Article
Immunology
Ferhat Guzel, Micol Romano, Erdi Keles, David Piskin, Seza Ozen, Hakan Poyrazoglu, Ozgur Kasapcopur, Erkan Demirkaya
Summary: This study describes the development and validation of an NGS-based multiplex array for targeted sequencing of nine genes associated with common AIDs, offering a cost-effective, comprehensive, and informative screening tool compared to other methods.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Oncology
Russell J. Diefenbach, Jenny H. Lee, Ashleigh Stewart, Alexander M. Menzies, Matteo S. Carlino, Robyn P. M. Saw, Jonathan R. Stretch, Georgina V. Long, Richard A. Scolyer, Helen Rizos
Summary: This study developed a custom panel for detecting TERT promoter mutations in ctDNA from melanoma patients. Analysis of patient samples showed a high detection rate for BRAF, NRAS, and TERT promoter mutations, and the panel demonstrated consistency with tissue biopsies.
FRONTIERS IN ONCOLOGY
(2022)
Article
Gastroenterology & Hepatology
Si-Yu He, Ying-Chun Li, Yong Wang, Hai-Lin Peng, Cheng-Lin Zhou, Chuan-Meng Zhang, Sheng-Lan Chen, Jian-Feng Yin, Mei Lin
Summary: This study used NGS to sequence stool DNA from CRC patients, screened specific genes or gene combinations suitable for diagnosis and prognostic prediction of CRC, and comprehensively evaluated their significance in diagnosing CRC and predicting patients' prognosis. The results of the study showed that TP53 and KRAS genes can be used for CRC screening, diagnosis, and prognostic prediction, and combined testing can improve the detection rate of CRC. Furthermore, new mutation sites were found that require further research to determine their clinical significance.
WORLD JOURNAL OF GASTROENTEROLOGY
(2022)
Article
Oncology
Hongsen Li, Liu Gong, Huanqing Cheng, Huina Wang, Xiaochen Zhang, Chuangzhou Rao, Zhangfa Song, Da Wang, Haizhou Lou, Feng Lou, Shanbo Cao, Hongming Pan, Yong Fang
Summary: This study investigated the molecular characterization of colorectal cancer with situs inversus totalis (SCRC), a rare condition. The results showed significant differences in mutated genes and mutational profiles between SCRC and non-SCRC patients. These findings contribute to personalized therapy and improved clinical management of SCRC patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Tonje Bjornetro, Paula A. A. Bousquet, Kathrine Roe Redalen, Anne-Marie Siebke Troseid, Torben Luders, Espen Stang, Adriana M. M. Sanabria, Christin Johansen, Anniken Jorlo Fuglestad, Christian Kersten, Sebastian Meltzer, Anne Hansen Ree
Summary: Recent studies have found that the entire mitochondrial genome can be secreted in extracellular vesicles (EVs), but the biological characteristics of this cell-free mitochondrial DNA (mtDNA) are not well understood. In this study, the mtDNA derived from plasma EVs of colorectal cancer patients was compared to that of whole blood, peripheral blood mononuclear cells, and tumor tissue. The results showed that EV mtDNA had more variants and low-level heteroplasmy compared to whole blood mtDNA. The EV mtDNA variants were mainly located in the coding regions and had a higher proportion of missense mutations compared to whole blood and tumor tissue.
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
Article
Biochemistry & Molecular Biology
Tao Zhou, Shidong Zhou, Yong Chen, Jun Wang, Ruina Zhang, Huan Xiang, Zihao Xia, Mengnan An, Xiuxiang Zhao, Yuanhua Wu
Summary: This study identified major plant viruses affecting cigar and flue-cured tobacco in Sichuan through deep sequencing and molecular techniques, and developed a fast detection method for these viruses.
MOLECULAR BIOLOGY REPORTS
(2022)
Article
Cell Biology
Marie-Delphine Lanic, Rene Guerin, Michel Wassef, Pauline Durdilly, Vinciane Rainville, Vincent Sater, Fabrice Jardin, Philippe Ruminy, Valerie Costes-Martineau, Marick Lae
Summary: A new targeted multiplexed next-generation sequencing method has been developed to accurately and rapidly detect gene fusions in salivary gland and sinonasal tumors. The method has been validated in 180 cases and shown to be consistent with conventional techniques, demonstrating its potential application in clinical settings.
