Targetable Genomic Alterations Research Articles

Abstract PO5-13-05: Comparison of whole exome, whole transcriptome genomic profiling and targeted sequencing with 50-gene panels

Abstract Introduction Genomic profiling to identify targetable genomic alterations is the standard of care in the management of advanced cancers, including breast cancer (BC), and is recommended by ASCO provisional clinical guidelines. Genomic panels of ≤50 genes are generally less expensive than larger panels but may miss targetable alterations. This study compared a comprehensive tumor-normal whole-exome, whole-transcriptome panel to four 50-gene panels. In addition, for triple-negative BC (TNBC), the budget impact of using a comprehensive panel versus 50-gene panels was estimated. Methods Gene lists derived from three commercially available 50-gene panels (A, B and C) and a customized pan-cancer gene panel list (D) were used. The genes listed on the custom panel were chosen by medical experts. Samples from BC patients that underwent OncoExTraTM testing from May 2018 through March 2023 were included. The OncoExTra assay uses tumor-normal whole exome and whole transcriptome sequencing to detect somatic single base substitutions, indels, copy number alterations, gene fusions and alternative transcripts. In this analysis, the focus was actionable biomarkers, defined as those with associated FDA-approved targeted therapies in any cancer type, those that made patients eligible for an active clinical trial, or those with evidence in guidelines or the literature for possible matched therapies in any cancer. The frequencies of patients who would have been missed (no actionable alterations identified) using only the genes on each 50-gene panel were summarized. It was assumed that any alteration involving a listed gene would be detected, maximizing the potential utility of each panel. For TNBC, the budget impact of shifting the 20% of patients currently tested with 50-gene panels to OncoExTra testing was estimated using a previously published model. Results A total of 2161 BC patient samples were included. Across all samples, between 11.9% and 28.1% of patients would have been missed by restricting to only 50 genes (Table 1). The proportion of missed patients across panels was highest in TNBC and lowest in HER2+ cancers. Major drivers of missed patients included absence of FGF3/4/19 (A-D), MAP3K1 (A-D), BRCA1/2 (A, B, C), CCND1 (B, C, D), and PTEN (A, D). Across the four panels, patients were missed due to actionable alterations in 96 to 126 genes. Tumor mutational burden and microsatellite instability, which are not reported in 50-gene panels, were high in 35 (1.6%) and 7 (0.3%) BC patient samples, respectively. Within a 1-million-member plan, 44 TNBC patients would be eligible for testing. If all these patients were tested with OncoExtra rather than a 50-gene panel, the increase in per-member-per-month costs ranges from $0.0104-0.0172, driven predominantly by increased matched therapy costs. Between two and five TNBC patients would be eligible to receive a different treatment with a comprehensive panel. Conclusions In BC, between 11.9% and 28.1% of patients with actionable alterations would have been missed by restricting analysis to the 50 genes found in these panels. Using a comprehensive profiling assay such OncoExTra led to the identification of additional TNBC patients with actionable alterations at a minimal budget impact. Table 1. BC patients (pts) with actionable alterations missed by each 50-gene panel. NS = subtype not specified. Citation Format: Snehal Thakkar, David Hall, Jess Hoag, Cynthia Flannery, Nishitha Therala, Anson Tharayanil, Jesse Ortendahl, Gebra Cuyun Carter, Gargi Basu. Comparison of whole exome, whole transcriptome genomic profiling and targeted sequencing with 50-gene panels [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-13-05.

Pamiparib as consolidation treatment after concurrent chemoradiotherapy of limited-stage small cell lung cancer: a single-arm, open-label phase 2 trial

BackgroundSmall cell lung cancer (SCLC) is highly invasive with poor prognosis, and its treatment has historically been hindered due to the absence of targetable driver genomic alterations. However, the high genomic instability and replication stress in SCLC have made poly(ADP-ribose) polymerases (PARPs) inhibitors a focus of research. Pamiparib is an orally available PARP1/2 inhibitor with high selectivity, strong PARP trapping activity, and excellent brain penetration. Utilizing pamiparib as consolidation maintenance therapy in limited-stage SCLC holds promise for improving survival outcomes and offering a viable therapeutic approach.MethodsThis single-arm, open-label phase II trial will enroll patients aged 18–75 years with histologically/cytologically confirmed, limited-stage SCLC who have not progressed following definitive platinum-based cCRT and have an ECOG PS of 0 or 1. Patients will be excluded if they have histologically confirmed mixed SCLC or NSCLC, or have undergone previous tumor resection, or can be treated with surgery or stereotactic body radiation therapy/stereotactic ablative radiation therapy. Participants will receive pamiparib 40 mg twice daily every 3 weeks within 2 to 6 weeks after cCRT for up to 1 year or until disease progression according to RECIST v1.1. The primary endpoint is the 1-year progression-free survival (PFS) rate assessed by investigators per RECIST v1.1. Secondary endpoints include PFS, objective response rate, and duration of response assessed by investigators per RECIST 1.1, overall survival, time to distant metastasis, and safety.DiscussionThe study will provide valuable data on the feasibility, safety, and effectiveness of pamiparib as a consolidation therapy after cCRT in patients with LS-SCLC. The correlation between molecular typing or gene expression profile of the disease and curative response will be further explored.Trial registrationNCT05483543 at clinicaltrials.gov.

