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Cancer Next Generation Sequencing

Mariko Murata
Infection and inflammation account for approximately 25% of cancer-causing factors. Inflammation-related cancers are characterized by mutagenic DNA lesions, such as 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8-nitroguanine. Our previous studies demonstrated the formation of 8-oxodG and 8-nitroguanine in the tissues of cancer and precancerous lesions due to infection (e.g., Opisthorchis viverrini-related cholangiocarcinoma, Schistosoma haematobium-associated bladder cancer, Helicobacter pylori-infected gastric cancer, human papillomavirus-related cervical cancer, Epstein-Barr virus-infected nasopharyngeal carcinoma) and pro-inflammatory factors (e...
October 20, 2018: Environmental Health and Preventive Medicine
Sadakatsu Ikeda, Sheryl K Elkin, Brett N Tomson, Jennifer L Carter, Razelle Kurzrock
Despite being one of the most common cancers, treatment options for prostate cancer are limited. Novel approaches for advanced disease are needed. We evaluated the relative rate of use of clinical-grade next generation sequencing (NGS) in prostate cancer, as well as genomic alterations identified and their potential actionability. Of 4864 patients from multiple institutions for whom NGS was ordered by physicians, only 67 (1.4%) had prostate cancer, representing 1/10 the ordering rate for lung cancer. Prostate cancers harbored 148 unique alterations affecting 63 distinct genes...
October 19, 2018: Cancer Biology & Therapy
Camila D M Campos, Sachindra S T Gamage, Joshua M Jackson, Malgorzata A Witek, Daniel S Park, Michael C Murphy, Andrew K Godwin, Steven A Soper
Cell-free DNA (cfDNA) is a liquid biopsy marker that can carry signatures (i.e., mutations) associated with certain pathological conditions. Therefore, the extraction of cfDNA from a variety of clinical samples can be an effective and minimally invasive source of markers for disease detection and subsequent management. In the oncological diseases, circulating tumor DNA (ctDNA), a cfDNA sub-class, can carry clinically actionable mutations and coupled with next generation sequencing or other mutation detection methods provide a venue for effective in vitro diagnostics...
October 19, 2018: Lab on a Chip
Masayuki Nagahashi, Yoshifumi Shimada, Hiroshi Ichikawa, Hitoshi Kameyama, Kazuaki Takabe, Shujiro Okuda, Toshifumi Wakai
Next generation sequencing (NGS) has been an invaluable tool to put genomic sequencing into clinical practice. The incorporation of clinically relevant target sequences into NGS-based gene panel tests has generated practical diagnostic tools that enabled individualized cancer-patient care. The clinical utility of gene panel testing includes investigation of the genetic basis for an individual's response to therapy, such as signaling pathways associated with a response to specific therapies, microsatellite instability and a hypermutated phenotype, and deficiency in the DNA double-strand break repair pathway...
October 18, 2018: Cancer Science
Tadayuki Kou, Masashi Kanai, Mayumi Kamada, Masahiko Nakatsui, Shigemi Matsumoto, Yasushi Okuno, Manabu Muto
Recent innovations in next-generation sequencing (NGS) technologies have enabled comprehensive genomic profiling of human cancers in the clinical setting. The ability to profile has launched a worldwide trend known as precision medicine, and the fusion of genomic profiling and pharmacogenomics is paving the way for precision medicine for cancer. The profiling is coupled with information about chemical therapies available to patients with specific genotypes. As a result, the chemogenomic space in play is not only the standard chemical and genome space but also the mutational genome and chemical space...
2018: Methods in Molecular Biology
Olga I Brovkina, Leila Shigapova, Daria A Chudakova, Marat G Gordiev, Rafael F Enikeev, Maxim O Druzhkov, Dmitriy S Khodyrev, Elena I Shagimardanova, Alexey G Nikitin, Oleg A Gusev
The Russian population consists of more than 100 ethnic groups, presenting a unique opportunity for the identification of hereditary pathogenic mutations. To gain insight into the landscape of heredity pathogenic variants, we employed targeted next-generation sequencing to analyze the germline mutation load in the DNA damage response and repair genes of hereditary breast and ovary cancer syndrome (HBOCS) patients of Tatar ethnicity, which represents ~4% of the total Russian population. Several pathogenic mutations were identified in DNA double-strand break repair genes, and the spectrum of these markers in Tatar patients varied from that previously reported for patients of Slavic ancestry...
