Impact Of Next-generation Sequencing Research Articles

The Impact of Next-generation Sequencing on Interobserver Agreement and Diagnostic Accuracy of Desmoplastic Melanocytic Neoplasms.

Next-generation sequencing (NGS) is increasingly being utilized as an ancillary tool for diagnostically challenging melanocytic neoplasms. It is incumbent upon the pathology community to perform studies assessing the benefits and limitations of these tools in specific diagnostic scenarios. One of the most challenging diagnostic scenarios faced by skin pathologists involves accurate diagnosis of desmoplastic melanocytic neoplasms (DMNs). In this study, 20 expert melanoma pathologists rendered a diagnosis on 47 DMNs based on hematoxylin and eosin sections with demographic information. After submitting their diagnosis, the experts were given the same cases, but this time with comprehensive genomic sequencing results, and asked to render a diagnosis again. Identification of desmoplastic melanoma (DM) improved by 7%, and this difference was statistically significant ( P <0.05). In addition, among the 15 melanoma cases, in the pregenomic assessment, only 12 were favored to be DM by the experts, while after genomics, this improved to 14 of the cases being favored to be DM. In fact, some cases resulting in metastatic disease had a substantial increase in the number of experts recognizing them as DM after genomics. The impact of the genomic findings was less dramatic among benign and intermediate-grade desmoplastic tumors (BIDTs). Interobserver agreement also improved, with the Fleiss multirater Kappa being 0.36 before genomics to 0.4 after genomics. NGS has the potential to improve diagnostic accuracy in the assessment of desmoplastic melanocytic tumors. The degree of improvement will be most substantial among pathologists with some background and experience in bioinformatics and melanoma genetics.

Impact of next-generation sequencing in biliary tract cancer treatment.

560 Background: Incorporating molecular profiling in BTC treatment has increased. With this study, we aimed to analyze the impact of molecular profiles on the survival of patients with BTC. Methods: This is the retrospective analysis of patients with biopsy-proven biliary tract cancer at our comprehensive cancer center GI oncology clinic from 2018-2022. Only patients with continued care at Lombardi Comprehensive Cancer Center were included in the study. Results: Of 217 patients screened; 160 patients were included in the final analysis. The mean age of the cohort was 63 years, and the majority were females (55%). In the order of frequency, intrahepatic cholangiocarcinoma (77.5%) was the most common type of cancer followed by extrahepatic cholangiocarcinoma (15.6%), and carcinoma of the Gallbladder (6.9%). Molecular profiling was performed in 49.4% of the patients and actionable mutations for FDA approved treatments or clinical trial enrollment were found in 42 patients (26.3%) of the patients. The spectrum of actionable mutations in decreasing order of frequency was KRAS (n=11), FGFR2 (n=9), IDH-1 (n=8), Her-2neu (n=5), BRCA1/2 (n=5), &amp; PD-L1(n=4). Patients who underwent molecular profiling had significantly better survival (43±5 months vs. 25±4, p 0.013). Notably, patients with actionable mutations had even better survival as compared to the rest of the cohort (52±8 months vs. 26±7 months, p 0.019). Conclusions: BTC exhibits diverse genetic alterations. Patients who underwent molecular profiling as a part of the treatment plan had better survival. Identifying actionable mutations was associated with even better survival.

Impact of next-generation sequencing on antimicrobial treatment in immunocompromised adults with suspected infections.

Prompt pathogen identification can have a substantial impact on the optimization of antimicrobial treatment. The objective of the study was to assess the diagnostic value of next-generation sequencing (NGS) for identifying pathogen and its clinical impact on antimicrobial intervention in immunocompromised patients with suspected infections. This was a retrospective study. Between January and August 2020, 47 adult immunocompromised patients underwent NGS testing under the following clinical conditions: 1) prolonged fever and negative conventional cultures; 2) new-onset fever despite empiric antimicrobial treatment; and 3) afebrile with suspected infections on imaging. Clinical data, including conventional microbial test results and antimicrobial treatment before and after NGS, were collected. Data were analyzed according to documented changes in antimicrobial treatment (escalated, no change, or de-escalated) after the NGS results. The median time from hospitalization to NGS sampling was 19 d. Clinically relevant pathogens were detected via NGS in 61.7% of patients (29/47), more than half of whom suffered from fungemia (n=17), resulting in an antimicrobial escalation in 53.2% of patients (25/47) and antimicrobial de-escalation in 0.2% of patients (1/47). Antimicrobial changes were mostly due to the identification of fastidious organisms such as Legionella, Pneumocystis jirovecii, and Candida. In the remaining three cases, NGS detected clinically relevant pathogens also detected by conventional cultures a few days later. The antimicrobial treatment was subsequently adjusted according to the susceptibility test results. Overall, NGS changed antimicrobial management in 55.3% (26/47) of patientst, and conventional culture detected clinically relevant pathogens in only 14.9% of patients (7/47). With its rapid identification and high sensitivity, NGS could be a promising tool for identifying relevant pathogens and enabling rapid appropriate treatment in immunocompromised patients with suspected infections.

