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Somatic mutation guideline

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https://www.readbyqxmd.com/read/29669169/genetic-testing-for-hereditary-prostate-cancer-current-status-and-limitations
#1
REVIEW
Jun Tu Zhen, Jamil Syed, Kevin Anh Nguyen, Michael S Leapman, Neeraj Agarwal, Karina Brierley, Xavier Llor, Erin Hofstatter, Brian Shuch
A significant proportion of prostate cancer diagnoses may be associated with a strong hereditary component. Men who have multiple single-gene polymorphisms and a family history of prostate cancer have a significantly greater risk of developing prostate cancer. Numerous single-gene alterations have been confirmed to increase the risk of prostate cancer. These include breast cancer genes 1 and 2 (BRCA1 and BRCA2, respectively), mutL homolog 1 (MLH1), mutS homologs 2 and 6 (MSH2 and MSH6, respectively), postmeiotic segregation increased 2 (PMS2), homeobox B13 (HOXB13), checkpoint kinase 2 (CHEK2), nibrin (NBN), BRCA1-interacting protein C-terminal helicase 1 (BRIP1), and ataxia telangiectasia mutated (ATM)...
April 18, 2018: Cancer
https://www.readbyqxmd.com/read/29507673/analysis-of-a-gene-panel-for-targeted-sequencing-of-colorectal-cancer-samples
#2
Klaus Højgaard Jensen, Jose M G Izarzugaza, Agnieszka Sierakowska Juncker, Rasmus Borup Hansen, Torben Frøstrup Hansen, Pascal Timshel, Thorarinn Blondal, Thomas Skøt Jensen, Eske Rygaard-Hjalsted, Peter Mouritzen, Michael Thorsen, Rasmus Wernersson, Henrik Bjørn Nielsen, Anders Jakobsen, Søren Brunak, Flemming Brandt Sørensen
Colorectal cancer (CRC) is a leading cause of death worldwide. Surgical intervention is a successful treatment for stage I patients, whereas other more advanced cases may require adjuvant chemotherapy. The selection of effective adjuvant treatments remains, however, challenging. Accurate patient stratification is necessary for the identification of the subset of patients likely responding to treatment, while sparing others from pernicious treatment. Targeted sequencing approaches may help in this regard, enabling rapid genetic investigation, and at the same time easily applicable in routine diagnosis...
February 6, 2018: Oncotarget
https://www.readbyqxmd.com/read/29498920/update-on-the-clinicopathology-of-pituitary-adenomas
#3
Chung Thong Lim, Márta Korbonits
Pituitary adenomas are the third most common central nervous system tumours and arise from the anterior pituitary within the pituitary fossa. The signs and symptoms of patients with pituitary adenomas vary from 'mass effects' caused by a large adenoma to features secondary to excess pituitary hormones produced by the functioning pituitary adenoma. Detailed histopathological assessment, based on novel classifications and the latest WHO guidelines, helps to categorise pituitary adenomas into different subtypes and identify features that, in some cases, help to predict their behaviour...
March 2, 2018: Endocrine Practice
https://www.readbyqxmd.com/read/29236352/iccs-escca-consensus-guidelines-to-detect-gpi-deficient-cells-in-paroxysmal-nocturnal-hemoglobinuria-pnh-and-related-disorders-part-1-clinical-utility
#4
Amy E Dezern, Michael J Borowitz
Paroxysmal nocturnal hemoglobinuria (PNH) arises as a consequence of the non-malignant clonal expansion of one or more hematopoietic stem cells with an acquired somatic mutation of the PIGA gene (Brodsky RA. Blood 113 (2009) 6522-6527). Progeny of affected stem cells are deficient in glycosyl phosphatidylinositol-anchored proteins (GPI-APs). This deficiency is readily detected by flow cytometry. Though this seems straightforward, the clinical utility of this testing requires that the ordering clinician understand not only the characteristics of the test, but also the biology of the underlying disease, and the clinical and laboratory manifestations in the individual patient...
January 2018: Cytometry. Part B, Clinical Cytometry
https://www.readbyqxmd.com/read/29204511/-smarca4-germline-gene-mutation-in-a-patient-with-epithelial-ovarian-a-case-report
#5
Reshma Muppala, Talia Donenberg, Marilyn S Huang, Matthew P Schlumbrecht
Background: SMARCA4 is gene whose protein product participates in chromatin remodeling. Somatic mutations in this gene are associated with non-small cell lung cancer and malignant rhabdoid tumors, and both germline and somatic mutations are seen with small cell carcinoma of the ovary, hypercalcemic type. To date, there are no data identifying an association with more common epithelial carcinomas of the ovary. Case: The patient is a 57-year-old female without any significant family history of cancer, diagnosed with high-grade serous carcinoma of the ovary...
