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Somatic mutation guideline

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https://www.readbyqxmd.com/read/27899194/strategies-for-clinical-implementation-of-screening-for-hereditary-cancer-syndromes
#1
REVIEW
Brandie Heald, Jessica Marquard, Pauline Funchain
Hereditary cancer syndromes generally account for 5%-10% of malignancies. While these syndromes are rare, affected patients carry significantly elevated risks of developing cancer, as do their at-risk relatives. Identification of these patients is critical to ensure timely and appropriate genetic testing relevant to cancer patients and their relatives. Several guidelines and tools are available to assist clinicians. Patients suspected to have hereditary cancer syndromes should be offered genetic testing in the setting of genetic counseling by a qualified genetics professional...
October 2016: Seminars in Oncology
https://www.readbyqxmd.com/read/27821315/current-perspectives-on-recommendations-for-brca-genetic-testing-in-ovarian-cancer-patients
#2
Ignace Vergote, Susana Banerjee, Anne-Marie Gerdes, Christi van Asperen, Christian Marth, Fatima Vaz, Isabelle Ray-Coquard, Dominique Stoppa-Lyonnet, Antonio Gonzalez-Martin, Jalid Sehouli, Nicoletta Colombo
Traditionally, BRCA genetic testing has been undertaken to identify patients and family members at future risk of developing cancer and patients have been referred for testing based on family history. However, the now recognised risk of ovarian cancer (OC) patients, even those with no known family history, harbouring a mutation in BRCA1/2, together with the first poly adenosine diphosphate ribose polymerase inhibitor (PARPi; olaparib [Lynparza]) being licenced for the treatment of BRCA-mutated OC, has led to reconsideration of referral criteria for OC patients...
December 2016: European Journal of Cancer
https://www.readbyqxmd.com/read/27764253/differential-dynamics-of-calr-mutant-allele-burden-in-myeloproliferative-neoplasms-during-interferon-alfa-treatment
#3
Lasse Kjær, Sabrina Cordua, Morten O Holmström, Mads Thomassen, Torben A Kruse, Niels Pallisgaard, Thomas S Larsen, Karin de Stricker, Vibe Skov, Hans C Hasselbalch
Discovery of somatic mutations in the calreticulin gene (CALR) has identified a subgroup of Philadelphia-negative chronic myeloproliferative neoplasms (MPN) with separate haematological characteristics and prognosis. CALR mutations serve as novel markers both of diagnostic value and as targets for monitoring molecular responses during therapy. Interferon-α (IFN) selectively targets the malignant clone in a subset of MPN patients and can induce both haematological and molecular remissions in CALR mutated essential thrombocythemia (ET) patients...
2016: PloS One
https://www.readbyqxmd.com/read/27678269/integration-of-next-generation-sequencing-in-clinical-diagnostic-molecular-pathology-laboratories-for-analysis-of-solid-tumours-an-expert-opinion-on-behalf-of-iqn-path-asbl
#4
Zandra C Deans, Jose Luis Costa, Ian Cree, Els Dequeker, Anders Edsjö, Shirley Henderson, Michael Hummel, Marjolijn Jl Ligtenberg, Marco Loddo, Jose Carlos Machado, Antonio Marchetti, Katherine Marquis, Joanne Mason, Nicola Normanno, Etienne Rouleau, Ed Schuuring, Keeda-Marie Snelson, Erik Thunnissen, Bastiaan Tops, Gareth Williams, Han van Krieken, Jacqueline A Hall
The clinical demand for mutation detection within multiple genes from a single tumour sample requires molecular diagnostic laboratories to develop rapid, high-throughput, highly sensitive, accurate and parallel testing within tight budget constraints. To meet this demand, many laboratories employ next-generation sequencing (NGS) based on small amplicons. Building on existing publications and general guidance for the clinical use of NGS and learnings from germline testing, the following guidelines establish consensus standards for somatic diagnostic testing, specifically for identifying and reporting mutations in solid tumours...
September 27, 2016: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/27650663/next-generation-testing-strategy-for-assessment-of-genomic-damage-a-conceptual-framework-and-considerations
#5
Kerry L Dearfield, B Bhaskar Gollapudi, Jeffrey C Bemis, R Daniel Benz, George R Douglas, Rosalie K Elespuru, George E Johnson, David J Kirkland, Matthew J LeBaron, Albert P Li, Francesco Marchetti, Lynn H Pottenger, Emiel Rorije, Jennifer Y Tanir, Veronique Thybaud, Jan van Benthem, Carole L Yauk, Errol Zeiger, Mirjam Luijten
For several decades, regulatory testing schemes for genetic damage have been standardized where the tests being utilized examined mutations and structural and numerical chromosomal damage. This has served the genetic toxicity community well when most of the substances being tested were amenable to such assays. The outcome from this testing is usually a dichotomous (yes/no) evaluation of test results, and in many instances, the information is only used to determine whether a substance has carcinogenic potential or not...
