Oncomine Focus Research Articles

Single-center analysis of a real-world cohort of patients with metastatic urothelial carcinoma evaluated by NGS: molecular landscape and efficacy of targeted therapies.

To describe the molecular profile of a real-world cohort of patients with metastatic urothelial carcinoma (mUC) and to evaluate the benefit of next-generation sequencing (NGS) panels in guiding therapy in patients with mUC and the outcomes of DNA-matched treatments recommended by a multidisciplinary molecular tumor board (MMTB). This was a single-center analysis of a real-world cohort of adult patients with mUC included in an ongoing trial that aimed to evaluate the clinical utility of NGS for solid tumors. Genomic analysis was performed for each patient, most of them using the Ion Torrent Oncomine Focus Assay. Genomic results were discussed during MMTB meetings. We included 43 patients with mUC treated with platinum-based combinations and immunotherapy. Twenty-five patients (58.1%; 95% CI 43.4-72.9) had at least one tumor pathogenic alteration. The MMTB classified 16 (48.5%) of the 33 tumor pathogenic alterations found in our real-world cohort of mUC patients as ESCAT I, which is the maximum grade of actionability. After excluding patients who were not candidates for targeted therapies, the MMTB provided guidance on matched therapy for seven patients. Among these patients, three achieved a partial response for an overall response rate of 42.9%, a median progression-free survival of 7.3months (95% CI 6.7-7.9) and a median overall survival of 10.9months (95% CI 2.4-19.5). We recommend that all patients with mUC undergo NGS at diagnosis given the high percentage of patients with pathogenic alterations in our real-world cohort and the efficacy data of patients treated with targeted therapies.

Feasibility and Impact of Embedding an Extended DNA and RNA Tissue-Based Sequencing Panel for the Routine Care of Patients with Advanced Melanoma in Spain.

Targeted NGS allows a fast and efficient multi-gene analysis and the detection of key gene aberrations in melanoma. In this study, we aim to describe the genetic alterations in a series of 87 melanoma cases using the oncomine focus assay (OFA), relate these results with the clinicopathological features of the patients, and compare them with our previous study results in which we used a smaller panel, the oncomine solid tumor (OST) DNA kit. Patients diagnosed with advanced melanoma at our center from 2020 to 2022 were included and DNA and RNA were extracted for sequencing. Common mutated genes were BRAF (29%), NRAS (28%), ALK, KIT, and MAP2K1 (5% each). Co-occurring mutations were detected in 29% of the samples, including BRAF with KIT, CTNNB1, EGFR, ALK, HRAS, or MAP2K1. Amplifications and rearrangements were detected in 5% of cases. Only BRAF mutation showed a significant statistical association with sun exposure. For patients with a given genetic profile, the melanoma survival and recurrence-free survival rates were equivalent, but not for stage and LDH values. This expanded knowledge of molecular alterations has helped to more comprehensively characterize our patients and has provided relevant information for deciding the best treatment strategy.

Effect of screening with a pan-TRK immunohistochemistry-based algorithm on NTRK fusion detection rates.

e15135 Background: Rearrangements in the NTRK1, NTRK2, and NTRK3 genes are clinical actionable and predictive of response to TRK kinase inhibitors in solid tumors. Their detection in clinical practice is a priority, but their low prevalence (0.25-1%) poses a diagnostic challenge. In this study, we describe our immunohistochemical-based and cost-effective approach for NTRK rearrangements detection. Methods: We implemented a comprehensive NTRK testing approach at a reference center that combined clinical criteria (e.g., iodine therapy-resistant thyroid cancer); molecular biomarkers (e.g., non-small-cell lung carcinoma negative for driver alterations, colorectal carcinoma with deficient MMR and/or microsatellite instability); and histopathological criteria (identifying tumor subtypes associated with NTRK fusions, such as breast secretory carcinoma). Automated immunohistochemistry (Ventana BenchMark ULTRA IHC/ISH System) using the antibody pan-TRK (Ventana, EPR17341) was used as a screening tool. Positive results were confirmed through molecular techniques, including Next Generation Sequencing, NGS (Oncomine Focus Assay, Thermo Fisher, based on DNA and RNA) and/or FISH (NTRK3 break-apart probe, Zytovision). Results: We evaluated 172 patients (99 female/73 male), with a mean age of 52 years (SD 23.8). Eighteen (18) patients with neoplasms expressing TRK proteins were identified. Confirmatory studies using NGS identified fusions in 7 cases. In instances of poor RNA quality, FISH techniques (NTRK3) were employed, confirming the findings in an additional 3 patients. Overall prevalence of NTRK fusions was 5.8%. Histological types included the following tumor types: Thyroid carcinoma, 4 patients (one medullary and 3 papillary carcinomas, two of them in the pediatric population); soft tissue sarcomas, 3 patients (2 corresponding to infantile fibrosarcoma and a soft tissue provisional entity, "NTRK-rearranged spindle cell neoplasm”); secretory carcinoma of the breast, one patient; secretory carcinoma of the salivary gland, one patient; colorectal carcinoma, one patient, with a deficient MMR phenotype. NTRK3 gene fusions were found in 10 patients, (6 fusions with ETV6 detected by NGS and 3 detected by FISH), and NTRK1 fusion in 1 case (fusion with LMNA detected by NGS). The positive predictive value of pan-TRK immunohistochemistry as a screening tool was 0.55. Conclusions: In our experience, the comprehensive screening approach based on morphological and clinical/ molecular inclusion criteria, along with the use of immunohistochemical techniques (pan-TRK antibody), significantly enhances the detection rate of NTRK fusions (5.8% vs. 0.25-1%). Additionally, FISH provides a valuable tool in samples with poor RNA quality. This approach allows for a reduction in the impact of costly testing, such as NGS, on the healthcare system.