Abstract 939: Comprehensive genomic and transcriptomic analysis to guide therapy for patients with metastatic solid tumors

Abstract Introduction: Precision oncology, which aims to profile tumors for identifying actionable alterations to guide therapy has become mainstream in cancer clinics. While most approaches focus on DNA aberrancies on targeted panels, not all patients’ tumors show targetable genomic alterations in these limited gene sets, indicating a need for more comprehensive methodologies combining whole exome (WES) and transcriptome sequencing (RNAseq) to direct a larger fraction of patients to therapies. Here, we aimed to compare the feasibility and utility of BostonGene’s (BG) analytical platform with WES and RNAseq to two targeted exome panels in identifying actionable alterations and therapy selection for patients with metastatic solid tumors. Methods: Study enrolled patients with solid tumors who have had next-generation-sequencing (NGS) testing with one of two tissue-based targeted exome sequencing panels, Oncomine (ThermoFisher, 148 genes), or MDA-MAPP (615 genes) with identification of no College of American Pathologists Tier-1 actionable DNA alterations between August 2022 and November 2023. Patients’ tissue and blood/saliva samples were subjected to BG’s NGS platform. An alteration-level actionability analysis was done upon receipt of WES results to inform treatment decision making, based on functional and therapeutic effects of the alterations detected. Results: A total of 64 patients were enrolled; testing was cancelled for 7 patients (10.9%) with samples showing <10% tumor content, while 5 patients’ reports were pending at the time of data analysis. Median turn-around time from consent to sample acquisition (SA) and from SA to available genomic profile were 8 and 15.5 days, respectively. 52 patients had NGS results representing a diverse group of tumor types, including sarcoma (n=11, 21.2%), head and neck (n=9, 17.3%) and mesothelioma (n=5, 9.6%). BG reported DNA alterations (mean: 3.75; median: 4) not shown by prior testing for 94.2% (49/52) of patients, whereby the most common alteration types included SNVs (43.1%), deletions (23.6%) and amplifications (11.8%). BG identified additional actionable DNA alterations (referred to as “AAs”; mean: 1.9, median: 2) in 32 (61.5%) patients, whereby majority of AAs were deletions (59.7%) and amplifications (27.4%). BG detected AAs in 58.8% (10/17) vs 62.9% (22/35) of patients for whom the same vs different samples were used across different tests compared (P=0.8). Of 32 patients with AAs, 7 (21.9%) were directed to DNA-informed treatments within 6 months based upon the new genomic findings reported by BG, 14 (43.8%) are being followed for treatment matching, while 11 (34.4%) were deceased. Discussion: Our results show the feasibility and utility of comprehensive molecular testing to match patients to WES-informed treatments within a clinically relevant time frame. Assessment of the additional benefit of RNA expression analysis is forthcoming. Citation Format: Burak Uzunparmak, Fei Su, Amber M. Johnson, Krystle Nomie, Nathan Fowler, Lile Kontselidze, Aleksander Bagaev, Anna Butusova, Ecaterina E. Dumbrava, Jordi Rodon-Ahnert, Siqing Fu, David S. Hong, Timothy A. Yap, Aung Naing, Sarina A. Piha-Paul, Daniel D. Karp, Paula R. Pohlmann, Apostolia M. Tsimberidou, Keyur P. Patel, Funda Meric-Bernstam. Comprehensive genomic and transcriptomic analysis to guide therapy for patients with metastatic solid tumors [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 939.

Abstract 3694: Genomic profiling of single cancer cells using the novel single-cell integrated mutational profiling of actionable cancer targets (scIMPACT) assay

Abstract Liquid biopsy provides opportunities to guide therapy decisions using biomarkers such as circulating tumor cells (CTCs) even years after the primary tumor resection. For this, novel methods permitting the genomic profiling of CTCs are needed to characterize systemic cancer spread and identify clinically targetable genomic alterations. Hence, we developed an assay based on the FDA-approved MSK-IMPACT® assay to analyze the genomes of single-cells. We present a series of benchmarking experiments using well-characterized cell lines to demonstrate the performance of our new Single-Cell Integrated Mutation Profiling of Actionable Cancer Targets (scIMPACT) assay.The scIMPACT assay was developed using Ampli1® WGA products of single-cell and pool samples. The workflow consists of an optimized library preparation protocol followed by targeted sequencing with the scIMPACT panel. A bioinformatics mutation calling workflow facilitates the detection of single nucleotide variations (SNVs), indels, and copy number variations (CNVs). To account for WGA associated bias, we developed an in-house proprietary machine learning based classifier algorithm. Two sample collectives were prepared and used for training and validating the workflow. The first collective, including genomic libraries of MDA-MB-453, BT474, BT549 and ZR-75.1 samples, was used for training of the mutation detection workflow. The second collective, consisting of HCC1395/HCC1395BL cell lines representing matched tumor and normal cells, was used to validate the performance of the assay. The scIMPACT assay identified somatic mutations in all WGA products as predicted from bulk gDNA samples and published literature. Notably, evidence of genetic heterogeneity was reported at the single cell level. Pertaining to the SNV detection, the training collective displayed 91% sensitivity and 96% specificity (AUC=0.98) while the validation collective demonstrated similar performance with 84% sensitivity and 96% specificity (AUC=0.90) proving the applicability of our workflow across different datasets. Furthermore, CNV analysis showed high concordance between matching gDNA and WGA samples. Our workflow enables mutational profiling with high specificity and sensitivity and accurate CNV detection in single cells. The scIMPACT assay has been successfully adapted to analyze samples at the single-cell level. Therefore, our method can be applied for the genomic profiling of patient-derived CTCs. Citation Format: Clara Chaiban, Adithi Ravikumar Varadarajan, Jonas Grote, Thomas Ragg, Isabell Blochberger, Vadim Dechand, Jens Warfsmann, Christoph A. Klein, Zbigniew T. Czyż. Genomic profiling of single cancer cells using the novel single-cell integrated mutational profiling of actionable cancer targets (scIMPACT) assay [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 3694.