November 2017: Gynecologic Oncology Reports
https://www.readbyqxmd.com/read/29200117/common-histologically-benign-tumors-of-the-brain
#6
Roy E Strowd, Jaishri O Blakeley
PURPOSE OF REVIEW: As a group, benign tumors account for the majority of primary neoplasms affecting the central nervous system (CNS). This article reviews the epidemiology, clinical presentation, neuroimaging features, and management of the most common of these tumors: meningiomas, schwannomas, and pituitary adenomas. RECENT FINDINGS: Awareness of the most common nonmalignant tumors of the CNS and their management guidelines is important as many of these tumors are managed conservatively, with neurologists playing a primary role in both surveillance and symptom management...
December 2017: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/29191607/pik3ca-mutation-as-a-distinctive-genetic-feature-of-non-small-cell-lung-cancer-with-chronic-obstructive-pulmonary-disease-a-comprehensive-mutational-analysis-from-a-multi-institutional-cohort
#7
Kenji Sawa, Yasuhiro Koh, Tomoya Kawaguchi, Satoshi Kambayashi, Kazuhisa Asai, Shigeki Mitsuoka, Tatsuo Kimura, Naruo Yoshimura, Naoki Yoshimoto, Akihito Kubo, Hideo Saka, Akihide Matsumura, Hideki Wanibuchi, Nobuyuki Yamamoto, Noritoshi Nishiyama, Kazuto Hirata
OBJECTIVES: Non-small cell lung cancer (NSCLC) and chronic obstructive pulmonary disease (COPD) have been proposed to have a mutual developmental mechanism, but their association has not been fully understood. We aimed to examine the association of the mutational landscape of NSCLC with co-morbid COPD. MATERIALS AND METHODS: A total of 197 surgical specimens of early stage NSCLC were retrospectively collected from two independent sources, namely, the Japan Molecular Epidemiology for Lung Cancer Study and the Osaka City University Hospital cohort from 2010 to 2013...
October 2017: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29162654/the-impact-of-hereditary-cancer-gene-panels-on-clinical-care-and-lessons-learned
#8
EDITORIAL
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/29118233/hairy-cell-leukemia-version-2-2018-nccn-clinical-practice-guidelines-in-oncology
#9
William G Wierda, John C Byrd, Jeremy S Abramson, Seema Bhat, Greg Bociek, Danielle Brander, Jennifer Brown, Asher Chanan-Khan, Steve E Coutre, Randall S Davis, Christopher D Fletcher, Brian Hill, Brad S Kahl, Manali Kamdar, Lawrence D Kaplan, Nadia Khan, Thomas J Kipps, Jeffrey Lancet, Shuo Ma, Sami Malek, Claudio Mosse, Mazyar Shadman, Tanya Siddiqi, Deborah Stephens, Nina Wagner, Andrew D Zelenetz, Mary A Dwyer, Hema Sundar
Hairy cell leukemia (HCL) is a rare type of indolent B-cell leukemia, characterized by symptoms of fatigue and weakness, organomegaly, pancytopenia, and recurrent opportunistic infections. Classic HCL should be considered a distinct clinical entity separate from HCLvariant (HCLv), which is associated with a more aggressive disease course and may not respond to standard HCL therapies. Somatic hypermutation in the IGHV gene is present in most patients with HCL. The BRAF V600E mutation has been reported in most patients with classic HCL but not in those with other B-cell leukemias or lymphomas...
November 2017: Journal of the National Comprehensive Cancer Network: JNCCN
https://www.readbyqxmd.com/read/29097733/discovery-of-targetable-genetic-alterations-in-advanced-non-small-cell-lung-cancer-using-a-next-generation-sequencing-based-circulating-tumor-dna-assay
#10
Helei Hou, Xiaonan Yang, Jinping Zhang, Zhe Zhang, Xiaomei Xu, Xiaoping Zhang, Chuantao Zhang, Dong Liu, Weihua Yan, Na Zhou, Hongmei Zhu, Zhaoyang Qian, Zhuokun Li, Xiaochun Zhang
Next-generation sequencing (NGS)-based circulating tumor DNA (ctDNA) assays have provided a new method of identifying tumor-driving genes in patients with advanced non-small cell lung carcinoma (NSCLC), especially in those whose cancer tissues are unavailable or in those that have acquired treatment resistance. Here, we describe a total of 119 patients with advanced EGFR-TKI-naive NSCLC and 15 EGFR-TKI-resistant patients to identify somatic SNVs, small indels, CNVs and gene fusions in 508 tumor-related genes...