Next-Generation Sequencing in Unexplained Intellectual Disability.

To determine the diagnostic yield of next generation sequencing (NGS) in patients with moderate/severe/profound intellectual disability (ID) unexplained by conventional tests and to assess the impact of definitive diagnosis on the clinical management and genetic counselling of these families. This was a ambi-directional study conducted at Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi. The study comprised 227 patients (prospective cohort - 126, retrospective cohort - 101) in whom NGS based tests were performed. The mean age of study cohort was 4.5 ± 4.4 y (2.5 mo to 37.3 y). The male: female ratio was 1.6:1. The overall diagnostic yield of NGS was 53.3% (121/227) with causative variants identified in 84 known ID genes. Autosomal recessive intellectual disability (ARID) (23.3%, 53/227) was the most common followed by autosomal dominant intellectual disability (ADID) (20.7%, 47/227) and X-linked intellectual disability (XLID) (9.2%, 21/227). The diagnostic yield was notably higher for ID plus associated condition group (55.6% vs. 20%) (p = 0.0075, Fisher's exact test) compared to isolated ID group. The impact of diagnosis on active or long-term management was observed in 17/121 (14%) and on reproductive outcomes in 26/121 (21.4%) families. There is paucity of data on molecular genetic spectrum of ID from India. The current study identifies extensive genetic heterogeneity and the impact of NGS in patients with ID unexplained by standard genetic tests. The study identified ARID as the most common cause of ID with additional implications for reproductive outcomes. It reiterates the importance of phenotype in genetic testing.

Impact of Next-Generation Sequencing in Diagnosis, Prognosis and Therapeutic Management of Acute Myeloid Leukemia/Myelodysplastic Neoplasms

For decades, the diagnosis, prognosis and thus, the treatment of acute myeloblastic leukemias and myelodysplastic neoplasms has been mainly based on morphological aspects, as evidenced by the French-American-British classification. The morphological aspects correspond quite well, in a certain number of particular cases, to particular evolutionary properties, such as acute myelomonoblastic leukemias with eosinophils or acute promyelocytic leukemias. Advances in biology, particularly “classical” cytogenetics (karyotype) and molecular cytogenetics (in situ hybridization), have made it possible to associate certain morphological features with particular molecular abnormalities, such as the pericentric inversion of chromosome 16 and translocation t(15;17) in the two preceding examples. Polymerase chain reaction techniques have made it possible to go further in these analyses by associating these karyotype abnormalities with their molecular causes, CBFbeta fusion with MYH11 and PML-RAR fusion in the previous cases. In these two examples, the molecular abnormality allows us to better define the pathophysiology of leukemia, to adapt certain treatments (all-transretinoic acid, for example), and to follow up the residual disease of strong prognostic value beyond the simple threshold of less than 5% of marrow blasts, signaling the complete remission. However, the new sequencing techniques of the next generation open up broader perspectives by being able to analyze several dozens of molecular abnormalities, improving all levels of management, from diagnosis to prognosis and treatment, even if it means that morphological aspects are increasingly relegated to the background.

The impact of next generation sequencing on the management of urothelial cell carcinoma.

e16576 Background: The urothelial carcinoma is commonly seen in urethra, bladder, ureter and renal pelvis. Targetable mutations included PD-L1, FGFR, PIK3CA, BRCA2, FBXW7, and Tumor mutation burden (TMB) greater than 10 Muts/Mb. Next genome sequencing is widely used to guide treatment of oncology patients; however, the efficacy of this practice is still not clear. Methods: Patients used in this study are from the Northwell Health Zuckerberg Cancer Center. This is a retrospective cohort study of patients with advanced urothelial carcinoma, who underwent next genome sequencing and received treatment based on targetable mutations. The primary objective for this study is to measure the response rate for patients with actionable gene aberrations on targetable treatment. Results: The RECIST 1.1 guidelines were used when identifying measurable lesions. Measurable lesions were identified as lymph nodes with a short axis ≥ 15 mm, or soft tissue lesions with a long axis ≥ 10 mm. Our sample size included 48 patients with urothelial carcinoma, these include bladder, ureter and renal pelvis cancers. Of these 48 patients, 21 received targetable treatment (16 males, 5 females), from those 21 only 20 had imaging before and after treatment. Most common mutations were TMB, PD-L1 and FGFR. 4 patients out of 20 had an overall response rate (20%), 3 had partial response (PR) and 1 had complete response (CR) to their respective targeted treatment. 11 patients had stable disease (SD). Thus disease control rate (DCR) was 15 out of 20 patients (75%) (when including PR, CR and SD out of 20 patients) had no progression of disease. Finally, 5 of the 20 patients had an overall progression of disease (PD). Conclusions: The results of our study indicate that next genome sequencing led to good treatment outcomes for patients previously heavily treated with advanced urothelial malignancy.