September 21, 2016: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/27560719/the-role-of-genetic-testing-in-the-selection-of-therapy-for-breast-cancer-a-review
#6
Polly Niravath, Burcu Cakar, Matthew Ellis
Importance: The application of next-generation sequencing (NGS) genomic testing for somatic mutations in breast oncology has been slower than anticipated due to issues with clinical applicability and natural heterogeneity of breast cancer. This review summarizes the state of the field and considers approaches for more effective implementation. Observations: While there is an emerging role for germline genetic testing potentially predicting sensitivity to platinum salts and PARP inhibitors, the data regarding somatic mutation for prediction of drug sensitivity remains controversial...
August 25, 2016: JAMA Oncology
https://www.readbyqxmd.com/read/27273966/molecular-assays-in-detecting-egfr-gene-aberrations-an-updated-her2-dependent-algorithm-for-interpreting-gene-signals-a-short-technical-report
#7
REVIEW
Evangelos Tsiambas, Vasileios Ragos, Alicia Y Lefas, Stavros N Georgiannos, Dimitrios N Rigopoulos, Georgios Georgakopoulos, Athanasios Stamatelopoulos, Dimitra Grapsa, Konstantinos Syrigos
Purpose: Among oncogenes that have already been identified and cloned, Epidermal Growth Factor Receptor (EGFR) remains one of the most significant. Understanding its deregulation mechanisms improves critically patients' selection for personalized therapies based on modern molecular biology and oncology guidelines. Anti-EGFR targeted therapeutic strategies have been developed based on specific genetic profiles and applied in subgroups of patients suffering by solid cancers of different histogenetic origin. Detection of specific EGFR somatic mutations leads to tyrosine kinase inhibitors (TKIs) application in subsets of them...
March 2016: Journal of B.U.ON.: Official Journal of the Balkan Union of Oncology
https://www.readbyqxmd.com/read/27240214/systems-medicine-in-colorectal-cancer-from-a-mathematical-model-toward-a-new-type-of-clinical-trial
#8
REVIEW
Nicoletta Castagnino, Massimo Maffei, Lorenzo Tortolina, Gabriele Zoppoli, Daniela Piras, Alessio Nencioni, Eva Moran, Alberto Ballestrero, Franco Patrone, Silvio Parodi
Current colorectal cancer (CRC) treatment guidelines are primarily based on clinical features, such as cancer stage and grade. However, outcomes may be improved using molecular treatment guidelines. Potentially useful biomarkers include driver mutations and somatically inherited alterations, signaling proteins (their expression levels and (post) translational modifications), mRNAs, micro-RNAs and long noncoding RNAs. Moving to an integrated system is potentially very relevant. To implement such an integrated system: we focus on an important region of the signaling network, immediately above the G1-S restriction point, and discuss the reconstruction of a Molecular Interaction Map and interrogating it with a dynamic mathematical model...
July 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27226207/evaluation-of-the-methods-to-identify-patients-who-may-benefit-from-parp-inhibitor-use
#9
REVIEW
Diana Lim, Joanne Ngeow
The effectiveness of poly (ADP-ribose) polymerase inhibitors (PARPi) in treating cancers associated with BRCA1/2 mutations hinges upon the concept of synthetic lethality and exemplifies the principles of precision medicine. Currently, most clinical trials are recruiting patients based on pathological subtypes or have included BRCA mutation analysis (germ line and/or somatic) as part of the selection criteria. Mounting evidence, however, suggests that these drugs may also be efficacious in tumors with defects in other genes involved in the homologous recombination repair pathway...
June 2016: Endocrine-related Cancer
https://www.readbyqxmd.com/read/27219889/recent-developments-in-primary-aldosteronism
#10
E Asbach, T A Williams, M Reincke
Primary aldosteronism (PA) is the most frequent endocrine cause of secondary arterial hypertension. Sporadic forms of PA caused mainly by an aldosterone producing adenoma (APA) or idiopathic adrenal hyperplasia (IAH) predominate; in contrast, familial forms (familial hyperaldosteronism types I, II and III) affect only a minor proportion of PA patients. Patient based registries and biobanks, international networks and next generation sequencing technologies have emerged over recent years. Somatic hot-spot mutations in the potassium channel GIRK4 (encoded by KCNJ5), in ATPases and a L-type voltage-gated calcium-channel correlate with the autonomous aldosterone production in approximately half of all APAs...
