Generation Sequencing Testing Research Articles

Phase II/III study of paclitaxel/carboplatin alone or combined with either trastuzumab and hyaluronidase-oysk or pertuzumab, trastuzumab, and hyaluronidase-zzxf in HER2 positive, stage I-IV endometrial serous carcinoma or carcinosarcoma (NRG-GY026).

TPS5641 Background: Uterine serous carcinoma and uterine carcinosarcoma are rare, high-risk uterine cancer subtypes that overexpress HER2 in up to 40% and 10% of cases, respectively. Phase II data demonstrated a benefit in adding trastuzumab in HER2 positive advanced and recurrent uterine serous carcinoma. Dual anti-HER2 therapy has the potential for further improvement in survival. Methods: This is a non-blinded, three-arm randomized phase II/III study. The primary objective is to evaluate the efficacy of trastuzumab and hyaluronidase-oysk (HERCEPTIN HYLECTA) or a fixed dose combination of pertuzumab, trastuzumab, and hyaluronidase-zzxf (PHESGO) in combination with paclitaxel/carboplatin in patients with HER2 positive uterine serous carcinoma or carcinosarcoma. The primary outcome of the phase II component is PFS. Depending on the phase II results, the study will progress to a phase III study of either two or three study arms. Patients in the control arm (Arm 1) receive carboplatin and paclitaxel every 3 weeks for 6 cycles. Patients on Arm 2 receive carboplatin and paclitaxel with trastuzumab and hyaluronidase-oysk every 3 weeks for 6 cycles plus one year of maintenance trastuzumab and hyaluronidase-oysk. Patients enrolled on Arm 3 receive carboplatin and paclitaxel with trastuzumab, pertuzumab, and hyaluronidase-zzxf every 3 weeks for 6 cycles plus one year of maintenance trastuzumab, pertuzumab, and hyaluronidase-zzxf . Those with an ongoing partial response may continue maintenance therapy for up to three years. Patients are eligible if they are diagnosed with chemo-naïve, non-recurrent stage IA-IVB myoinvasive uterine serous or carcinosarcoma. All tumors must be HER2 positive as defined by the ASCO/CAP Breast Cancer 2018 guidelines (testing performed locally). Tumors may also be HER2 positive based on next generation sequencing testing. Patients may have measurable, non-measurable, or no measurable disease and may have a plan for vaginal brachytherapy . Key exclusion criteria include severe heart disease or interstitial lung disease. The phase II portion of this study is open and enrolling. Clinical trial information: NCT05256225 .

Effect of plasma-based molecular testing in patients with newly diagnosed advanced NSCLC on initiation of targeted agents in patients with targetable genomic alterations: A real world experience from the Middle East.

e20514 Background: The treatment of metastatic non-small cell lung cancer ( m-NSCLC) is personalized and driven by mutational profiling of the tumour tissue at diagnosis. This study evaluates the additional clinical utility of plasma based molecular testing towards shortening time to initiation of treatment and detection of targetable mutations in a cohort of patients with newly diagnosed m-NSCLC. Methods: This is a retrospective analysis of patients with newly diagnosed advanced NSCLC referred to the Thoracic Oncology Program between September 2021 to December 2023, who underwent “paired” plasma based circulating tumour ( ct-DNA ) and tissue based next generation sequencing (NGS) testing (done less than 4 weeks apart). ct-DNA testing was performed using the Oncomine Pancancer NGS Assay (Thermo Scientific) that screens for single nucleotide variants (SNV) in hotspot regions of 52 and common fusions involving 12 genes respectively. Tissue NGS testing was performed using Oncomine Comprehensive Assay Plus (Thermo Scientific); a panel covering ~500 genes capable of identifying all single nucleotide variants, indels, fusions and copy number variants (CNV). Patient demographics and clinicopathological characteristics were collected by retrospective review of electronic medical records (EMR). Results: Among 36 patients, the median age was 66.0 years (range: 32-66), 25 (69.4%) were males, and 16 (44.4%) were never smokers. Thirty (83.3%) had adenocarcinoma and 33 (91.67%) had stage IV NSCLC. The mutation detection rate of ct-DNA was 66.7% with a concordance of 58.3% between ct-DNA and tissue NGS testing. The median turnaround time (TAT) from sample collection to reporting were12 days (IQR:8-15) and 14 days (IQR:9-24.50) for ct-DNA and tissue NGS testing respectively. Among 31 patients who started treatment, the median time to initiation of 1st line treatment was 26 days from date of first visit (IQR:18-42). Fifteen(41.7%), 6(16.7%) and 10(27.8%) started first line targeted therapy, chemotherapy and chemoimmunotherapy respectively. Twenty-three(63.89%) had targetable mutations (EGFR Exon 19 or 21, EGFR Exon 20 insertion, ALK, ROS1, MET Exon1 4 skipping, ROS1 or KRAS12C detected either in ct-DNA or tissue). Fifteen (65.21%) out of these 23 started targeted therapy as their 1st line treatment and of these 8 (53.3%) were initiated on targeted agents prior to availability of tissue NGS reports. Conclusions: Though our TAT for ct-DNA and tissue based NGS testing was similar, ct-DNA based NGS testing enables earlier initiation of targeted treatment for newly diagnosed advanced NSCLC patients with targetable mutations. In the real world, this increases access to targeted agents and may translate to a subsequent improvement in survival outcomes.

