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Next generation sequencing AND cancer

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https://www.readbyqxmd.com/read/29168077/progress-and-challenges-of-sequencing-and-analyzing-circulating-tumor-cells
#1
REVIEW
Zhongyi Zhu, Si Qiu, Kang Shao, Yong Hou
Circulating tumor cells (CTCs) slough off primary tumor tissues and are swept away by the circulatory system. These CTCs can remain in circulation or colonize new sites, forming metastatic clones in distant organs. Recently, CTC analyses have been successfully used as effective clinical tools to monitor tumor progression and prognosis. With advances in next-generation sequencing (NGS) and single-cell sequencing (SCS) technologies, scientists can obtain the complete genome of a CTC and compare it with corresponding primary and metastatic tumors...
November 22, 2017: Cell Biology and Toxicology
https://www.readbyqxmd.com/read/29167892/association-of-prognostic-value-of-primary-tumor-location-in-stage-iii-colon-cancer-with-ras-and-braf-mutational-status
#2
Julien Taieb, Hampig Raphael Kourie, Jean-François Emile, Karine Le Malicot, Ralyath Balogoun, Josep Tabernero, Enrico Mini, Gunnar Folprecht, Jean-Luc Van Laethem, Claire Mulot, Olivier Bouché, Thomas Aparicio, Pierre Michel, Josef Thaler, John Bridgewater, Eric Van Cutsem, Géraldine Perkins, Come Lepage, Ramon Salazar, Pierre Laurent-Puig
Importance: We know of no data on the prognostic value of primary tumor location (PTL) according to BRAF, RAS, and microsatellite instability (MSI) status in patients who have undergone resection for colon cancer (CC) and have been treated with current standard adjuvant chemotherapy. Objective: To determine the prognostic and predictive value of PTL according to BRAF, RAS, and MSI status in patients with stage III CC receiving adjuvant treatment with FOLFOX (folinic acid [leucovorin calcium], fluorouracil, and oxaliplatin) with or without cetuximab...
November 22, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/29167028/corrigendum-to-validation-of-a-next-generation-sequencing-panel-for-detection-of-hotspot-cancer-mutations-in-a-clinical-laboratory-journal-information-pathology-research-and-practice-2017-volume-213-issue-2-pages-98-105
#3
Reza Shahsiah, Jenefer DeKoning, Saeed Samie, Seyed Ziaeddin Latifzadeh, Zahra Mehdizadeh Kashi
No abstract text is available yet for this article.
December 2017: Pathology, Research and Practice
https://www.readbyqxmd.com/read/29165888/molecular-pathology-and-thyroid-fna
#4
REVIEW
D N Poller, S Glaysher
This review summarises molecular pathological techniques applicable to thyroid FNA. The molecular pathology of thyroid tumours is now fairly well understood. Molecular methods may be used as a rule-in test for diagnosis of malignancy in thyroid nodules, eg BRAF V600E point mutation, use of a seven-gene mutational panel (BRAF V600E, RAS genes, RET/PTC or PAX8/PPARG rearrangement), or as a comprehensive multigene next-generation sequencing panel, eg ThyroSeq v2. Molecular methods can also be applied as rule-out tests for malignancy in thyroid nodules, eg Afirma or ThyroSeq v2 or as markers of prognosis, eg TERT promoter mutation or other gene mutations including BRAF V600E, TP53 and AKT1, and as tests for newly defined tumour entities such as non-invasive follicular thyroid neoplasm with papillary like nuclei, or as a molecular marker(s) for targeted therapies...
December 2017: Cytopathology: Official Journal of the British Society for Clinical Cytology
https://www.readbyqxmd.com/read/29165687/investigation-of-the-relationship-between-radiation-dose-and-gene-mutations-and-fusions-in-post-chernobyl-thyroid-cancer
#5
Alexey A Efanov, Alina V Brenner, Tetiana I Bogdanova, Lindsey M Kelly, Pengyuan Liu, Mark P Little, Abigail I Wald, Maureen Hatch, Liudmyla Y Zurnadzy, Marina N Nikiforova, Vladimir Drozdovitch, Kiyohiko Mabuchi, Mykola D Tronko, Stephen J Chanock, Yuri E Nikiforov
Background: Exposure to ionizing radiation during childhood is a well-established risk factor for thyroid cancer. However, the genetic mechanisms of radiation-associated carcinogenesis remain not fully understood. Methods: In this study, we used targeted next-generation sequencing and RNA-Seq to study 65 papillary thyroid cancers (PTCs) from patients in the Ukrainian-American cohort with measurement-based iodine-131 (I-131) thyroid doses received as a result of the Chernobyl accident...