June 2016: Experimental and Clinical Endocrinology & Diabetes
https://www.readbyqxmd.com/read/27191687/nephroblastomatosis-or-wilms-tumor-in-a-fourth-patient-with-a-somatic-pik3ca-mutation
#11
Karen W Gripp, Laura Baker, Vinay Kandula, Katrina Conard, Mena Scavina, Joseph A Napoli, Gregory C Griffin, Mihir Thacker, Rachel G Knox, Graeme R Clark, Victoria E R Parker, Robert Semple, Ghayda Mirzaa, Kim M Keppler-Noreuil
Wilms tumor and nephroblastomatosis are associated with syndromic conditions including hemihyperplasia. Hemihyperplasia is genetically heterogeneous and may be the result of genomic abnormalities seen in Beckwith-Wiedemann syndrome, mosaic chromosome or genomic abnormalities, or somatic point mutations. Somatic missense mutations affecting the PI3K-AKT-MTOR pathway result in segmental overgrowth and are present in numerous benign and malignant tumors. Here, we report a fourth patient with asymmetric overgrowth due to a somatic PIK3CA mutation who had nephroblastomatosis or Wilms tumor...
October 2016: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/27148575/lessons-learned-from-the-application-of-whole-genome-analysis-to-the-treatment-of-patients-with-advanced-cancers
#12
Janessa Laskin, Steven Jones, Samuel Aparicio, Stephen Chia, Carolyn Ch'ng, Rebecca Deyell, Peter Eirew, Alexandra Fok, Karen Gelmon, Cheryl Ho, David Huntsman, Martin Jones, Katayoon Kasaian, Aly Karsan, Sreeja Leelakumari, Yvonne Li, Howard Lim, Yussanne Ma, Colin Mar, Monty Martin, Richard Moore, Andrew Mungall, Karen Mungall, Erin Pleasance, S Rod Rassekh, Daniel Renouf, Yaoqing Shen, Jacqueline Schein, Kasmintan Schrader, Sophie Sun, Anna Tinker, Eric Zhao, Stephen Yip, Marco A Marra
Given the success of targeted agents in specific populations it is expected that some degree of molecular biomarker testing will become standard of care for many, if not all, cancers. To facilitate this, cancer centers worldwide are experimenting with targeted "panel" sequencing of selected mutations. Recent advances in genomic technology enable the generation of genome-scale data sets for individual patients. Recognizing the risk, inherent in panel sequencing, of failing to detect meaningful somatic alterations, we sought to establish processes to integrate data from whole-genome analysis (WGA) into routine cancer care...
October 2015: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27095580/thin-and-thick-primary-cutaneous-melanomas-reveal-distinct-patterns-of-somatic-copy-number-alterations
#13
Valentina Montagnani, Matteo Benelli, Alessandro Apollo, Chiara Pescucci, Danilo Licastro, Carmelo Urso, Gianni Gerlini, Lorenzo Borgognoni, Lucio Luzzatto, Barbara Stecca
Cutaneous melanoma is one of the most aggressive type of skin tumor. Early stage melanoma can be often cured by surgery; therefore current management guidelines dictate a different approach for thin (<1mm) versus thick (>4mm) melanomas. We have carried out whole-exome sequencing in 5 thin and 5 thick fresh-frozen primary cutaneous melanomas. Unsupervised hierarchical clustering analysis of somatic copy number alterations (SCNAs) identified two groups corresponding to thin and thick melanomas. The most striking difference between them was the much greater abundance of SCNAs in thick melanomas, whereas mutation frequency did not significantly change between the two groups...
May 24, 2016: Oncotarget
https://www.readbyqxmd.com/read/27041411/genetic-testing-in-pancreatic-ductal-adenocarcinoma-implications-for-prevention-and-treatment
#14
REVIEW
Mary Linton B Peters, Jennifer F Tseng, Rebecca A Miksad
PURPOSE: This article reviews the progress to date and future directions for investigation of germline and somatic genetic testing to inform pancreatic adenocarcinoma (PDAC) treatment, screening, and prevention strategies. METHODS: We searched PubMed to identify recent articles regarding genetic testing in pancreatic cancer, including both germline and somatic testing, and recent genome-wide association studies. References were specifically hand searched as relevant...
July 2016: Clinical Therapeutics
https://www.readbyqxmd.com/read/26995877/-companion-diagnostics-for-solid-tumors
#15
REVIEW
Atsushi Watanabe
Companion diagnostics (CoDx) will likely continue to rapidly increase in number and application to disease areas including solid tumors, for example EGFR for gefitinib and ALK fusion gene for crizotinib in non-small-cell lung cancer; KRAS against the use of cetuximab and panitumumab in colorectal cancer; HER2 for trastuzumab in breast cancer. CoDx are an indispensable part of personalized medicine and pharmacogenomics. In CoDx development, there are still many challenges, such as the business model promoting cooperation between diagnostics and pharmaceutical companies, and also the regulations related to CoDx...
