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Laura Torrens, Sarah Moody, Ana Carolina de Carvalho, Mariya Kazachkova, Behnoush Abedi-Ardekani, Saamin Cheema, Sergey Senkin, Thomas Cattiaux, Ricardo Cortez Cardoso Penha, Joshua R Atkins, Valérie Gaborieau, Priscilia Chopard, Christine Carreira, Ammal Abbasi, Erik N Bergstrom, Raviteja Vangara, Jingwei Wang, Stephen Fitzgerald, Calli Latimer, Marcos Diaz-Gay, David Jones, Jon Teague, Felipe Ribeiro Pinto, Luiz Paulo Kowalski, Jerry Polesel, Fabiola Giudici, José Carlos de Oliveira, Pagona Lagiou, Areti Lagiou, Marta Vilensky, Dana Mates, Ioan N Mates, Lidia Mrb Arantes, Rui Reis, Jose Roberto V Podesta, Sandra V von Zeidler, Ivana Holcatova, Maria Paula Curado, Cristina Canova, Elenora Fabianova, Paula A Rodríguez-Urrego, Laura Humphreys, Ludmil B Alexandrov, Paul Brennan, Michael R Stratton, Sandra Perdomo
Tobacco smoke, alone or combined with alcohol, is the predominant cause of head and neck cancer (HNC). Here, we further explore how tobacco exposure contributes to cancer development by mutational signature analysis of 265 whole-genome sequenced HNC from eight countries. Six tobacco-associated mutational signatures were detected, including some not previously reported. Differences in HNC incidence between countries corresponded with differences in mutation burdens of tobacco-associated signatures, consistent with the dominant role of tobacco in HNC causation...
April 17, 2024: medRxiv
#2
Chong Chu, Viktor Ljungström, Antuan Tran, Hu Jin, Peter J Park
Insertion of active retroelements-L1s, Alu s, and SVAs-can disrupt proper genome function and lead to various disorders including cancer. However, the role of de novo retroelements (DNRTs) in birth defects and childhood cancers has not been well characterized due to the lack of adequate data and efficient computational tools. Here, we examine whole-genome sequencing data of 3,244 trios from 12 birth defect and childhood cancer cohorts in the Gabriella Miller Kids First Pediatric Research Program. Using an improved version of our tool xTea (x-Transposable element analyzer) that incorporates a deep-learning module, we identified 162 DNRTs, as well as 2 pseudogene insertions...
April 16, 2024: medRxiv
#3
JOURNAL ARTICLE
Anders Edsjö, Hege G Russnes, Janne Lehtiö, David Tamborero, Eivind Hovig, Albrecht Stenzinger, Richard Rosenquist
In the last decades, the development of high-throughput molecular assays has revolutionised cancer diagnostics, paving the way for the concept of personalised cancer medicine. This progress has been driven by the introduction of such technologies through biomarker-driven oncology trials. In this review, strengths and limitations of various state-of-the-art sequencing technologies, including gene panel sequencing (DNA and RNA), whole-exome/whole-genome sequencing and whole-transcriptome sequencing, are explored, focusing on their ability to identify clinically relevant biomarkers with diagnostic, prognostic and/or predictive impact...
May 2, 2024: Journal of Internal Medicine
#4
JOURNAL ARTICLE
Stephen-John Sammut, Jacob D Galson, Ralph Minter, Bo Sun, Suet-Feung Chin, Leticia De Mattos-Arruda, Donna K Finch, Sebastian Schätzle, Jorge Dias, Oscar M Rueda, Joan Seoane, Jane Osbourn, Carlos Caldas, Rachael J M Bashford-Rogers
B cells and T cells are important components of the adaptive immune system and mediate anticancer immunity. The T cell landscape in cancer is well characterized, but the contribution of B cells to anticancer immunosurveillance is less well explored. Here we show an integrative analysis of the B cell and T cell receptor repertoire from individuals with metastatic breast cancer and individuals with early breast cancer during neoadjuvant therapy. Using immune receptor, RNA and whole-exome sequencing, we show that both B cell and T cell responses seem to coevolve with the metastatic cancer genomes and mirror tumor mutational and neoantigen architecture...
