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.
Article
Oncology
James P. Solomon, Soo-Ryum Yang, Noura J. Choudhury, Ryan N. Ptashkin, Nasrin Eslamdoost, Christina J. Falcon, Axel Martin, Andrew Plodkowski, Clare Wilhelm, Ronglai Shen, Marc Ladanyi, Michael Berger, Yanming Zhang, Alexander Drilon, Maria E. Arcila
Summary: This study validated and optimized the utility of next-generation sequencing (NGS) in assessing MET copy number alterations, achieving high concordance, sensitivity, and specificity. MET copy gains and amplifications were found in certain malignancies, with high-level/focal amplification associated with targeted therapy response.
CLINICAL CANCER RESEARCH
(2022)
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
Oncology
Xiao-Bo Wu, Shu-Ling Hou, Qiao-Hua Zhang, Ning Jia, Min Hou, Wen Shui
Summary: This study investigated the features of ctDNA mutated genes in lymphoma subtypes and found significant correlation between genetic alterations in ctDNA and clinical indices. The genetic heterogeneity across lymphoma subtypes was observed, indicating potential implications for therapeutic targets and risk-adaptive therapies.
FRONTIERS IN ONCOLOGY
(2022)
Article
Microbiology
Melanie A. Mallory, Weston C. Hymas, Keith E. Simmon, Michael T. Pyne, Jeffery B. Stevenson, Adam P. Barker, David R. Hillyard, Kimberly E. Hanson
Summary: This study developed and validated an amplicon-based Ion Torrent NGS method for simultaneous analysis of CMV resistance mutations in multiple genes. Compared to standard Sanger sequencing, the NGS assay had a low error rate and high accuracy, and generated high-quality sequence from low viral load specimens. The assay showed excellent agreement with Sanger and detected resistance mutations missed by Sanger in low-frequency variants.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Oncology
Min Ruan, Lipeng Liu, Benquan Qi, Xiaoyan Chen, Lixian Chang, Aoli Zhang, Fang Liu, Shuchun Wang, Xiaoming Liu, Xiaojuan Chen, Li Zhang, Ye Guo, Yao Zou, Yingchi Zhang, Yumei Chen, LiXia Liu, Shanbo Cao, Feng Lou, Chengcheng Wang, Xiaofan Zhu
Summary: This study validates the diagnostic role of circulating tumor DNA in pediatric AML based on next-generation sequencing, showing that ctDNA can mirror genomic information from bone marrow and detect mutations exclusively. Monitoring ctDNA with NGS-based assays provides valuable information for precision treatment in pediatric AML.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Min-Ying Sun, Fang-Qin Lin, Lu-Jia Chen, Hong Li, Wei-Quan Lin, Hong-Yan Du, Xue-Xi Yang, Ming Li
Summary: Liquid biopsy by detecting circulating tumor DNA (ctDNA) has potential advantages in cancer monitoring and prediction, serving as a potential biomarker for evaluation, prediction, and clinical management guidance of metastatic breast cancer patients undergoing chemotherapy. Results show that ctDNA mutation levels are associated with tumor size, HER2 status, and poor survival outcomes, indicating its potential in assessing treatment efficacy and guiding clinical decisions.
Article
Oncology
Szilvia Lilla Csoma, Judit Bedekovics, Gergo Veres, Anita arokszallasi, Csilla Andras, Gabor Mehes, Attila Mokanszki
Summary: In the era of personalized oncology, next-generation sequencing plays a crucial role in identifying genetic aberrations in biliary tract cancers. Our study demonstrates that liquid biopsy of peripheral blood can effectively monitor the molecular genetic profile and chemotherapy response in BTCs, providing a minimally invasive testing approach for precision oncology treatment.
Article
Oncology
Marina Berger, Andrea Thueringer, Doritt Franz, Nadia Dandachi, Emina Talakic, Georg Richtig, Erika Richtig, Peter Michael Rohrer, Lukas Koch, Ingrid Hildegard Wolf, Catharina Koch, Barbara Margaretha Rainer, Maximilian Koeller, Martin Pichler, Hanno Gerritsmann, Karl Kashofer, Ariane Aigelsreiter
Summary: The study evaluated the use of NGS technology in predicting and monitoring treatment response in metastatic melanoma patients through ctDNA analysis. The research found potential in using NGS gene panels for monitoring disease burden during therapy, although statistically significant results were not observed in this cohort.