Impact of next generation sequencing on a clinicians’ first line treatment decision in patients with stage IV non-small cell lung cancer.

e21160 Background: National Comprehensive Cancer Network (NCCN) guidelines strongly recommend biomarker testing for patients with advanced non-small cell lung cancer (NSCLC), specifically with broad, panel-based sequencing via NGS. Our study characterized how clinicians utilized NGS testing to make first line treatment decisions in patients with stage IV NSCLC. Methods: We conducted a cross-sectional study of members within an integrated healthcare system (Kaiser Permanente Southern California) diagnosed with stage IV NSCLC who completed NGS testing (Strata Oncology) between May 2019 to June 2021. Treatment start dates were used to divide patients into those who started treatment before and after NGS results, and those who did not receive treatment after NGS results. Patients harboring alterations in seven genes (EGFR, ALK, ROS-1, BRAF, KRAS, RET, and MET) were considered candidates for targeted first line therapy. Results: A sample of 760 patients with stage IV NSCLC completed NGS testing. The mean time from NGS order to result was 25 days. Of the 760 in the sample, 284 (37%) and 262 (34%) initiated treatment before and after NGS results were reported, respectively, while the remaining 214 (28%) did not receive any treatment up to 120 days after the NGS results were reported. 43% (323/760) of the sample was found to have a targetable mutation on NGS, of whom only 38% (124/323) initiated first line treatment with a targeted therapy. 56/124 (45%) were treated with targeted therapy prior to NGS results and 68/124 (55%) were treated with targeted therapy after NGS results. 61% (118/193) of EGFR, ALK, or ROS mutated patients started targeted therapy. 67/323 with a driver mutation did not receive any treatment and were referred to hospice. For those patients who initiated targeted therapy prior to NGS results, it suggests that clinicians ordered single gene testing in parallel with NGS, and that these results were available prior to NGS. Conclusions: NGS tests results were not exclusively used to inform first line treatment decisions in most patients with stage IV NSCLC, as most patients found to have a targetable mutation, were not treated with targeted therapy. Possible explanations include lengthy turnaround times for NGS testing and the availability of more timely single gene testing.

An Overview of Molecular Basis and Genetic Modification of Floral Organs Genes: Impact of Next-Generation Sequencing.

In plant development, flowering is the most widely studied process. Floral forms show large diversity in different species due to simple variations in basic architecture. To determine the floral gene expression during the past decade, MADS-box genes have identified as key regulators in both reproductive and vegetative plant development. Traditional genetics and functional genomics tools are now available to elucidate the expression and function of this complex gene family on a much larger scale. Moreover, comparative analysis of the MADS-box genes in diverse flowering and non-flowering plants, boosted by various molecular technologies such as ChIP and next-generation DNA sequencing, contributes to our understanding of how this important gene family has expanded during the evolution of land plants. Likewise, the big data analysis revealed combined activity of transcriptional regulators and floral organ identity factors regulate the flower developmental programs. Thus, with the help of cutting-edge technologies like RNA-Sequencing, sex determination is now better understood in few non-model plants Therefore, the recent advances in next-generation sequencing (NGS) should enable researchers to identify the full range of floral gene functions, which will significantly help to understand plant development and evolution. This review summarizes the floral homeotic genes in model and non-model species to understand the flower development genes and dioecy evolution.

EP04.01-020 Impact of Next-Generation Sequencing on Treatment Choice Among Patients with Metastatic NSCLC from the CHUM University Center

Early identification of actionable mutations with precise molecular testing, such as Next-Generation Sequencing (NGS), has changed the management of patients with metastatic lung cancer. We report real-world data showing how NGS has become an essential tool in determining each patient’s molecular profile and allowing the individualization of cancer treatment.