Genetic profiles of oligometastatic non-small cell lung cancer and corresponding brain metastases.

In patients with oligometastatic non-small cell lung cancer, systemic therapy in combination with local ablative treatment of the primary tumor and all metastatic sites is associated with improved prognosis. For patient selection and treatment allocation, further knowledge about the molecular characteristics of the oligometastatic state is necessary. Here, we performed a genetic characterization of primary non-small cell lung cancer and corresponding brain metastases. We retrospectively identified patients with oligometastatic non-small cell lung cancer and synchronous (<3 months) or metachronous (>3 months) brain metastases who underwent surgical resection of both primary tumor and brain metastases. Mutation profiling of formalin-fixed paraffin-embedded tumor cell blocks was performed by targeted next generation sequencing using the oncomine focus assay panel. Sequencing was successful in 46 paired samples. An oncogenic alteration was present in 31 primary tumors (67.4%) and 40 brain metastases (86.9%). The alteration of the primary tumors was preserved in the corresponding brain metastases in 29 out of 31 cases (93.5%). The most prevalent oncogenic driver in both primary tumors and brain metastases was a KRAS mutation (n = 21). In 16 patients (34.8%), the brain metastasis harbored additional oncogenic alterations. The presence of a private genetic alteration in the brain metastasis was an independent predictor of shorter overall survival. In oligometastatic non-small cell lung cancer, brain metastases retain the main genetic alterations of the primary tumors. Patients may profit from targeted inhibition of mutated KRAS. Additional private genetic alterations in the brain metastases are dismal.

Abstract A004: Clinical test design affects tumor tissue and ctDNA FGFR gene status in metastatic urothelial cancer: a prospective study

Abstract Fibroblast growth factor receptor (FGFR) gene alterations are common in urothelial cancer (UC) and targetable with erdafitinib. The co-approved companion diagnostic is an amplicon-based tumor tissue test that detects a limited number of recurrent FGFR alterations. However, FGFR status may change during disease progression, and rare FGFR alterations not typically covered by existing tests may be of clinical importance. Therefore, in a prospective pan-Canadian study (NCT06129084), we compared standard archival tissue testing to broad targeted sequencing of cell-free circulating tumor DNA (ctDNA) to detect FGFR alterations in UC. Eligible patients had progressing metastatic UC and were undergoing tissue FGFR testing. Blood was drawn at study enrollment and plasma cell-free DNA and matched white blood cell DNA underwent deep-targeted sequencing with a hybridization capture panel including the introns and exons of FGFR1-4 and the common breakpoint region of TACC3. Archival tissue selection and testing was initiated by the treating physician and typically used the Oncomine Focus assay. 210 patients were enrolled across 12 sites, and 140 patients have tissue and ctDNA results available for concordance assessment. 43/140 (31%) of cell-free DNA samples had low tumor fraction (&amp;lt;0.5%) and were considered inconclusive. For the remaining 97 same-patient tissue and ctDNA pairs, FGFR status was identical in 88 (91%). In 7 of 9 discordant cases, the tissue was negative, but ctDNA was positive for FGFR alterations: these were enriched for FGFR3-TACC3 fusions (4/7). Two discordant fusions had canonical breakpoints that can be identified by current amplicon-based companion diagnostics, indicating potential spatiotemporal heterogeneity in somatic FGFR status. The other two discordant (ctDNA-only) fusions had non-canonical breakpoints that are not amenable to detection by current amplicon-based companion diagnostics. In two mutation discordant cases (S249C positive in ctDNA only), lack of signal in tumor tissue could be explained by the presence of additional FGFR3 variants within 25bp of S249 and in cis - disrupting primer binding sites. There were only two cases of tissue-only FGFR alterations among the 97 evaluable pairs (FGFR3-TACC3 fusion, S249C). ctDNA testing of metastatic UC with a broad capture-based approach covering all exons and introns of FGFR genes can identify additional alterations not detected with current amplicon-based companion diagnostics applied to archival tissue. Our results support ctDNA testing as a valuable adjunct to tissue testing, but not as a replacement due to the high frequency of inconclusive ctDNA results, secondary to tumor fraction below the threshold. Assay design, including target enrichment technique, is a significant source of variability in tissue and ctDNA FGFR status and should be carefully considered in future clinical biomarker testing strategies. Citation Format: David C. Müller, Gillian Vandekerkhove, Andrew J. Murtha, Jack V.W. Bacon, Carlos Vasquez-Rios, Maria Stephenson, Kimia Rostin, Elena Schönlau, Connor Wells, Sunil Parimi, Krista Noonan, Naveen S. Basappa, Jenny J. Ko, Daygen Finch, Nimira Alimohamed, Tarek A. Bismar, Gang Wang, Andreas Papadakis, Lucia Nappi, Matti Annala, Cecily Q. Bernales, Alan Spatz, Kim N. Chi, Alexander W. Wyatt, Bernhard J. Eigl. Clinical test design affects tumor tissue and ctDNA FGFR gene status in metastatic urothelial cancer: a prospective study [abstract]. In: Proceedings of the AACR Special Conference on Bladder Cancer: Transforming the Field; 2024 May 17-20; Charlotte, NC. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(10_Suppl):Abstract nr A004.