Prolonged response to entrectinib in an adult patient with recurrent glioblastoma harboring a GOPC::ROS1 fusion

Introductory paragraph Data on the use of targeted therapies in glioma are still limited and the identification of useful targetable mutations is still under investigation. Among all the relevant alterations identified through next generation sequencing (NGS) tests, ROS1 alterations can rarely be found in gliomas, and the most common of them is GOPC::ROS1 fusion. Targeted therapies, such as entrectinib, are available for such alterations. Hereby, the case of a patient affected by GOPC::ROS1 fused glioblastoma and treated with entrectinib is presented; this patient achieved a complete and prolonged response with no relevant toxicities from the treatment.

Abstract PO3-14-11: Association between BRCA alterations detected by circulating tumor DNA and germline mutations in breast cancer patients: a retrospective mono-institutional analysis

Abstract Background: PARP inhibitors (PARPi) are a standard of care for breast cancer (BC) patients (pts) with germline BRCA (gBRCA) mutation, with benefit demonstrated also in patients with somatic (s) BRCA1/2 mutations. The use of circulating tumor (ct) DNA testing allows to detect resistant and actionable alterations in BC, but it could be associated with the incidental identification of germinal mutations. The aim of this study was to describe the incidence of both, somatic and germinal BRCA1/2 alterations, and the impact on the therapeutic outcomes in a retrospective BC cohort with clinical ctDNA testing for their BC. Materials and methods: A retrospective cohort of 245 BC pts that underwent ctDNA analysis (Guardant 360) between August 2014 and May 2023 at Weill Cornell Medical College was identified. Pts with at least a BRCA1/2 alteration, including variant of uncertain significant (VUS) and synonymous, were enrolled in the study. A descriptive analysis was performed. Results: Among 35 patients included, 34 had metastatic disease, the median age was 61 years old (IQR 40-67), and 65.7% were post-menopausal at diagnosis. 57.1% of pts had hormone receptor positive/HER2 negative (HR+/HER2-) BC, 20% had HER2 positive disease and 22.9% were triple-negative (TN) BC. Ten (28.6%) and 20 (57.1%) pts had a sBRCA1 or a sBRCA2 alteration on ctDNA, respectively; 5 pts (14.3%) had a coexisting sBRCA1/2 mutation. The median variant allele frequency (VAF) was 1.2% for BRCA1 and 2.7% for BRCA2 alterations. Furthermore, 53.3% and 6.7% of sBRCA1 and 40% and 8% of sBRCA2 mutations were identified as VUS and synonymous, respectively. The most common associated genomic alterations included TP53 (62.9%), ESR1 (20%) and PI3KCA (52%) with a median number of 4 variants (IQR 2-7). Next generation sequencing (NGS) testing on tissue was available for 3 patients: two demonstrated concordance with BRCA alterations detected by ctDNA, whereas no alteration in BRCA1/2 genes was found for the third patient despite the tissue analysis was performed at the same time of the ctDNA. Germline testing was available for 24 (69%) pts; a corresponding gBRCA1 mutation was found for 3 pts (VAF 48.6%-84.3%), and a gBRCA2 for 8 pts (VAF 26.7%-49.5%). Due to the small sample size, a univocal VAF cut-off to detect gBRCA1/2 mutations could not be calculated. Twenty-nine pts had a sBRCA1/2 mutation detected by ctDNA test before starting a new therapy; of these 55.2% had HR+/HER2- disease, while 17.2% and 27.6% were HER2 positive and TN BC, respectively. The median progression free survival (mPFS) was 10.3 (3.2-17.4) months (ms) and the 1-year and 2-year overall survival (OS) rates were 82.3% and 70.5%, respectively. The mPFS was 10.3 ms (0-25.0) for patients (n=16) that underwent chemotherapy, 5.6 ms (0-15.1) for those who had received endocrine therapy (n=9), and not reached for patients treated with PARPi (n=4). Conclusions: ctDNA analysis allows the detection of sBRCA1/2 mutations that could be missed by tissue-based testing. The identification of BRCA alterations on ctDNA could guide the use of germline testing even when these are present at a lower VAF than expected, with relevant impact on the therapeutic choices and family screening. Further evaluation to establish the impact of sBRCA1/2 detected by ctDNA on the therapeutic algorithm decision are needed. Citation Format: Letizia Pontolillo, Eleonora Nicolò, Laura Munoz Arcos, Carolina Reduzzi, Mara Serena Serafini, Amanda Kaylan Strickland, Nadia Bayou, Jeannine Donahue, Elisabetta Molteni, Lorenzo Gerratana, Diana Giannarelli, Eleni Andreopoulou, Emilio Bria, Massimo Cristofanilli. Association between BRCA alterations detected by circulating tumor DNA and germline mutations in breast cancer patients: a retrospective mono-institutional analysis [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 PO3-14-11.

