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Journal articles on the topic 'GENEXUS'

Author: Grafiati
Published: 2 June 2025
Last updated: 31 July 2025

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1

Sedova, Marina, Alexy Ongpin, Jennifer Burke, et al. "Abstract 764: Fully automated sample-to-report NGS workflow for comprehensive genomic profiling for myeloid neoplasms." Cancer Research 82, no. 12_Supplement (2022): 764. http://dx.doi.org/10.1158/1538-7445.am2022-764.

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Abstract Introduction: Myeloid malignancies are associated with a broad and diverse set of genomic alterations, including SNVs, insertions, deletions and gene fusions. Comprehensive characterization of genetic mutations in hematological disorders currently requires a variety of diagnostic tests and takes multiple days to complete. We developed a fully automated NGS Myeloid Assay that offers an easy to use sample-to-report workflow and the capability for processing up to 8 samples per day. Methods: The Genexus System is comprised of two software linked instruments, the Genexus Purification Syst
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2

Oliveira, Douglas Hamilton, and Vandré Felipe de Oliveira Nicolau. "Comunicação SMTP em aplicações Genexus – um comparativo entre a linguagem nativa e a não nativa." Revista Processando o Saber 03, no. 01 (2011): 82–99. https://doi.org/10.5281/zenodo.15571842.

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O artigo visa demonstrar a comunicação de aplicações GENEXUS com servidores de e-mails utilizando o protocolo SMTP que é responsável pelo envio de mensagens de correio eletrônico, para isso serão comentados duas formas de envio: a forma nativa do GENEXUS com a utilização de variáveis que, na verdade, são objetos instanciados de classes especificas do GENEXUS que tratam do protocolo SMTP e a outra forma usando linguagem externa não nativa que, no caso, será a linguagem da Microsoft C#.NET no framewo
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3

Reibán-Lucero, Franklin I., and Diego M. Cordero-Guzmán. "Catálogo de refactorización de código fuente para la herramienta CASE GeneXus." Polo del Conocimiento 4, no. 6 (2019): 173. http://dx.doi.org/10.23857/pc.v4i6.1005.

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<p style="text-align: justify;">La herramienta de ingeniería de software asistido por computador (CASE) GeneXus se utiliza para desarrollar software en base a la abstracción del conocimiento, permite modelar entidades del mundo real y definir sus características y comportamiento de forma declarativa pero también permite crear objetos basados en lógica procedural cuya construcción depende exclusivamente del desarrollador pues la herramienta no brinda asistencia de ningún tipo para el desarrollo, esto implica que no se verifique exhaustivamente la congruencia con el conocimiento que se cap
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4

Zochowski, Kayla, Dinesh Cyanam, Geoffrey Lowman, et al. "Abstract 42: High-throughput next-generation sequencing research solutions for detection of oncology variants, gene fusion events, and key oncology endpoints." Cancer Research 82, no. 12_Supplement (2022): 42. http://dx.doi.org/10.1158/1538-7445.am2022-42.

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Abstract Introduction: The Ion Torrent Genexus System has redefined the genomic profiling paradigm as the first fully-integrated, next-generation sequencing (NGS) research platform to provide an automated sample-to-report workflow with results in a single day. With a purification instrument, an enhanced chip architecture, and downstream reporting, the Genexus System provides a convenient solution to enable oncology research. Here we highlight the oncology research applications and high-throughput NGS capabilities of the Genexus System with Oncomine Comprehensive Assay Plus (OCA Plus), an oncol
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5

Casuga, Iris, Frances Chan, Milton Huynh, et al. "Abstract 2944: Rapid and accurate variant calling of FFPE samples with the Genexus System." Cancer Research 82, no. 12_Supplement (2022): 2944. http://dx.doi.org/10.1158/1538-7445.am2022-2944.

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Abstract Next-Generation Sequencing technology has enhanced oncology research by enabling the detection of all cancer related variants into one assay for research and drug discovery programs. The Oncomine࣪ Comprehensive Assay v3, a pan-cancer panel, used with the Ion Torrent࣪ Genexus࣪ System allows for formalin-fixed paraffin embedded (FFPE) samples to be examined across 161 unique genes in an automated sample to result workflow in 30hrs. This study demonstrates ≥ 95% Sensitivity and PPV for detecting SNV, Indel, and Copy Number variants of clinical FFPE samples along with fusions. When tested
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Kreston, Sarah, Claire Gould, Kylie Blair, Leisa Jackson, Janice Riley, and Gary A. Pestano. "Abstract 5547: Evaluation of two clinically focused targeted NGS systems for liquid biopsy testing shows a high level of concordance in resulting actionable mutations." Cancer Research 83, no. 7_Supplement (2023): 5547. http://dx.doi.org/10.1158/1538-7445.am2023-5547.