Clinical impact of panel gene sequencing on therapy of advanced cancers of the digestive system: a retrospective, single center study

BackgroundPanel gene sequencing is an established diagnostic tool for precision oncology of solid tumors, but its utility for the treatment of cancers of the digestive system in clinical routine is less well documented.MethodsWe retrospectively identified patients with advanced or metastatic gastrointestinal, pancreaticobiliary or hepatic cancers who received panel gene sequencing at a tertiary university hospital from 2015 to 2022. For these cases, we determined the spectrum of genetic alterations, clinicopathological parameters and treatment courses. Assessment of actionability of genetic alterations was based on the OncoKB database, cancer-specific ESMO treatment guidelines, and recommendations of the local molecular tumor board.ResultsIn total, 155 patients received panel gene sequencing using either the Oncomine Focus (62 cases), Comprehensive (91 cases) or Childhood Cancer Research Assay (2 cases). The mean age of patients was 61 years (range 24–90) and 37% were female. Most patients suffered from either colorectal cancer (53%) or cholangiocellular carcinoma (19%). 327 genetic alterations were discovered in 123 tumor samples, with an average number of 2.1 alterations per tumor. The most frequently altered genes were TP53, KRAS and PIK3CA. Actionable gene alterations were detected in 13.5–56.8% of tumors, according to ESMO guidelines or the OncoKB database, respectively. Thirteen patients were treated with targeted therapies based on identified molecular alterations, with a median progression-free survival of 8.8 months.ConclusionsActionable genetic alterations are frequently detected by panel gene sequencing in patients with advanced cancers of the digestive tract, providing clinical benefit in selected cases. However, for the majority of identified actionable alterations, sufficient clinical evidence for targeted treatments is still lacking.

Abstract 6158: Tumor genomic heterogeneity in non-small cell lung cancer (NSCLC) patients from Latin America

Abstract Motivation: Life prospects of non-small cell lung cancer (NSCLC) patients have greatly improved over the last decades with the adoption of tumor genomic profiling. A better understanding of the mutational landscape has allowed for a more precise molecular characterization and the development of more effective treatment alternatives. However, tumors present a widespread heterogeneity, and many challenges remain to fully comprehend the influencing factors. Of particular importance is the Latin America population which i) is commonly underrepresented in clinical trials and large-scale epidemiological studies, ii) presents higher incidence and mortality rates in comparison to the developed world, and iii) is constituted by a genetically admixed population. Our research attempts to close this gap by investigating the interplay between sociodemographic, clinical, and lifestyle factors, and the effect these exert on the mutational profiles of Latin-American NSCLC patients. Methodology: The study population is derived from the NIRVANA study, a cross-sectional multicenter observational study aiming to characterize and validate molecular diagnostic technologies for NSCLC patients in Chile, Brazil, and Peru. Between July 2015 to October 2018, 5030 NSCLC patients were recruited from 37 centers, meeting inclusion criteria of age ≥18, histologically or cytological proven NSCLC diagnostic, and naïve treatment. Exclusion criteria included prior chemotherapy treatment and refusal to give informed consent. Primary or metastatic NSCLC samples were collected during standard of care biopsy and processed for the DNA and RNA isolation. Next Generation Sequencing (NSG) genomics profiles were obtained using the Oncomine Focus Assay (OFA). Covariates of interest, including sociodemographic, clinical, and lifestyle factors, were assessed at enrollment. QC-approved genomic profiles were obtained for 1864 participants. Results and Conclusions: The prevalence of mutations and fusions in the eight most relevant NSCLC genes (EGFR, KRAS, ALK, MET, RET, BRAF, ROS1 and ERBB2) varies based on sociodemographic, clinical and lifestyle characteristics. Clear distinctions emerged in the prevalence of EGFR, KRAS and ERBB2 mutations among the three countries (EGFR: 20.9%, 17.6%, 35.3%; KRAS: 21.8%, 15.6%, 10.3%; ERBB2: 2.8%, 3.3%, 4.4% for Brazil, Chile, and Peru, respectively). Furthermore, distinct association patterns were identified between the prevalence of genetic alterations and the studied factors, with attributes such as sex, tobacco use and ethnicity mostly influencing the occurrence of EGFR, ALK and ROS1 alterations. These findings provide novel insights into NSCLC studies among Latin-American patients, potentially serving as guidelines for more tailored strategies in the overall management of this underrepresented population. Citation Format: Javiera Garrido, Evelin González, Gonzalo Sepúlveda-Hermosilla, Matias Freire, Alejandro Blanco, Solange Rivas, Katherine Marcelain, Gareth I. Owen, Carolina Ibañez, Alejandro Corvalan, Marcelo Garrido, Rodrigo Assar, Rodrigo Lizana, Javier Cáceres-Molina, Diego Ampuero, Liliana Ramos, Paola Pérez, Osvaldo Aren, Sara Chernilo, Cristina Fernández, María Loreto Spencer, Jacqueline Flores, Giuliano Bernal, Mónica Ahumada, Germán Rasse, Carolina Sánchez, Maria Galli de Amorim, Gabriela Branco, Diana Noronha Nunes, Emmanuel Dias-Neto, Helano C. Freitas, NIRVANA team, Ricardo Armisén. Tumor genomic heterogeneity in non-small cell lung cancer (NSCLC) patients from Latin America [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6158.