Comprehensive Molecular Profiling and Clinicopathological Characteristics of Gastric-Type Mucinous Carcinoma of the Uterine Cervix in Japanese Women.

Gastric-type mucinous carcinoma (GAS) of the uterine cervix is the most common adenocarcinoma that develops independently of human papillomavirus infection; it is typically diagnosed at an advanced stage and has a poorer prognosis than usual-type endocervical adenocarcinoma. Few studies have examined the molecular profile of GAS, but genetic alterations in TP53 and STK11 have been repeatedly reported. We analyzed the clinicopathological characteristics and molecular profile of GAS. Fresh-frozen tissue specimens and formalin-fixed paraffin-embedded (FFPE) tissues from 13 patients with GAS treated between January 2000 and December 2020 were analyzed. We performed next-generation sequencing on eight fresh-frozen GAS specimens using the Cancer Hotspot Panel v2 (cases 1-8) and the FoundationOne companion diagnostic (F1CDx) assay on six FFPE samples (cases 8-13). Seventy-four genomic alterations were identified in 42 genes. In order of frequency, TP53, ATRX, CDKN2A, KRAS, APC, and STK11 were altered in at least three cases. Targetable genomic alterations were identified in all six patients' specimens analyzed using the F1CDx assay. GAS harbors various genomic alterations associated with sustained activation of signaling pathways or cell cycle regulation in addition to abnormalities in TP53, and precision medicine based on molecular profiling will be necessary to overcome GAS.

From the identification of actionable molecular targets to the generation of faithful neuroblastoma patient-derived preclinical models

BackgroundNeuroblastoma (NB) represents the most frequent and aggressive form of extracranial solid tumor of infants. Although the overall survival of patients with NB has improved in the last years, more than 50% of high-risk patients still undergo a relapse. Thus, in the era of precision/personalized medicine, the need for high-risk NB patient-specific therapies is urgent.MethodsWithin the PeRsonalizEd Medicine (PREME) program, patient-derived NB tumors and bone marrow (BM)-infiltrating NB cells, derived from either iliac crests or tumor bone lesions, underwent to histological and to flow cytometry immunophenotyping, respectively. BM samples containing a NB cells infiltration from 1 to 50 percent, underwent to a subsequent NB cells enrichment using immune-magnetic manipulation. Then, NB samples were used for the identification of actionable targets and for the generation of 3D/tumor-spheres and Patient-Derived Xenografts (PDX) and Cell PDX (CPDX) preclinical models.ResultsEighty-four percent of NB-patients showed potentially therapeutically targetable somatic alterations (including point mutations, copy number variations and mRNA over-expression). Sixty-six percent of samples showed alterations, graded as “very high priority”, that are validated to be directly targetable by an approved drug or an investigational agent. A molecular targeted therapy was applied for four patients, while a genetic counseling was suggested to two patients having one pathogenic germline variant in known cancer predisposition genes. Out of eleven samples implanted in mice, five gave rise to (C)PDX, all preserved in a local PDX Bio-bank. Interestingly, comparing all molecular alterations and histological and immunophenotypic features among the original patient’s tumors and PDX/CPDX up to second generation, a high grade of similarity was observed. Notably, also 3D models conserved immunophenotypic features and molecular alterations of the original tumors.ConclusionsPREME confirms the possibility of identifying targetable genomic alterations in NB, indeed, a molecular targeted therapy was applied to four NB patients. PREME paves the way to the creation of clinically relevant repositories of faithful patient-derived (C)PDX and 3D models, on which testing precision, NB standard-of-care and experimental medicines.

Methylthioadenosine Phosphorylase Genomic Loss in Advanced Gastrointestinal Cancers

Abstract Background One of the most common sporadic homozygous deletions in cancers is 9p21 loss, which includes the genes methylthioadenosine phosphorylase (MTAP), CDKN2A, and CDKN2B, and has been correlated with worsened outcomes and immunotherapy resistance. MTAP-loss is a developing drug target through synthetic lethality with MAT2A and PMRT5 inhibitors. The purpose of this study is to investigate the prevalence and genomic landscape of MTAP-loss in advanced gastrointestinal (GI) tumors and investigate its role as a prognostic biomarker. Materials and Methods We performed next-generation sequencing and comparative genomic and clinical analysis on an extensive cohort of 64 860 tumors comprising 5 GI cancers. We compared the clinical outcomes of patients with GI cancer harboring MTAP-loss and MTAP-intact tumors in a retrospective study. Results The prevalence of MTAP-loss in GI cancers is 8.30%. MTAP-loss was most prevalent in pancreatic ductal adenocarcinoma (PDAC) at 21.7% and least in colorectal carcinoma (CRC) at 1.1%. MTAP-loss tumors were more prevalent in East Asian patients with PDAC (4.4% vs 3.2%, P = .005) or intrahepatic cholangiocarcinoma (IHCC; 6.4% vs 4.3%, P = .036). Significant differences in the prevalence of potentially targetable genomic alterations (ATM, BRAF, BRCA2, ERBB2, IDH1, PIK3CA, and PTEN) were observed in MTAP-loss tumors and varied according to tumor type. MTAP-loss PDAC, IHCC, and CRC had a lower prevalence of microsatellite instability or elevated tumor mutational burden. Positive PD-L1 tumor cell expression was less frequent among MTAP-loss versus MTAP-intact IHCC tumors (23.2% vs 31.2%, P = .017). Conclusion In GI cancers, MTAP-loss occurs as part of 9p21 loss and has an overall prevalence of 8%. MTAP-loss occurs in 22% of PDAC, 15% of IHCC, 8.7% of gastroesophageal adenocarcinoma, 2.4% of hepatocellular carcinoma, and 1.1% of CRC and is not mutually exclusive with other targetable mutations.