May 2024: Nature Immunology
#5
JOURNAL ARTICLE
Jiaqi Liu, Lijun Dai, Qiang Wang, Chenghao Li, Zhichao Liu, Tongyang Gong, Hengyi Xu, Ziqi Jia, Wanyuan Sun, Xinyu Wang, Minyi Lu, Tongxuan Shang, Ning Zhao, Jiahui Cai, Zhigang Li, Hongyan Chen, Jianzhong Su, Zhihua Liu
Detecting early-stage esophageal squamous cell carcinoma (ESCC) and precancerous lesions is critical for improving survival. Here, we conduct whole-genome bisulfite sequencing (WGBS) on 460 cfDNA samples from patients with non-metastatic ESCC or precancerous lesions and matched healthy controls. We develop an expanded multimodal analysis (EMMA) framework to simultaneously identify cfDNA methylation, copy number variants (CNVs), and fragmentation markers in cfDNA WGBS data. cfDNA methylation markers are the earliest and most sensitive, detectable in 70% of ESCCs and 50% of precancerous lesions, and associated with molecular subtypes and tumor microenvironments...
May 2, 2024: Nature Communications
#6
JOURNAL ARTICLE
Qing Fan, Chaoran Xia, Xiaoqun Zeng, Zhen Wu, Yuxing Guo, Qiwei Du, Maolin Tu, Xinanbei Liu, Daodong Pan
Nitrite has the potential risk of hypoxic poisoning or cancer in pickled food. In our previous study, Limosilactobacillus fermentum ( L. fermentum ) RC4 is effective in nitrite degradation by producing nitrite reductase B (NirB). To investigate the detailed mechanism from the genome, response, and regulation of NirB, the whole-genome sequence of L. fermentum RC4 was analyzed, the L. fermentum -EGFP- nir B with enhanced green fluorescent protein (EGFP) labeled the nitrite reductase large subunit nir B, and the recombined L...
2024: Current research in food science
#7
JOURNAL ARTICLE
Alicia M Braxton, Ashley L Kiemen, Mia P Grahn, André Forjaz, Jeeun Parksong, Jaanvi Mahesh Babu, Jiaying Lai, Lily Zheng, Noushin Niknafs, Liping Jiang, Haixia Cheng, Qianqian Song, Rebecca Reichel, Sarah Graham, Alexander I Damanakis, Catherine G Fischer, Stephanie Mou, Cameron Metz, Julie Granger, Xiao-Ding Liu, Niklas Bachmann, Yutong Zhu, YunZhou Liu, Cristina Almagro-Pérez, Ann Chenyu Jiang, Jeonghyun Yoo, Bridgette Kim, Scott Du, Eli Foster, Jocelyn Y Hsu, Paula Andreu Rivera, Linda C Chu, Fengze Liu, Elliot K Fishman, Alan Yuille, Nicholas J Roberts, Elizabeth D Thompson, Robert B Scharpf, Toby C Cornish, Yuchen Jiao, Rachel Karchin, Ralph H Hruban, Pei-Hsun Wu, Denis Wirtz, Laura D Wood
Pancreatic intraepithelial neoplasias (PanINs) are the most common precursors of pancreatic cancer, but their small size and inaccessibility in humans make them challenging to study1 . Critically, the number, dimensions and connectivity of human PanINs remain largely unknown, precluding important insights into early cancer development. Here, we provide a microanatomical survey of human PanINs by analysing 46 large samples of grossly normal human pancreas with a machine-learning pipeline for quantitative 3D histological reconstruction at single-cell resolution...
May 1, 2024: Nature
#8
JOURNAL ARTICLE
Katrina O'Halloran, Hesamedin Hakimjavadi, Moiz Bootwalla, Dejerianne Ostrow, Rhea Kerawala, Jennifer A Cotter, Venkata Yellapantula, Kristiyana Kaneva, Nitin R Wadhwani, Amy Treece, Nicholas K Foreman, Sanda Alexandrescu, Jose Velazquez Vega, Jaclyn A Biegel, Xiaowu Gai
Little is known regarding the genomic alterations in chordoma, with the exception of loss of SMARCB1, a core member of the SWI/SNF complex, in poorly differentiated chordomas. A TBXT duplication and rs2305089 polymorphism, located at 6q27, are known genetic susceptibility loci. A comprehensive genomic analysis of the nuclear and mitochondrial genomes in pediatric chordoma has not yet been reported. In this study, we performed whole exome and mitochondrial DNA (mtDNA) genome sequencing on 29 chordomas from 23 pediatric patients...
May 1, 2024: Molecular Cancer Research: MCR
#9
JOURNAL ARTICLE
Saptarshi Chakraborty, Zoe Guan, Caroline E Kostrzewa, Ronglai Shen, Colin B Begg
Numerous studies over the past generation have identified germline variants that increase specific cancer risks. Simultaneously, a revolution in sequencing technology has permitted high-throughput annotations of somatic genomes characterizing individual tumors. However, examining the relationship between germline variants and somatic alteration patterns is hugely challenged by the large numbers of variants in a typical tumor, the rarity of most individual variants, and the heterogeneity of tumor somatic fingerprints...