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Abstract Introduction: The use of blood-based molecular diagnostics is increasingly becoming routine in clinical oncology practice. The purpose of this study was to evaluate variant resulting concordance for the four major somatic variant classes using two clinical next-generation sequencing (NGS) systems for conducting highly sensitive blood-based analyses. All donor specimens were de-identified remnants from patients previously diagnosed with advanced NSCLC. We utilized two independent panels, systems and bioinformatic pipelines that are focused on clinical testing for key actionable variant
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7

Lowman, Geoffrey Marc, Dinesh Cyanam, Emily Norris, et al. "Abstract 232: Fully automated comprehensive genomic profiling for detection of cancer variants, gene fusions, and complex oncology endpoints." Cancer Research 83, no. 7_Supplement (2023): 232. http://dx.doi.org/10.1158/1538-7445.am2023-232.

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Abstract Introduction: We present the comprehensive genomic profiling performance of the Ion Torrent Genexus system using the Oncomine Comprehensive Assay Plus (OCA Plus), a 500+ gene targeted AmpliSeq-based oncology research panel that evaluates DNA variants (including copy number alterations), RNA fusions, and key oncology research endpoints including tumor mutational burden (TMB), microsatellite instability (MSI), and homologous recombination repair deficiency (HRD) via characterization of genomic instability by the newly introduced Genomic Instability Metric (GIM). Methods: The Ion Torrent
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8

Low, Siew-Kee Kee, Ken Uchibori, Rie Hayashi, et al. "Evaluation of Genexus system that automates specimen-to-report for cancer genomic profiling within a day using liquid biopsy." Journal of Clinical Oncology 38, no. 15_suppl (2020): 3538. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.3538.

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3538 Background: Genomic profiling of patients’ tumors using NGS system help in facilitating molecular-guided therapy. The turnaround time from specimen to report by the NGS system is important to deliver result timely for clinical decisions. The Genexus Integrated Sequencer automates all steps of the targeted NGS workflow starting from nucleic acid of formalin-fixed paraffin-embedded tissues or plasma that significantly reduce laborious procedures. Importantly, the whole specimen-to-report workflow delivers results in a single day. In this study, we evaluated detection rate of alteration usin
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9

Schageman, Jeoffrey. "Oncomine Dx Express CE-IVD liquid biopsy assay for non-small cell lung cancer: Performance review and analytical validation." Journal of Clinical Oncology 41, no. 16_suppl (2023): e21218-e21218. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e21218.

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e21218 Background: Clinical diagnostics assays for oncology are becoming more readily available due to the advancement and democratization of Next-Generation Sequencing (NGS). Additionally, liquid biopsy can be used in NGS to detect genetic variants in circulating tumor DNA and RNA. Liquid biopsy is a less invasive option compared to traditional biopsy methods for early detection and continuous monitoring of cancer treatment outcomes. Here, we discuss screening of over 3,500 non-small cell lung cancer (NSCLC) samples, and the analytical validation of the Oncomine Dx Express Test (ODxET) and Ge
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10

Burke, Jennifer, Frances Chen, Jiajie Huang, Geoffrey Lowman, Timothy Looney, and Marina Sedova. "69 Automated TRB locus haplotype analysis by long-amplicon TCRB chain sequencing for potential immune-related adverse events biomarker research." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A75. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0069.

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BackgroundIdentifying potential predictive biomarkers for immune related adverse events (irAEs) following checkpoint blockade inhibition (CPI) remains an outstanding goal of immune-oncology translational research. Polymorphism with the T cell receptor variable gene (TRBV) has been proposed as a potential risk factor for irAEs owing to a potential link between TRBV polymorphism and chronic autoimmune disease. Efforts to interrogate the potential biomarker utility of TRBV polymorphism have been hampered by the repetitive nature of the TRB locus. Our research has demonstrated a method for inferri
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11

Jiwani, Shahanawaz, Jerald P. Radich, Maria Saeed, et al. "Rapid Clinical Mutation Screening for AML Using the Genexus Platform." Blood 142, Supplement 1 (2023): 2288. http://dx.doi.org/10.1182/blood-2023-188270.

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Introduction: The promise of “precision medicine” is using therapeutic agents matched to the inferred biology of a patient's particular disease. In acute myeloid leukemia this approach demands fast and accurate assessment of the mutation and cytogenetic landscape of each AML case. The NCI Myeloid Malignancies Molecular Analysis for Therapy Choice program (“myeloMATCH”) is a precision medicine clinical trial initiative across the NCI National Clinical Trials Network for patients with newly diagnosed acute myeloid leukemia and myelodysplasia. In myeloMATCH the goal is to have cytogenetic and mut
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De Luca, Caterina, Francesco Pepe, Gianluca Russo, et al. "Technical Validation of a Fully Integrated NGS Platform in the Real-World Practice of Italian Referral Institutions." Journal of Molecular Pathology 4, no. 4 (2023): 259–74. http://dx.doi.org/10.3390/jmp4040022.