2018: Frontiers in Oncology
Yi Ma, Lijie He, Qianwen Huang, Shuang Zheng, Zhiqiang Zhang, Hongshi Li, Shuang Liu
BACKGROUND: Prostate cancer is a heterogeneous disease, meaning patients would benefit from different treatment strategies based on their molecular stratification. In recent years, several genomic studies have identified prostate cancers with defects in DNA repair genes. It is known that the PARP inhibitor, olaparib, has a significant synthetic lethal effect on tumors with BRCA 1/2 mutations, particularly in ovarian and breast cancer. CASE PRESENTATION: In this study, we describe a patient with metastatic castration-resistant prostate cancer (mCRPC) containing a BRCA2 germline mutation who underwent olaparib treatment...
October 17, 2018: BMC Medical Genetics
Yuanyuan Song, Peng Liu, Yu Huang, Yanfang Guan, Xiaohong Han, Yuankai Shi
BACKGROUND: Leptomeningeal metastases (LM) are much more frequent in patients of non-small lung cancer (NSCLC) harboring epidermal growth factor receptor (EGFR) mutations. Osimertinib, a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) shows promising efficacy for LM. OBJECTIVE: The aim of this study was to analyze the concentration of osimertinib and gene variation of circulating tumor DNA (ctDNA) in human plasma and cerebrospinal fluid (CSF)...
October 17, 2018: Current Cancer Drug Targets
William Tabayoyong, Ashish M Kamat
PURPOSE OF REVIEW: We summarize the current literature regarding the available urinary biomarkers for the detection and surveillance of bladder cancer. RECENT FINDINGS: Four urinary biomarkers have FDA approval for the detection of bladder cancer; however, they have not supplanted cystoscopy and urine cytology as the gold standard. Recent technological advances in next-generation sequencing have allowed the field of urinary biomarker research to move beyond protein biomarkers and now include genomic, transcriptomic, and epigenetic panels...
October 17, 2018: Current Urology Reports
(no author information available yet)
The FDA granted marketing authorization to the first-ever next-generation sequencing assay for detecting minimal residual disease in patients with acute lymphoblastic leukemia or multiple myeloma.
October 16, 2018: Cancer Discovery
Bishal Gyawali, Howard Jack West
No abstract text is available yet for this article.
October 11, 2018: JAMA Oncology
Charu Aggarwal, Jeffrey C Thompson, Taylor A Black, Sharyn I Katz, Ryan Fan, Stephanie S Yee, Austin L Chien, Tracey L Evans, Joshua M Bauml, Evan W Alley, Christine A Ciunci, Abigail T Berman, Roger B Cohen, David B Lieberman, Krishna S Majmundar, Samantha L Savitch, Jennifer J D Morrissette, Wei-Ting Hwang, Kojo S J Elenitoba-Johnson, Corey J Langer, Erica L Carpenter
Importance: The clinical implications of adding plasma-based circulating tumor DNA next-generation sequencing (NGS) to tissue NGS for targetable mutation detection in non-small cell lung cancer (NSCLC) have not been formally assessed. Objective: To determine whether plasma NGS testing was associated with improved mutation detection and enhanced delivery of personalized therapy in a real-world clinical setting. Design, Setting, and Participants: This prospective cohort study enrolled 323 patients with metastatic NSCLC who had plasma testing ordered as part of routine clinical management...
October 11, 2018: JAMA Oncology
Huiping Li, Yaping Xu, Fangyuan Zhao, Guohong Song, Hope S Rugo, Yan Zhang, Ling Yang, Xiaoran Liu, Bin Shao, Liang Yang, Yaxin Liu, Ran Ran, Ruyan Zhang, Yanfang Guan, Lianpeng Chang, Xin Yi
Through next generation sequencing, this study evaluated the circulating tumor DNA (ctDNA) of advanced breast cancer patients to prospectively explore the relationship between specific DNA mutations and prognosis as well as therapeutic decision making. The target region covered 1021 gene totally. Clinical characteristics, treatment and outcome data were collected. We analyzed progression-free survival (PFS) from first-line therapy and overall survival (OS), and found that their endpoints were correlated with observed gene mutations...
2018: American Journal of Cancer Research
Riku Katainen, Iikki Donner, Tatiana Cajuso, Eevi Kaasinen, Kimmo Palin, Veli Mäkinen, Lauri A Aaltonen, Esa Pitkänen
Next-generation sequencing (NGS) is routinely applied in life sciences and clinical practice, but interpretation of the massive quantities of genomic data produced has become a critical challenge. The genome-wide mutation analyses enabled by NGS have had a revolutionary impact in revealing the predisposing and driving DNA alterations behind a multitude of disorders. The workflow to identify causative mutations from NGS data, for example in cancer and rare diseases, commonly involves phases such as quality filtering, case-control comparison, genome annotation, and visual validation, which require multiple processing steps and usage of various tools and scripts...