Abstract PO1-08-11: The survival rate of hereditary breast cancer in young women of Kazakh population

Abstract Background The study focused on determining survival rates between breast cancer patients with various germinal mutations and those without mutations among Kazakh women. Methods The study included 222 female patients of Kazakh ethnic group diagnosed with stage I-IV stage breast cancer at the age up to 40 years old. DNA samples were tested by next-generation sequencing on the MiSeq Illumina platform using Trusight Cancer kit for the analysis of 94 genes and 287SNPs. Information about dates of diagnosis and death retried from cancer registry system. Survival analyses were performed and compared mutation carriers and non-carriers subgroups. The 5-year survival was calculated using the Kaplan-Meier method. Results Next generation sequencing test identified 11 various pathogenic mutations in 57(25.7%) of overall 222 patients. The 5-year survival analysis for mutation carriers were 72.1%and 82.1% for non-carriers, with no statistically significant difference(P0.232). When stratified by mutational type, the 5-year survival rates were 71.8% for BRCA1 carriers, 81.3% for BRCA2, 53.35% for TP53 and 50% for moderate risk gene PALB2 mutation. These findings suggest that mutations in certain genes may be associated with differences in survival outcomes. Conclusions In breast cancer patients of Kazakh population similar to the world prevalence and predictive value of germline mutations have been found. A subcohort of mutation carriers and non-carriers demonstrated no significant difference in 5-year survival rate which may be associated with an early onset of disease, high-risk predictor of poor prognosis. Long-term survival and detailed PFS will be published according to information of follow-up visits and the cancer register system. Citation Format: Dilyara Kaidarova, Nazgul Omarbayeva, Aliya Abdrakhmanova, Oxana Shatkovskaya, Dilyar Omarov. The survival rate of hereditary breast cancer in young women of Kazakh population [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 PO1-08-11.

Chinese expert consensus on the analytical validation of tumor comprehensive genomic profiling next generation sequencing testing (2024 edition)

In hospital laboratories-developed testing is of great significance for the clinical testing products that has not been approved by the National Medical Product Administration and is urgently needed to meet clinical practice needs. With the development of cancer precision medicine in recent years, comprehensive genomic profiling (CGP) has become an important means and method for the detection of drug targets, precise molecular typing, and immunotherapy biomarkers in cancer patients. However, there is still a lack of unified understanding and consensus on clinical testing standards and application specifications for laboratory-developed testing in the hospitals. The Molecular Pathology Collaboration Group of the Cancer Experts Committee of the Chinese Anti-Cancer Association and the Molecular Pathology Group of the Pathology Branch of the Chinese Medical Association initiated the expert consensus on relevant specifications for analytical validation of CGP next-generation sequencing (NGS) testing in Chinese hospitals. Combined with domestic clinical practice, refer to domestic and foreign literatures, from the background of the laboratory-developed testing, analytical validation scenarios, evaluation indicators and variation ranges, sample types and quantities covered by analytical validation, clinical performance and drug efficacy determination, and site personnel for analytical validation, quality control, inter-laboratory quality evaluation and document management, etc. After the discussion by the expert group, 12 expert consensuses were formed to provide reference for the analytical validation and clinical application of tumor CGP NGS testing in Chinese hospitals, so as to promote the laboratory-developed testing applications in Chinese hospitals.

Value of Next Generation Sequencing (NGS) testing in advanced cancer patients

Aims: The availability of targeted therapies for oncology patients is increasing. Available genomic tests to identify treatment-eligible patients include single gene tests and gene panel tests, including the whole-exome, whole-transcriptome OncoExTraTM test. We assessed the costs and clinical benefits of test choice. Methods: A Microsoft Excel-based model was developed to evaluate test choice in patients with advanced/metastatic non-small cell lung cancer (NSCLC), breast, prostate, and colorectal cancer. Treatment pathways were based on NCCN guidelines and medical expert opinion. Inputs were derived from published literature. Annual economic results and lifetime clinical results with OncoExTra testing were projected per-tested-patient and compared with single gene testing and no testing. Separately, results were estimated for a US health plan without the OncoExTra test and with its use in 5% of patients. Results: Compared with no genomic testing, OncoExTra test use increased costs by $4,915 per patient; however, 82%-92% of individuals across tumor types were identified as eligible for targeted therapy or a clinical trial. Compared with single gene testing, OncoExTra test use decreased costs by $9,966 per-patient-tested while increasing use of approved or investigational targeted therapies by 20%. When considering a hypothetical health plan with 1 million members, 858 patients were eligible for genomic testing. Using the OncoExTra test in 5% of those eligible, per-member per-month costs decreased by $0.003, ranging from cost-savings of $0.026 in NSCLC patients to a $0.009 increase in prostate cancer patients. Cost-savings were driven by reduced treatment costs with increased clinical trial enrollment and reduced direct and indirect medical costs associated with targeted treatments. Conclusions: Limitations include the required simplifications in modeling complex conditions that may not fully reflect evolving real-world testing and treatment patterns. Compared to single-gene testing, results indicate that using NGS test such as OncoExTra identified more actionable alterations, leading to improved outcomes and reduced costs.