Impact of next-generation sequencing (NGS) on the diagnosis of gliomas according to the WHO-2016 and WHO-2021 classification in routine clinical practice.

e14022 Background: The WHO-2016 classification of central nervous system tumors introduced molecular data to perform the diagnosis, especially in gliomas. The cIMPACT-NOW updates and the WHO-2021 classification have consolidated this need, and today a comprehensive structured diagnosis is indicated. Therefore, we study the impact of the use of NGS in changing the diagnosis of gliomas in routine clinical practice. Methods: We have carried out a systematic search of glioma patients operated between January 2008 and September 2021 and diagnosed according to WHO-2016 and cIMPACT-NOW updated criteria at our academic medical center in Spain. All included patients were reclassified to WHO-2021 according to pathological data. Subsequently, we analyzed whether the application of NGS led to a change in the WHO-2016 or WHO-2021 diagnosis. We also analyzed the median of tumor mutation burden (TMB), variants of unknown significance (VUSs), potential enrollment eligible (PENs) and cancer-related alterations (CRAs). Results: Although our center serves a population of 1.8 million people, the scarcity of biopsied material and the difficulty of accessing NGS early enough limited the recruitable patients to 22. Of them 17 patients (77.27%) remained after NGS results with the same WHO-2016 and WHO-2021 diagnosis and in 5 (22.73%) it involved a change in diagnosis (Table). No PENs were detected for any patient. A median of 4 CRAs and 6 VUSs were detected per patient. The median TMB was 1.89 mutations per megabase. Conclusions: The scarce quality biopsied material and the limited access to NGS restrict its use in gliomas. Despite this, its impact in diagnosis cannot be ignored, in our study the diagnosis changed in 1 out of 3.18 patients regardless of the classification used. With these data we recommend increasing the effort to facilitate NGS to glioma patients early enough. Further studies remain essential to determine the impact of NGS results in treatment.[Table: see text]

Effectiveness of nationwide insurance coverage for next-generation sequencing in advanced colorectal cancer: A real-world data study.

3602 Background: Next-generation sequencing (NGS) has been covered by Korean national health insurance since March 2017 for patients with advanced colorectal cancer (CRC). We explored the clinical and socioeconomic impact of NGS compared with that of a single gene test (SGT) alone. Methods: From the nationwide database, we identified patients who 1) are diagnosed with advanced CRC classified as a distant disease using Summary Stage between March 1, 2017, and December 31, 2018; 2) had NGS or SGT within 2 months after diagnosis of advanced CRC. Multivariate logistic regression with covariates including age, sex, Charlson comorbidity index, insurance type, year of diagnosis, and region and type of hospital with the initial diagnosis was conducted to identify factors affecting the performance of NGS. We conducted 1:3 propensity score matching to minimize the impact of confounding factors. The median overall survival and the adjusted hazard ratio (aHR) were estimated using the Kaplan-Meier method and the Cox proportional hazard model, respectively. We calculated the total medical cost, and per patient per year (PPPY) cost adjusted for the survival period. Results: Among 5,029 patients with advanced CRC, 655 patients were identified as NGS group and 1,995 as SGT group after matching. Old age, low household income, rural location, and non-tertiary hospital were all characteristics that reduced the likelihood of obtaining an NGS test. The NGS group showed significantly favorable survival compared to the SGT group (median survival 29.2 vs. 24.9 months, P =.031; adjusted hazard ratio [HR] 0.86, P =.034). The total medical cost was lower in the NGS group ($55,445) than the SGT group ($57,989), and the PPPY cost was also lower in the NGS group ($44,879 and $49,734, respectively). Conclusions: We found that some socioeconomic factors such as age, insurance type, region, and hospital type may hamper the implementation of NGS. Also, lowering the barrier of NGS tests by reimbursing NGS in a specific clinical setting may have survival and cost-benefit in patients with advanced CRC.

Clinical implications of next-generation sequencing on pediatric solid tumors.