Article
Microbiology
Michael T. Pyne, Keith E. Simmon, Melanie A. Mallory, Weston C. Hymas, Jeffery Stevenson, Adam P. Barker, David R. Hillyard
Summary: HIV-1 antiretroviral therapy management requires sequencing of different portions of the HIV-1 pol gene. Traditional Sanger sequencing has limited ability to detect minor variants. Next generation sequencing enables detection of variants at frequencies as low as 1%, allowing for earlier detection of resistance. However, implementation of NGS in the clinical laboratory is hindered by complicated design and analysis.
JOURNAL OF CLINICAL MICROBIOLOGY
(2022)
Article
Immunology
William F. Wright, Patricia J. Simner, Karen C. Carroll, Paul G. Auwaerter
Summary: Despite the continued prevalence of infectious diseases as the main cause of fever of unknown origin, advancements in molecular technologies offer hope in transforming the investigation of this condition by potentially replacing traditional microbial identification methods.
CLINICAL INFECTIOUS DISEASES
(2022)
Article
Medicine, General & Internal
Weibi Chen, Yingfeng Wu, Yan Zhang
Summary: This study demonstrates that mNGS combined with mPCR can be an effective method for the etiological diagnosis and clinical surveillance of HSV-1 encephalitis.
FRONTIERS IN MEDICINE
(2022)
Article
Oncology
Chul Seung Lee, Hoon Seok Kim, Jeoffrey Schageman, In Kyu Lee, Myungshin Kim, Yonggoo Kim
Summary: Circulating tumor DNA (ctDNA) is a minimally invasive biomarker that can be analyzed using next-generation sequencing (NGS) to evaluate its clinical and analytical performance in colorectal cancer (CRC) patients. Postoperative ctDNA detection can serve as a valuable marker for identifying the risk of recurrence or persistent tumor lesions in patients with CRC.
Letter
Oncology
Steven Olsen, Yoshiaki Nakamura
Summary: A comprehensive genomic profiling (CGP) using plasma-based next-generation sequencing was conducted in a real-world database of metastatic colorectal cancer (mCRC) in the United States. The study revealed potentially actionable genomic profiles for approximately one-third of the patients, and around 60% of all tested patients received treatment consistent with the CGP results in each line of treatment. These findings suggest the potential role of CGP prior to multiple lines of mCRC treatment.
Review
Oncology
Salma Abbes, Simone Baldi, Hayet Sellami, Amedeo Amedei, Leila Keskes
Summary: Colorectal cancer (CRC) is the third most common malignancy and second most deadly cancer worldwide, with a higher incidence in developed countries. It is a heterogeneous genomic disease with various alterations contributing to its development. Previous screening efforts for CRC have been limited by performance issues and low penetrance of standard screening tools, but the advent of next-generation sequencing (NGS) has revolutionized the identification of novel genomic CRC characteristics and understanding of its carcinogenesis. This review focuses on the diagnostic tools used for CRC screening, with an emphasis on recent NGS approaches and their role in identifying clinically actionable targets for personalized medicine.
WORLD JOURNAL OF GASTROINTESTINAL ONCOLOGY
(2023)
Review
Oncology
Youngjun Park, Dominik Heider, Anne-Christin Hauschild
Summary: In recent years, advancements in next-generation sequencing and artificial intelligence have led to the development of various algorithms and applications. Integrating systems biology and machine learning has been crucial in addressing challenges posed by big data. Machine learning algorithms and network-based models play a key role in analyzing NGS data effectively.
Article
Health Policy & Services
Catherine D. Darker, Martina Mullin, Louise Doyle, Michelle Tanner, David McGrath, Lena Doherty, Katrin Dreyer-Gibney, Emer M. Barrett, Deirdre Flynn, Patricia Murphy, Jo-Hanna H. Ivers, Eilish Burke, Michele Ryan, Mary McCarron, Paula Murphy, Orla Sheils, David Hevey, Aisling Leen, Leah Keogh, Breda Walls, Annemarie E. Bennett, Freja Petersen, Ann Nolan, Joe M. Barry
Summary: This article introduces the 'Healthy Trinity' initiative at Trinity College Dublin, aiming to promote the health and wellbeing of staff and students through a multi-faceted approach and collaborative efforts. The initiative achieved some successes and encountered challenges by focusing on both individual and organizational responsibility.