Is Immunotherapy Beneficial in Patients with Oncogene-Addicted Non-Small Cell Lung Cancers? A Narrative Review

Over the past 20 years, there has been a paradigm shift in the care of patients with non-small cell lung cancer (NSCLC), who now have a range of systemic treatment options including targeted therapy, chemotherapy, immunotherapy (ICI), and antibody–drug conjugates (ADCs). A proportion of these cancers have single identifiable alterations in oncogenes that drive their proliferation and cancer progression, known as “oncogene-addiction”. These “driver alterations” are identified in approximately two thirds of patients with lung adenocarcinomas, via next generation sequencing or other orthogonal tests. It was noted in the early clinical development of ICIs that patients with oncogene-addicted NSCLC may have differential responses to ICI. The toxicity signal for patients with oncogene-addicted NSCLC when treated with ICIs also seemed to differ depending on the alteration present and the specific targeted agent used. Developing a greater understanding of the underlying reasons for these clinical observations has become an important area of research in NSCLC. In this review, we analyze the efficacy and safety of ICI according to specific mutations, and consider possible future directions to mitigate safety concerns and improve the outcomes for patients with oncogene-addicted NSCLC.

GATA2 Mutation with Bone Marrow Failure. A Review of Ordering Next Generation Sequencing Testing while Triaging Bone Marrows in Patients with Cytopenias – Pathologists Challenge

Abstract Introduction/Objective GATA2 (germline) mutations are a cause of bone marrow (BM) failure in younger patients characterized by pancytopenia and hypoplastic BM with minimal or no dysplasia. These cases may have negative cytogenetic (CG)/FISH (FH) results and are diagnosed by next-generation sequencing (NGS) testing. We present a case where GATA2 testing was performed on a repeat BM resulting in delayed diagnosis. Insurance companies challenge providers and pathologists with frequent claims denials, thus the need to revise pre-authorization (PA) policies for triaging BMs in real time. We also reviewed our data where NGS was performed in patients with cytopenias, negative morphology (MO), flow cytometry (FC) & CG/FH studies. Methods/Case Report We did a retrospective analysis and selected 455 BMs (2018 to 2022) where the clinical indication was cytopenias and had negative MO, FC, CG, and FH. We evaluated MO again with NGS results to ensure diagnostic features were not overlooked. Results (if a Case Study enter NA) The index case was a 22-year-old female failing to show abnormality by MO, FL, CG, or FH. The patient continued to have cytopenias; BM was performed a year later and NGS showed GATA2 mutation. This prompted a retrospective analysis of 455 BMs as described under methods. 101/455 (22%) cases revealed abnormal NGS results with pathogenic mutation resulting in amended reports. 42/455 (9%) cases revealed mutations consistent with clonal hematopoiesis of indeterminate potential (CHIP) or clonal cytopenia of undetermined significance (CCUS). Conclusion 1) PA policy for BM triaging is not practical since a decision for NGS testing is made in real-time; 2) Claim denials lead to underutilization of NGS, thus resulting in delayed patient care; 3) NGS may show pathogenic mutation despite negative MO/FL/CG/FH results; and 4) Insurance companies need to consider reviewing local coverage determination (LCD) policy for hematopoietic disorders as these tests are medically necessary, thus not requiring PA.

Next-Generation Sequencing Testing and Triaging of Bone Marrow Samples: Indications, Pre-authorization and Medical Necessity for Patient Care