Clinical and Genetic Characteristics of Early and Advanced Gastric Cancer.

Gastric cancer (GC) persists as the fourth most prevalent cause of global cancer-related mortality, presenting a challenge due to the scarcity of available therapeutic strategies. Precision medicine is crucial not only in the treatment but also in the management of GC. We performed gene panel sequencing with Oncomine focus assay comprising 52 cancer-associated genes and MSI analysis in 100 case-matched gastric cancer cases. A comprehensive analysis of clinical and genetic characteristics was conducted on these genetic results and clinicopathological findings. Upon comparison of clinicopathological characteristics, significant differences between early gastric cancer (EGC) and advanced gastric cancer (AGC) were observed in tumor location (p = 0.003), Lauren classification (p = 0.015), T stage (p = 0.000), and N stage (p = 0.015). The six most frequently mutated genes were PIK3CA (29%, 10/35), ERBB2 (17%, 6/35), KRAS (14%, 5/35), ALK (6%, 2/35), ESR1 (6%, 2/35), and FGFR3 (6%, 2/35). Regarding genetic variation, there was a tendency for the N stage to be higher in GC patients with mutated genes (p = 0.014). The frequency of mutations in GC patients was statistically significantly higher in AGC (n = 24) compared to EGC (n = 11) (odds ratio, 2.792; 95% confidence interval, 1.113 to 7.007; p = 0.026). Six of the ten GC patients carrying mutated genes and exhibiting MSI were classified into intestinal-type and undifferentiated GC, with the location of the tumor being in the lower-third. Among these patients, five harbored mutated PIK3CA, while the remaining patient had a mutation in ALK. Conclusions: AGC patients more frequently exhibited alterations of PIK3CA, KRAS, and ERBB2 as somatic oncogenic drivers, and displayed a higher prevalence of cumulative genetic events, including increased rates of PIK3CA mutations, enhanced detection of immunotherapy biomarkers, and mutations of the ESR1 gene.

Genomic profiling in advanced NSCLC in Italy: First results of NERoNE (NSCLC Emilia Romagna Next Generation Sequencing Evaluation) project.

e21077 Background: The NERoNE Project evaluates the use of Next Generation Sequencing (NGS) in molecular profiling of advanced NSCLC (aNSCLC) patients (pts) in three Oncology Units (OU) of Emilia Romagna Region aiming to clarify the impact of such extensive tool in characterizing different NSCLC subpopulations. Methods: Since January 2020 to December 2022, 970 sequential aNSCLC pts from three OU (AUSL-IRCCS of Reggio Emilia, Modena University Hospital and IRST Meldola) were profiled by NGS. Samples from Modena and Reggio Emilia were analyzed at Modena University Hospital Molecular Pathology Lab using Myriapod IL- 56G, Cancer Panel DNA, Cancer Panel RNA, Oncomine DX Target Test Assay, Oncomine Focus Assay. Samples from IRST Meldola were processed at its Molecular Diagnostic Unit by Myriapod NGS cancer panel DNA e RNA, Oncomine Focus Assay and Oncomine Comprehensive Assay v3.We considered molecular alterations with available target therapies in Italy: EGFR mutations (mut) (exon 18,19,20,21), KRAS mut, BRAF V600E mut, ALK, ROS1, RET and NTRK rearrangements, MET exon 14 skipping mut, ErbB2 mut, FGFR 1-3 mut. PDL1 expression was assessed by standard immunohistochemistry on 486 pts. Results: Among 970 pts, 501 with at least one mut (52%) were considered for analysis: 266 were female (53%), mean age was 69 ± 11 years (min-max: 33-94) and 473 pts (94%) had adenocarcinoma. Molecular features are listed in table 1. Distribution of mut among ages, categorized as &lt; 60, 60-70 and &gt; 70 y, was similar, EGFR activating mut were most prevalent in females; KRAS mut (G12C and non G12C) were most prevalent in males; 41 pts had co-mutations (8.2%): the most frequent co-mut were EGFR mut (27%). PDL1 expression was &lt; 1% 129 (27%), 1-49% 211 (43,4%) and ≥50% 146 pts (30%). The majority of pts with EGFR activating mut had PDL1 &lt; 50%. Conclusions: NERoNE evaluates data from NGS profiling of three OU mapping key actionable molecular alterations in a large population of aNSCLC also accounting for PDL1 status. This preliminary analysis will be the starting point for further evaluations in order to improve the personalized approach to aNSCLC. [Table: see text]

Comparison between liquid biopsy and tissue NGS in two cohorts of advanced NSCLC.

