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
Yiping Liu, Hanlin Chen, Hua Bao, Jinfeng Zhang, Runda Wu, Lingjun Zhu
Summary: This study identified FBXW7 alterations in colorectal cancer patients and found that these mutations were associated with higher tumor mutation burden, microsatellite instability, and lower chromosomal instability scores. Patients with FBXW7 mutations showed better overall survival, but those with the R465C mutation had worse overall survival compared to other FBXW7 mutations and to all other patients. In patients with microsatellite instability, the FBXW7 mutated group showed higher rates of M1 macrophage, CD8+ T cell, and regulatory T cell infiltration, as well as enrichment of multiple immune-related gene sets.
FRONTIERS IN ONCOLOGY
(2023)
Article
Oncology
Arnaud Bayle, Debora Basile, Simon Garinet, Bastien Rance, Pierre Laurent-Puig, Helene Blons, Julien Taieb, Geraldine Perkins
Summary: This study evaluated the role of NGS targeted panels in digestive oncology, showing that it allows for an exhaustive search for molecular abnormalities and provides patients with more opportunities for targeted therapies. Regular updates and further studies are needed for better analysis of prognostic factors.
Article
Chemistry, Analytical
Chu Cheng, Zhongjie Fei, Pengfeng Xiao, Huan Huang, Guohua Zhou, Zuhong Lu
Summary: The ability to accurately identify SNPs or low-abundance mutations is crucial for early disease diagnosis, but current high-throughput sequencing platforms have limitations in accuracy. A correctable decoding sequencing strategy is proposed, based on adding a mixture of natural nucleotide and cyclic reversible termination (CRT) for cyclic sequencing. This strategy demonstrates high feasibility and efficiency, with an error rate lower than Sanger sequencing. It also allows for the detection of known mutation sites using information from a single sequencing run.
Article
Oncology
Simona Bruzas, Sherko Kuemmel, Hakima Harrach, Elisabeth Breit, Beyhan Ataseven, Alexander Traut, Anna Rueland, Athina Kostara, Ouafaa Chiari, Christine Dittmer-Grabowski, Mattea Reinisch
Summary: NGS-matched treatment improved clinical outcomes in a subset of metastatic breast cancer patients, with some showing increased survival periods after receiving targeted therapy.
Article
Oncology
Sara Lahoz, Adela Rodriguez, Laia Fernandez, Teresa Gorria, Reinaldo Moreno, Francis Esposito, Helena Oliveres, Santiago Albiol, Tamara Sauri, David Pesantez, Gisela Riu, Miriam Cuatrecasas, Pedro Jares, Leire Pedrosa, Estela Pineda, Antonio Postigo, Antoni Castells, Aleix Prat, Joan Maurel, Jordi Camps
Summary: The mutational status of certain genes can be useful for improving therapeutic decision making and clinical management of cancer patients. This study investigates the prognostic and predictive value of actionable mutated genes in metastatic colorectal cancer (mCRC). Through targeted gene sequencing, SMAD4 and FBXW7 mutations were identified as negative prognostic markers in TP53-driven tumors, improving the ability to discriminate high-risk patients. This information can provide a molecular rationale for prognostic stratification and personalized treatment in mCRC patients.
Article
Pharmacology & Pharmacy
Samuel D. Chorlton, Gordon Ritchie, Tanya Lawson, Elizabeth McLachlan, Marc G. Romney, Nancy Matic, Christopher F. Lowe
Summary: A next-generation sequencing (NGS) assay was developed for CMV antiviral drug resistance (AVDR) testing, which using MinION technology detected additional mutations compared to traditional Sanger sequencing. Through the application of an online bioinformatics pipeline, barriers associated with MinION and NGS in clinical laboratories were eliminated.
ANTIVIRAL RESEARCH
(2021)
Article
Genetics & Heredity
Anita Sveen, Bjarne Johannessen, Ina A. Eilertsen, Bard Rosok, Marie Gulla, Peter W. Eide, Jarle Bruun, Kushtrim Kryeziu, Leonardo A. Meza-Zepeda, Ola Myklebost, Bjorn A. Bjornbeth, Rolf Skotheim, Arild Nesbakken, Ragnhild A. Lothe
Summary: Only a subset of mutations in microsatellite stable colorectal cancers were expressed, and the expressed mutation dose may provide an opportunity for more fine-tuned biomarker interpretations.