Abstract Introduction/Objective Bone marrow biopsy (BMBx) is an invasive procedure and samples are usually obtained for diagnosis, staging and prognosis of hematolymphoid disorders (HDs). Given the need for WHO and ICC classification of HDs; the Next Generation Sequencing (NGS) testing (in addition to other esoteric testing) has become relevant and medically necessary. It is important to triage BMBx in real-time based on clinical indications; however, pathologists are challenged by limited published guidelines as well as need for pre-authorization (PA) thus resulting in claim denials. Methods/Case Report Retrospective analysis was performed (2018 to 2022) on 1610 BMBx submitted for various clinical indications. These were categorized as follows: Cytopenias 220 (MDS); Cytosis 250 (MPN); Lymphomas work-up 350 (LY), acute leukemias 440 (AL) and plasma cell disorders 350 (PCD). In addition to esoteric testing; the decision was made to perform NGS testing based on preview of aspirate slides, clinical history and CBC. Results (if a Case Study enter NA) Providers initially ordered NGS in 10% of cases; however, NGS was added later by pathologists in 30% of BMBx samples. Abnormal NGS results were obtained as follows: MDS (70%); MPN (75%); LY (15%); AL (90%) and PCD (40%). NGS testing provided clinically useful data for MDS, MPN and AL groups. Even though LY and PCD groups also yielded positive results; the concurrent esoteric testing (Flow, FISH and Cytogenetics) was useful thus making indication of NGS in these two subset groups less indicated. Conclusion Appropriate triaging of BMBx for NGS testing is medically necessary for following reasons: 1) Enables precise diagnosis in a timely manner; 2) to avoid repeat BMBx if triaging guidelines are followed; and 3) decision to order NGS is made in real-time as BMBx are time sensitive samples thus eliminating the need for PA as this study emphasize that NGS has become standard of care in the work-up of HDs.

Using Next Generation Sequencing (NGS) tests in routine oncology practice in Croatia: Results of a nationally representative survey of oncologists

Using Next Generation Sequencing (NGS) tests in routine oncology practice in Croatia: Results of a nationally representative survey of oncologists

PATH-63. NEXT GENERATION SEQUENCING FOR CNS TUMORS IN CHILDREN; DOES IT ADD VALUE IN A MIDDLE-INCOME COUNTRY SETUP?

Abstract INTRODUCTION Advances in molecular diagnostics led to improved targeted interventions in the treatment of pediatric CNS tumors. However, the capacity to do these diagnostics is limited in LMICs, and consequently their value is questionable. METHODS We reviewed our experience of Next Generation Sequencing (NGS) testing (TruSight RNA Pan-Cancer seq panel) for pediatric CNS tumors at KHCC/Jordan (March/2022- April/2023). Paraffin blocks’ scrolls were shipped to Sickkids laboratory based on local multidisciplinary team recommendations. We reviewed patients’ clinical characteristics, tumor types and the impact on treatment. RESULTS There were 16 boys and 16 girls; median age at time of testing was 9.5 years (range, 0.9- 21.9 years). Twenty samples were sent at diagnosis and twelve upon tumor progression. Main diagnoses were Low-grade glioma (15), High-grade glioma (10), and other tumors (7). Reasons for NGS testing were: to find a molecular target (20), and to characterize more tumor/behavior (12). The median time from shipping the samples to receive the NGS result was 22 days (range, 15-49 days) at a cost of US$1000. Twenty (63%) tumors had targetable alterations (MAPK/PI3K inhibitors (16), NTRK inhibitors (2), check point inhibitors (2)). Two rare BRAF mutations were identified (BRAFp.G469A, BRAFp.K601E). One tumor diagnosed initially as undifferentiated round-cell sarcoma found to have NAB2::STAT6 fusion and re-diagnosed as aggressive metastatic solitary fibrous tumor. Eight patients received targeted therapy; Dabrafenib/Trametinib (5), Pembrolizumab (2), Entrectinib (1), while radio-chemotherapy was used in the others. Three patients died from disease progression (one used Entrectinib). CONCLUSIONS Sent abroad NGS testing was feasible, however local capacity building is necessary. In this highly selected tumor cohort, high percentage of targetable alterations were identified. NGS was helpful to characterize tumors more and to offer alternative therapies. Nevertheless, interpretation of the significance of NGS results and access to those “new” therapies continues to be a challenge in LMICs

Quality control patterns in comprehensive genomic testing of malignancies.

456 Background: Molecular genetic testing is a crucial tool to detect genetic alterations in tumor samples and can aid in identifying targeted therapies for patients. Next generation sequencing (NGS) testing is a comprehensive technology to detect a broad spectrum of targetable biomarkers with a high sensitivity, while providing a cost- and time-effective strategy compared to other molecular genetic tests such as Sanger sequencing. NGS requires a minimum sufficient genetic material to detect a true mutation and report a significant result. Methods: In our study, we have analyzed NGS results from clinical samples from different organs or malignancies, obtained from 278 patients (median age 55, average age of 64, range 20-89) were analyzed. The specimens were collected between September 2005 and December 2022 from adenocarcinomas, not otherwise specified (NOS, 34.95%), metastatic adenocarcinomas, NOS (13.42%); metastatic carcinomas, NOS (4.49%), and others (47.14%). A total of 5127 individual results were reported. NGS testing (DNA-seq and RNA-seq) was performed and reported by Caris Life Sciences. Results: From our molecular genetic results analysis, 28 specimens (n= 12 female, 16 male) were reported to be ‘Quantity Not Sufficient’ (QNS), representing 9.45% of all specimens tested. To further understand the patterns of reported QNS, we identified the prevalence of QNS results in various tumor types. The majority of QNS results occurred in adenocarcinomas (NOS) representing 45.16%; followed by metastatic adenocarcinoma (NOS), 16.33%; and glioblastoma, 6.45%. The majority of specimen sites with QNS reported were the liver 15.12%, lung (NOS) 13.71%, and the prostate (NOS) 12.10%. Conclusions: Understanding patterns of QNS can be helpful to optimize testing and sampling strategies specifically for tissues with a high prevalence of insufficient quantity of genetic material. Additionally, analyzing and comparing biomarkers and their QNS pattern can be supportive to identify testing errors and improve testing methodologies.