November 2015: Rinsho Byori. the Japanese Journal of Clinical Pathology
https://www.readbyqxmd.com/read/26895645/-spanish-consensus-statement-for-diagnosis-and-treatment-of-paroxysmal-nocturnal-haemoglobinuria
#16
Ana Villegas, Beatriz Arrizabalaga, Santiago Bonanad, Enrique Colado, Anna Gaya, Ataúlfo González, Isidro Jarque, Ramiro Núñez, Emilio Ojeda, Alberto Orfao, José-María Ribera, Vicente Vicente, Álvaro Urbano-Ispizua
Paroxysmal nocturnal haemoglobinuria (PNH) is an acquired clonal disorder of the haematopoietic progenitor cells due to a somatic mutation in theX-linked phosphatidylinositol glycan class A gene. The disease is characterized by intravascular haemolytic anaemia, propensity to thromboembolic events and bone marrow failure. Other direct complications of haemolysis include dysphagia, erectile dysfunction, abdominal pain, asthenia and chronic renal failure (65% of patients). The disease appears more often in the third decade of life and there is no sex or age preference...
March 18, 2016: Medicina Clínica
https://www.readbyqxmd.com/read/26880610/microsatellite-instability-as-a-biomarker-for-pd-1-blockade
#17
REVIEW
Jonathan C Dudley, Ming-Tseh Lin, Dung T Le, James R Eshleman
Initial results by Le and colleagues, which were published in the June 25, 2015 issue of the New England Journal of Medicine, report significant responses of cancers with microsatellite instability (MSI) to anti-PD-1 inhibitors in patients who failed conventional therapy. This finding fits into a broader body of research associating somatic hypermutation and neoepitope formation with response to immunotherapy, with the added benefit of relying on a simple, widely used diagnostic test. This review surveys the pathogenesis and prognostic value of MSI, diagnostic guidelines for detecting it, and the frequency of MSI across tumors, with the goal of providing a reference for its use as a biomarker for PD-1 blockade...
February 15, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/26782803/critical-pitfalls-in-the-use-of-braf-mutation-as-a-diagnostic-tool-in-thyroid-nodules-a-case-report
#18
Elisabetta Kuhn, Moira Ragazzi, Michele Zini, Davide Giordano, Davide Nicoli, Simonetta Piana
Thyroid fine-needle aspiration (FNA) cytology is the primary tool for the diagnostic evaluation of thyroid nodules. BRAF mutation analysis is employed as an ancillary tool in indeterminate cases, as recommended by the American Thyroid Association management guidelines. Hereby, we report the case of a 73-year-old woman who presented an 8-mm-size, ill-defined, left thyroid nodule. FNA resulted "suspicious for papillary thyroid carcinoma". BRAF mutation status was analyzed, and somatic BRAF (V600E) mutation identified...
September 2016: Endocrine Pathology
https://www.readbyqxmd.com/read/26697194/proficiency-of-dna-repair-genes-and-microsatellite-instability-in-operated-colorectal-cancer-patients-with-clinical-suspicion-of-lynch-syndrome
#19
Isabella Nicácio de Freitas, Fábio Guilherm Caserta Maryssael de Campos, Venâncio Avancini Ferreira Alves, Juliana Magalhães Cavalcante, Dirce Carraro, Renata de Almeida Coudry, Márcio Augusto Diniz, Sérgio Carlos Nahas, Ulysses Ribeiro
BACKGROUND: Lynch syndrome (LS) diagnosis is underestimated, and most of the patients remain undetected after colorectal resections. The study aims to assess the frequency of LS in patients undergoing surgical treatment for colorectal cancer (CRC). METHODS: A total of 458 CRC patients were operated from January 2005 to December 2008. Positive CRC family history (FH) was present in 118 (25.8%) patients. Histologic sections were reviewed for microsatellite instability (MSI) criteria (Bethesda guidelines), immunohistochemical (IHC) analysis for MLH1, MSH2, MSH6, PMS2 proteins, through the avidin-biotin-peroxidase complex, MSI (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) and BRAF somatic mutation...
December 2015: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/26654542/-novel-methods-and-their-applicability-in-the-evaluation-of-the-genetic-background-of-endocrine-system-tumours
#20
REVIEW
Attila Patócs, István Likó, Henriett Butz, Kornélia Baghy, Károly Rácz
The technical developments leading to revolution in clinical genetic testing offer new approaches for patients with cancer. From one mutation or one gene approach the scale of genetic testing moved to whole exome or whole genome scale. It is well known that many tumours are genetically determined and they are part of familial tumour syndromes. In addition, some mutations indicate specific molecular targeted therapies. Although sampling and sample preparation are different for testing germline and somatic mutations, the technical background of the analysis is the same...
December 20, 2015: Orvosi Hetilap
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