November 18, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29165356/fast-detection-of-a-brca2-large-genomic-duplication-by-next-generation-sequencing-as-a-single-procedure-a-case-report
#6
Marcella Nunziato, Flavio Starnone, Barbara Lombardo, Matilde Pensabene, Caterina Condello, Francesco Verdesca, Chiara Carlomagno, Sabino De Placido, Lucio Pastore, Francesco Salvatore, Valeria D'Argenio
The aim of this study was to verify the reliability of a next generation sequencing (NGS)-based method as a strategy to detect all possible BRCA mutations, including large genomic rearrangements. Genomic DNA was obtained from a peripheral blood sample provided by a patient from Southern Italy with early onset breast cancer and a family history of diverse cancers. BRCA molecular analysis was performed by NGS, and sequence data were analyzed using two software packages. Comparative genomic hybridization (CGH) array was used as confirmatory method...
November 22, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29163793/rapid-ultra-low-coverage-copy-number-profiling-of-cell-free-dna-as-a-precision-oncology-screening-strategy
#7
Daniel H Hovelson, Chia-Jen Liu, Yugang Wang, Qing Kang, James Henderson, Amy Gursky, Scott Brockman, Nithya Ramnath, John C Krauss, Moshe Talpaz, Malathi Kandarpa, Rashmi Chugh, Missy Tuck, Kirk Herman, Catherine S Grasso, Michael J Quist, Felix Y Feng, Christine Haakenson, John Langmore, Emmanuel Kamberov, Tim Tesmer, Hatim Husain, Robert J Lonigro, Dan Robinson, David C Smith, Ajjai S Alva, Maha H Hussain, Arul M Chinnaiyan, Muneesh Tewari, Ryan E Mills, Todd M Morgan, Scott A Tomlins
Current cell-free DNA (cfDNA) next generation sequencing (NGS) precision oncology workflows are typically limited to targeted and/or disease-specific applications. In advanced cancer, disease burden and cfDNA tumor content are often elevated, yielding unique precision oncology opportunities. We sought to demonstrate the utility of a pan-cancer, rapid, inexpensive, whole genome NGS of cfDNA approach (PRINCe) as a precision oncology screening strategy via ultra-low coverage (~0.01x) tumor content determination through genome-wide copy number alteration (CNA) profiling...
October 27, 2017: Oncotarget
https://www.readbyqxmd.com/read/29163380/focused-review-cytotoxic-and-antioxidant-potentials-of-mangrove-derived-streptomyces
#8
REVIEW
Hooi-Leng Ser, Loh Teng-Hern Tan, Jodi Woan-Fei Law, Kok-Gan Chan, Acharaporn Duangjai, Surasak Saokaew, Priyia Pusparajah, Nurul-Syakima Ab Mutalib, Tahir Mehmood Khan, Bey-Hing Goh, Learn-Han Lee
Human life expectancy is rapidly increasing with an associated increasing burden of chronic diseases, such as neurodegenerative diseases and cancer. However, there is limited progress in finding effective treatment for these conditions. For this reason, members of the genus Streptomyces have been explored extensively over the past decades as these filamentous bacteria are highly efficient in producing bioactive compounds with human health benefits. Being ubiquitous in nature, streptomycetes can be found in both terrestrial and marine environments...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29162654/the-impact-of-hereditary-cancer-gene-panels-on-clinical-care-and-lessons-learned
#9
Volkan Okur, Wendy K Chung
Mutations in hereditary cancer syndromes account for a modest fraction of all cancers; however, identifying patients with these germline mutations offers tremendous health benefits to both patients and their family members. There are about 60 genes that confer a high lifetime risk of specific cancers, and this information can be used to tailor prevention, surveillance, and treatment. With advances in next-generation sequencing technologies and the elimination of gene patents for evaluating genetic information, we are now able to analyze multiple genes simultaneously, leading to the widespread clinical use of gene panels for germline cancer testing...
November 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29160420/next-generation-sequencing-based-genomic-profiling-fostering-innovation-in-cancer-care
#10
Gustavo S Fernandes, Daniel F Marques, Daniel M Girardi, Maria Ignez F Braghiroli, Renata A Coudry, Sibele I Meireles, Artur Katz, Paulo M Hoff
OBJECTIVES: With the development of next-generation sequencing (NGS) technologies, DNA sequencing has been increasingly utilized in clinical practice. Our goal was to investigate the impact of genomic evaluation on treatment decisions for heavily pretreated patients with metastatic cancer. METHODS: We analyzed metastatic cancer patients from a single institution whose cancers had progressed after all available standard-of-care therapies and whose tumors underwent next-generation sequencing analysis...