Cost-effectiveness analysis of Next generation sequencing tests in critically ill pediatric patients

Abstract Rare genetic diseases in the pediatric population constitute an urgent global public health issue; overall, more than 300 million people are affected worldwide. Next Generation Sequencing techniques, as Whole genome sequencing (WGS) and Whole exome sequencing (WES), have proven to be significantly supportive in diagnosing these complex conditions. The aim is to evaluate the cost-effectiveness of WGS versus WES in pediatric patients with suspected genetic disorders. A Bayesian Markov model was calibrated among this target population, comparing WGS to WES. Model parameters were retrieved from the scientific literature. Costs and benefits were discounted at a rate of 3%. A lifetime time horizon and the National Health Service perspective was chosen. The Eurozone threshold, ranging from €30,000 to €50,000, was adopted. Markov Chain Monte Carlo was used as the simulation method for Bayesian inference. Uncertainty was explored through a probabilistic sensitivity analysis (PSA) and a value of information analysis (VOI), illustrated through Cost-Effectiveness Acceptability Curve (CEAC) and Expected Value of Perfect Information (EVPI). Results were reported as Incremental Cost-Effectiveness Ratio (ICER), expressed as euros per additional diagnosis. The base case findings highlighted that WGS was cost-effective with an ICER of €31,973. The CEAC showed that for all thresholds over the ICER, WGS had the highest probability of being cost-effective. The EVPI per patient was estimated to be €6,535 on a threshold of €50,000/diagnosis. In addition to being cost-effective, WGS could allow early genetic diagnosis shortening the diagnostic odyssey. The use of WGS in the diagnostic workup has the potential to revolutionise personalised medicine and to play a significant role in achieving SDG 3 by providing personalised healthcare, identifying genetic risk factors for diseases, and informing public health policies for a target population that represents the human capital of the future. Key messages • This analysis informs that WGS is cost-effective and possibly cost-saving in the long term. • WGS could be implemented in the diagnostic workup of children with suspected rare disorders.

Next generation sequencing (NGS) testing for cancer patients at a safety NET hospital.

e18563 Background: Next Generation Sequencing (NGS) testing is gradually becoming an essential aspect of cancer care. However, numerous studies have shown that non-White patients are under-represented in both precision oncology clinical trials and molecular testing. Highland General Hospital (HGH) is a community safety-net hospital in Oakland, California serving primarily Black, Hispanic and Asian patients. In an effort to increase health equity, in August 2020 we began to offer NGS testing with Tempus Labs, Inc. for our cancer patients. The purpose of this study is to document this experience and highlight the genomic profile of our patient population. Methods: This is a retrospective chart review study. Patients were included if their tumor biopsy was sent for NGS testing from August 2020 to December 2022. A total of 165 patients had their samples sent for NGS, of which 148 were included in this study and 17 were excluded due to lack of sufficient tissue. Patient demographic data and predictive biomarkers were collected. For the purposes of this study, we defined predictive biomarkers as those that predict likelihood of response or lack of response to therapy as recommended by National Comprehensive Cancer Network guidelines. Results: The racial distribution of our patient sample is shown in the table below. Consistent with the patient population of HGH, our sample included mostly Black (32.4%), Hispanic (26.4%), and Asian (21.6%) patients. Non-Small Cell Lung Cancer (NSCLC) and colorectal cancer (CRC) were the two most common malignancies sequenced at 34.5% and 25.7%, respectively. For NSCLC patients, 54.9% had predictive biomarkers, with EGFR and KRAS being the most common driver mutations. For CRC patients, 60.5% had predictive biomarkers, with 73.9% of those being NRAS/KRAS and 13.0% being high tumor mutational burden. Full results to be presented. Conclusions: Based on our experience, it is feasible and informative to provide NGS testing for patients at safety-net hospitals. NGS testing allows for the most appropriate treatment selection for each patient, which can translate into better outcomes. Moreover, due to the unique demographics of patients from these hospitals, NGS tests can provide valuable information about the tumor genomic profiles of these underrepresented patients. This data can help improve drug development research and close the health equity gap. [Table: see text]

Clinical analysis of the presence of comutations in patients with EGFR-mutated NSCLC.