HEALTH PROMOTION INTERNATIONAL
(2023)
Letter
Surgery
Corrado Pedrazzani, Cristian Conti, Angelo Di Vittori, Giulia Turri, Laura Bernardoni, Andrea Mafficini, Claudio Luchini, Armando Gabbrielli, Aldo Scarpa, Alfredo Guglielmi
ASIAN JOURNAL OF SURGERY
(2023)
Article
Oncology
Marie Auvray Kuentz, Helene Blons, Anne Paule Gimenez-Roqueplo, Just Pierre-Alexandre, Pierre Laurent-Puig, Arnaud Mejean, Stephane Oudard, Virginie Verkarre
Summary: This study identified a new VCP::TFE3 fusion gene caused by a t(X;9)(p11.23;p13.3) translocation through whole transcriptome sequencing. The patient showed typical morphological features of TFE3-rearranged RCC and demonstrated positive TFE3 immunostaining and break-apart fluorescence in situ hybridization. The patient received surgery and five lines of therapy, including 24 months of stable disease with the MET inhibitor cabozantinib, resulting in an overall survival of 7 years. Besides expanding the spectrum of TFE3 rearrangement partners, this study emphasizes the complexity of these tumors and supports the development of translational programs in renal cancer.
GENES CHROMOSOMES & CANCER
(2023)
Article
Neurosciences
Karen M. Ryan, Paul Smyth, Gordon Blackshields, Laura Kranaster, Alexander Sartorius, Orla Sheils, Declan M. McLoughlin
Summary: MiRNA expression changes in the hippocampus were examined using next-generation sequencing technology during electroconvulsive stimulation in rats. Six miRNAs were found to be significantly differentially expressed, and some of these miRNAs were also altered in patients with depression receiving medication treatment. These findings may provide insights into the mechanism of action of electroconvulsive therapy and the neurobiology of depression.
MOLECULAR NEUROBIOLOGY
(2023)
Article
Pathology
Riziero Esposito Abate, Melanie H. Cheetham, Jennifer A. Fairley, Raffaella Pasquale, Alessandra Sacco, Wolstenholme Nicola, Zandra C. Deans, Simon J. Patton, Nicola Normanno
Summary: Tumor mutational burden (TMB) is an agnostic biomarker for immune checkpoint inhibitors, but its testing methods are not standardized. A pilot external quality assessment (EQA) scheme validated the materials and procedures for TMB testing and found significant variability in the results.
Article
Medicine, Research & Experimental
Simon Garinet, Audrey Didelot, Laetitia Marisa, Guillaume Beinse, Marine Sroussi, Francoise Le Pimpec-Barthes, Elizabeth Fabre, Laure Gibault, Pierre Laurent-Puig, Sophie Mouillet-Richard, Antoine Legras, Helene Blons
Summary: We identified a miR-200 based RNA signature that can distinguish the heterogeneity of Epithelial-to-mesenchymal transition (EMT) and predict the survival of lung adenocarcinoma patients. This signature can stratify patients into high- and low-risk groups independently of tumor stage for prognostic evaluation.
JOURNAL OF TRANSLATIONAL MEDICINE
(2023)
Article
Cell Biology
Julia Kaellberg, Alexandra Harrison, Valerie March, Santa Berzina, Ivan Nemazanyy, Oliver Kepp, Guido Kroemer, Sophie Mouillet-Richard, Pierre Laurent-Puig, Valerie Taly, Wenjin Xiao
Summary: The high mortality rate in colorectal cancer (CRC) is mainly due to drug resistance caused by intratumor heterogeneity (ITH). This study investigated the interaction between different molecular subtypes of CRC cells and found that coculturing CMS1 and CMS4 cells increased their resistance to the chemotherapeutic agent 5-fluorouracil (5-FU) and promoted cellular invasion. The secretome of CMS1 cells played a protective role for CMS4 cells against 5-FU treatment and mediated the transfer of metabolites between CMS1 and CMS4 cells.
CELL DEATH & DISEASE
(2023)
Review
Oncology
Ana Regina de Abreu, Ken Op de Beeck, Pierre Laurent-Puig, Valerie Taly, Leonor Benhaim
Summary: Currently available methods for detecting colorectal cancer (CRC) at an early stage and monitoring its progression during treatment are not always sensitive and specific enough. Circulating tumor DNA (ctDNA) has the potential to address this issue and personalize treatment for each patient at every stage of the disease. This review article provides an up-to-date overview of the clinical use and future directions of ctDNA in CRC management.