October 2017: Clinics
https://www.readbyqxmd.com/read/29158372/enhancing-next-generation-sequencing-guided-cancer-care-through-cognitive-computing
#11
Nirali M Patel, Vanessa V Michelini, Jeff M Snell, Saianand Balu, Alan P Hoyle, Joel S Parker, Michele C Hayward, David A Eberhard, Ashley H Salazar, Patrick McNeillie, Jia Xu, Claudia S Huettner, Takahiko Koyama, Filippo Utro, Kahn Rhrissorrakrai, Raquel Norel, Erhan Bilal, Ajay Royyuru, Laxmi Parida, H Shelton Earp, Juneko E Grilley-Olson, D Neil Hayes, Stephen J Harvey, Norman E Sharpless, William Y Kim
BACKGROUND: Using next-generation sequencing (NGS) to guide cancer therapy has created challenges in analyzing and reporting large volumes of genomic data to patients and caregivers. Specifically, providing current, accurate information on newly approved therapies and open clinical trials requires considerable manual curation performed mainly by human "molecular tumor boards" (MTBs). The purpose of this study was to determine the utility of cognitive computing as performed by Watson for Genomics (WfG) compared with a human MTB...
November 20, 2017: Oncologist
https://www.readbyqxmd.com/read/29158289/next-generation-panel-sequencing-identifies-nf1-germline-mutations-in-three-patients-with-pheochromocytoma-but-no-clinical-diagnosis-of-neurofibromatosis-type-1
#12
Laura Gieldon, Jimmy Rusdian Masjkur, Susan Richter, Roland Därr, Marcos Lahera, Daniela E Aust, Silke Zeugner, Andreas Rump, Karl Hackmann, Andreas Tzschach, Andrzej Januszewicz, Aleksander Prejbisz, Graeme Eisenhofer, Evelin Schroeck, Mercedes Robledo, Barbara Klink
Objective Our objective was to improve molecular diagnostics in patients with hereditary pheochromocytoma and paraganglioma (PPGL) by using next generation sequencing (NGS) multi-gene panel analysis. Derived from this study we here present three cases that were diagnosed with NF1 germline mutations but did not have a prior clinical diagnosis of Neurofibromatosis Type 1 (NF1). Design We performed genetic analysis of known tumor predisposition genes, including NF1, using a multi-gene NGS enrichment-based panel applied to a total of 1029 PPGL patients...
November 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29157215/integration-of-rna-seq-data-with-heterogeneous-microarray-data-for-breast-cancer-profiling
#13
Daniel Castillo, Juan Manuel Gálvez, Luis Javier Herrera, Belén San Román, Fernando Rojas, Ignacio Rojas
BACKGROUND: Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more recent Next Generation Sequencing technologies, such as RNA-Seq. In any case, information from microarrays is truthful and robust, thus it can be exploited through the integration of microarray data with RNA-Seq data. Additionally, information extraction and acquisition of large number of samples in RNA-Seq still entails very high costs in terms of time and computational resources...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29156800/comparative-molecular-analyses-of-left-sided-colon-right-sided-colon-and-rectal-cancers
#14
Mohamed E Salem, Benjamin A Weinberg, Joanne Xiu, Wafik S El-Deiry, Jimmy J Hwang, Zoran Gatalica, Philip A Philip, Anthony F Shields, Heinz-Josef Lenz, John L Marshall
Tumor sidedness has emerged as an important prognostic and predictive factor in the treatment of colorectal cancer. Recent studies demonstrate that patients with advanced right-sided colon cancers have a worse prognosis than those with left-sided colon or rectal cancers, and these patient subgroups respond differently to biological therapies. Historically, management of patients with metastatic colon and rectal cancers has been similar, and colon and rectal cancer patients have been grouped together in large clinical trials...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29154802/microrna-profiling-in-mda-mb-231-human-breast-cancer-cell-exposed-to-the-phaleria-macrocarpa-boerl-fruit-ethyl-acetate-fraction-pmeaf-through-iilumina-hi-seq-technologies-and-various-in-silico-bioinformatics-tools
#15
Nowroji Kavitha, Soundararajan Vijayarathna, Shanmugapriya, Chern Ein Oon, Yeng Chen, Jagat R Kanwar, Vasu Punj, Sreenivasan Sasidharan
ETHNOPHARMACOLOGICAL RELEVANCE: Phaleria macrocarpa (Scheff) Boerl, is a famous traditional medicinal plant which exhibited cytotoxicity against various cancerous cells. Traditionally, P. macrocarpa has been used to control cancer, impotency, hemorrhoids, diabetes mellitus, allergies, liver and heart disease, kidney disorders, blood diseases, acne, stroke, migraine, and various skin diseases. AIM OF THE STUDY: Recent studies have demonstrated a potent anticancer potential of P...