November 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29082853/cancer-gene-profiling-in-non-small-cell-lung-cancers-reveals-activating-mutations-in-jak2-and-jak3-with-therapeutic-implications
#11
Shuyu D Li, Meng Ma, Hui Li, Aneta Waluszko, Tatyana Sidorenko, Eric E Schadt, David Y Zhang, Rong Chen, Fei Ye
BACKGROUND: Next-generation sequencing (NGS) of cancer gene panels are widely applied to enable personalized cancer therapy and to identify novel oncogenic mutations. METHODS: We performed targeted NGS on 932 clinical cases of non-small-cell lung cancers (NSCLCs) using the Ion AmpliSeq™ Cancer Hotspot panel v2 assay. RESULTS: Actionable mutations were identified in 65% of the cases with available targeted therapeutic options, including 26% of the patients with mutations in National Comprehensive Cancer Network (NCCN) guideline genes...
October 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29065433/primary-aldosteronism-the-next-five-years
#12
John W Funder
The management of primary aldosteronism is widely varied within various published guidelines, with very little in the way of data supporting the choice of one variation over others. Current estimates of prevalence are probably accurate for aldosterone producing adenoma, but fall very short of that for bilateral adrenal hyperplasia. Discovery at the level of basic science has proven illuminating over the past 6 years in terms of unilateral disease and both somatic and germline mutations, with much less focus on the much more common bilateral disease; Attempts at harmonization have begun - for example, criteria for complete/partial/absent cure after adrenalectomy for unilateral disease; again focus on bilateral disease is muted...
December 2017: Hormone and Metabolic Research, Hormon- und Stoffwechselforschung, Hormones et Métabolisme
https://www.readbyqxmd.com/read/28890946/oncokb-a-precision-oncology-knowledge-base
#13
Debyani Chakravarty, Jianjiong Gao, Sarah M Phillips, Ritika Kundra, Hongxin Zhang, Jiaojiao Wang, Julia E Rudolph, Rona Yaeger, Tara Soumerai, Moriah H Nissan, Matthew T Chang, Sarat Chandarlapaty, Tiffany A Traina, Paul K Paik, Alan L Ho, Feras M Hantash, Andrew Grupe, Shrujal S Baxi, Margaret K Callahan, Alexandra Snyder, Ping Chi, Daniel Danila, Mrinal Gounder, James J Harding, Matthew D Hellmann, Gopa Iyer, Yelena Janjigian, Thomas Kaley, Douglas A Levine, Maeve Lowery, Antonio Omuro, Michael A Postow, Dana Rathkopf, Alexander N Shoushtari, Neerav Shukla, Martin Voss, Ederlinda Paraiso, Ahmet Zehir, Michael F Berger, Barry S Taylor, Leonard B Saltz, Gregory J Riely, Marc Ladanyi, David M Hyman, José Baselga, Paul Sabbatini, David B Solit, Nikolaus Schultz
PURPOSE: With prospective clinical sequencing of tumors emerging as a mainstay in cancer care, there is an urgent need for a clinical support tool that distills the clinical implications associated with specific mutation events into a standardized and easily interpretable format. To this end, we developed OncoKB, an expert-guided precision oncology knowledge base. METHODS: OncoKB annotates the biological and oncogenic effect and the prognostic and predictive significance of somatic molecular alterations...
July 2017: JCO Precision Oncology
https://www.readbyqxmd.com/read/28833575/in-vivo-pig-a-and-micronucleus-study-of-the-prototypical-aneugen-vinblastine-sulfate
#14
Svetlana L Avlasevich, Carson Labash, Dorothea K Torous, Jeffrey C Bemis, James T MacGregor, Stephen D Dertinger
The Pig-a assay is being used in regulatory studies to evaluate the potential of agents to induce somatic cell gene mutations and an OECD test guideline is under development. A working group involved with establishing the guideline recently noted that representative aneugenic agents had not been evaluated, and to help fill this data gap Pig-a mutant phenotype and micronucleated reticulocyte frequencies were measured in an integrated study design to assess the mutagenic and cytogenetic damage responses to vinblastine sulfate exposure...