Prevalence of targetable genomic alterations in young women with advanced breast cancer: a cross-sectional study.

Approximately 5% of breast cancers each year are diagnosed in young women < 40 years who tend to have worse clinical outcomes. We compared genomic alterations using comprehensive genomic profiling (CGP) of tumor tissue among very young women (< 30 years) and young women (30-39 years) compared to women ≥ 40 years at diagnosis. 2049 advanced breast cancer cases were submitted to Foundation Medicine within a 22-month window for CGP. Hybrid-capture based CGP was performed to evaluate all classes of genomic alterations. Tumor mutational burden was determined on at least 0.8 Mbp of sequenced DNA and microsatellite instability was determined on at least 95 loci. Immunocyte PD-L1 expression was determined by immunohistochemistry. Of the total cases, 28 (1.37%) were < 30 years,159 (7.76%) were 30-39 years, and 1862 (90.87%) were ≥ 40 at time of diagnosis. Breast tumors were less likely to be estrogen receptor positive in younger women (54% of < 30 years, p > 0.05; 60% of 30-39 years, p < 0.001; 69.4% of ≥ 40 years) and more likely to be triple negative (43%, p = 0.05; 33%, p = 0.05; 26.1% respectively). Young women had higher rates of BRCA1 mutations (17.9% <30 years, p < 0.001; 10.1% 30-39 years, p < 0.001; 2.6% ≥40 years), but lower rates of CDH1 (7.1% <30 years, p > 0.05; 5.0% 30-39 years, p < 0.001; 15.4% ≥40 years) and PIK3CA mutations (17.9% <30 years, p = 0.02; 17.6% 30-39 years, p < 0.001; 40.0% ≥40 years). Our findings contribute to the growing literature demonstrating unique genetic profiles among young women diagnosed with breast cancer, compared to older women.

Baseline mutational profiles of patients with carcinoma of unknown primary origin enrolled in the CUPISCO study

Patients with unfavorable carcinoma of unknown primary origin (CUP) have an extremely poor prognosis of ∼1 year or less, stressing the need for more tailored treatments, which are currently being tested in clinical trials. CUPISCO (NCT03498521) was a phase II randomized study of targeted therapy/cancer immunotherapy versus platinum-based chemotherapy in patients with previously untreated, unfavorable CUP, defined as per the European Society for Medical Oncology guidelines. We present a preliminary, descriptive molecular analysis of 464 patients with stringently diagnosed, unfavorable CUP enrolled in the CUPISCO study. Genomic profiling was carried out on formalin-fixed, paraffin-embedded tissue to detect genomic alterations and assess tumor mutational burden and microsatellite instability. Overall, ∼32% of patients carried a potentially targetable genomic alteration, including PIK3CA, FGFR2, ERBB2, BRAFV600E, EGFR, MET, NTRK1, ROS1, and ALK. Using hierarchical clustering of co-mutational profiles, 10 clusters were identified with specific genomic alteration co-occurrences, with some mirroring defined tumor entities. Results reveal the molecular heterogeneity of patients with unfavorable CUP and suggest that genomic profiling may be used as part of informed decision-making to identify the potential primary tumor and targeted treatment options. Whether stringently diagnosed patients with unfavorable CUP benefit from targeted therapies in a similar manner to those with matched known primaries will be a key learning from CUPISCO.

Integration of Genomic Sequencing Drives Therapeutic Targeting of PDGFRA in T-Cell Acute Lymphoblastic Leukemia/Lymphoblastic Lymphoma.

Patients with relapsed or refractory T-cell acute lymphoblastic leukemia (T-ALL) or lymphoblastic lymphoma (T-LBL) have limited therapeutic options. Clinical use of genomic profiling provides an opportunity to identify targetable alterations to inform therapy. We describe a cohort of 14 pediatric patients with relapsed or refractory T-ALL enrolled on the Leukemia Precision-based Therapy (LEAP) Consortium trial (NCT02670525) and a patient with T-LBL, discovering alterations in platelet-derived growth factor receptor-α (PDGFRA) in 3 of these patients. We identified a novel mutation in PDGFRA, p.D842N, and used an integrated structural modeling and molecular biology approach to characterize mutations at D842 to guide therapeutic targeting. We conducted a preclinical study of avapritinib in a mouse patient-derived xenograft (PDX) model of FIP1L1-PDGFRA and PDGFRA p.D842N leukemia. Two patients with T-ALL in the LEAP cohort (14%) had targetable genomic alterations affecting PDGFRA, a FIP1-like 1 protein/PDGFRA (FIP1L1-PDGFRA) fusion and a novel mutation in PDGFRA, p.D842N. The D842N mutation resulted in PDGFRA activation and sensitivity to tested PDGFRA inhibitors. In a T-ALL PDX model, avapritinib treatment led to decreased leukemia burden, significantly prolonged survival, and even cured a subset of mice. Avapritinib treatment was well tolerated and yielded clinical benefit in a patient with refractory T-ALL. Refractory T-ALL has not been fully characterized. Alterations in PDGFRA or other targetable kinases may inform therapy for patients with refractory T-ALL who otherwise have limited treatment options. Clinical genomic profiling, in real time, is needed for fully informed therapeutic decision making.

