8 years (mean: 2.7 y); 3 patients were alive and well from 4 to 6 years; and 2 patients had metastases when last seen but were lost to follow-up thereafter. The importance of recognizing this distinctive and aggressive variant of non-small cell lung carcinoma lies in avoiding confusion with a sarcoma or other types of malignancy.

Tumour-derived somatic variants (~50 gene panel) can now be reliably assessed from plasma to provide minimally invasive tumour profiling. Successful implementation of this ISO15189 accredited service resulted in: 1) Appropriate molecular profiling of patients where tumour tissue is unavailable or inaccessible; 2) r apid TAT of NGS; 3) results to oncologists; 4) capturing potential cases of tumour heterogeneity; 5) timely switching of therapy at progression following the detection of resistance mutations via simple blood plasma sample. This study provides an NGS implementation roadmap for clinical diagnostic pathology departments that have increased demands for advanced diagnostics of DNA and fusions via NGS on blood samples.

The advancement of high-throughput sequencing technologies has highlighted the complexity of pathobiology and revealed recurrently mutated genes involved. However, uncommon mutations, such as those found in the ALK and IDH1 genes associated with CIUC, could represent new treatment targets. Lastly, the results obtained in this study fully correlate with the molecular profile reported for gastrointestinal tumors.

This study highlights the performance, capabilities, and efficiency of conventional and rapid NGS platforms. In clinical practice, selecting the right platform should be dependent on throughput requirements and sample size for efficient molecular tumor profiling. In time-sensitive settings like lung cancer, the strategic use of technology and expertise becomes crucial for prompt clinical management.

This study confirms the value of molecular testing in the differential diagnosis of CNS tumors, as well as in prognostic and therapeutic implications. It is necessary to increase the database of CNS tumor sequencing to identify markers of prognostic and therapeutic relevance alternatives for these poorly accessible neoplasms, with limited treatments and unfavorable prognoses.

These results demonstrate the feasibility of using cytology samples as an alternative source of tumour DNA for mutation profiling in NSCLC across a genetically diverse patient cohort. Implementation of this into the clinical pathway has potential to significantly reduce the turnaround time of vital results to aid treatment decisions and improve therapy outcomes in NSCLC. Further validation studies are warranted to corroborate these findings in a larger patient cohort and assist in overcoming the current limitations of tissue biopsy.

The use of DNA/RNA NGS panels is essential to detect patients that are candidates for directed therapies.

20% of NSCLC in our cohort show MTAP deficiency by IHC. IHC is more sensitive than targeted panel-based NGS to detect MTAP deficiency in NSCLC. The results of ongoing analyses to explore reasons for the lower sensitivity of NGS will be presented at the congress.

Tumour-derived somatic variants can now be reliably assessed from plasma to provide minimally invasive tumour profiling. Successful implementation of this accredited service resulted in:Appropriate molecular profiling of patients where tumour tissue is unavailable or inaccessible.Rapid TAT of plasma NGS results.

We were able to demonstrate the usefulness of SN for reliable rapid molecular results. We successfully incorporated the workflow for tissue handling and processing among our clinical, cytopathology, and molecular teams. Molecular results were available at the same time as the cytologic diagnosis, allowing for timely reporting of a comprehensive diagnosis. This approach is particularly useful in patients with advanced disease requiring urgent management.

Our NGS programme in mCRC allows the optimization of tissue samples for initial molecular profile assessment and the access to innovative therapies in almost half of pts with an actionable target. Additional prospective studies including cost-effectiveness analysis are crucial before implementing NGS in the diagnosis setting of mCRC in health systems.

One patient received nivolumab for MSI-H recurrent GBM (ESCAT IIIB) but progressed within 3 months of commencing treatment. Despite advances in our understanding of the pathogenesis of these high grade gliomas and improved awareness of molecular targets, the delivery of targeted therapy to patients with HGG remains challenging. Rapid access to targeted therapy via compassionate access programmes and improved availability and access to clinical trials for patients with rare cancers and molecular alterations, is paramount.

BAY 2927088 led to rapid, substantial, and durable responses in pts with pretreated HER2-mutant NSCLC. The safety profile was consistent with previously reported data. These data support the further clinical development of BAY 2927088 in pts with HER2-mutant NSCLC.

Patients with shorter PFS with prior 1 st line EGFR-TKI are more likely to have MET amp. The efficacy of standard PBC post EGFR-TKI in patients with MET CNG is limited. Current MET-targeted therapy may not be effective for EGFR-mutated NSCLC harboring MET poly after progression on EGFR-TKI.

These data clearly show the potential for a fresh EBUS pathway to improve patient care through viability and rapidity of predictive testing for SOC therapy and trial decision-making, benefitting from higher RNA success and markedly reduced TATs. These results also support the use of first-line assessment of fresh EBUS over FFPE, reducing multidisciplinary laboratory work burden and increasing availability of FFPE material for additional predictive biomarker processes.

Our study showed that frozen cytology pellets may have equivalent diagnostic value to frozen tissue for NGS analyses. Bronchial cytology specimens are usually used only for cytology, but NGS analysis is possible if enough cells are collected to create pellet specimens. In particular, the frozen cytology pellets obtained by endobronchial ultrasound-guided transbronchial needle aspiration yielded sufficient amounts of DNA.

Remnant samples are typically not an option due to limited yields from a standard blood draw, thus contrived standards are especially needed. Expanded variant content and improvements in the methods used to produce the Seraseq ctDNA Mutation Mix v4 materials will enable advancements in the blood-based NGS clinical diagnostics space.

Higher Ki67 gene expression was associated with recurrences (p=0.042) Increased PI3K pathway activity, independent of PIK3CA mutations, may play a role in the recurrence of early-stage breast cancer with low and intermediate 21-gene RS. Pathway analysis can help to identify high-risk patients in this setting.

Our study comprises one of the largest retrospective studies in solid tumors of different sources in the Mexican population, giving new perspectives and evidence about our genomic profiles and mutational prevalence. It also highlights the feasibility of a small NGS panel that represents cost effectiveness for a latin american landscape. Among the comparison between the molecular profiles of the global databases, it is important to distinguish that the allele frequency of EGFR in the Mexican population is significantly higher, similar to the data reported in the Asian population

In this study, we found that KRAS-G12D mutation is significantly associated with poor prognosis, remaining significant after adjusting for clinicopathologic characteristics and co-occurring mutations among LUAD patients.

Taken together, our comparison ofIon PGMTM Dx system and GenexusTM integrated sequencer indicates that the latter exhibits superior performance with significantly higher total reads, mapped reads, and mean depth, leading to a faster turnaround time and improved detection of clinically relevant variants. This underscores its potential for enhanced precision in clinical applications.

In summary, our results indicate that CSF-cfTNA analysis with the Genexus-OPA can provide clinically relevant information in patients with brain metastases with short TAT.

The population prevalence-based coverage ranged from 89.2% to 100.0% across targets and exceeded 99.0% in aggregate. The assay demonstrated >97% concordance with respect to the comparator method.

Conclusion FNB provides a better quality specimen with preserved architecture than FNA. FNB samples were more suitable for NGS testing in lung cancer diagnosis.

Our results suggest that short read NGS-based assays may miss a significant number of clinically actionable KIT variants, and that follow-up of KIT and PDGFRA NGS-negative cases by alternative testing modalities should be considered.