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Aims: To date, precision medicine has played a pivotal role in the clinical administration of solid-tumor patients. In this scenario, a rapidly increasing number of predictive biomarkers have been approved in diagnostic practice or are currently being investigated in clinical trials. A pitfall in molecular testing is the diagnostic routine sample available to analyze predictive biomarkers; a scant tissue sample often represents the only diagnostical source of nucleic acids with which to conduct molecular analysis. At the sight of these critical issues, next-generation sequencing (NGS) platform
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13

Jasti, Madhuri, Swasti Raut, Diarra Hassell, et al. "Abstract 3671: Analytical performance of the Oncomine™ Dx Express Test, a CE-IVD NGS liquid biopsy assay for identification of clinically relevant variants." Cancer Research 84, no. 6_Supplement (2024): 3671. http://dx.doi.org/10.1158/1538-7445.am2024-3671.

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Abstract For in vitro Diagnostic use only. Not available in all regions including the United States. Introduction Minimally invasive blood-based liquid biopsy using cell-free total nucleic acid (cfTNA) and next generation sequencing (NGS) has substantially evolved in the field of clinical diagnostics for oncology, for detection of molecular therapeutic targets in non-small cell lung cancer (NSCLC). Here we describe analytical validation results for cfTNA using the CE-IVD Oncomine™ Dx Express Test (ODxET) assay, a qualitative in vitro diagnostic test that uses targeted NGS technology, the Ion T
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14

Dhawale, Tejaswini, Valentina Nardi, Charlotte Wang, et al. "Impact of Ultra Rapid Molecular Profiling on Treatment Delays and Healthcare Utilization of Patients Hospitalized for Acute Leukemia." Blood 144, Supplement 1 (2024): 5058. https://doi.org/10.1182/blood-2024-208059.

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Background Molecular testing is fundamental to treatment decisions in patients with acute leukemia. The impact of rapid molecular profiling on the timing of treatment initiation and healthcare utilization in patients hospitalized for suspected acute leukemia has not been described. Methods We conducted a retrospective chart review of patients hospitalized and treated for suspected acute leukemia at Massachusetts General Hospital between September 2023 and April 2024. We conducted a detailed workflow analysis comparing the time to obtaining molecular profiling results from admission [“time to r
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15

Matsumoto, Shingo, Takaya Ikeda, Kiyotaka Yoh, et al. "Impact of rapid multigene assays with short turnaround time (TAT) on the development of precision medicine for non-small cell lung cancer (NSCLC)." Journal of Clinical Oncology 39, no. 15_suppl (2021): 9094. http://dx.doi.org/10.1200/jco.2021.39.15_suppl.9094.

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9094 Background: A variety of oncogene drivers have been identified in NSCLC and molecularly-stratified precision medicine has led to improved survival in advanced NSCLC. Next-generation sequencing (NGS)-based testing is utilized to detect actionable gene alterations; however, the TAT of NGS is often too long to translate into clinical decision making. Thus, rapid multi-gene testing alternatives are needed. Methods: A lung cancer genomic screening project (LC-SCRUM-Asia) capturing clinical outcome was established in 2013 to identify patients with oncogene drivers and to support the development
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16

Siepert, Nicholas, Jeoffrey Schageman, Jian Gu, et al. "Abstract 5601: Oncomine™ dx express CE-IVD liquid biopsy assay for non-small cell lung cancer: Performance review and analytical validation." Cancer Research 83, no. 7_Supplement (2023): 5601. http://dx.doi.org/10.1158/1538-7445.am2023-5601.

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Abstract Introduction - Clinical diagnostics assays for oncology are becoming more readily available due to the advancement and democratization of Next-Generation Sequencing (NGS). Additionally, liquid biopsy can be used in NGS to detect genetic variants in circulating tumor DNA and RNA. Liquid biopsy is a less invasive option compared to traditional biopsy methods for early detection and continuous monitoring of cancer treatment outcomes. Here, we discuss screening of over 3,500 non-small cell lung cancer (NSCLC) samples, and the analytical validation of the Oncomine™ Dx Express Test (ODxET)
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17

Normanno, Nicola, José Carlos Machado, Edoardo Pescarmona, et al. "European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors." International Journal of Molecular Sciences 24, no. 18 (2023): 13788. http://dx.doi.org/10.3390/ijms241813788.

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Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal
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18

Sheffield, Brandon S., Andrea Beharry, Joanne Diep, et al. "Point of Care Molecular Testing: Community-Based Rapid Next-Generation Sequencing to Support Cancer Care." Current Oncology 29, no. 3 (2022): 1326–34. http://dx.doi.org/10.3390/curroncol29030113.

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Purpose: Biomarker data are critical to the delivery of precision cancer care. The average turnaround of next-generation sequencing (NGS) reports is over 2 weeks, and in-house availability is typically limited to academic centers. Lengthy turnaround times for biomarkers can adversely affect outcomes. Traditional workflows involve moving specimens through multiple facilities. This study evaluates the feasibility of rapid comprehensive NGS using the Genexus integrated sequencer and a novel streamlined workflow in a community setting. Methods: A retrospective chart review was performed to assess
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19

Eno, Celeste, Wenjuan Zhang, and Eric Vail. "27. Review and comparison of the Oncomine Myeloid Assay GX v2 on Genexus System." Cancer Genetics 268-269 (November 2022): 10. http://dx.doi.org/10.1016/j.cancergen.2022.10.030.