April 30, 2024: Genetic Epidemiology
#10
JOURNAL ARTICLE
Yuxing Chen, Chaoyu Xiao, Qingxin Fan, Ye Zhang, Qiu Huang, Yunsheng Ou
BACKGROUND: The extracellular matrix (ECM) modeling induced by the metalloproteinases is a vital characteristic for tumor progression. Previous studies mainly focus on the functions of two subgroups of metalloproteinases: matrix metalloproteinases (MMPs) and a disintegrin and metalloproteases (ADAMs) in tumors. The roles of another important group: the ADAMs with thrombospondin motifs (ADAMTS) remain unclear. This study aimed to perform a pan-cancer analysis of procollagen N-propeptidase subgroup of ADAMTS (PNPSA)...
April 12, 2024: Frontiers in Bioscience (Landmark Edition)
#11
JOURNAL ARTICLE
Prajwal Ghimire, Ben Kinnersley, Golestan Karami, Prabhu Arumugam, Richard Houlston, Keyoumars Ashkan, Marc Modat, Thomas C Booth
BACKGROUND: Immunotherapy is an effective "precision medicine" treatment for several cancers. Imaging signatures of the underlying genome (radiogenomics) in glioblastoma patients may serve as preoperative biomarkers of the tumor-host immune apparatus. Validated biomarkers would have the potential to stratify patients during immunotherapy clinical trials, and if trials are beneficial, facilitate personalized neo-adjuvant treatment. The increased use of whole genome sequencing data, and the advances in bioinformatics and machine learning make such developments plausible...
2024: Neuro-oncology advances
#12
JOURNAL ARTICLE
V G Druzhinin, E D Baranova, P S Demenkov, L V Matskova, A V Larionov
Recent studies have shown that the bacterial microbiome of the respiratory tract influences the development of lung cancer. Changes in the composition of the microbiome are observed in patients with chronic inflammatory processes. Such microbiome changes may include the occurrence of bacteria that cause oxidative stress and that are capable of causing genome damage in the cells of the host organism directly and indirectly. To date, the composition of the respiratory microbiome in patients with various histological variants of lung cancer has not been studied...
April 2024: Vavilovskii Zhurnal Genetiki i Selektsii
#13
JOURNAL ARTICLE
Zhishan Chen, Xingyi Guo, Ran Tao, Jeroen R Huyghe, Philip J Law, Ceres Fernandez-Rozadilla, Jie Ping, Guochong Jia, Jirong Long, Chao Li, Quanhu Shen, Yuhan Xie, Maria N Timofeeva, Minta Thomas, Stephanie L Schmit, Virginia Díez-Obrero, Matthew Devall, Ferran Moratalla-Navarro, Juan Fernandez-Tajes, Claire Palles, Kitty Sherwood, Sarah E W Briggs, Victoria Svinti, Kevin Donnelly, Susan M Farrington, James Blackmur, Peter G Vaughan-Shaw, Xiao-Ou Shu, Yingchang Lu, Peter Broderick, James Studd, Tabitha A Harrison, David V Conti, Fredrick R Schumacher, Marilena Melas, Gad Rennert, Mireia Obón-Santacana, Vicente Martín-Sánchez, Jae Hwan Oh, Jeongseon Kim, Sun Ha Jee, Keum Ji Jung, Sun-Seog Kweon, Min-Ho Shin, Aesun Shin, Yoon-Ok Ahn, Dong-Hyun Kim, Isao Oze, Wanqing Wen, Keitaro Matsuo, Koichi Matsuda, Chizu Tanikawa, Zefang Ren, Yu-Tang Gao, Wei-Hua Jia, John L Hopper, Mark A Jenkins, Aung Ko Win, Rish K Pai, Jane C Figueiredo, Robert W Haile, Steven Gallinger, Michael O Woods, Polly A Newcomb, David Duggan, Jeremy P Cheadle, Richard Kaplan, Rachel Kerr, David Kerr, Iva Kirac, Jan Böhm, Jukka-Pekka Mecklin, Pekka Jousilahti, Paul Knekt, Lauri A Aaltonen, Harri Rissanen, Eero Pukkala, Johan G Eriksson, Tatiana Cajuso, Ulrika Hänninen, Johanna Kondelin, Kimmo Palin, Tomas Tanskanen, Laura Renkonen-Sinisalo, Satu Männistö, Demetrius Albanes, Stephanie J Weinstein, Edward Ruiz-Narvaez, Julie R Palmer, Daniel D Buchanan, Elizabeth A Platz, Kala Visvanathan, Cornelia M Ulrich, Erin Siegel, Stefanie Brezina, Andrea