e22012 Background: To assess the impact of next-generation sequencing (NGS) on Chinese pediatric cancer, we reported the first study of largest cohort in Chinese children with genomic landscape and highlighted the potential application with respect to molecular diagnosis and predictive biomarkers etc. Methods: A retrospective analysis was conducted on patients aged &lt; 19 years diagnosed with solid tumors sequenced by targeted NGS panel. Somatic variants were analyzed following CAP/CLIA-certificated workflows, including Single Nucleotide Variant (SNV), Copy Number Variation (CNV), large insertion and deletions (Lindel) and gene rearrangements. Results: A total of 356 patients enrolled with three major cancer types including osteosarcoma (OS) (n = 78), rhabdomyosarcoma (RMS) (n = 51), Ewing sarcoma (EWS) (n = 13). Hepatocellular carcinoma (n = 9), medulloblastomas (n = 7) and colorectal adenocarcinoma (n = 5) were also included. 3487 somatic alterations were identified, TP53 (16%), EWSR1 (8.7%), CDKN2A (7.8%), BCOR (7%) and RB1 (5.6%) rank the top five reported. TP53 (21% % vs 7.9%), RB1 (10% vs 5.3%) mutations showed higher frequency in OS and BCOR (14% vs 17.6%) showed lower frequency in RMS compared to published paper (Gröbner et al 2018). We found PIK3CA mutations presented in RMS with 11.7% frequency, twice than reported (5.8%), mostly occurring at the known oncogenic codon E545. The obscure boundary of soft tissue tumor and bone tumor perplexed the pathologic diagnosis, NGS provide an important auxiliary examination. In 140 soft tissue tumor and bone tumor patients, 14.2% patients were further diagnosed with different subtype, 4.2% patients with unknown subtype were diagnosed with a specified subtype by supportive genetic alterations. Moreover, 41.5% (138/356) patients received treatment recommended . Twelve NTRK-fusions were detected and the patients were recommended therapy method upon Larotrectinib, recruitment in matched clinical trial is still on-going. Conclusions: We investigated the different genetic profiling of Chinese pediatric solid cancer and found the clinical value of NGS in pathological diagnosis and biomarker discovery.

Effectiveness of nationwide insurance coverage for next-generation sequencing in advanced non–small cell lung cancer: A real-world data study.

9134 Background: Next-generation sequencing (NGS) has been covered by Korean national health insurance since March 2017 for patients with advanced non-small cell lung cancer (NSCLC). We explored the clinical and socioeconomic impact of NGS compared with that of a single gene test (SGT) alone. Methods: From the nationwide database, we identified patients who 1) are diagnosed with advanced NSCLC classified as a distant disease using Summary Stage between March 1, 2017, and December 31, 2018; 2) had NGS or SGT within 2 months after diagnosis of advanced NSCLC. Patients with squamous cell carcinoma were excluded. We conducted multivariate logistic regression to identify factors (e.g., age, sex, Charlson comorbidity index, insurance type, year of diagnosis, and region and type of hospital with the initial diagnosis) affecting the performance of NGS. Further, we divided the cohort into subgroups based on whether patients received treatment targeting epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) mutations (group A) or not (group B). We conducted 1:5 propensity score matching for each group to minimize the impact of confounding factors. The median overall survival and the adjusted hazard ratio (aHR) for death were estimated using the Kaplan-Meier method and the Cox proportional hazard model, respectively. We calculated the total medical cost, and per patient per year (PPPY) cost adjusted for the survival period. Results: Among 10,247 patients with advanced NSCLC, 768 patients were identified as group A and 1,596 as group B after matching. Old age, low household income, and rural region were factors negatively impacting on having NGS tests. In Group A, we did not find a significant difference in survival outcome between the NGS cohort and the SGT cohort (median survival 31.6 vs. 27.5 months, P =.331; aHR 0.80, P =.204). In contrast, significantly favorable survival was observed for the NGS group in Group B (median survival 14.1 vs. 9.5 months, P =.023; aHR 0.80, P =.009). Although the total medical cost was higher in the NGS group ($39,145) than the SGT group ($36,207) for Group B, the PPPY cost was lower in the NGS group ($57,502 and $63,293, respectively). Conclusions: Socioeconomic factors hampering the implementation of NGS were identified. Lowering the barrier by covering the NGS cost publicly in a specific clinical setting may have survival and cost-benefit in patients with advanced NSCLC.

A review on the application of bioinformatics tools in food microbiome studies.

There is currently a transformed interest toward understanding the impact of fermentation on functional food development due to growing consumer interest on modified health benefits of sustainable foods. In this review, we attempt to summarize recent findings regarding the impact of Next-generation sequencing and other bioinformatics methods in the food microbiome and use prediction software to understand the critical role of microbes in producing fermented foods. Traditionally, fermentation methods and starter culture development were considered conventional methods needing optimization to eliminate errors in technique and were influenced by technical knowledge of fermentation. Recent advances in high-output omics innovations permit the implementation of additional logical tactics for developing fermentation methods. Further, the review describes the multiple functions of the predictions based on docking studies and the correlation of genomic and metabolomic analysis to develop trends to understand the potential food microbiome interactions and associated products to become a part of a healthy diet.