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20

Arjuna, Srividya, Mauli Shah, Antonio Dono, et al. "SDPS-44 RAPID DETECTION OF MUTATIONS IN CSF-CFTNA WITH THE GENEXUS INTEGRATED SEQUENCER." Neuro-Oncology Advances 5, Supplement_3 (2023): iii25. http://dx.doi.org/10.1093/noajnl/vdad070.098.

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Abstract Brain metastases commonly arise in patients with lung and breast carcinomas and pose distinctive clinical challenges. Genomic alterations are fundamental for diagnosis and therapy selection in cancer patients. However, the turn-around-time (TAT) of standard next generation sequencing (NGS) assays is a limiting factor in the timely delivery of genomic information for clinical decision making. The GenexusTM Sequencer automates the NGS workflow delivering results in less than 24hrs. The Oncomine Precision Assay (OPA) evaluates somatic mutations, copy number variations and fusions in hot-
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21

Echeverria, Delvis. "Tiempo de Respuestas y Experiencia de Usuario Estudio Experimental." Revista Latinoamericana de Ingenieria de Software 4, no. 5 (2016): 231. http://dx.doi.org/10.18294/relais.2016.231-234.

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La investigación está fundamentada por un estudio experimental, enfocado en la evaluación del comportamiento de los usuarios finales interactuando con tiempos de respuestas en <br />aplicaciones reales. Se tomará como base el aporte de los autores Doherty y Thadani, investigadores de IBM relacionado con los tiempos de respuestas, y las investigaciones de Jacob Nielsen. Se llevarán a cabo un test con usuarios finales, y se expondrán optimizaciones a través de del uso de herramientas que contribuirán a mejorar los tiempos de respuestas de las aplicaciones web. Todo esto engloba una primera
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22

Siepert, Nicholas, Emilia Ostrowska, Luming Qu He, et al. "Abstract 5030: Evaluation of different blood collection tubes for liquid biopsy NGS applications." Cancer Research 84, no. 6_Supplement (2024): 5030. http://dx.doi.org/10.1158/1538-7445.am2024-5030.

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Abstract Intro: Liquid biopsy is fast becoming a standard practice in oncology research due to recent advancements in Next Generation Sequencing (NGS). To detect genetic variants, whole blood samples are collected in blood collection tubes (BCTs) and fractionated to obtain plasma which is then used to isolate cell free nucleic acid (cfNA) for analysis. While the limited availability of cfNA is a challenge in liquid biopsy, storage condition and duration between blood collection and fractionation have a significant impact on the quantity and quality of the cfNA due to degradation and genomic DN
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Liu, Xiaowei, Kritika Krishnamurthy, and D. Yitzchak Goldstein. "P692: Impact of sample age on RNA sequencing metrics from FFPE tissues using ion torrent Genexus Integrated Sequencer." Genetics in Medicine Open 3 (2025): 103061. https://doi.org/10.1016/j.gimo.2025.103061.

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24

Buglioni, S., E. Gallo, C. Ercolani, et al. "Clinical Feasibility of NGS Liquid Biopsy Analysis in NSCLC Patients Using Oncomine Precision Assay with Genexus™ Integrated Sequencer." Journal of Liquid Biopsy 1 (November 2023): 100017. http://dx.doi.org/10.1016/j.jlb.2023.100017.

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25

Liu, Xiaowei, Kritika Krishnamurthy, and D. Yitzchak Goldstein. "P744: Comparative analysis of Ion Torrent sequencing platforms: Unveiling enhanced performance and precision with the Genexus integrated sequencer in clinical applications." Genetics in Medicine Open 2 (2024): 101648. http://dx.doi.org/10.1016/j.gimo.2024.101648.

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26

Ilié, Marius, Jonathan Benzaquen, Véronique Hofman, et al. "Accurate Detection of SARS-CoV-2 by Next-Generation Sequencing in Low Viral Load Specimens." International Journal of Molecular Sciences 24, no. 4 (2023): 3478. http://dx.doi.org/10.3390/ijms24043478.

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As new SARS-CoV-2 variants emerge, there is an urgent need to increase the efficiency and availability of viral genome sequencing, notably to detect the lineage in samples with a low viral load. SARS-CoV-2 genome next-generation sequencing (NGS) was performed retrospectively in a single center on 175 positive samples from individuals. An automated workflow used the Ion AmpliSeq SARS-CoV-2 Insight Research Assay on the Genexus Sequencer. All samples were collected in the metropolitan area of the city of Nice (France) over a period of 32 weeks (from 19 July 2021 to 11 February 2022). In total, 7
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27

Vivancos Sánchez, Catalina, María Isabel Esteban Rodríguez, Alberto Peláez García, et al. "Clinical Impact of a Next-Generation Sequencing Approach for Glioblastoma Patients." Cancers 17, no. 5 (2025): 744. https://doi.org/10.3390/cancers17050744.