P11.02.B DO GENOMIC ALTERATIONS INFLUENCE THE DEVELOPMENT OF BRAIN METASTASES IN ADVANCED AND METASTATIC NON-SMALL CELL LUNG CANCER?

Abstract BACKGROUND Lung cancer is the most common cause of cancer deaths worldwide. Development of brain metastases (BM) in patients with advanced (Stage III) and metastatic (Stage IV) non-small cell lung cancer (NSCLC) is linked with poor prognosis. Identifying mutations associated with BM development could influence screening and determine targeted treatment paradigms. We aimed to establish BM prevalence and incidence in patients with advanced and metastatic NSCLC, stratified by genomic alterations. MATERIAL AND METHODS A systematic review and meta-analysis was conducted in accordance with PRISMA guidelines (PROSPERO ID CRD42022315915). Three databases were searched, and articles published between January 2000-May 2022 included (Search date 30th April 2022). Prevalence at diagnosis, and incidence of new BM per year were obtained, including patients with EGFR, ALK, KRAS, ROS1, RET, MET, and other genomic alterations. Pooled incidence rates were calculated using random effects models. RESULTS Of 960 articles identified, 65 were included in the study (24,784 patients). Pooled BM prevalence at diagnosis was 28.6% (45 studies, 95% Confidence Interval [CI] 26.1-31.0), and highest in patients with ALK (34.9%) and RET translocations (32.2%). With a median follow-up of 24 months, the per-year incidence of new BM was 12.5% in the wild-type group (14 studies, 95% CI 10.9-15.9). Incidence in the subgroups with different genomic alterations was 15.6% in the EGFR group (16 studies, 95% CI 11.4-21.2), 17.0% in the ALK group (6 studies, 95% CI 11.3-25.8), 9.8% in the KRAS group (4 studies, 95% CI 5.5-17.5), 12.5% in the ROS1 group (3 studies, 95% CI 5.7-27.6), and 11.8% in the RET group (2 studies, 95% CI 8.0-17.5). At the end of the follow-up period, a median of 55.0% of patients had BM (IQR 44.2-67.8). CONCLUSION This is the first study to show prevalence, and incidence of BM development in advanced and metastatic NSCLC, stratified by genomic alterations. Our data indicates a higher prevalence and incidence of BM in patients with targetable genomic alterations. This supports brain imaging at staging and follow-up, underlining the need for NSCLC therapies with brain penetrance and efficacy.

Molecular testing in non-small cell lung cancer: A consensus recommendation

Introduction: Lung cancer remains an important cause of cancer-related mortality in Singapore, with a greater proportion of non-smokers diagnosed with non-small cell lung cancer (NSCLC) in the past 2 decades. The higher prevalence of targetable genomic alterations in lung cancer diagnosed in Singapore compared with countries in the West, as well as the expanding therapeutic landscape for NSCLC in the era of precision medicine, are both factors that underscore the importance of efficient and effective molecular profiling. Method: This article provides consensus recommendations for biomarker testing for early-stage to advanced NSCLC. These recommendations are made from a multidisciplinary group of lung cancer experts in Singapore with the aim of improving patient care and long-term outcomes. Results: The recommendations address the considerations in both the advanced and early-stage settings, and take into account challenges in the implementation of biomarker testing as well as the limitations of available data. Biomarker testing for both tumour tissue and liquid biopsy are discussed. Conclusion: This consensus statement discusses the approaches and challenges of integrating molecular testing into clinical practice for patients with early- to late-stage NSCLC, and provides practical recommendations for biomarker testing for NSCLC patients in Singapore.

Genomic biomarker testing and treatment in advanced NSCLC: Practice patterns and barriers in a global survey of oncology point-of-care mobile app users.

e21004 Background: Appropriate molecular testing and oncogene-directed treatment planning are essential best practices for managing patients with advanced non-small cell lung cancer (aNSCLC) who are potential candidates for targeted therapy. Understanding real-world practices and challenges among oncology health care professionals (HCPs) is necessary to inform the development of digital tools and other initiatives that support optimal care. Methods: From 12/2022 to 01/2023, 142 HCPs who treat aNSCLC completed an online survey related to NSCLC genomic biomarker testing and treatment planning. Participants were recruited from a global cohort of HCPs who are active users of an oncology point-of-care mobile app following the launch of an NSCLC decision-support tool and educational intervention. Results: Participants included medical oncologists (87%), surgical oncologists (3%), pulmonologists (2%), and nurses (4%) from 62 countries. Most (72%) reported providing care for ≥5 pts/month with aNSCLC; 27.5% provide care for ≥20 pts/month. HCPs reported testing the following genomic biomarkers in 100%, 50-99%, 1-49%, and 0% of patients with aNSCLC, respectively: EGFR (44%, 23%, 27%, 4%), ALK (41%, 20%, 29%, 8%), ROS1 (32%, 19%, 23%, 22%), BRAF (23%, 20%, 23%, 31%), NTRK (12%, 14%, 22%, 47%), HER2 (11%, 17%, 27%, 42%), KRAS (23%, 15%, 25%, 33%), RET (13%, 13%, 25%, 44%), MET exon 14 (15%, 12%, 27%, 42%). Reported barriers varied in frequency (Table 1), with the most common involving biomarker test turnaround time. The majority of HCPs reported often or sometimes feeling that “results take too long,” and they (80%) and/or their patients (81%) are eager to start treatment. HCPs also commonly reported often or sometimes not being sure about which tests to order (45%), when to test (43%), which 1st-line therapy to select (45%), which 2nd- or later-line therapy to select (57%), and how to manage adverse events of oncogene-targeted therapy (50%). Conclusions: In current real-world practice, the majority of HCPs report suboptimal testing for targetable genomic alterations ( EGFR, ALK, ROS1, BRAF, NTRK, HER2, KRAS, RET, and MET exon 14) in patients with aNSCLC. Identified common barriers represent opportunities for future interventions to improve biomarker-directed NSCLC care. [Table: see text]