November 14, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/29154079/clinical-performance-of-a-next-generation-sequencing-assay-thyroseq-v2-in-the-evaluation-of-indeterminate-thyroid-nodules
#16
Aida Taye, Dillon Gurciullo, Brett A Miles, Ashita Gupta, Randall P Owen, William B Inabnet, Jessica N Beyda, Jennifer L Marti
BACKGROUND: Molecular testing with the Thyroseq v2 next generation sequencing panel ("Thyroseq") is used to estimate the risk of cancer in indeterminate thyroid nodules. METHODS: We analyzed 156 indeterminate thyroid nodules evaluated with Thyroseq, across 3 institutions. Thyroseq data and surgical pathology were matched via pathologic re-review. A result was considered Thyroseq positive if molecular alterations were annotated on the report with malignancy probability >30%...
November 16, 2017: Surgery
https://www.readbyqxmd.com/read/29153095/circulating-cell-free-dna-mutation-patterns-in-early-and-late-stage-colon-and-pancreatic-cancer
#17
Eveline E Vietsch, Garrett T Graham, Justine N McCutcheon, Aamir Javaid, Giuseppe Giaccone, John L Marshall, Anton Wellstein
Cancer is a heterogeneous disease harboring diverse subclonal populations that can be discriminated by their DNA mutations. Environmental pressure selects subclones that ultimately drive disease progression and tumor relapse. Circulating cell-free DNA (ccfDNA) can be used to approximate the mutational makeup of cancer lesions and can serve as a marker for monitoring disease progression at the molecular level without the need for invasively acquired samples from primary or metastatic lesions. This potential for molecular analysis makes ccfDNA attractive for the study of clonal evolution and for uncovering emerging therapeutic resistance or sensitivity...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29153093/next-generation-sequencing-and-molecular-cytogenetic-characterization-of-etv6-lyn-fusion-due-to-chromosomes-1-8-and-12-rearrangement-in-acute-myeloid-leukemia
#18
Edmond S K Ma, Thomas S K Wan, Chun Hang Au, Dona N Ho, Shing Yan Ma, Margaret H L Ng, Tsun Leung Chan
In a newly diagnosed patient with acute myeloid leukemia (AML) and complex cytogenetics and negative for gene mutations associated with myeloid neoplasms, RNA sequencing by next-generation sequencing (NGS) through a large cancer-related gene panel showed ETV6-LYN leukemic fusion transcript. Breakpoint analysis of the NGS reads showed fusion of exon 5 of the ETV6 gene to exon 8 of the LYN gene. Metaphase fluorescence in situ hybridization (FISH) inferred a four-break rearrangement of three chromosomes, namely 1, 8 and 12...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29152076/profiling-tumour-heterogeneity-through-circulating-tumour-dna-in-patients-with-pancreatic-cancer
#19
Patricia Adamo, Caroline M Cowley, Christopher P Neal, Vilas Mistry, Karen Page, Ashley R Dennison, John Isherwood, Robert Hastings, JinLi Luo, David A Moore, Pringle J Howard, Martins L Miguel, Catrin Pritchard, Margaret Manson, Jacqui A Shaw
The majority of pancreatic ductal adenocarcinomas (PDAC) are diagnosed late so that surgery is rarely curative. Earlier detection could significantly increase the likelihood of successful treatment and improve survival. The aim of the study was to provide proof of principle that point mutations in key cancer genes can be identified by sequencing circulating free DNA (cfDNA) and that this could be used to detect early PDACs and potentially, premalignant lesions, to help target early effective treatment. Targeted next generation sequencing (tNGS) analysis of mutation hotspots in 50 cancer genes was conducted in 26 patients with PDAC, 14 patients with chronic pancreatitis (CP) and 12 healthy controls with KRAS status validated by digital droplet PCR...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29151929/identification-of-circular-rna-signature-in-bladder-cancer
#20
Xiao Yang, Wenbo Yuan, Jun Tao, Peng Li, Chengdi Yang, Xiaheng Deng, Xiaolei Zhang, Jingyuan Tang, Jie Han, Jingzi Wang, Pengchao Li, Qiang Lu, Min Gu
Circular RNA (circRNA) comprises a class of endogenous species of RNA consisting of a circular loop that is crucial for genetic and epigenetic regulation. The significance of circRNA in bladder cancer (BCa) remains to be investigated. Here we performed genome‑wide circRNA analysis of 5 paired tumour and adjacent normal tissue samples from BCa patients via next generation sequencing (NGS) technology. Next we confirmed NGS data in a separate set of 32 paired BCa samples using quantitative real-time reverse transcription polymerase chain reaction...
2017: Journal of Cancer
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