TEST:

TruSight Oncology 500 Assay

The diagnostic parameters exhibited high accuracy, including a positive predictive value, negative predictive value, and overall diagnostic accuracy. This study underscores NxClinical as a reliable software for identifying clinically relevant gene alterations using NGS TSO500, offering valuable insights for personalized cancer treatment strategies based on CNA analysis.

A computational drug repurposing approach may assist in identifying novel repurposing events in cancer patients with no access to standard therapies. Further validation is needed to confirm a precision oncology approach using drug repurposing.

P=N/A; Our data suggest detectable pre-treatment KRASG12C ctDNA as a marker for poor prognosis, and on-treatment ctDNA clearance as a marker for treatment response. We identified KRAS amplifications as a potential recurring resistance mechanism to sotorasib. Identifying patients with superior prognosis could aid in optimizing time of treatment initiation, and identifying patients at risk of early progression could allow for earlier treatment decisions.

Furthermore, plasma ctDNA detection of new MMR gene mutations not present in the initial tissue biopsy may provide an early indication of the development of chemotherapy resistance. Additional clinical validation in larger cohorts is needed.

This is the first study of its kind to establish long-term mesothelioma organoid cultures from malignant pleural effusions and report on their utility to test individuals' chemotherapeutic sensitivities ex vivo.

MYC amplifications had a prognostic influence on survival, whereas ARID1A gene mutations were correlated with microvascular invasion. These may serve as prognostic biomarkers and should be validated in large, independent cohort.

Assays for GI assessment not only show a high concordance with each other but also in correlation with Myriad myChoice. Thus, almost all of the assays included here can be used effectively to assess HRD-associated GI in the clinical setting. This is important as PARPi treatment on the basis of these tests is compliant with European Medicines Agency approvals, which are methodologically not test-bound.

TSO500 and F1CDx showed robust analytical performance for TMB assessment with TSO500 showing stronger concordance of TMB with high PD-L1 expression. As the paradigm for the management of early-resected NSCLC continues to evolve, understanding TMB and the mutation landscape may help advance clinical outcomes for this subset of patients.

We demonstrate the utility of PanelCAT by analyzing two large NGS panels (Illumina TruSight Oncology 500, and Qiagen Human Pan Cancer Panel) to validate the advertised target genes, quantify targeted exons and mutations, and identify differences between panels. PanelCAT will enable institutions and researchers to catalogue and visualize NGS panel target regions independent of the manufacturer, promote transparency of panel limitations, and share this information with employees and requisitioners.

The genomic profiling performed using biopsies from young colorectal cancer patients provides a unique ability to identify the potential “genomic triggers� for the development and progression of cancer in these patients. In this study, in addition to known colorectal cancer associated gene mutations, we identified recurrent missense mutations in DDR2 oncogene. This information can be further used to develop not only targeted treatment options for these patients but also to design new screening protocols for identifying high risk patients for optimal surveillance.

Comparable results were obtained from targeted sequencing depending on sample purity, preservation method, and read depth.CIN signatures are a new set of emerging biomarkers that reflect the diversity of defective pathways that have operated in a tumor, which require robust genome-wide copy number profiles. These CIN signatures can be used to predict response to cytotoxic agents and targeted therapies and could ultimately help guide therapy selection in patients.

NF2 mutations have been identified in a variety of morphologic types of Renal cell cancer. However, we were surprised by the number of cases with NF2 mutation in tumors that also harbor the FH (HLRCC) mutation. NF2 tumors have been reported to have an aggressive behavior, and FH cancers are also known to have poor survival.

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.

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.

This is the largest cohort present in the Literature of EOC PT and matched BM characterized with a multi-omics analysis. The intersection of LAMC3 and MYC target genes within the MET signalling network, a pathway recognized for bolstering cell motility, introduces a compelling avenue for future research.