Clinical benefit of personalized treatment following high throughput sequencing in metastatic melanoma: A national retrospective study.

e21534 Background: Despite the approval of effective therapies in metastatic melanoma, durable benefit concerns only a fraction of patients and new therapeutic options are still needed. Next generation sequencing is now widely available to screen for targetable genomic alterations. Clinical impact of personalized medicine strategies in melanoma, outside classical targeting, have little been reported yet. Methods: By means of the Group of Cutaneous Oncology of the French Society of Dermatology, we retrospectively included all metastatic melanoma patients, aged 18 and over, for whom a molecular testing has identified one, or more, actionable molecular alterations and who received molecularly matched therapy accordingly, between 2018 and 2022. We excluded patients with only BRAF, NRAS or CKIT alterations and patients who received molecularly matched therapy for less than 15 days. Response was evaluated using RECIST 1.1 criteria. Results: We included 26 patients, median age was 63 years [24-89] and sex ratio 2.7. They had been heavily pretreated (58% have received 3 or more previous lines of treatment); 77% had 3 or more metastatic sites; 58% elevated LDH levels; and 42% and 35% had brain and liver metastasis respectively; 69 % had an ECOG PS 0 or 1. Actionable molecular alterations affected MAP kinase pathway in 12/26 cases: 10 of them received trametinib for GNA11 mutations (n = 4), MAP2K1 mutations (n = 2), CBL mutation (n = 1), NF1 loss (n = 1), FYCO1-RAF1 fusion (n = 1) and KRAS amplification (n = 1) while tipifarnib was given for an HRAS mutation and sunitinib for a CBL mutation. Cell cycle pathway was targeted in 7/26 cases with abemaciclib for a CDKN2A/B mutation, palbociclib for CDKN2A deletion, ribociclib and binimetinib for concurrent loss of CDKN2A and NRAS mutations (n = 2) and siremaldin and ribociclib for CCND1 amplification and MDM2/ CDK4 amplification (n = 2). PIK3CA pathway was targeted with alpelisib (n = 1) and with sirolimus for 1 PTEN mutation. EGFR, ALK and MET mutations were targeted using afatinib, alectinib and cabozantanib respectively. BRCA spectrum ( ATM and BRCA1) was targeted with olaparib in 2 patients in combination with dabrafenib and trametinib for one patient who had relapsed under this therapy. 11/26 patients responded to this molecularly matched strategy with 4 partial responses and 7 stable diseases including 5 ≥ 6 months stable diseases, with a median follow-up of 8 months [1-54]. Among responders, median duration of response was 6.5 months [2.5-13] and 3 are still ongoing. Responding patients had GNA11 (n = 2), MAP2K1, FYCO1-RAF1, HRAS, ATM, CCND1 (n = 2), MDM2/ CDK4 and CDKN2A/NRAS (n = 2) alterations. Conclusions: High throughput sequencing followed by matched targeted therapy is a promising approach in metastatic melanoma patients refractory to approved treatments, underlying the importance of access to molecular testing and molecular tumor boards.

Amplification of wild-type RET and clinical response to selpercatinib for non–small-cell lung cancer (NSCLC).

9123 Background: RET rearrangements and RET kinase domain mutations represent targetable genomic alterations in various cancer types. However, the frequency and characteristics of RET amplification in cancer and its potential role as a targetable oncogenic driver are not well-characterized. Methods: In a pan-cancer cohort of patients at the Dana-Farber Cancer Institute (DFCI) whose tumors underwent next-generation sequencing (NGS), we evaluated the frequency of wild-type (wt) RET amplification (defined as ≥6 copies) in the absence of RET rearrangements or activating mutations. We validated our findings using merged data from the TCGA, GENIE, and China Pan-Cancer datasets. Results: The frequency of wt RET amplification across all cancers was 0.08% (28/34,463) in the DFCI cohort and 0.16% (145/91,466) in the validation cohort. In NSCLC, the frequency of RET amplification was 0.10% (5/4773) in the DFCI cohort and 0.13% (15/11,622) in the validation cohort. Other cancer types with RET amplification included hepatobiliary cancer, prostate cancer, and breast cancer, among others. For 22 RET-amplified cases with available copy number data , the median RET gene copy number was 7 (range 6-36). Among 20 RET-amplified NSCLCs, 10 had no other known driver mutations, and 10 had concurrent driver mutations (including MET exon 14 skipping, MET amplification, KRAS G12C/S/D, EGFR L858R, EGFR exon 20 insertion, and EGFR exon 19 deletion). In cases with available smoking status, 5 out of 6 patients with RET-amplified NSCLC had a history of tobacco use. A 69-year-old man with unresectable stage III NSCLC had disease recurrence after chemoradiation and durvalumab. Both the initial and recurrent biopsy samples showed focal high-level RET amplification (22 and 28 copies, respectively); genomic and RNA sequencing showed no other driver mutations or RET rearrangements. He experienced partial response to the selective RET inhibitor selpercatinib with decrease of both intracranial and systemic tumor burden. Conclusions: Amplification of wt RET represents a novel, targetable, rare molecular subset of NSCLC and other cancers.