e21043 Background: Molecular testing is mandatory in advanced non-small cell lung cancer (NSCLC) due to prognostic and therapeutic implications. Correlation between blood and tissue next-generation sequencing (NGS) has recently been demonstrated. Methods: A retrospective observational study of two cohorts of NSCLC patients who underwent liquid biopsy at the time of advanced disease diagnosis was conducted. In cohort 1 (N = 129), liquid biopsy was performed using a 74 genes panel (Guardant360 CDx). In cohort 2 (N = 149), NGS was performed in peripheral blood using a 63 genes panel (FoundationOne Liquid CDx). For tissue NGS analysis, Oncomine Precision Assay and Oncomine Focus Assay, with 50 and 52 genes, respectively, were performed. Data were analyzed in both cohorts independently, and compared by statistical descriptive methods. Results: In cohort 1, 74/129 (57.4%) were men and 55/129 (42.6%) were non-smokers or had a ≤ 20-pack-year tobacco history. The most frequent histology was adenocarcinoma (99/129; 76.7%). In 14/129 (10.9%) patients, a second determination of NGS in peripheral blood was necessary and 1/129 (0.8%) had a total of three determinations. Tissue NGS was not performed in 32/129 (24.8%) because of insufficient sample. In cohort 2, 99/149 (66.4%) were men and 48/149 (32.2%) were non-smokers or had a ≤ 20-pack-year tobacco history. The most frequent histology was adenocarcinoma (99/149; 66.4%). Tissue NGS was not performed in 40/149 (26.8%) due to insufficient sample (26/40; 65%) or technical difficulties to perform a biopsy (14/40; 35%). In cohort 1, pathogenic mutations were detected in 119/129 (92.2%) and in 62/97 (63.9%) patients (p &lt; 0.001), with median time to obtain results of 11 (IQR 9-14) and 29 (IQR 22-39) days for blood and tissue NGS, respectively (p &lt; 0.001). Actionable mutations included alterations of levels I-II according to ESCAT and were found in 40/129 (31%) and 33/97 (34%) patients using blood and tissue NGS, respectively (p = 0.63). In cohort 2, circulating tumor DNA was not detected in 5/149 (3.5%) patients. Pathogenic mutations were found in 123/149 (82.6%) and in 71/109 (65.1%) patients (p = 0.001), with median time to obtain results of 15 (IQR 14-15) and 27 (IQR 16-27) days for blood and tissue NGS, respectively (p &lt; 0.001). Actionable mutations were detected in 41/149 (27.5%) and 41/109 (37.6%) using blood and tissue NGS, respectively (p = 0.08). Targeted therapy was given to 31/129 (24%) and 39/149 (26.2%) patients in cohort 1 and 2, respectively. Conclusions: To our knowledge, this is the first retrospective observational study where liquid biopsy and tissue NGS are compared in two different cohorts of patients with advanced NSCLC. Time to obtain results was shorter for blood NGS than tissue sequencing, and liquid biopsy provided molecular information in cases in which tissue NGS is not available. Further studies to identify patients in which liquid biopsy could replace tissue analysis are needed.

The Glioma-IRE project − Molecular profiling in patients with glioma: steps toward an individualized diagnostic and therapeutic approach

BackgroundThis study aimed to characterize the genetic profile of patients with glioma and discuss the impact of next-generation sequencing in glioma diagnosis and treatment.MethodsBetween 2019 and 2022, we analyzed the genetic profile of 99 patients with glioma through the Oncomine Focus Assay. The assay enables the detection of mutations in 52 driver genes, including single nucleotide variants (SNVs), copy number variants (CNVs), and gene fusions. We also collected and analyzed patients’ clinic characteristics and treatment outcomes.ResultsOver a period of 35 months, 700 patients with glioma followed by our neuro-oncology unit were screened, and 99 were enrolled in the study; most of the patients were excluded for inadequate non-morphological MRI or lack/inadequacy of the tissue samples. Based on our findings, most patients with glioma present mutations, such as SNVs, CNVs or gene fusions. Our data were similar to those reported by The Cancer Genome Atlas Program in terms of frequency of SNVs and CNVs, while we observed more cases of gene fusions. Median overall survival, progression-free survival, and time to progression were significantly lower for patients with grade VI glioblastoma than those with other gliomas. Only four patients were offered a targeted treatment based on the mutation detected; however, only one received treatment, the others could not receive the selected treatment because of worsening clinical status.ConclusionRoutine timely molecular profiling in patients with glioma should be implemented to offer patients an individualized diagnostic approach and provide them with advanced targeted therapy options if available.

Performance Characteristics of Oncomine Focus Assay for Theranostic Analysis of Solid Tumors, A (21-Months) Real-Life Study.

Next generation sequencing analysis is crucial for therapeutic decision in various solid tumor contexts. The sequencing method must remain accurate and robust throughout the instrument lifespan allowing the biological validation of patients' results. This study aims to evaluate the long-term sequencing performances of the Oncomine Focus assay kit allowing theranostic DNA and RNA variants detection on the Ion S5XL instrument. We evaluated the sequencing performances of 73 consecutive chips over a 21-month period and detailed the sequencing data obtained from both quality controls and clinical samples. The metrics describing sequencing quality remained stable throughout the study. We showed that an average of 11 × 106 (±0.3 × 106) reads were obtained using a 520 chip leading to an average of 6.0 × 105 (±2.6 × 105) mapped reads per sample. Of 400 consecutive samples, 95.8 ± 16% of amplicons reached the depth threshold of 500X. Slight modifications of the bioinformatics workflow improved DNA analytical sensitivity and allowed the systematic detection of expected SNV, indel, CNV, and RNA alterations in quality controls samples. The low inter-run variability of DNA and RNA-even at low variant allelic fraction, amplification factor, or reads counts-indicated that our method was adapted to clinical practice. The analysis of 429 clinical DNA samples indicated that the modified bioinformatics workflow allowed detection of 353 DNA variants and 88 gene amplifications. RNA analysis of 55 clinical samples revealed 7 alterations. This is the first study showing the long-term robustness of the Oncomine Focus assay in clinical routine practice.