Impact of next generation sequencing in hematopoietic stem cell transplantation in children with non-DNA breakage defect inherited bone marrow failure syndromes

Impact of next generation sequencing in hematopoietic stem cell transplantation in children with non-DNA breakage defect inherited bone marrow failure syndromes

Impact of Next-generation Sequencing on Interobserver Agreement and Diagnosis of Spitzoid Neoplasms.

Atypical Spitzoid melanocytic tumors are diagnostically challenging. Many studies have suggested various genomic markers to improve classification and prognostication. We aimed to assess whether next-generation sequencing studies using the Tempus xO assay assessing mutations in 1711 cancer-related genes and performing whole transcriptome mRNA sequencing for structural alterations could improve diagnostic agreement and accuracy in assessing neoplasms with Spitzoid histologic features. Twenty expert pathologists were asked to review 70 consultation level cases with Spitzoid features, once with limited clinical information and again with additional genomic information. There was an improvement in overall agreement with additional genomic information. Most significantly, there was increase in agreement of the diagnosis of conventional melanoma from moderate (κ=0.470, SE=0.0105) to substantial (κ=0.645, SE=0.0143) as measured by an average Cohen κ. Clinical follow-up was available in all 70 cases which substantiated that the improved agreement was clinically significant. Among 3 patients with distant metastatic disease, there was a highly significant increase in diagnostic recognition of the cases as conventional melanoma with genomics (P<0.005). In one case, none of 20 pathologists recognized a tumor with BRAF and TERT promoter mutations associated with fatal outcome as a conventional melanoma when only limited clinical information was provided, whereas 60% of pathologists correctly diagnosed this case when genomic information was also available. There was also a significant improvement in agreement of which lesions should be classified in the Spitz category/WHO Pathway from an average Cohen κ of 0.360 (SE=0.00921) to 0.607 (SE=0.0232) with genomics.

Impact of Next-Generation Sequencing on Treatment Choices for Patients with Acute Myeloid Leukemia

INTRODUCTION: Until recently, therapy options for patients with acute myeloid leukemia (AML) were limited. This is changing due to advent of CLIA-approved next generation sequencing (NGS) panels and development of multiple new anti-leukemia agents. Examples are the recent approval of a FLT3 and IDH2 inhibitors. Multiple other targeted agents are currently being studied in clinical trials for AML. The aim of our study was to evaluate the impact of a NGS panel on the clinical practice at a major clinical trial research center. We report the experience in 1171 patients with AML who had a NGS panel evaluation as part of their clinical care during 2012-2015. METHODS : We included all AML patients for whom an NGS-based analysis for the detection of somatic mutations in the coding sequence of a total of 28 or 53 genes was performed between October 2012 and October 2015. Clinical and demographic data were obtained from clinical records. 17 genes ( ALK, CSF1R, FGFR1, FGFR2, FGFR3, FLT3, IDH1, IDH2, JAK2, KDR, KRAS, NPM1, NRAS, PDGFRA, PRPN11, RET and TP53) were considered potentially actionable due to the possibility to be targeted with established or investigational therapies, either directly or indirectly. Statistical analyses were performed with the IBM SPSS Statistics 23.0 software. RESULTS: A total of 732 patients (62.5%) were evaluated using the 28 gene panel and 439 patients (37.5%) using the 53 gene panel. 36% of patients were evaluated frontline (n=421), 27.6% during treatment (n=313) and 37.4% (n=437) at relapse. The median time to inform the results were 9 days (range 2-90). Median age at AML diagnosis was 62 years (range 10-92). Baseline characteristics are shown in Table 1. 881 patients (75%) had at least one detectable mutation: 669 (57.1%) on a potential actionable gene and 502 (42.9%) on non-actionable genes. The most frequently potentially actionable mutation was IDH2 (n=196; 16.7%), followed by TP53 (N=174; 14.9%), NPM1 (n=163; 13.9%), NRAS (n=129; 11.0%), IDH1 (n=116; 9.9%) and KRAS (n=66; 5.6%), present on more than 5% of the patients. The frequency of all identified mutations is shown in Fig. 1A. A total of 421 patients (36.0%) were evaluated at initial diagnosis, with 404 patients subsequently starting therapy for their AML. 277 (65.8%) of these had potentially targetable alterations, and only 5 (1.8%) of these patients were treated with a targeted agent. 437 patients (37.4%) patients were evaluated at the time of relapse/refractory with 388 patients (88.6%) starting new therapy. 281 (72.4%) of these treated patients had a targetable mutation and 46 (16.4%) of them were treated with a target agent. Therefore, considering only patients with an actionable mutation, patients with relapse/refractory AML were more likely to receive targeted therapy than those at diagnosis (16.4% vs 1.8%, p The 614 remaining patients (91.8%) never received a targeted therapy. 9.5% of these patients (n=58) never return to the institution after the mutation analysis and 16.6% (n=102) responded to another therapy. For the remaining 434 patients, documentation of discussion of enrollment in a clinical trial was present on 82.9% (n=358): 85.8% (n=307) enrolled in a clinical trial not involving actionable mutations and 10.1% (n=36) were not eligible owing to poor status or other causes. CONCLUSION: NGS technologies can be used to identify a significant proportion of patients (57%) with potentially actionable mutations. However, until 2015, only a small proportion of patients (8.2%) with AML and actionable alterations were treated with targeted therapy. Relapse/refractory patients were more likely to receive targeted agents than those at initial diagnosis. Possible reasons are: 1) delays in NGS results and physicians not willing to wait to start treatment; 2) presumption that standard therapies may be better than investigational target agents. Personalized medicine based on mutation profiles in AML remains an area under development, but a dramatic increase in the proportion of patients treated with a target agent were observed in 4 years. The results of current clinical trials may change the way we treat these patients. Disclosures Takahashi: Symbio Pharmaceuticals: Consultancy. Jabbour: Bristol-Myers Squibb: Consultancy. Cortes: ARIAD: Consultancy, Research Funding; Novartis Pharmaceuticals Corporation: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; ImmunoGen: Consultancy, Research Funding; Teva: Research Funding; Sun Pharma: Research Funding; BMS: Consultancy, Research Funding. DiNardo: AbbVie: Honoraria, Research Funding; Agios: Honoraria, Research Funding; Novartis: Honoraria, Research Funding; Celgene: Honoraria, Research Funding; Daiichi-Sankyo: Honoraria, Research Funding. Daver: Otsuka America Pharmaceutical, Inc.: Consultancy; Bristol-Myers Squibb Company: Consultancy, Research Funding; Kiromic: Research Funding; Jazz: Consultancy; Pfizer Inc.: Consultancy, Research Funding; Novartis Pharmaceuticals Corporation: Consultancy; Incyte Corporation: Honoraria, Research Funding; Sunesis Pharmaceuticals, Inc.: Consultancy, Research Funding; Immunogen: Research Funding; Karyopharm: Consultancy, Research Funding; Daiichi-Sankyo: Research Funding. Pemmaraju: Cellectis: Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Incyte: Consultancy, Honoraria; Stemline: Consultancy, Honoraria, Research Funding; LFB: Consultancy, Honoraria, Research Funding. Kantarjian: Amgen: Research Funding; ARIAD: Research Funding; Novartis: Research Funding; Bristol-Meyers Squibb: Research Funding; Delta-Fly Pharma: Research Funding; Pfizer: Research Funding.