Deep learning-based ensemble model using hematoxylin and eosin (H&amp;E) whole slide images (WSIs) for the prediction of MET mutations in non-small cell lung cancer (NSCLC).

e13578 Background: The MET proto-oncogene is involved in tumorigenesis and progression and has emerged as an attractive targetable genomic alteration in NSCLC. However, it has not been actively tested in NSCLC due to the lack of a cost-effective screening tool. We developed a deep-learning based model to predict genomic profiles from H&amp;E WSI and applied it to MET pathologic mutations in NSCLC. The prediction model is based on an ensemble model trained not solely on H&amp;E images but also on multi-layered semantic contents that were produced by a pre-trained AI analyzer, Lunit SCOPE IO. Methods: The model was trained on the MET aberration (exon 14 skipping, n=191; pathogenic mutation, n=109) and paired wild-type dataset (n=500). To extract deep features from raw H&amp;E images, a self-supervised vision transformer was used, and an AI-based pathology profiling analyzer extracted semantic contents such as the spatial information of tumor cells, lymphocytes, cancer epithelium, and cancer stroma. A set of classifiers was trained based on the two features, and the ensemble of these features was used to improve robustness. Following cross-validation, the model was applied to an independent clinical dataset with MET sequencing results from The Cancer Genome Atlas (TCGA) LUAD and LUSC datasets (n=914), Samsung Medical Center (SMC, n=361), and Chonnam National University Hospital (CNUH, n=54). Results: The best cross-validation performances of the models predicting MET aberration measured by mean area under the receiver operating characteristic curve (AUROC) were 0.772 when trained by only H&amp;E images (HE-only), 0.788 by AI semantic content with MLP classifier (AISC-MLP), and 0.803 by AISC with random forest (AI-RF), respectively. An ensemble of the three models showed an increased AUROC of 0.837 in the training dataset by cross-validation. These models were applied to the external validation dataset (n=1,329), including 20 (1.5%) MET exon 14 skipping and known pathologic mutations. The mean AUROC to predict MET aberration by the ensemble model was 0.817 with 95% sensitivity, 64.7% specificity. The AUROC of TCGA, SMC, and CNUH cohorts were 0.815, 0.802, and 0.812, respectively. Conclusions: An AI-based ensemble model combining H&amp;E images with semantic contents extracted from pre-developed AI models significantly improved the accuracy and robustness of MET pathogenic mutation prediction using an H&amp;E sample in NSCLC. These findings allow for cost-effective screening for MET alterations.

Abstract 3391: Dual inhibition of RAS and the IGF2/IGF1R pathways: a potential targeting strategy for RAS-mutated embryonal rhabdomyosarcoma

Abstract Background: Mutations in RAS is reported in embryonal rhabdomyosarcoma (ERMS). Upregulation of IGF2/IGF1R axis and IGF2 overexpression is a common finding. Targeting RAS downstream is associated with high toxicity. Combination therapies targeting parallel pathways is necessary to overcome treatment resistance. Dual inhibition of RAS downstream and IGF2/IGF1R axis can be a potential mechanism of targeted treatment. The efficacy of this mechanism was studied using a microcancer 3D exvivo tumor cell viability assay in a KRAS mutant ERMS. Design: Tumor was collected for a high-risk pediatric ERMS patient. Comprehensive genomic analysis, for identification of targetable genomic alterations, was performed by integrating WES, MPseq and RNAseq. Tumor spheroids grown in 3D environment were tested against multiple single drugs and combinations. The tumor viability was assed employing the Cell Titer Glow Luminescent Cell Viability Assay. Results were expressed as nMATP and were shown as drug-response curve exhibiting the ATP concentration changes at Cmax. Results: Genomic findings included an oncogenic KRAS (G12D) mutation. BAY-293 has a partial cell killing response as a single agent. Given to the presence of IGF2 over-expression, IGF2/IGF1R pathway was targeted by linsitinib. Addition of BAY-293 to linsitinib led to enhanced effectiveness of this agent (Table 1). Conclusion: Combination of comprehensive genomic profiling and a laboratory-based 3D micro-cancer model using the patient’s own tumor is an effective way to determine drug efficacy. Targeting RAS pathway by single agents, increases the possibility of resistance. Dual targeting of downstream pathways by MEK and PI3K pathway inhibition is highly toxic, and the clinical usage of this combination is limited. Our results have indicated inhibition of IGF-1R/IGF2 axis in combination with other agents targeting RAS pathway, can be a potential method to address these limitations. ABEL 1. Summary of molecular alterations and targeting methods Molecular alteration Drug Target Kill% at Cmax KRAS (G12D) Mutation BAY-293 RAS-SOS1 interaction 55.3 Trametinib MEK1/2 88.3 Selumetinib MEK1/2 76 Paxalisib PI3K/mTOR 89.7 Samotolisib PI3K/mTOR 92.9 Copanlisib PI3K 95.2 Perifosine AKT 89.2 IGF2 Over-expression Linsitinib IGF-1R/InsR 84.1 BMS-754807 IGF-1R/InsR 67.4 NTRK2 mutation Larotrectinib NTRK 41.9 KMT2D mutation Panobinostat HDAC 85.3 Combinations Kill% at Cmax BAY-293+Selumetinib 100 BAY-293+Samotolisib 100 BAY-293+Paxalisib 99.7 BAY-293+Linsitinib 97.5 Selumetinib+Samotolisib 93.1 Citation Format: Dorsay Sadeghian, Wan-Hsin Lin, James Smadbeck, Alan Panheiter, Michael Barrett, Alexa F. Mccune, Giannoula Karagouga, Sarah Johnson, Ryan W. Feathers, Faye R. Harris, Lindsey Kinsella, Taylor Berry, John Cheville, Panos Anastasiadis, Candace Granberg, Patricio Gargollo, Vasmatzis George. Dual inhibition of RAS and the IGF2/IGF1R pathways: a potential targeting strategy for RAS-mutated embryonal rhabdomyosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3391.