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Objectives: The purpose of this study is to assess the clinical impact of next-generation sequencing (NGS), as an increasingly available and advantageous tool, for glioblastoma patients. Methods: Adult patients aged less than 65, and surgically treated for glioblastoma between 2010–2021, were included. Tumor samples were analyzed with NGS using the Oncomine Comprehensive v3 (OCA) panel and Ion Reporter Genexus v5.9.1 (Thermo Fisher Scientific). Results: Thirty-two patients were included, with a median age of 47.7 years and a median overall survival of 25 months. Identification of mutations by
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28

Andrew, Georgia M., Laura W. Dillon, Maria Saeed, et al. "Evaluation of a Rapid Automated Next Generation Sequencing Assay for Precision Medicine in Acute Myeloid Leukemia." Blood 138, Supplement 1 (2021): 4444. http://dx.doi.org/10.1182/blood-2021-148926.

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Abstract Background: In the last decade there have been significant advances in diagnosing and classifying adult acute myeloid leukemia (AML) based on genomic profiling, enabling risk-stratification and targeted therapies. In 2017 the US FDA approved the first gene mutation targeted therapies for AML with multiple additional targeted therapies since approved or in development. Given the typical acuity of AML at initial presentation however and the current turnaround time for next-generation sequencing (NGS) assays, most patients will start definitive initial therapy before all potentially targ
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Frady, Lauren, Desiree Unselt, John Pufky, Fernando Torres, Jennifer Sims, and Jennifer Mason. "Abstract 528: Automated liquid biopsy pan-cancer genomic profiling panel demonstrates utility for screening of targeted biomarkers." Cancer Research 82, no. 12_Supplement (2022): 528. http://dx.doi.org/10.1158/1538-7445.am2022-528.

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Abstract Background: Liquid biopsy testing has demonstrated the utility of capturing the heterogeneity of solid tumors and relevant actionable mutations using a less invasive sample collection method. The Genexus™ Integrated Sequencer provides a viable pathway to deploy an automated platform for a sensitive pan-cancer liquid biopsy assay to meet the needs of quick turn-around and cost effectiveness for multi-site implementation. The Oncomine™ Precision Assay GX (OPAGX) is an amplicon-based next-generation sequencing (NGS) assay that enables detection of biomarkers across 50 genes from both sol
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Unselt, Desiree, Lauren Frady, John Pufky, Fernando Torres, Jennifer Sims, and Jennifer Mason. "Abstract 2290: Quick turnaround NGS assay for the characterization of biomarkers in FFPE tissue." Cancer Research 82, no. 12_Supplement (2022): 2290. http://dx.doi.org/10.1158/1538-7445.am2022-2290.

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Abstract Background: Genomic profiling of a tumor to characterize clinically relevant variants has become critically important for cancer diagnosis and prognosis, as well as in driving therapeutic decision making. As such, there is a growing need for rapid inline assessment of somatic variants in genes of key interest in oncology. The Oncomine™ Precision Assay on the Ion Torrent Genexus Sequencer (OPAGX) is an amplicon-based automated next-generation sequencing (NGS) assay that enables quick turnaround genomic profiling of biomarkers across 50 genes from solid tissue. The complete workflow, in
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Heeke, Simon, Dzifa Duose, Srividya Arjuna, et al. "Abstract 3776: Association of baseline ctDNA EGFR mutation detection with clinical outcome in the phase II RAMOSE trial assessing ramucirumab plus osimertinib versus osimertinib in EGFR mutant non-small cell lung cancer." Cancer Research 85, no. 8_Supplement_1 (2025): 3776. https://doi.org/10.1158/1538-7445.am2025-3776.

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Abstract Background: While third-generation EGFR TKIs such as osimertinib have improved outcomes in EGFR-mutant non-small cell lung cancer (NSCLC), responses remain transient, and resistance develops often. We recently reported primary efficacy results from the phase II RAMOSE trial showing that the combination of osimertinib with the VEGFR2 antagonist ramucirumab improved progression-free survival (PFS) over osimertinib monotherapy (24.8 months [mo] vs 15.6 mo, HR 0.55 (95% CI, 0.32-0.93, p=0.023), establishing this regimen as a promising approach to improve clinical outcomes. However, biomar
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Guo, Fei, Yubo Lang, Guannan Long, et al. "Ion Torrent ™ Genexus ™ Integrated Sequencer and ForeNGS Analysis Software—An automatic NGS-STR workflow from DNA to profile for forensic science." Forensic Science International: Genetics 61 (November 2022): 102753. http://dx.doi.org/10.1016/j.fsigen.2022.102753.

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33

Pickle, Loni, Andrew Hatch, Gokhan Yavas, et al. "Abstract 4416: Rapid, low-input, targeted NGS workflow for DNA methylation." Cancer Research 84, no. 6_Supplement (2024): 4416. http://dx.doi.org/10.1158/1538-7445.am2024-4416.