An investigation into the impact of next generation sequencing on the use of targeted treatments in glioblastoma.

2035 Background: Next-generation sequencing (NGS) provides clinicians immense amounts of information about a patient’s cancer. NGS allows the detection of a wide range of gene alterations undetectable by older techniques. This has the promise to help guide clinicians in their decision-making as genetic alterations can be both prognostic and predictive. NGS may reveal new treatment options for patients with glioblastoma. The goal of this project was to evaluate how often NGS results influence the use of targeted treatment agents in glioblastoma. This study did not investigate the impact of NGS on reclassification of cancers, prognosis, or treatment decisions outside of the use of targeted therapy. Methods: We conducted a retrospective chart review to see if adult glioblastoma patients received treatments for potentially actionable gene alterations and for fusion variants because of NGS. Here we looked at alterations labeled as actionable from the Tempus company’s NGS results. We collected diagnosis and treatment information from the Electronic Medical Record and from the Electronic Data Warehouse. We examined if patients after receiving NGS would receive targeted treatment, as that likely indicated these treatments were given due to NGS indication. We excluded cytotoxic chemotherapy agents and bevacizumab as these therapies are utilized regardless of a targeted gene indication. This analysis excluded treatments received in clinical trials in which enrollment was independent of NGS. This analysis looked at the proportion of patients with actionable alterations that were treated with targeted agents. Results: 261 glioblastoma patients were found on NGS to have mutations which were potentially actionable. Thirty-three of these patients (12.6%) received a respective targeted therapy, and the other 228 patients (87.4%) did not receive an NGS guided targeted therapy. 97 patients had EGFR copy number gains or EGFR gain of function mutations of which 21 were treated with depatuxizumab mafodotin, and one additional patient who was treated with ABBV 321. Of the NGS treatment guided therapies, depatuxizumab mafodotin was the most used targeted agent in our sample set. Additionally, there were 30 patients with fusion variants and 11 of them were FGFR3-TACC3 fusions. Of these 11, 4 received targeted regimens (36.4%) with either TAS-120, pemigatinib, erdafitinib, or erdafitinib with ponatinib. The other fusion variants were not acted upon. Conclusions: These preliminary results suggest that NGS data currently does not frequently impact treatment decisions for glioblastoma. Although this study is limited by being a single institution study, future efforts include expanding this analysis to multiple institutions. With improvements in therapeutics as well as with wider availability of NGS testing, sequencing data may impact a larger percentage of glioblastoma patients.