CANTRK: A Canadian Ring Study to Optimize Detection of NTRK Gene Fusions by Next-Generation RNA Sequencing

The Canadian NTRK (CANTRK) study is an interlaboratory comparison ring study to optimize testing for neurotrophic receptor tyrosine kinase (NTRK) fusions in Canadian laboratories. Sixteen diagnostic laboratories used next-generation sequencing (NGS) for NTRK1, NTRK2, or NTRK3 fusions. Each laboratory received 12 formalin-fixed, paraffin-embedded tumor samples with unique NTRK fusions and two control non-NTRK fusion samples (one ALK and one ROS1). Laboratories used validated protocols for NGS fusion detection. Panels included Oncomine Comprehensive Assay v3, Oncomine Focus Assay, Oncomine Precision Assay, AmpliSeq for Illumina Focus, TruSight RNA Pan-Cancer Panel, FusionPlex Lung, and QIAseq Multimodal Lung. One sample was withdrawn from analysis because of sample quality issues. Of the remaining 13 samples, 6 of 11 NTRK fusions and both control fusions were detected by all laboratories. Two fusions, WNK2::NTRK2 and STRN3::NTRK2, were not detected by 10 laboratories using the Oncomine Comprehensive or Focus panels, due to absence of WNK2 and STRN3 in panel designs. Two fusions, TPM3::NTRK1 and LMNA::NTRK1, were challenging to detect on the AmpliSeq for Illumina Focus panel because of bioinformatics issues. One ETV6::NTRK3 fusion at low levels was not detected by two laboratories using the TruSight Pan-Cancer Panel. Panels detecting all fusions included FusionPlex Lung, Oncomine Precision, and QIAseq Multimodal Lung. The CANTRK study showed competency in detection of NTRK fusions by NGS across different panels in 16 Canadian laboratories and identified key test issues as targets for improvements.

HER2 Copy Number and Resistance Mechanisms in Patients with HER2-positive Advanced Gastric Cancer Receiving Initial Trastuzumab-based Therapy in JACOB Trial.

In JACOB trial, pertuzumab added to trastuzumab-chemotherapy did not significantly improve survival of patients with HER2-positive metastatic gastric cancer, despite 3.3 months increase versus placebo. HER2 copy-number variation (CNV) and AMNESIA panel encompassing primary resistance alterations (KRAS/PIK3CA/MET mutations, KRAS/EGFR/MET amplifications) may improve patients' selection for HER2 inhibition. In a post hoc analysis of JACOB on 327 samples successfully sequenced by next-generation sequencing (NGS; Oncomine Focus DNA), HER2 CNV, HER2 expression by IHC, and AMNESIA were correlated with overall response rate (ORR), progression-free survival (PFS), and overall survival (OS) by univariable/multivariable models. Median HER2 CNV was 4.7 (interquartile range, 2.2-16.9). HER2 CNV-high versus low using the median as cutoff was associated with longer median PFS (10.5 vs. 6.4 months; HR = 0.48; 95% confidence interval: 0.38-0.62; P < 0.001) and OS (20.3 vs. 13.0 months; HR = 0.54; 0.42-0.72; P < 0.001). Combining HER2 CNV and IHC improved discriminative ability, with better outcomes restricted to HER2-high/HER2 3+ subgroup. AMNESIA positivity was found in 51 (16%), with unadjusted HR = 1.35 (0.98-1.86) for PFS; 1.43 (1.00-2.03) for OS.In multivariable models, only HER2 CNV status remained significant for PFS (P < 0.001) and OS (P = 0.004). Higher ORR was significantly associated with IHC 3+ [61% vs. 34% in 2+; OR = 3.11 (1.89-5.17)] and HER2-high [59% vs. 43% in HER2-low; OR = 1.84 (1.16-2.94)], with highest OR in the top CNV quartile. These biomarkers were not associated with treatment effect of pertuzumab. HER2 CNV-high assessed by NGS may be associated with better ORR, PFS, and OS in a JACOB subgroup, especially if combined with HER2 3+. The negative prognostic role of AMNESIA requires further clinical validation.

19P Deciphering the role of precision oncology in the treatment of biliary tract cancer in daily routine practice: Retrospective analysis from the cancer center Upper Austria

BackgroundThe routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized.MethodsWe performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression.ResultsA potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol.ConclusionsWe could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC.Legal entity responsible for the studyThe authors.FundingHas not received any funding.DisclosureAll authors have declared no conflicts of interest. BackgroundThe routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized. The routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized. MethodsWe performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression. We performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression. ResultsA potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol. A potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol. ConclusionsWe could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC. We could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC.