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Abstract DNA methylation is a fundamental epigenetic process that regulates human gene expression. In cancer, methylation changes promote proliferation networks and metastasis. Development of biomarkers for methylation will be enabled by flexible, fast, low-input next generation sequencing workflows. We describe the first Ion AmpliSeq™ Methylation targeted panel and protocol on the turn-key Genexus™ Integrated Sequencer as part an ongoing collaboration with Ontario Institute for Cancer Research (OICR) to detect and predict response in early stage breast cancer and improve diagnostics for Black
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Huang, Jiajie, Haigang Gu, Janet Orton, et al. "Abstract 328: A comprehensive genomic profiling of myeloid malignancies demonstrates mutational spectrum of DNA variants, FLT3-ITDs, and gene fusions." Cancer Research 84, no. 6_Supplement (2024): 328. http://dx.doi.org/10.1158/1538-7445.am2024-328.

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Abstract Introduction: Myeloid malignancies encompass diverse hematopoietic disorders, including acute myeloid leukemia (AML), myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS), chronic myeloid leukemia (CML), chronic myelomonocytic leukemia (CMML), and juvenile myelomonocytic leukemia (JMML). We developed two assays to address the genetic complexity of myeloid malignancies, OncomineTM Myeloid Assay and OncomineTM Myeloid Assay GX v2, detecting mutations in 45 DNA genes and >30 fusion driver genes, including >700 fusion isoforms. Our panel includes genetic alter
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Ilié, Marius, Véronique Hofman, Christophe Bontoux, et al. "Setting Up an Ultra-Fast Next-Generation Sequencing Approach as Reflex Testing at Diagnosis of Non-Squamous Non-Small Cell Lung Cancer; Experience of a Single Center (LPCE, Nice, France)." Cancers 14, no. 9 (2022): 2258. http://dx.doi.org/10.3390/cancers14092258.

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The number of genomic alterations required for targeted therapy of non-squamous non-small cell lung cancer (NS-NSCLC) patients has increased and become more complex these last few years. These molecular abnormalities lead to treatment that provides improvement in overall survival for certain patients. However, these treated tumors inexorably develop mechanisms of resistance, some of which can be targeted with new therapies. The characterization of the genomic alterations needs to be performed in a short turnaround time (TAT), as indicated by the international guidelines. The origin of the tiss
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Gaal, Orsolya I., Andrei Ungureanu, Bogdan Pop, et al. "The Genomic Landscape of Romanian Non-Small Cell Lung Cancer Patients: The Insights from Routine NGS Testing with the Oncomine Dx Target Panel at the PATHOS Molecular Pathology Laboratory." Cancers 17, no. 12 (2025): 1947. https://doi.org/10.3390/cancers17121947.

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Background: Comprehensive molecular profiling is essential for precision oncology in non-small cell lung cancer (NSCLC). However, genomic data from Eastern European populations, including Romania, remain limited. Methods: We analyzed 398 consecutive NSCLC cases tested at the PATHOS Molecular Pathology Laboratory (Cluj-Napoca, Romania) between April 2024 and February 2025 using the Ion Torrent™ Genexus™ System and the Oncomine™ Dx Target Test, which evaluates SNVs/indels in 46 genes, fusions in 23 genes, and CNVs in 19 genes from FFPE samples. Results: The cohort was predominantly male (66%) wi
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Colac, Svetlana, Olga Burduniuc, and Mariana Apostol. "GENETIC SIGNIFICANCE AND TRACKING OF CIRCULATING SARS-COV-2 VARIANTS IN THE REPUBLIC OF MOLDOVA." Romanian Archives of Microbiology and Immunology 83, no. 3 (2024): 148–54. https://doi.org/10.54044/rami.2024.03.02.

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Tracking the circulating variants of the SARS-CoV-2 virus and identifying new genetic variations provide a high-resolution perspective with many advanced applications, ranging from developing diagnostic tests and vaccines to real-time data for public health measures. This study aimed to investigate and assess the genetic variants of SARS-CoV-2 circulating in the Republic of Moldova to improve COVID-19 response strategies. A retrospective descriptive study was carried out in the National Public Health Agency virology laboratory. The study analysed 417 biological samples collected from patients
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Nicholas, Champica, Andrea Beharry, Anna M. Bendzsak, et al. "Point of Care Liquid Biopsy for Cancer Treatment—Early Experience from a Community Center." Cancers 16, no. 14 (2024): 2505. http://dx.doi.org/10.3390/cancers16142505.

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Liquid biopsy is rapidly becoming an indispensable tool in the oncologist’s arsenal; however, this technique remains elusive in a publicly funded healthcare system, and real-world evidence is needed to demonstrate utility and feasibility. Here, we describe the first experience of an in-house point of care liquid biopsy program at a Canadian community hospital. A retrospective review of consecutive cases that underwent plasma-based next-generation sequencing (NGS) was conducted. Liquid biopsy was initiated at the discretion of clinicians. Sequencing followed a point of care workflow using the G
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Kropf, Jacqueline, Elim Kuo, Jorge Cusco, Jennifer Tseng, Amy Iarrobino Laughlin, and Wang L. Cheung. "Impact of tissue biomarker testing by in-house platform on result times in metastatic non-small cell lung cancer." JCO Oncology Practice 19, no. 11_suppl (2023): 49. http://dx.doi.org/10.1200/op.2023.19.11_suppl.49.