Pts received boserolimab 30 mg IV Q6W plus pembro 400 mg IV Q6W for 18 cycles plus nab-paclitaxel 100 mg/m2 (3 weeks on [days 1, 8, and 15]/1 week off). In pts with TNBC and tumors expressing PD-L1 at the cutoff of CPS <10, triple therapy with boserolimab, pembro, and chemo had acceptable safety and showed preliminary evidence of antitumor activity regardless of baseline TcellinfGEP expression or TMB status.

They were randomly assigned to the control group of FLOX (oxaliplatin, 5-fluorouracil, folinic acid) Q2W or the experimental group of alternating 2 cycles each of FLOX Q2W and nivolumab Q2W, with prespecified break periods. TMB >5 mut/Mb was associated with tumor KRAS or BRAF driver mutation and remarkably long PFS in first-line treatment of patients with abdominal metastases from MSS-CRC with alternating short-course oxaliplatin-based chemotherapy and ICB.

The Illumina TruSight Oncology 500 assay also detects immunotherapy biomarkers for tumor mutational burden (TMB) and microsatellite instability (MSI) in DNA samples. The Illumina TruSight Oncology 500 assay also offers a combined RNA/DNA workflow that also allows for the assessment of fusion events.In this poster, we show the utility of the Biomek NGeniuS Next Generation Library Prep System to perform the Illumina TruSight Oncology 500 assay, which saves researchers valuable hands-on time and offers a highly streamlined setup process for users new to liquid handling automation.Confidential - Company Proprietary

In summary, the results showed that all the acceptance criteria were met and the TSO500 assay can be utilized for genomic profiling of FFPE tumor samples. The study also identified a few limitations of the Illumina LRM software e.g. potential false positive SNV within a indel background, potential false negative of complex indel, and the challenge of long indel detection.

A marked portion of patients with iCCA exhibits both SD- and LD-iCCA in different tumour regions. In case of the presence of histopathological heterogeneity, mutational profiling should be considered to avoid missing therapeutically relevant genetic alterations.

K-4CAREâ„¢ assay provides comprehensive and reliable genomic information that fulfills all guideline-based biomarker testing for both targeted therapy and immunotherapy. Integration of ctDNA tracking helps clinicians to further monitor treatment response and ultimately provide well-rounded care to cancer patients.

A radiosensitizing effect can be confirmed after treatment with AZD0156, Afatinib or Alpelisib in three organoid lines using this assay so far. Establishment of HNSCC organoids was successful using our workflow. These 3D models can be used to screen for potential radiosensitizers. For validation, we established an organoid formation assay to determine the clonogenic survival as an important endpoint in radiobiology.

MSI estimation using NGS is suitable as a quick screening tool. Since thresholds for MSI-H might differ enormously between entities, additional IHC testing is recommended at least in samples where VUS or pathogenic mutations are found in one of the mismatch repair genes. Downloaded from http://karger.com/ort/article-pdf/47/Suppl.

WGS could be performed in half of all EBUS-TBNA aspirates, which points to the enormous potential of EBUS-TBNA as source material for large, well-curated discovery-based studies for novel and more effective predictors of treatment response. Comprehensive panel sequencing is possible in the vast majority of fresh EBUS-TBNA aspirates and enhances the detection of actionable mutations over current clinical testing.

Despite the limitation of sample size, our study identified actionable alterations in 28% of tumor samples submitted to CGP. A high level of evidence of clinical activity according to OncoKB criteria was noted in 41% of actionable alterations. These findings underscore the importance of comprehensive genomic profiling in managing sarcomas.

These results suggest that HT, AHT and PTL are a continuum of the same process that can exhibit follicular or marginal zone growth patterns. A similar concept was described in pediatric follicular and marginal zone lymphomas. An acquisition of same mutations could be explained by sharing similar microenvironment in the thyroid gland of both tumors.

Bone sarcomas associated with infarcts exhibit genomic instability, with pronounced copy number variations, especially in Chromosome 12. CDKN2A/B homozygous deletion is highly prevalent, whereas TP53 alterations appear less frequent than in osteosarcomas. MDM2 amplification and H3.3-G34 mutations are recurrent (33%).