1206P HER2 copy number variation (CNV), HER2 expression and primary resistance mechanisms in patients (pts) with HER2-positive metastatic gastric or gastroesophageal junction cancer (mGC/GEJC) receiving first-line chemotherapy (CT) + trastuzumab (T) +/- pertuzumab (P) in the JACOB trial

In JACOB trial, P added to T-CT did not significantly improve overall survival (OS) in pts with HER2+ mGC/GEJC despite a 3.3 mos increase vs placebo. We previously showed a negative prognostic role of AMNESIA panel, including KRAS/PIK3CA/MET mutations and KRAS/EGFR/MET amplifications (Pietrantonio et al, CCR 2018), whereas higher HER2 CNV may be associated with better outcomes on T. These biomarkers may allow to better identify pts with higher benefit from HER2 inhibition. Among 780 pts enrolled in JACOB and 580 with available baseline tumor DNA, 327 samples were sequenced by Oncomine Focus DNA assay. In a post-hoc analysis, HER2 CNV, HER2 expression by IHC and AMNESIA were correlated with overall response rate (ORR), progression-free survival (PFS) and OS by uni-/multivariable models. Median HER2 CNV was 4.7 (IQR 2.2-16.9). By pooling treatment arms, HER2-high vs low status using the median as the cut-off value was associated with longer PFS (mPFS: 10.5 vs 6.4 mos; hazard ratio (HR)=0.48, 95%CI: 0.38-0.62; p<.001) and OS (mOS: 20.3 vs 13.0 mos; HR=0.54, 0.42-0.72; p<.001). Combining HER2 CNV and IHC improved the discriminative ability, with better outcomes restricted to HER2-high/HER2 3+ subgroup. AMNESIA positivity was found in 51 (16%), with unadjusted HR=1.35 (0.98-1.86) for PFS; 1.43 (1.00-2.03) for OS. HER2-high subgroup was enriched for AMNESIA-neg and HER2 3+ status. In multivariable models with main variables including treatment arm, only HER2 CNV status remained statistically significant for PFS (p<.001) and OS (p=.004). Higher ORR was significantly associated with IHC 3+ [61% vs 34% in 2+; odds ratio(OR)=3.11 (1.89-5.17)] and HER2-high [59% vs 43% in HER2-low; OR=1.84 (1.16-2.94), with highest OR in the top CNV quartile. The selected biomarkers were not associated with activity and efficacy of P added to T-CT. HER2-high CNV assessed by NGS is associated with significantly better ORR, PFS, OS in a pts subgroup from the JACOB trial, independent from treatment arm and especially if combined with HER2 3+.

Costs of Next-Generation Sequencing Assays in Non-Small Cell Lung Cancer: A Micro-Costing Study.

Background: Next-generation sequencing (NGS) of tumor genomes has changed and improved cancer treatment over the past few decades. It can inform clinicians on the optimal therapeutic approach in many of the solid and hematologic cancers, including non-small lung cancer (NSCLC). Our study aimed to determine the costs of NGS assays for NSCLC diagnostics. Methods: We performed a micro-costing study of four NGS assays (Trusight Tumor 170 Kit (Illumina), Oncomine Focus (Thermo Fisher), QIAseq Targeted DNA Custom Panel and QIASeq Targeted RNAscan Custom Panel (Qiagen), and KAPA HyperPlus/SeqCap EZ (Roche)) at the StemCore Laboratories, the Ottawa Hospital, Canada. We used a time-and-motion approach to measure personnel time and a pre-defined questionnaire to collect resource utilization. The unit costs were based on market prices. The cost data were reported in 2019 Canadian dollars. Results: Based on a case throughput of 500 cases per year, the per-sample cost for TruSight Tumor 170 Kit, QIASeq Targeted DNA Custom Panel and QIASeq Targeted RNAscan Custom Panel, Oncomine Focus, and HyperPlus/SeqCap EZ were CAD 1778, CAD 599, CAD 1100 and CAD 1270, respectively. The key cost drivers were library preparation (34–60%) and sequencing (31–51%), followed by data analysis (6–13%) and administrative support (2–7%). Conclusions: Trusight Tumor 170 Kit was the most expensive NGS assay for NSCLC diagnostics; however, an economic evaluation is required to identify the most cost-effective NGS assay. Our study results could help inform decisions to select a robust platform for NSCLC diagnostics from fine needle aspirates, and future economic evaluations of the NGS platforms to guide treatment selections for NSCLC patients.

Proposal of a molecular testing algorithm for differentiated thyroid cancer (DTC).