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
Biochemistry & Molecular Biology
Pasquale Tripodi
Summary: This review examines the application of genomic technologies in studying the diversity of tomatoes, with a focus on next-generation sequencing strategies and methods. It also discusses how genomics has provided insights into the domestication process of tomatoes and presents perspectives on utilizing natural variation for breeding purposes through pan-genome construction and graphical pan-genome development.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Medicine, Research & Experimental
Lee-Moay Lim, Wen-Yu Chung, Daw-Yang Hwang, Chih-Chuan Yu, Hung-Lung Ke, Peir-In Liang, Ting-Wei Lin, Siao Muk Cheng, A-Mei Huang, Hung-Tien Kuo
Summary: This study compares the genetic alterations in urothelial carcinoma (UC) developed after kidney transplantation (UCKT) and in UC in patients on hemodialysis (UCHD). Specific gene mutations were found in UCKT, potentially contributing to the understanding of the molecular pathogenesis of urothelial carcinoma.
JOURNAL OF TRANSLATIONAL MEDICINE
(2022)
Article
Oncology
Hee Young Na, Jeong Hwan Park, Sun Ah Shin, Sejoon Lee, Heonyi Lee, Heejoon Chae, HoKyung Choung, Namju Kim, Jin-Haeng Chung, Ji Eun Kim
Summary: This study investigated genetic alterations in ocular and extraocular sebaceous carcinoma in Korean patients, revealing distinct genetic differences between the two types of tumors and identifying important prognostic molecular markers. Mutations in potentially actionable genes were noted, suggesting consideration of clinical trials in intractable cases.
Article
Oncology
Carlotta Antoniotti, W. Michael Korn, Federica Marmorino, Daniele Rossini, Sara Lonardi, Gianluca Masi, Giovanni Randon, Veronica Conca, Alessandra Boccaccino, Gianluca Tomasello, Alessandro Passardi, Jeff Swensen, Clara Ugolini, Matthew Oberley, Emiliano Tamburini, Mariaelena Casagrande, Valeriy Domenyuk, Gabriella Fontanini, Mirella Giordano, Jim Abraham, David Spetzler, Alfredo Falcone, Heinz-Josef Lenz, Chiara Cremolini
Summary: This study conducted comprehensive genomic profiling of tumour samples from metastatic colorectal cancer patients, revealing a strong association between high TMB and MSI-H, and suggested an optimal threshold of 17 mut/Mb for predicting MSI status. Additionally, actionable mutations were identified in 21% of the patients.
EUROPEAN JOURNAL OF CANCER
(2021)
Article
Oncology
Juan A. Santamaria-Barria, Chikako Matsuba, Adam Khader, Anthony J. Scholar, Mary Garland-Kledzik, Trevan D. Fischer, Richard Essner, Matthew P. Salomon, Joshua M. V. Mammen, Melanie Goldfarb
Summary: This study analyzed melanoma samples and identified age-related mutational differences, as well as potential targetable mutations for personalized therapies.
JOURNAL OF SURGICAL ONCOLOGY
(2023)
Article
Urology & Nephrology
Matthew P. Deek, Kim Van der Eecken, Ryan Phillips, Neil R. Parikh, Pedro Isaacsson Velho, Tamara L. Lotan, Amar U. Kishan, Tobias Maurer, Paul C. Boutros, Christopher Hovens, Matthew Abramowtiz, Alan Pollack, Neil Desai, Bradley Stish, Felix Y. Feng, Mario Eisenberger, Michael Carducci, Kenneth J. Pienta, Mark Markowski, Channing J. Paller, Emmanuel S. Antonarakis, Alejandro Berlin, Piet Ost, Phuoc T. Tran
Summary: Somatic mutational profiles across the spectrum of metastatic castration-sensitive prostate cancer reveal associations between TP53 mutations and clinical outcomes in patients with oligometastasis, indicating a potential biological definition of oligometastasis beyond numerical classifications. Mutation analysis in TP53 and DNA double-strand break repair genes may help predict the number of metastases and clinical outcomes in patients with mCSPC.