Pathogenic genomic alterations in Chinese pancreatic cancer patients and their therapeutical implications.

Approximately 90% of pancreatic ductal adenocarcinoma (PDAC) cases are driven by the untargetable non-G12C KRAS mutations, and only a small subset of patients are eligible for FDA-approved precision therapies. The practice of precision therapy in pancreatic cancer was limited by the paucity of targetable genetic alterations, especially in the Asian population. To explore therapeutic targets in 499 Chinese PDAC patients, a deep sequencing panel (OncoPanscan™, Genetron health) was used to characterize somatic alterations including point mutations, indels, copy number alterations, gene fusions as well as pathogenic germline variants. We performed genomic profiling in 499 Chinese PDAC patients, which revealed somatic driver mutations in KRAS, TP53, CDKN2A, SMAD4, ARID1A, RNF43, and pathogenic germline variants (PGVs) in cancer predisposition genes including BRCA2, PALB2, and ATM. Overall, 20.4% of patients had targetable genomic alterations. About 8.4% of patients carried inactivating germline and somatic variants in BRCA1/2 and PALB2, which were susceptible to platinum and PARP inhibitors therapy. Patients with KRAS wild-type disease and early-onset pancreatic cancer (EOPC) harbored actionable mutations including BRAF, EGFR, ERBB2, and MAP2K1/2. Compared to PGV-negative patients, PGV-positive patients were younger and more likely to have a family history of cancer. Furthermore, PGVs in PALB2, BRCA2, and ATM were associated with high PDAC risk in the Chinese population. Our results demonstrated that a genetic screen of actionable genomic variants could facilitate precision therapy and cancer risk reduction in pancreatic cancer patients of Asian ethnicity.

Genomic profiling to provide new treatment opportunities in ampullary carcinoma.

582 Background: Ampullary carcinoma (AC) is a rare heterogeneous group of diseases with an abysmal prognosis. Treatment options are limited, and the molecular landscape of this disease and its therapeutic implications have been incompletely explored. Here, we aim to provide a clinical and genomic characterization of AC and explore opportunities for precision oncology. Methods: Patients diagnosed with AC and treated at a single tertiary institution between 2010 and 2022 were reviewed. Molecular profiles were analyzed by applying an in-house exome-targeted panel or the FoundationOne CDx panel. Gene mutations were categorized into molecular pathways and potentially targetable alterations were classified according to the ESCAT scale. Overall survival (OS) and disease-free survival (DFS) were estimated by using the Kaplan-Meier method. Results: We included 64 patients with a median age of 66 years, 51.6% were women, most were classified as pancreatobiliary tumours (PB, 58.3%), followed by intestinal (INT, 33.3%) and mixed histologies (8.3%). 18.8%, 23.4%, 32.8% and 25.0% of the patients were diagnosed at stage I, II, III and IV, respectively. 81.2% of the patients were treated with surgery. The INT subtype was enriched in WNT pathway alterations (28.6 vs 6.2%, p=0.02) and showed a non-significant enrichment in the apoptotic pathway (57.1 vs 34.4%, p=0.08). Conversely, BP showed a non-significant enrichment in HRR pathway alterations (16.7 vs 54.5%, p=0.3). The frequency of KRAS mutations were similar in both subtypes (38.1 vs 37.5%). Potentially actionable molecular alterations were found in 46.7% of the patients (9 ERBB2, 8 HRD, 8 PI3KCA, 2 MSI, 2 BRAF, 2 PTEN and 1 KRAS G12C). Importantly, KRASwt tumours were enriched in potentially targetable alterations (ESCAT I-IIIA), including 20% ERBB2 amplification/mutations, 6% MSI and 3% BRCA1. 6 patients received matched targeted therapies during their disease course, 66% of which responded and 100% stable disease, with a median TTD of 7 months. Conclusions: More than 45% of AC harbor potentially targetable genomic alterations that may provide novel therapeutic opportunities and enhance personalized medicine in this rare disease entity.

Next-Generation Sequencing for Advanced Breast Cancer: What the Way to Go?

The rapid implementation of precision medicine tools in diagnosing and treating breast cancer (BC) has widened the potential therapeutic options for patients. The applications of gene sequencing, including next-generation gene sequencing (NGS), have led to numerous questions on how to validate, implement, interpret, prioritize and operationalize precision medicine tools to deliver meaningful and impactful interventions. Limited benefit has been portended with earlier experiences of NGS-driven treatment, in BC. However, the development and use of frameworks of clinical actionability of genomic alterations, for example, detected with NGS, has resulted in better patient selection, and potentially higher therapeutic value. The European Society for Medical Oncology Scale for Clinical Actionability of molecular Targets (ESCAT) is a framework that includes five tiers of clinical actionability, with tier 1 reserved for approved drugs with demonstrated benefits for targetable genomic alterations. The re-analysis of clinical studies by grouping the genomic alterations and matched drugs with ESCAT, in high vs lower tiers has demonstrated a significant benefit portended by high tiers alterations, with the availability of efficacious treatments. As a result, frameworks for actionability, like ESCAT, should be fundamental in developing and implementing NGS-driven, and broadly, precision medicine research and treatments.