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49 Background: Biomarker testing for actionable mutations is standard of care for patients diagnosed with metastatic non-small cell, non-squamous cell lung cancer. However, testing via third-party laboratories can take weeks to result, leading to treatment decision delays identified at our own institution. Methods: We conducted a retrospective chart review of metastatic non-small cell, non-squamous cell lung cancer patients treated at Orlando Regional Medical Center before (6/1/2021-5/31/2022) as well as after (1/1/2023-5/31/2023) the initiation of in-house next generation sequencing (NGS) tis
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40

Huang, Ping, Chia Chou, and Ronghui Huang. "Seasonal Modulation of Tropical Intraseasonal Oscillations on Tropical Cyclone Geneses in the Western North Pacific." Journal of Climate 24, no. 24 (2011): 6339–52. http://dx.doi.org/10.1175/2011jcli4200.1.

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Abstract The seasonal modulation of tropical intraseasonal oscillation (TISO) on tropical cyclone (TC) geneses over the western North Pacific Ocean (WNP) is investigated in three periods of the WNP TC season: May–June (MJ), July–September (JAS), and October–December (OND). The modulation of the TISO–TC geneses over the WNP is strong in MJ, while it appears weaker in JAS and OND. In MJ, TISO propagates northward via two routes, the west route through the South China Sea and the east route through the WNP monsoon trough region, which are two clustering locations of TC geneses. TISO can synchrono
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Chen, Tsing-Chang, Jenq-Dar Tsay, Jun Matsumoto, and Jordan Alpert. "Impact of the Summer Monsoon Westerlies on the South China Sea Tropical Cyclone Genesis in May." Weather and Forecasting 32, no. 3 (2017): 925–47. http://dx.doi.org/10.1175/waf-d-16-0189.1.

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Abstract After the onset of the Southeast Asian summer monsoon in mid-May, the South China Sea (SCS) trough is deepened by the intensified monsoon westerlies to facilitate the development of a synoptic cyclonic shear flow. This shear flow forms an environment favorable for the SCS tropical storm (TS)/typhoon (TY) genesis triggered by the surge of this monsoon circulation. This genesis mechanism has not been well documented. Seventeen named SCS TS/TY geneses in May over 1979–2016 occurred under the following environmental conditions/processes: 1) with its maximum located south of 15°N, the inte
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42

Raskin, William, Parneet Cheema, Kirstin Perdrizet, Marco Iafolla, Shaan Dudani, and Brandon Sheffield. "Rapid point of care NGS in colorectal cancer." Journal of Clinical Oncology 40, no. 4_suppl (2022): 172. http://dx.doi.org/10.1200/jco.2022.40.4_suppl.172.

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172 Background: Next generation sequencing (NGS) is the laboratory cornerstone of precision oncology treatment. In advanced colorectal cancer (CRC), current guidelines recommend testing RAS, BRAF and MMR biomarkers as standard of care. The added value of comprehensive genomic profiling is so far unclear. Traditional NGS operations are complicated, requiring specialized equipment and personnel. In many jurisdictions, cancer patients are treated in publicly-funded community hospitals, where NGS is not typically utilized and access to testing via send-out services is associated with lengthy turna
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43

Chen, Guanghua, and Chia Chou. "Joint Contribution of Multiple Equatorial Waves to Tropical Cyclogenesis over the Western North Pacific." Monthly Weather Review 142, no. 1 (2014): 79–93. http://dx.doi.org/10.1175/mwr-d-13-00207.1.

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Abstract A composite study is performed to examine the differences in equatorial wave behaviors and large-scale background patterns during tropical cyclone (TC) genesis. After removing TC contamination, Madden–Julian oscillation (MJO), equatorial Rossby (ER) wave, mixed Rossby–gravity (MRG) wave, and tropical depression (TD)-type disturbance (jointly referred to as the MT wave) are quantified to evaluate the attribution of TC geneses. Given that TC geneses are attributed to a single wave or multiple waves, the eight categories are specified based on the moderate thresholds. The TC geneses rela
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Pérez-Alarcón, Albenis, Rogert Sorí, José Carlos Fernández-Alvarez, Raquel Nieto, and Luis Gimeno. "Moisture Sources for Tropical Cyclones Genesis in the Coast of West Africa through a Lagrangian Approach." Environmental Sciences Proceedings 4, no. 1 (2020): 3. http://dx.doi.org/10.3390/ecas2020-08126.