October 15, 2018: Nature Protocols
Victor T G Lin, Lisle M Nabell, Sharon A Spencer, William R Carroll, Shuko Harada, Eddy S Yang
Salivary duct carcinoma (SDC) is a rare and aggressive malignancy for which limited data exist to guide treatment decisions. With the advent of advanced molecular testing and tumor genomic profiling, clinicians now have the ability to identify potential therapeutic targets in difficult-to-treat cancers such as SDC. This report presents a male patient with widely metastatic SDC found on targeted next-generation sequencing to have a BRAF p.V600E mutation. He experienced a prolonged and robust response to first-line systemic chemotherapy with dabrafenib and trametinib...
October 2018: Journal of the National Comprehensive Cancer Network: JNCCN
Winnie S Liang, Christopher Dardis, Adrienne Helland, Shobana Sekar, Jonathan Adkins, Lori Cuyugan, Daniel Enriquez, Sara Byron, Andrew S Little
Chordoma is a rare, orphan cancer arising from embryonal precursors of bone. Surgery and radiotherapy (RT) provide excellent local control, often at the price of significant morbidity due to the structures involved and the need for relatively high doses of RTare not typically curative; however, recurrence remains high. Although our understanding of the genetic changes that occur in chordoma is evolving rapidly, this knowledge has yet to translate into treatments. We performed comprehensive DNA (paired tumor/normal whole exome and shallow whole genome) and RNA (tumor whole transcriptome) next-generation sequencing analyses of archival sacral and clivus chordoma specimens...
October 15, 2018: Cold Spring Harbor Molecular Case Studies
Valeria Pecce, Marialuisa Sponziello, Giuseppe Damante, Francesca Rosignolo, Cosimo Durante, Livia Lamartina, Giorgio Grani, Diego Russo, Cira Rosaria di Gioia, Sebastiano Filetti, Antonella Verrienti
Synonymous mutations continue to be filtered out from most large-scale cancer genome studies, but several lines of evidence suggest they can play driver roles in neoplastic disease. We investigated a case of an aggressive, apparently sporadic medullary thyroid carcinoma (MTC) harboring a somatic RET p.Cys634Arg mutation (a known MTC driver). A germ-line RET substitution (p.Cys630=) had also been found but was considered clinically irrelevant because of its synonymous nature. Next generation sequencing (NGS) of the tumor tissues revealed that the RET mutations were in cis...
October 15, 2018: PLoS Genetics
Daniel M Altmann
The field of cancer immunology stepped into the limelight this year when James P. Allison and Tasuku Honjo received the Nobel Prize in Physiology or Medicine for their discovery of cancer therapy by inhibition of negative immune regulation. Among many exciting advances contributing to the coming of age of tumour immunology as a viable clinical specialty has been the ability to progress from the initial elucidation of tumour antigens, such as the melanoma antigen, MAGE-1, to high-throughput sequencing facilitating identification of T cell epitopes from diverse tumour neoantigens...
November 2018: Immunology
Brent O'Carrigan, Joline Si Jing Lim, Awais Jalil, Samuel John Harris, Dionysis Papadatos-Pastos, Udai Banerji, Juanita Lopez, Johann Sebastian de Bono, Timothy Anthony Yap
BACKGROUND: Greater understanding of the molecular classification of breast cancer has permitted the development of rational drug design strategies. In a phase I clinical trial setting, molecular profiling with next-generation sequencing of individual tumour samples has been employed to guide treatment. METHODS: We conducted a retrospective evaluation of clinical outcomes of patients with metastatic breast cancer (MBC) treated in phase I clinical trials at our institution to assess the benefit of molecularly matched compared to non-matched treatments...
October 15, 2018: British Journal of Cancer
Jai N Patel, Ioana Braicu, Kirsten M Timms, Cara Solimeno, Placede Tshiaba, Julia Reid, Jerry S Lanchbury, Silvia Darb-Esfahani, Mahrukh K Ganapathi, Jalid Sehouli, Ram N Ganapathi
BACKGROUND: Homologous recombination deficiency (HRD) is shown to predict response to DNA-damaging therapies in patients with high-grade serous ovarian cancer (HGSOC); however, changes in HRD during progression remains unknown. METHODS: HRD scores were evaluated in paired primary and/or recurrent HGSOC samples (N = 107) from 54 patients with adjuvant platinum-based chemotherapy. BRCA1/2 mutation, BRCA1 methylation, loss of heterozygosity (LOH), and HRD scores were characterised using tumour DNA-based next-generation sequencing assays...
October 15, 2018: British Journal of Cancer
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