"Five genes showed a different mutational status across samples and/or panels: 4 discordant results involved NBF samples. In conclusion, acid-deprived fixatives (GAF and ADF) guarantee the highest DNA preservation/sequencing performance, thus allowing more complex molecular profiling of tissue samples."

This study estimated TMB cut-off values for commercially available CGP panels. The results showed a good performance of all panels on clinical samples and the calculated cut-offs support better accuracy measures for TSO500. The validated cut-off values can drive clinical interpretation of TMB testing in clinical research and clinical practice.

Conclusions In our cohort, NRG-1 alterations resulted frequently associated with poor prognosis and main oncogene alterations and/or loss of function of oncosuppressor genes. Further investigations are needed.

Comparison between the Illumina and Myriad assays showed that overall HRD status, the individual components of BRCA analysis, and HRD GIS detection results were highly concordant (>93%), suggesting the TSO 500 HRD assay will approach the analytical accuracy of the FDA-approved Myriad assay.

Conclusion The IMPRESS-NORWAY trial has thus far revealed prevalent and potentially clinically significant genetic alterations among the enrolled gynaecological cancer patients. Further investigation is needed to determine the representativeness of these findings for the patient group and to evaluate the efficacy of targeted treatments in gynaecological cancer therapy.

In our cohort of 83 tumour profiling results analyzed, 11% had P/LP tumour variants confirmed to be germline. Early age at diagnosis is an important factor in both contexts: a clinical suspicion of a HCS and tumour-only recommendations. Our study emphasizes the need for ongoing collaboration between disciplines to integrate a germline follow-up of relevant tumour variants and optimize patient care in precision oncology.

Conclusions Our results support the role of extensive CGP as a tool for detecting targetable alterations thus potentially allowing patients' access to innovative treatments. Information on therapeutic choices following profiling and prognostic outcomes is currently being gathered.

In this study, we demonstrate the feasibility of an in-house NGS pathway to yield patient-specific ctDNA variants with high fidelity between solid and ctDNA for patients undergoing AC treatment at a high-volume center. We identified predictors of ctDNA variant yield in AC based on disease volume (PCI), tumor grade, and CD8+ lymphocyte infiltration. Future studies are underway to explore the utility of this pathway to inform patient-specific ctDNA assays as biomarkers of response to therapy, minimal residual disease, and disease recurrence in AC patients.

We demonstrated that approximately 2.0% of patients with metastatic solid cancers have RAF1 aberrations according to NGS of tumor specimens.

Hybrid capture sequencing using TSO500 panel is feasible to analyse clinical samples from patients with NSCLC and is an efficient tool for screening actionable GAs.

However, this novel data shows how tumour content and minor change in site of node sampling can impact TMB. Further study is needed on whether all node aspirates should be combined in 1 sample, or whether testing independent nodes using smears is needed.

This case report aims to warn of the possibility that other driver mutations may be associated with the diagnosis of TCCRP, such as IDH1 R132 and not just IDH2 R172, and that a comprehensive testing approach of the IDH1/2 genes might be more accurate in these cases.

73 of 84 patients were treated with traditional neoadjuvant chemotherapy plus trastuzumab meanwhile 13 of 84 received neoadjuvant chemotherapy plus trastuzumab and pertuzumab. We would like to acknowledge the contribution of Multi-specialistic Biobank Research Core Facility G-STeP, Fondazione Policlinico Universitario "A. Gemelli" IRCCS (Biobank-FPG) who provided the bio-resources.

"We developed the Seraseq HRD reference materials to meet the needs of laboratories looking to analyze HRD in cancer patient samples. The HRD status of each material was evaluated using several assays using different measurement approaches. Although the materials showed similar trends and concordance among formats, there was variability in GIS across the methods tested."

The key benefits from automating our laboratory workflows include increased throughput and error reduction.