e21001 Background: EGFR mutation is the most common treatable molecular alteration in non-small cell lung cancer (NSCLC), in particular in adenocarcinoma it can be found in 10-15% of our patients (spanish population). But the presence of other commutations in EGFR mutated tumors and its implications has not been well characterized. Methods: We selected patients diagnosed with EGFR mutation non-small cell lung carcinoma (NSCLC) from February 2021 to March 2022 from 4 hospitals in Madrid (most of them from Fundación Jimenez Diaz University Hospital). EGFR status and the presence of commutations was determined by using the AVENIO Tumor Tissue Targeted Kit (a Next Generation Sequencing test). PD-L1 status was determined by immunohistochemistry assay (22C3 pharmDx). Molecular and clinicopathological characteristics were collected and we performed a descriptive analysis of our population. Results: Of the 48 patients evaluated, 68.8% were women and 31.3% were men. 73% were ECOG 0 and 23% ECOG 1 and only 44% were non-smokers, being 18.8% smokers and 37% ex-smokers, most of them with low consumption. The 91.7% were adenocarcinomas and 8.3% were squamous carcinomas. 43.7% were PD-L1 negative and 10.4% were high expressors (PD-L1 > 50%). Of the stage at diagnosis, 60.4% were stage IV and 16.7% were stage III, with 22.9% being stage I and II. Of the Stage IV patients, 87.7% debuted as patients with high disease burden, with only 13.3% being oligometastatic (oligometastatic being understood as those with less than 5 metastases in 3 different organs, including the primary tumor). 40% of them had brain metastasis at the diagnosis. Of the mutational profile, 50% had an exon 19 deletion, 25% had an L858R mutation and the rest had infrequent mutations (12.5% amplification, 10.4% exon 20 insertion and 6.3% exon 18 mutations). In our cases, we evidence that 56.25% of the patients, analyzed by NGS, had another mutation. Of all of them the most frequent was p53 (seen in 55% of the commutated cases), being less frequent others, such as MET and APC amplification (4.2%) and others with a 2.1% (PI3K, BAP1, KRAS, ALKt or HER2 amplification). Finally, we analyzed the progression-free survival (PFS) and overall survival (OS) of commutated patients vs. non-commutated treated with Osimertinib as a first line treatment and, although it was statistically non-significant due to the small sample size (11 vs 9) and the short follow-up, a very positive trend was seen (log-rank test p = 0.055 and p = 0.136 respectively). Conclusions: With the development of NGS, the presence of other commutations besides EGFR have implications that are still unknown, but it appears that it may cause worse OS and PFS. This should be studied in larger cohorts with longer follow-up.

EE321 Cost Impact of Next Generation Sequencing Testing in NSCLC with and without RNA Sequencing

Identifying cancer patients who may benefit from targeted therapies is essential for treatment decisions. Due to the large number of potential oncogenic drivers in advanced non-small cell lung cancer (NSCLC), next-generation sequencing (NGS) is guideline-recommended for identifying actionable targets to inform treatment decisions. Multiple testing options incorporating DNA and/or RNA sequencing are available. Given the potential for improved detection of actionable fusions using RNA sequencing, we examined the costs associated with these testing options.

Resolution of an insidious and migratory Mycobacterium tuberculosis-associated secondary organizing pneumonia: a case report and literature review

BackgroundOrganizing pneumonia (OP) is a rare interstitial lung disease. Secondary organizing pneumonia (SOP) caused by Mycobacterium tuberculosis (MTB) is extremely rare. Migratory MTB-associated SOP is more deceptive and dangerous. When insidious tuberculosis (TB) is not recognized, SOP would be misdiagnosed as cryptogenic organizing pneumonia (COP). Use of steroid hormone alone leads to the progression of TB foci or even death. Clues of distinguishing atypical TB at the background of OP is urgently needed.Case presentationA 56-year-old female patient was hospitalized into the local hospital because of cough and expectoration for more than half a month. Her medical history and family history showed no relation to TB or other lung diseases. Community-acquired pneumonia was diagnosed and anti-infection therapy was initialized but invalid. The patient suffered from continuous weigh loss. More puzzling, the lesions were migratory based on the chest computed tomography (CT) images. The patient was then transferred to our hospital. The immunological indexes of infection in blood and pathogenic tests in sputum and the bronchoalveolar lavage fluid were negative. The percutaneous lung puncture biopsy and pathological observation confirmed OP, but without granulomatous lesions. Additionally, pathogen detection of the punctured lung tissues by metagenomics next generation sequencing test (mNGS) were all negative. COP was highly suspected. Fortunately, the targeted next-generation sequencing (tNGS) detected MTB in the punctured lung tissues and MTB-associated SOP was definitely diagnosed. The combined therapy of anti-TB and prednisone was administrated. After treatment for 10 days, the partial lesions were significantly resorbed and the patient was discharged. In the follow-up of half a year, the patient was healthy.ConclusionsIt is difficult to distinguish SOP from COP in clinical practice. Diagnosis of COP must be very cautious. Transient small nodules and cavities in the early lung image are a clue to consider TB, even though all pathogen tests are negative. tNGS is also a powerful tool to detect pathogen, ensuring prompt diagnosis of TB-related SOP. For clinicians in TB high burden countries, we encourage them to keep TB in mind before making a final diagnosis of COP.