Article
Oncology
Jonathan M. Tsai, Aaron N. Hata, Jochen K. Lennerz
Summary: Comprehensive genetic profiling using next-generation sequencing is crucial in precision oncology, where accurate variant annotation plays a key role. This article highlights inconsistencies in variant annotation for the MET D1228N exon 19 resistance mutations, emphasizing the importance of avoiding erroneous interpretation when annotated on different transcripts.
Article
Oncology
Panagiota Economopoulou, Aris Spathis, Ioannis Kotsantis, Eirini Maratou, Maria Anastasiou, Myrto K. Moutafi, Maria Kirkasiadou, Anastasios Pantazopoulos, Maria Giannakakou, Daniel L. Edelstein, Hillary Sloane, Johannes Fredebohm, Frederick S. Jones, Anastasios Kyriazoglou, Niki Gavrielatou, Periklis Foukas, Ioannis Panayiotides, Amanda Psyrri
Summary: The aim of this pilot study was to evaluate somatic mutations in tumor and circulating DNA samples from HNSCC patients and assess the association of changes in ctDNA levels with survival. The study included 62 HNSCC patients treated with surgery or radical chemoradiotherapy. Tumor DNA was extracted from plasma and tumor tissue, and the presence of pathogenic variants in four genes was assessed.
Article
Biochemistry & Molecular Biology
Kseniya Khamina, Andreas B. Diendorfer, Susanna Skalicky, Moritz Weigl, Marianne Pultar, Teresa L. Krammer, Catharine Aquino Fournier, Amy L. Schofield, Carolin Otto, Aaron Thomas Smith, Nina Buchtele, Christian Schoergenhofer, Bernd Jilma, Bernhard J. H. Frank, Jochen G. Hofstaetter, Regina Grillari, Johannes Grillari, Klemens Ruprecht, Christopher E. Goldring, Hubert Rehrauer, Warren E. Glaab, Matthias Hackl
Summary: The plasma levels of tissue-specific microRNAs can serve as diagnostic, disease severity and prognostic biomarkers. Combining diverse microRNAs into biomarker signatures using multivariate statistics is powerful in terms of tissue and condition specific microRNA shedding into the plasma.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Masato Kojima, Takanori Harada, Takahiro Fukazawa, Sho Kurihara, Ryo Touge, Isamu Saeki, Shinya Takahashi, Eiso Hiyama
Summary: In this study, single-cell next-generation sequencing of circulating tumor cells (CTCs) from neuroblastoma (NB) patients was performed. The findings showed that the isolation rate of CTCs was associated with disease progression, and single-cell RNA sequencing revealed upregulated genes related to angiogenesis and cell cycle in CTCs. These results indicate the utility of single-cell CTC sequencing in characterizing NB tumor biology and metastasis mechanisms.
Article
Virology
Calesta Hui Yi Teo, Nurul Hannah Binte Norhisham, Ogestelli Fabia Lee, Siyu Png, Chean Nee Chai, Gabriel Yan, Julian Wei-Tze Tang, Chun Kiat Lee
Summary: The HIV genotypic resistance test is crucial for managing HIV/AIDS patients, and high-throughput sequencing is a reliable and sensitive alternative method for detecting low-abundance covert mutations and drug resistance.
Article
Oncology
Bassel Nazha, Tony Z. Zhuang, Hiba Dada, Leylah M. Drusbosky, Jacqueline T. Brown, Deepak Ravindranathan, Bradley C. Carthon, Omer Kucuk, Jamie Goldman, Viraj A. Master, Mehmet Asim Bilen
Summary: This study evaluated the genomic landscape of adrenocortical carcinoma (ACC) using blood-based DNA testing. The findings suggest that a significant proportion of ACC patients have actionable mutations, which could inform personalized treatment options or clinical trials for this aggressive malignancy.