Gsur, Peter T Campbell, Jenny Chang-Claude, Michael Hoffmeister, Hermann Brenner, Martha L Slattery, John D Potter, Kostas K Tsilidis, Matthias B Schulze, Marc J Gunter, Neil Murphy, Antoni Castells, Sergi Castellví-Bel, Leticia Moreira, Volker Arndt, Anna Shcherbina, D Timothy Bishop, Graham G Giles, Melissa C Southey, Gregory E Idos, Kevin J McDonnell, Zomoroda Abu-Ful, Joel K Greenson, Katerina Shulman, Flavio Lejbkowicz, Kenneth Offit, Yu-Ru Su, Robert Steinfelder, Temitope O Keku, Bethany van Guelpen, Thomas J Hudson, Heather Hampel, Rachel Pearlman, Sonja I Berndt, Richard B Hayes, Marie Elena Martinez, Sushma S Thomas, Paul D P Pharoah, Susanna C Larsson, Yun Yen, Heinz-Josef Lenz, Emily White, Li Li, Kimberly F Doheny, Elizabeth Pugh, Tameka Shelford, Andrew T Chan, Marcia Cruz-Correa, Annika Lindblom, David J Hunter, Amit D Joshi, Clemens Schafmayer, Peter C Scacheri, Anshul Kundaje, Robert E Schoen, Jochen Hampe, Zsofia K Stadler, Pavel Vodicka, Ludmila Vodickova, Veronika Vymetalkova, Christopher K Edlund, W James Gauderman, David Shibata, Amanda Toland, Sanford Markowitz, Andre Kim, Stephen J Chanock, Franzel van Duijnhoven, Edith J M Feskens, Lori C Sakoda, Manuela Gago-Dominguez, Alicja Wolk, Barbara Pardini, Liesel M FitzGerald, Soo Chin Lee, Shuji Ogino, Stephanie A Bien, Charles Kooperberg, Christopher I Li, Yi Lin, Ross Prentice, Conghui Qu, Stéphane Bézieau, Taiki Yamaji, Norie Sawada, Motoki Iwasaki, Loic Le Marchand, Anna H Wu, Chenxu Qu, Caroline E McNeil, Gerhard Coetzee, Caroline Hayward, Ian J Deary, Sarah E Harris, Evropi Theodoratou, Stuart Reid, Marion Walker, Li Yin Ooi, Ken S Lau, Hongyu Zhao, Li Hsu, Qiuyin Cai, Malcolm G Dunlop, Stephen B Gruber, Richard S Houlston, Victor Moreno, Graham Casey, Ulrike Peters, Ian Tomlinson, Wei Zheng
Genome-wide association studies (GWAS) have identified more than 200 common genetic variants independently associated with colorectal cancer (CRC) risk, but the causal variants and target genes are mostly unknown. We sought to fine-map all known CRC risk loci using GWAS data from 100,204 cases and 154,587 controls of East Asian and European ancestry. Our stepwise conditional analyses revealed 238 independent association signals of CRC risk, each with a set of credible causal variants (CCVs), of which 28 signals had a single CCV...
April 26, 2024: Nature Communications
#14
JOURNAL ARTICLE
Jun Akiba, Sachiko Ogasawara, Hirohisa Yano
BACKGROUND/AIM: Advancements in genetic analysis technologies have led to establishment of molecular classifications systems for primary liver cancers. The correlation between pathological morphology and genetic mutations in hepatocellular carcinoma (HCC) is becoming increasingly evident. To construct appropriate experimental models, it is crucial to select cell lines based on their morphology and genetic mutations. In this study, we conducted comprehensive genetic analyses of primary liver cancer cell lines and examined their correlations with morphology...
2024: Cancer Genomics & Proteomics
#15
JOURNAL ARTICLE
Siwei Wang, Fanchen Meng, Peng Chen, Yang Lv, Min Wu, Haimeng Tang, Hua Bao, Xue Wu, Yang Shao, Jie Wang, Juncheng Dai, Lin Xu, Xiaoxiao Wang, Rong Yin
OBJECTIVE: Although low-dose computed tomography has been proven effective to reduce lung cancer-specific mortality, a considerable proportion of surgically resected high-risk lung nodules were still confirmed pathologically benign. There is an unmet need of a novel method for malignancy classification in lung nodules. METHODS: We recruited 307 patients with high-risk lung nodules who underwent curative surgery, and 247 and 60 cases were pathologically confirmed malignant and benign lung lesions, respectively...