Prevalence of next generation sequencing testing and targetable mutations in cholangiocarcinoma.

e16194 Background: Cholangiocarcinoma (CCA) is an aggressive cancer with a poor prognosis. However, next-generation sequencing (NGS) of tumors and new mutation-targeted therapies have the potential to greatly improve treatment outcomes while reducing the systemic toxicities of traditional chemotherapy. In this study, we examined clinical characteristics, treatment outcomes and the use of NGS profiling in a diverse South Florida population of CCA patients to identify mutations as potential therapeutic targets. Methods: We included patients treated at Jackson and University of Miami Health Systems who were diagnosed with CCA between 2018 and 2021. Clinical and demographic characteristics were obtained through retrospective chart review and entered into a REDCap database. We analyzed the association between clinical characteristics, treatment outcomes, use of NGS and race/ethnicity using Pearson’s Chi-square and Kruskal Wallis tests. Results: The majority of our sample, n = 140, had intrahepatic CCA (iCCA), n = 97, followed by extrahepatic CCA (eCCA), n = 27, and perihilar CCA (pCCA), n = 16. Stage, based on AJCC 8th edition, was most advanced in iCCA and pCCA; 56% had stage III or higher, compared to only 26.2% of eCCA patients. In addition, the median size of the largest iCCA tumor, 7 cm, was significantly larger than that of pCCA, 2.4 cm, and eCCA, 2.2 cm, p = 0.001. NGS was performed in significantly more iCCA cases, 72.2%, compared to pCCA, 37.5%, and eCCA, 59.3%, p = 0.04. TP53 mutations were most common across all CCA subtypes. Other common mutations included CDKN2A, CDKN2B, ERBB2, KRAS, FGFR2, IDH1, and ARID1A, of which only IDH1 and FGFR2 are targetable mutations. There were no significant differences across CCA subtypes in receipt of targeted therapy; overall, 17.1% of patients received targeted therapy. There were no racial differences in stage at presentation or survival in any CCA subtype. While there were numerical differences in the proportion of patients receiving targeted therapy (13.6% of Black, 12.8% of White, and 21.3% of Hispanic), these differences were not statistically significant. Conclusions: There are significant differences in the presentation of CCA subtypes. Examination of NGS results in a larger sample of CCA patients will help expand knowledge on CCA’s mutational profile and permit examination of potential racial disparities in survival or rates of NGS. This work also highlights the need for further targeted therapies against other common mutations in CCA. [Table: see text]

Usefulness and real-world outcomes of next generation sequencing testing in patients with cancer: an observational study on the impact of selection based on clinical judgement.

Next Generation Sequencing (NGS) panels are increasingly used in advanced patients with cancer to guide therapy. There is, however, controversy about when should these panels be used, and about their impact on the clinical course. In an observational study of 139 patients with cancer having an NGS test [from January 1st, 2017 to December 30th, 2020, in two hospitals (Hospital Universitario de La Princesa and Hospital Universitario Quironsalud Madrid) from Spain], we evaluated whether the clinical course (progression-free survival, PFS) was influenced by drug-based criteria [druggable alterations, receiving a recommended drug, having a favourable ESCAT category (ESMO Scale for Clinical Actionability of molecular Targets)] or clinical judgement criteria. In 111 of 139 cases that were successfully profiled, PFS was not significantly influenced by either having druggable alterations [median PFS for patients with druggable alterations was 170 (95% C.I.: 139-200) days compared to 299 (95% C.I.: 114-483) for those without; p=0.37], receiving a proposed matching agent [median PFS for patients receiving a genomics-informed drug was 195 days (95% C.I.: 144-245), compared with 156 days for those that did not (95% C.I.: 85-226); p=0.50], or having favourable ESCAT categories [median PFS for patients with ESCAT I-III was 183 days (95% C.I.: 104-261), compared with 180 (95% C.I.:144-215) for patients with ESCAT IV-X; p=0.87]. In contrast, NGS testing performed within clinical judgement showed a significantly improved PFS [median PFS for patients that were profiled under the recommended scenarios was 319 days (95% C.I.: 0-658), compared to 123 days (95% C.I.: 89-156) in the non-recommended categories; p=0.0020]. According to our data, real-world outcomes after NGS testing provide evidence of the benefit of clinical judgement in patients with either advanced cancers that routinely need multiple genetic markers, patients with advanced rare cancers, or patients that are screened for molecular clinical trials. By contrast, NGS does not seem to be valuable when performed in cases with a poor PS, rapidly progressing cancer, short expected lifetime, or cases with no standard therapeutic options. RC, NR-L and MQF are recipients of the PMP22/00032 grant, funded by the ISCIII and co-funded by the European Regional Development Fund (ERDF). The study also received funds from the CRIS Contra el Cancer Foundation.