e18090 Background: In the growing era of precision medicine and tumor-agnostic therapies, the molecular testing of DTC is becoming mandatory to optimize diagnostic and therapeutical strategies. Even if the most frequent oncogenic events, occurring in a mutually exclusive manner, are BRAF V600E, followed by RAS, gene fusions mainly occurring in RET, NTRK1-3, and ALK genes have been also found. In this scenario, the definition of a molecular testing algorithm to be implemented for clinical practice is needed, in order to optimize resources and time for better clinical patient management. Methods: Gene mutations and gene fusions were evaluated on DNA and RNA extracted from cytologic or histologic samples. Mutations were tested using a lab-developed multi-gene panel able to analyze the hot-spot regions of 28 genes (total of 343 amplicons, 21.77 kb); gene fusions were tested using the Oncomine Focus assay panel. Results: Molecular characterization was performed on a total of 63 DTC (50 papillary thyroid carcinoma - PTC, 8 – follicular thyroid carcinoma - FTC, 5 – hurthle cell carcinoma - HCC) by the treating clinician for diagnostic, prognostic or clinical reasons. In 27 cases (42.8%) at least one DNA mutation was detected, 17 cases (26.9%) were positive for gene fusion rearrangement, in only 2 cases (3.1%) both DNA mutations and gene rearrangements were found and in the remaining 17 (26.9%) cases no DNA mutations or rearrangements were detected. Among mutated-subgroup, BRAF V600E mutation was the most common (14 of 63 cases – 22.2%), followed by RAS mut (9 cases – 14.2%: 4 NRAS, 3 HRAS, and 3 KRAS), both as single event in 7 and 4 cases respectively. Substitutions in TERT promoter region was found in 16 cases (25.3%), of which 14 as secondary event. Other mutations in TP53 (4 cases –6.3 %, of which 2 as single event), PIK3CA (1 case – 1.5%), AKT1(1 case – 1.5%), and RNF43 (1 case – 1.5%) were detected. Among riarranged subgroup, RET fusions and NTRK1-3 was found in 8 cases respectively (12.6%), while ALK fusion was found 1 case (1.5%). The concomitant mutational and fusion events found in 2 cases were the following: 1) HRAS and PAX8/PPARG; 2) PIK3CA/TP53/TERT and RET/CCDC6. Conclusions: As expected, BRAF and RAS mutations represent the most common genetic events in DTC and occur in a mutual exclusive manner. However, in about 30% of patients, mostly of young age, with papillary histology and lymph nodal involvement, a clinically actionable gene rearrangement has been found. Thus, we propose a two-step molecular testing algorithm with a first-level test to identify the most common mutations and a second-level test, including less common mutations and gene rearrangements, if the genes analyzed with the first level test are wild-type. The second-level test may be performed up-front in cases where there are clinicopathologic features suggestive of fusion gene TC gene or in clinically aggressive unconventional cases for which molecular therapy is being considered.

Recurrent Alterations in the MAPK pathway in Sporadic Pyogenic Granuloma of Childhood.

Pyogenic granuloma is one of the most common vascular tumours. The cause of pyogenic granuloma was previously thought to be an inflammatory reaction with consecutive stimulation of endothelial cell proliferation. However, recent studies suggest that pyogenic granuloma may be driven by constitutive activation of the mitogen-activated protein kinase pathway. The aim of this study was to investigate the molecular profile of sporadic pyogenic granuloma of childhood, using a systematic approach scrutinizing potential aberrations within different oncogenic pathways. Within a retrospective setting pyogenic granuloma of 15 patients was analysed by targeted next generation sequencing using the Oncomine Focus Assay, which includes genes of key tumorigenic signalling pathways. Activating mutations were found in 4 out of 15 cases (27%). Two HRAS hotspot mutations (p.Gly13Arg, p.Ala59Thr), 1 BRAF (p.Val600Glu) mutation and a novel, previously not reported, MAP2K1 hotspot mutation (p.Glu203Lys) were identified. It is notable that all of these genes are involved in constitutive mitogen-activated protein kinase signalling. This study increases the range of underlying genetic alterations in pyogenic granuloma by identifying novel oncogenic mutations in crucial mitogen-activated protein kinase pathway genes. The results provide supporting evidence that activated mitogen-activated protein kinase signalling is a key driver in the pathogenesis of pyogenic granuloma, which might be exploited by targeted treatment approaches for selected cases.

NTRK Gene Fusion Detection in a Pan-Cancer Setting Using the Idylla GeneFusion Assay

Recently, approval of tyrosine receptor kinase (TRK) inhibitors by Food and Drug Administration and European Medicines Agency in NTRK fusion-positive cancer types has led to a variety of proposed testing algorithms. In this study, performance of the fully automated Idylla GeneFusion Assay was assessed in a set of clinically relevant cancer types, including glioblastoma, non-small-cell lung cancer, microsatellite instability-positive colorectal cancer, and thyroid carcinoma. Analysis with the Idylla GeneFusion Assay revealed significant differences in baseline RNA expression profile between the different cancer types, which corresponded to both literature and pan-TRK immunohistochemical staining. Compared with the RNA-based Oncomine Focus Assay, the Idylla GeneFusion Assay demonstrated an overall percentage agreement, positive percentage agreement, and negative percentage agreement of 92.7%, 81.8%, and 93.8%, respectively; and the pan-TRK immunohistochemistry demonstrated an overall percentage agreement, positive percentage agreement, and negative percentage agreement of 82.1%, 45.5%, and 85.7%, respectively. These findings highlighted the importance of tailoring NTRK testing algorithms per cancer type. In a small subset, data from the RNA-based Archer FusionPlex Assay were also available. NTRK fusion detection efficiency was compared between the four NTRK testing modalities, with a high concordance between the PCR-based methods. Last, RNA degradation was observed when using the Idylla GeneFusion Assay on snap frozen tissue samples as these are nonfixated. This might be countered by increasing the amount of sample input. To conclude, the Idylla GeneFusion Assay has shown a clear potential in identifying NTRK fusions.