April 24, 2024: Journal of Thoracic and Cardiovascular Surgery
#16
JOURNAL ARTICLE
Emma Titmuss, Irene S Yu, Erin D Pleasance, Laura M Williamson, Karen Mungall, Andrew J Mungall, Daniel J Renouf, Richard Moore, Steven J M Jones, Marco A Marra, Janessa J Laskin, Kerry J Savage
Immune checkpoint inhibitors (ICIs) are increasingly used in the treatment of many tumor types, and durable responses can be observed in select populations. However, patients may exhibit significant immune-related adverse events (irAEs) that may lead to morbidity. There is limited information on whether the presence of specific germline mutations may highlight those at elevated risk of irAEs. We evaluated 117 patients with metastatic solid tumors or hematologic malignancies who underwent genomic analysis through the ongoing Personalized OncoGenomics (POG) program at BC Cancer and received an ICI during their treatment history...
March 30, 2024: Current Oncology
#17
REVIEW
Rocco Spagnuolo, Giuseppe Guido Maria Scarlata, Maria Rosaria Paravati, Ludovico Abenavoli, Francesco Luzza
Helicobacter pylori ( H. pylori ) infection is a prevalent global health issue, associated with several gastrointestinal disorders, including gastritis, peptic ulcers, and gastric cancer. The landscape of H. pylori treatment has evolved over the years, with increasing challenges due to antibiotic resistance and treatment failure. Traditional diagnostic methods, such as the urea breath test, stool antigen test, and endoscopy with biopsy, are commonly used in clinical practice. However, the emergence of antibiotic-resistant strains has led to a decline in treatment efficacy, necessitating a re-evaluation of common diagnostic tools...
April 12, 2024: Antibiotics
#18
JOURNAL ARTICLE
Jie Zhang, Ye Wang, Shiyang Hou, Xiaoqian Chi, Danyang Ding, Mei Xue, Mengqiao Zhang, Jing Wang, Junfang Shuai, Haiying Sun, Qiang Gao, Chunbo Kang
Colorectal cancer (CRC) is one of the most common malignancies worldwide. The 5‑year survival rate of patients diagnosed with the early stages of the disease is markedly higher than that of patients in the advanced stages. Therefore, identifying novel biomarkers and drug targets for CRC is critical for clinical practice. Zinc finger protein 169 (ZNF169) is a crucial transcription factor, and its role in CRC remains to be explored. The present study aimed to investigate the clinical relevance, function and underlying mechanisms of ZNF169 in CRC growth and proliferation...
June 2024: Oncology Reports
#19
JOURNAL ARTICLE
Alexandra N Demetriou, Frances Chow, David W Craig, Michelle G Webb, D Ryan Ormond, James Battiste, Arnab Chakravarti, Howard Colman, John L Villano, Bryan P Schneider, James K C Liu, Michelle L Churchman, Gabriel Zada
BACKGROUND: Glioblastoma exhibits aggressive growth and poor outcomes despite treatment, and its marked variability renders therapeutic design and prognostication challenging. The Oncology Research Information Exchange Network (ORIEN) database contains complementary clinical, genomic, and transcriptomic profiling of 206 glioblastoma patients, providing opportunities to identify novel associations between molecular features and clinical outcomes. METHODS: Survival analyses were performed using the Logrank test, and clinical features were evaluated using Wilcoxon and chi-squared tests with q -values derived via Benjamini-Hochberg correction...
2024: Neuro-oncology advances
#20
JOURNAL ARTICLE
Yuwei Zhang, Yichen Yang, Yue Ma, Ying Liu, Zhaoxiang Ye
BACKGROUND: Tumor mutational burden (TMB) is a promising biomarker for immunotherapy. The challenge of spatial and temporal heterogeneity and high costs weaken its power in clinical routine. The aim of this study is to estimate TMB preoperatively using a volumetric CT-based radiomic signature (rMB). METHODS: Seventy-one patients with resectable lung adenocarcinoma (LUAD) who underwent whole-exome sequencing (WXS) from 2011 to 2014 were enrolled from the institutional biobank of Tianjin Medical University Cancer Institute and Hospital (TMUCIH)...
2024: Frontiers in Genetics
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