January 2018: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28771233/impact-of-germline-and-somatic-brca1-2-mutations-tumor-spectrum-and-detection-platforms
#15
REVIEW
H Wu, X Wu, Z Liang
The BRCA1/2 genes are long and complex and mutation carriers are at risk of developing malignancies, mainly of gynecological origin. Various mutations arise in these genes and their characterization is a time-consuming, cost intensive, complicated process. Tumors of BRCA1/2 origin have distinct molecular and histological features that can impact responses to therapy. Therefore, detection of these mutations constitutes an important step in the risk assessment, prevention strategy and treatment of subjects. Although Sanger sequencing is the gold standard for the detection of genetic mutations, several next generation sequencing-based high throughput platforms have been developed and adapted for the detection of BRCA1/2 mutations...
October 2017: Gene Therapy
https://www.readbyqxmd.com/read/28760304/diagnostic-prognostic-and-predictive-utility-of-recurrent-somatic-mutations-in-myeloid-neoplasms
#16
REVIEW
Umang Patel, Rajyalakshmi Luthra, L Jeffrey Medeiros, Keyur P Patel
The classification and risk stratification of myeloid neoplasms, including acute myeloid leukemia, myelodysplastic syndromes, myelodysplastic syndromes/myeloproliferative neoplasms, and myeloproliferative neoplasms, have increasingly been guided by molecular genetic abnormalities. Gene expression analysis and next-generation sequencing have led to the ever increasing discovery of somatic gene mutations in myeloid neoplasms. Mutations have been identified in genes involved in epigenetic modification, RNA splicing, transcription factors, DNA repair, and the cohesin complex...
July 2017: Clinical Lymphoma, Myeloma & Leukemia
https://www.readbyqxmd.com/read/28642172/egfr-t790m-ctdna-testing-platforms-and-their-role-as-companion-diagnostics-correlation-with-clinical-outcomes-to-egfr-tkis
#17
REVIEW
Zhiyong Liang, Ying Cheng, Yuan Chen, Yanping Hu, Wei-Ping Liu, You Lu, Jie Wang, Ye Wang, Gang Wu, Jian-Ming Ying, He-Long Zhang, Xu-Chao Zhang, Yi-Long Wu
Somatic mutation in the epidermal growth factor receptor (EGFR) predict clinical response to EGFR tyrosine kinase inhibitors in non-small cell lung cancer (NSCLC) and is a promising target for personalised medicine. EGFR mutations have prognostic value. Initially patients respond well to tyrosine kinase inhibitors but finally they would develop resistance and about 50% of this resistance can be attributed to the emergence of EGFR resistant mutation, T790M. This necessitates the need for genetic testing for clinical management of patients...
September 10, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28561687/new-insight-into-the-biology-risk-stratification-and-targeted-treatment-of-myelodysplastic-syndromes
#18
Mintallah Haider, Eric J Duncavage, Khalid F Afaneh, Rafael Bejar, Alan F List
In myelodysplastic syndromes (MDS), somatic mutations occur in five major categories: RNA splicing, DNA methylation, activated cell signaling, myeloid transcription factors, and chromatin modifiers. Although many MDS cases harbor more than one somatic mutation, in general, there is mutual exclusivity of mutated genes within a class. In addition to the prognostic significance of individual somatic mutations, more somatic mutations in MDS have been associated with poor prognosis. Prognostic assessment remains a critical component of the personalization of care for patient with MDS because treatment is highly risk adapted...
2017: American Society of Clinical Oncology Educational Book
https://www.readbyqxmd.com/read/28521741/the-rainfall-plot-its-motivation-characteristics-and-pitfalls
#19
Diana Domanska, Daniel Vodák, Christin Lund-Andersen, Stefania Salvatore, Eivind Hovig, Geir Kjetil Sandve
BACKGROUND: A visualization referred to as rainfall plot has recently gained popularity in genome data analysis. The plot is mostly used for illustrating the distribution of somatic cancer mutations along a reference genome, typically aiming to identify mutation hotspots. In general terms, the rainfall plot can be seen as a scatter plot showing the location of events on the x-axis versus the distance between consecutive events on the y-axis. Despite its frequent use, the motivation for applying this particular visualization and the appropriateness of its usage have never been critically addressed in detail...
May 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28463398/using-funseq2-for-coding-and-non-coding-variant-annotation-and-prioritization
#20
Priyanka Dhingra, Yao Fu, Mark Gerstein, Ekta Khurana
The identification of non-coding drivers remains a challenge and bottleneck for the use of whole-genome sequencing in the clinic. FunSeq2 is a computational tool for annotation and prioritization of somatic mutations in coding and non-coding regions. It integrates a data context made from large-scale genomic datasets and uses a high-throughput variant prioritization pipeline. This unit provides guidelines for installing and running FunSeq2 to (a) annotate and prioritize variants, (b) incorporate user-defined annotations, and (c) detect differential gene expression...
May 2, 2017: Current Protocols in Bioinformatics
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