Article
Oncology
A. Lambert, J. Salleron, M. Lion, M. Rouyer, N. Lozano, A. Leroux, J. L. Merlin, Alexandre Harle
PATHOLOGY & ONCOLOGY RESEARCH
(2019)
Article
Multidisciplinary Sciences
Claire Franczak, Ludovic Dubouis, Pauline Gilson, Marie Husson, Marie Rouyer, Jessica Demange, Agnes Leroux, Jean-Louis Merlin, Alexandre Harle
Article
Biochemistry & Molecular Biology
Charlene Thiebaut, Amand Chesnel, Jean-Louis Merlin, Maelle Chesnel, Agnes Leroux, Alexandre Harle, Helene Dumond
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Article
Multidisciplinary Sciences
Pauline Gilson, Claire Franczak, Ludovic Dubouis, Marie Husson, Marie Rouyer, Jessica Demange, Marie Perceau, Agnes Leroux, Jean-Louis Merlin, Alexandre Harle
Review
Biochemistry & Molecular Biology
Pauline Gilson, Guillaume Drouot, Andrea Witz, Jean-Louis Merlin, Philippe Becuwe, Alexandre Harle
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2019)
Review
Biochemistry & Molecular Biology
Shaun M. Kandathil, Joe G. Greener, David T. Jones
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
(2019)
Article
Multidisciplinary Sciences
Stephane Busca, Julia Salleron, Romain Boidot, Jean-Louis Merlin, Alexandre Harle
SCIENTIFIC REPORTS
(2019)
Review
Oncology
Pauline Gilson, Jean-Louis Merlin, Alexandre Harle
Summary: Microsatellite instability (MSI) is a molecular marker for defects in the mismatch repair system (dMMR) and is linked to higher cancer risk. MSI tumors show mutations throughout the genome, with a focus on microsatellite (MS) DNA repeat sequences. Assessment of MSI/dMMR status is commonly done with immunohistochemistry or PCR, but newer methods based on tumor tissue or plasma samples are emerging trends.
Review
Cell Biology
Joe G. Greener, Shaun M. Kandathil, Lewis Moffat, David T. Jones
Summary: This passage discusses the application of machine learning in the analysis of biological data and provides guidance for experimentalists. The increasing scale and complexity of biological data have led to a growing use of machine learning in biology.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2022)
Review
Chemistry, Medicinal
Jul Dardare, Andrea Witz, Jean-Louis Merlin, Agathe Bochnakian, Paul Toussaint, Pauline Gilson, Alexandre Harle
Summary: Pancreatic ductal adenocarcinoma (PDAC) has a poor prognosis, mainly due to late-stage diagnosis. EMT plays a significant role in PDAC, not only related to cancer progression and metastasis, but also potentially becoming a new therapeutic target.
Article
Multidisciplinary Sciences
Shaun M. Kandathil, Joe G. Greener, Andy M. Lau, David T. Jones
Summary: The study presents a deep learning-based method for predicting protein structure, which reduces preprocessing time and directly outputs main chain coordinates. The approach is fast, easy to use, and produces accurate structural models. It enables large-scale modeling of proteins on minimal hardware.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Pauline Gilson, Jean-Louis Merlin, Alexandre Harle
Summary: Malignant tumors exhibit high levels of heterogeneity at both molecular and phenotypic levels, which poses challenges for patient management. This heterogeneity exists between patients and even within a single patient over space and time. Current treatment decision-making often only considers the molecular characteristics of a limited tumor tissue sample, without taking into account the complexity and continuous evolution of bulk tumors. This review explores the extent of tumor heterogeneity, focusing on intra-tumor heterogeneity (ITH), and discusses the mechanisms that promote and sustain this diversity in cancers. The clinical implications of ITH in the management of cancer patients are summarized, along with discussions on current approaches to adequately appreciate ITH.
Article
Oncology
Julie Egea, Julia Salleron, Sophie Gourgou, Ahmet Ayav, Valerie Laurent, Beata Juzyna, Alexandre Harle, Thierry Conroy, Aurelien Lambert
Summary: The study suggests that clinical and biological evaluation, alongside traditional imaging examinations, can yield a more reliable detection of tumor progression in patients with pancreatic cancer, leading to early treatment and potentially better outcomes.
Review
Oncology
Margaux Betz, Vincent Massard, Pauline Gilson, Andrea Witz, Julie Dardare, Alexandre Harle, Jean-Louis Merlin
Summary: Endocrine therapy is the main treatment for hormone receptor-positive breast cancer, and mutations in the ESR1 gene are a common mechanism of resistance. Liquid biopsies using circulating cell-free DNA have shown promise in detecting ESR1 mutations for disease monitoring. This review discusses the latest advances in this field and compares different techniques for analyzing the ESR1 gene.