Review
Oncology
Nicolo Caldonazzi, Paola Chiara Rizzo, Albino Eccher, Ilaria Girolami, Giuseppe Nicolo Fanelli, Antonio Giuseppe Naccarato, Giuseppina Bonizzi, Nicola Fusco, Giulia d'Amati, Aldo Scarpa, Liron Pantanowitz, Stefano Marletta
Summary: The assessment of lymph node metastases is important in cancer staging and prognosis. By applying artificial intelligence to whole slide images, the automatic detection of metastatic cells can be achieved, leading to increased diagnostic quality. This study reviews the literature on using AI for the assessment of metastases in lymph nodes in whole slide images.
Review
Oncology
Anastasios Gkountakos, Filippo M. M. Martelli, Nicola Silvestris, Michele Bevere, Mario De Bellis, Laura Alaimo, Elena Sapuppo, Francesca Masetto, Aldo Mombello, Michele Simbolo, Elena Bariani, Michele Milella, Matteo Fassan, Aldo Scarpa, Claudio Luchini
Summary: Pancreatic ductal adenocarcinoma (PDAC) and distal cholangiocarcinoma (dCCA) are aggressive tumors with limited treatment options. They share histomolecular features, making differential diagnosis challenging, but also have significant differences with clinical implications. PDAC and dCCA have different prognosis and oncogenic targets, highlighting the importance of accurate diagnosis and targeted treatments.
Review
Oncology
Albrecht Stenzinger, Arndt Vogel, Ulrich Lehmann, Angela Lamarca, Paul Hofman, Luigi Terracciano, Nicola Normanno
Summary: Cholangiocarcinomas are a heterogeneous group of tumors with distinct genomic alterations. Next-generation sequencing is a powerful tool for identifying gene variants and guiding personalized treatment for patients with cholangiocarcinomas. Understanding the use of NGS in molecular profiling is crucial for healthcare professionals to optimize treatment outcomes.
CANCER TREATMENT REVIEWS
(2024)
Article
Oncology
Nicola Normanno, Antonella De Luca, Riziero Esposito Abate, Alessandro Morabito, Michele Milella, Fabrizio Tabbo, Giuseppe Curigliano, Cristina Masini, Paolo Marchetti, Giancarlo Pruneri, Valentina Guarneri, Giovanni L. Frassineti, Gianpiero Fasola, Vincenzo Adamo, Bruno Daniele, Rossana Berardi, Florinda Feroce, Evaristo Maiello, Carmine Pinto
Summary: The Italian Register of Actionable Mutations is a multicentric observational study that collects next-generation sequencing data of patients with advanced solid tumors. The study identifies the rate of actionable mutations and highlights the utility of comprehensive genomic profiling in selected cancer patients.
EUROPEAN JOURNAL OF CANCER
(2023)
Article
Oncology
Maximiliano Gelli, Christophe Desterke, Mohamed Amine Bani, Valerie Boige, Charles Ferte, Peggy Dartigues, Bastien Job, Geraldine Perkins, Pierre Laurent-Puig, Diane Goere, Jacques R. R. Mathieu, Jerome Cartry, Michel Ducreux, Fanny Jaulin
Summary: This study aims to elucidate the primary tumor transcriptomic signatures associated with distinct metastatic routes in colorectal cancer (CRC). By analyzing the transcriptomic mRNA sequencing, gene set enrichment analyses and immunohistochemistry of primary tumor specimens, we identified a 61-gene signature that distinguishes between liver and peritoneal metastatic routes. The application of this transcriptomic signature could potentially identify new therapeutic targets for stage IV CRC and contribute to individualized follow-up programs in stage II-III CRC.
Review
Biochemistry & Molecular Biology
Federica Danzi, Raffaella Pacchiana, Andrea Mafficini, Maria T. Scupoli, Aldo Scarpa, Massimo Donadelli, Alessandra Fiore
Summary: Tumour cells possess the ability to reprogram their metabolism in order to support tumor growth, progression, and resistance. This reprogramming involves significant changes in bioenergetic, biosynthetic, and redox status to meet the increased energetic demands of the cells. Recent advancements in biochemical technologies, such as metabolomics and fluxomics, have provided researchers with powerful tools to study cancer metabolism and gain a better understanding of its complex activities on both qualitative and mechanistic levels. Additionally, the development of single-cell analysis technologies and functional genomic screening have further enhanced our ability to investigate cancer biology, identify biomarkers, and discover new therapeutic targets and treatment strategies.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2023)