The Johns Hopkins Molecular Tumor Board Precision Oncology elective for Medical Oncology fellows.

11035 Background: The accelerated impact of next generation sequencing (NGS) in clinical decision making requires the integration of cancer genomics and precision oncology focused training into medical oncology education. The Johns Hopkins Molecular Tumor Board (JH MTB) is a multi-disciplinary effort focused on integration of NGS findings with critical evidence interpretation to generate personalized recommendations tailored to the genetic footprint of individual patients. Methods: The JH MTB and the Medical Oncology Fellowship Program have developed a 3-month precision oncology elective for fellows in their research years. Commencing fall of 2020, the goals of this elective are to enhance the understanding of NGS platforms and findings, advance the interpretation and characterization of molecular assay outputs by use of mutation annotators and knowledgebases and ultimately master the art of matching NGS findings with available therapies. Fellow integration into the MTB focuses on mentored case-based learning in mutation characterization and ranking by levels of evidence for actionability, with culmination in form of verbal presentations and written summary reports of final MTB recommendations. A mixed methods questionnaire was administered to evaluate progress since elective initiation. Results: Three learners who have participated as of February 2021 were included. Of the two who had completed the MTB elective, each have presented at least 10 cases, with at least 1 scholarly publication planned. All indicated strong agreement that MTB elective had increased their comfort with interpreting clinical NGS reports as well as the use of knowledgebases and variant annotators. Exposure to experts in the field of molecular precision oncology, identification of resources necessary to interpret clinical NGS reports, development of ability to critically assess various NGS platforms, and gained familiarity with computational analyses relevant to clinical decision making were noted as strengths of the MTB elective. Areas of improvement included ongoing initiatives that involve streamlining variant annotation and transcription of information for written reports. Conclusions: A longitudinal elective in the JHU MTB has been found to be preliminarily effective in promoting knowledge mastery and creating academic opportunities related to the clinical application of precision medicine. Future directions will include leveraging of the MTB infrastructure for research projects, learner integration into computational laboratory meetings, and expansion of the MTB curriculum to include different levels of learners from multiple medical education programs. Continued elective participation will be key to understanding how best to facilitate adaptive expertise in assigning clinical relevance to genomic findings, ultimately improving precision medicine delivery in patient care and trial development.

Survey study of barriers to evidence-based decision-making in oncology care using next-generation sequencing.

e18757 Background: Next-generation sequencing (NGS) has the potential to accelerate precision medicine in oncology by informing efficient and improved clinical treatment decision-making. However, discussions on the utility of NGS in clinical practice are ongoing. This survey study examined clinical utility barriers to adoption of NGS into oncologic care. Methods: A cross-sectional online survey was sent to a nationally representative sample of oncologists/hematologists, surgeons, and pathologists (N=201). The survey gathered information on physician demographics, practice characteristics, perceived barriers to NGS testing, and potential strategies for increasing adoption. Results: Almost all physicians in the sample (99.5%) reported using NGS. Physicians reported the following aspects of NGS as the most valuable: ability to guide decision-making (73.1%), more accurate identification of corresponding treatment (56.7%), comprehensive genomic coverage (54.2%), efficient technology with faster turnaround time (49.8%), and more accurate diagnosis or prognosis (41.3%). Physicians reported that NGS results guided treatment decisions for 63% of patients (Range: 2% - 100%). Over 85% of physicians reported that confidence in interpreting results and availability of clinical guidelines were important in undertaking NGS. Correspondingly, limited evidence of clinical utility was a top barrier to testing (80.1%), with pathologists and surgeons more likely than oncologists/hematologists to consider this. Overall, 76% of physicians shared that strategies to alleviate these clinical utility barriers included increased evidence, standardized guidelines, and interpretation support. Conclusions: Given the high uptake of NGS testing in this physician sample, but the lower rates of application of test results to guide treatment, the clinical impact of NGS may not be fully optimized. This discrepancy highlights the ongoing need for real-world evidence to better understand and further optimize the evolving role of NGS in the context of the overall management of the cancer patient. [Table: see text]