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Atmospheric moisture transport plays an important role in the genesis of tropical cyclones (TCs). In this study, the moisture sources associated with the genesis of TCs in the tropical Atlantic Ocean near West Africa, from June to November in the period 1980–2018, were identified. To detect the location of the TCs geneses, the HURDAT2 database from the National Hurricane Center was used. Additionally, global outputs of the Lagrangian FLEXPART model were used to determine the moisture sources that provided water vapor for the genesis of TCs. This model permitted us to track backward in time the
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45

D’Agnano, Vito, Fabio Perrotta, Giulia Maria Stella, et al. "Molecular Diagnostic Yield and Safety Profile of Ultrasound-Guided Lung Biopsies: A Cross-Sectional Study." Cancers 16, no. 16 (2024): 2860. http://dx.doi.org/10.3390/cancers16162860.

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Background: The recent advances in precision oncology for lung cancer treatment has focused attention on the importance of obtaining appropriate specimens for tissue diagnosis as well as comprehensive molecular profiling. CT scan-guided biopsies and bronchoscopy are currently the main procedures employed for tissue sampling. However, growing evidence suggests that ultrasound-guided biopsies may represent an effective as well as safe approach in this diagnostic area. This study explores the safety and the diagnostic yield for cancer molecular profiling in ultrasound-guided percutaneous lung les
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Chen, Tsing-Chang, Jenq-Dar Tsay, and Ming-Chang Yen. "Genesis and Development of Spring Rainstorms in Northern Southeast Asia: Southwest China–Northern Indochina and the Northern South China Sea." Monthly Weather Review 145, no. 12 (2017): 4949–76. http://dx.doi.org/10.1175/mwr-d-17-0059.1.

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During May and June, the monsoon rainfall in northern Southeast Asia is primarily produced by rainstorms. At the mature stage, these storms, coupled with a midtropospheric subsynoptic-scale trough, produce rainfall ≥50 mm (6 h)−1and exhibit a cyclonic surface vortex. With a scale ~ O(102) km, rainstorms during the period of 1979–2016 are identified with station and satellite observations, along with assimilation data. Several dynamic processes of rainstorm geneses are disclosed by an extensive analysis. 1) Maximum occurrence of rainstorm geneses is located in the midtroposphere of two regions
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Sarda, Shrutii, David Merrill, Heesun Shin, et al. "680 Automated Ion torrent based solution enables accurate gut microbiome quantification of bacterial species relevant to research in cancer and its response to immunotherapy." Journal for ImmunoTherapy of Cancer 8, Suppl 3 (2020): A719. http://dx.doi.org/10.1136/jitc-2020-sitc2020.0680.

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BackgroundA low-cost targeted solution to profiling gut microbial diversity is sequencing of the 16S rRNA gene; however, it is often insufficient to gain species level resolution due to high homology across different bacteria. Therefore, we developed a first-of-its-kind targeted sequencing solution that supplements 16S gene targets, with highly species-specific primers for a cohort of 73 bacteria associated with research in diabetes, cancer and its response to immunotherapy, gastrointestinal and auto-immune disorders. This assay performs at 100% sensitivity and specificity for the species-leve
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48

Rappenglück, Michael A. "Natural Iron Silicides: A Systematic Review." Minerals 12, no. 2 (2022): 188. http://dx.doi.org/10.3390/min12020188.

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This review systematically presents all finds of geogenic, impact-induced, and extraterrestrial iron silicide minerals known at the end of 2021. The respective morphological characteristics, composition, proven or reasonably suspected genesis, and possible correlations of different geneses are listed and supported by the available literature (2021). Artificially produced iron silicides are only dealt with insofar as the question of differentiation from natural minerals is concerned, especially regarding dating to pre-industrial and pretechnogenic times.
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JASTI, MADHU, Sergio Hernandez, Nick Siepert, et al. "Abstract 5018: Evaluation of whole blood fractionation conditions for optimal liquid biopsy NGS applications." Cancer Research 84, no. 6_Supplement (2024): 5018. http://dx.doi.org/10.1158/1538-7445.am2024-5018.

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Abstract “For research use only. Not for diagnostic procedures.” Introduction: Liquid biopsy is a non-invasive alternative to tissue biopsies for cancer profiling using cell-free total nucleic acids (cfTNA; including cell free DNA (cfDNA) and cell free RNA (cfRNA)), the biological analytes derived from tumor cells floating in blood. However, it is crucial to optimize the whole blood fractionation workflows, since limited access to a suitable centrifuge at blood collection sites poses a challenge to this critical fractionation step, causing delays in processing the blood, leading to decreased s
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50

O Reilly, Mary, Bruce Moran, Kieran Sheahan, et al. "Oncomine panel testing in the clinical management of colorectal cancer: An Irish experience." Journal of Clinical Oncology 43, no. 4_suppl (2025): 212. https://doi.org/10.1200/jco.2025.43.4_suppl.212.

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212 Background: Early onset colorectal cancer (EOCRC) is defined as colorectal cancer (CRC) in those under the age of 50. It has been hypothesized that the molecular signatures of EOCRC could differ from those of late onset CRC (LOCRC). Next Generation Sequencing (NGS) using the Oncomine Precision Assay is a useful tool to guide treatment decisions based on the presence or absence of oncogene drivers. While not all of these mutations currently influence the clinical management of CRC patients, ongoing research on the function of these genes and the development of new drugs could offer insights
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