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Somatic mutation guideline

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https://www.readbyqxmd.com/read/28642172/egfr-t790m-ctdna-testing-platforms-and-their-role-as-companion-diagnostics-correlation-with-clinical-outcomes-to-egfr-tkis
#1
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...
June 19, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28561687/new-insight-into-the-biology-risk-stratification-and-targeted-treatment-of-myelodysplastic-syndromes
#2
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
#3
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
#4
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
https://www.readbyqxmd.com/read/28447726/a-three-caller-pipeline-for-variant-analysis-of-cancer-whole-exome-sequencing-data
#5
Ze-Kun Liu, Yu-Kui Shang, Zhi-Nan Chen, Huijie Bian
Rapid advancements in next generation sequencing (NGS) technologies, coupled with the dramatic decrease in cost, have made NGS one of the leading approaches applied in cancer research. In addition, it is increasingly used in clinical practice for cancer diagnosis and treatment. Somatic (cancer‑only) single nucleotide variants and small insertions and deletions (indels) are the simplest classes of mutation, however, their identification in whole exome sequencing data is complicated by germline polymorphisms, tumor heterogeneity and errors in sequencing and analysis...
May 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28329407/regulatory-requirements-for-genotoxicity-assessment-of-plant-protection-product-active-ingredients-impurities-and-metabolites
#6
REVIEW
Ewan D Booth, Paul J Rawlinson, Priscila Maria Fagundes, Kevin A Leiner
Active ingredients in plant protection products are subject to rigorous safety assessment during their development, including assessment of genotoxicity. Plant protection products are used for agriculture in multiple regions and for the registration of active ingredients it is necessary to satisfy the data requirements of these different regions. There are no overarching global agreements on which genotoxicity studies need to be conducted to satisfy the majority of regulatory authorities. The implementation of new OECD guidelines for the in vitro micronucleus, transgenic rodent somatic and germ cell gene mutation and in vivo comet assays, as well as the revision of a number of other OECD test guidelines has resulted in some changes to data requirements...
March 22, 2017: Environmental and Molecular Mutagenesis
https://www.readbyqxmd.com/read/28286680/utility-of-myd88-in-the-differential-diagnosis-and-choice-of-second-line-therapy-in-a-case-of-nonsecretory-lymphoplasmacytic-lymphoma-versus-free-light-chain-waldenstrom-s-macroglobulinemia
#7
D Kazmierski, M L Palomba, C Barsigian
The MYD88 L265P somatic variant (MYD88) has a high prevalence in Waldenstrom's Macroglobulinemia (WM), a form of lymphoplasmacytic lymphoma (LPL) associated with monoclonal IgM. Although the role of MYD88 in WM was initially reported in 2012, it was not until 2016 that MYD88 testing was included in the National Cancer Care Network (NCCN) Guidelines. We present a case illustrating the utility of MYD88 status in distinguishing atypical forms of WM from marginal zone lymphoma (MZL) and in selecting second-line therapy with ibrutinib...
2017: Case Reports in Hematology
https://www.readbyqxmd.com/read/28276433/renal-cell-carcinoma
#8
REVIEW
James J Hsieh, Mark P Purdue, Sabina Signoretti, Charles Swanton, Laurence Albiges, Manuela Schmidinger, Daniel Y Heng, James Larkin, Vincenzo Ficarra
Renal cell carcinoma (RCC) denotes cancer originated from the renal epithelium and accounts for >90% of cancers in the kidney. The disease encompasses >10 histological and molecular subtypes, of which clear cell RCC (ccRCC) is most common and accounts for most cancer-related deaths. Although somatic VHL mutations have been described for some time, more-recent cancer genomic studies have identified mutations in epigenetic regulatory genes and demonstrated marked intra-tumour heterogeneity, which could have prognostic, predictive and therapeutic relevance...
March 9, 2017: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/28195261/immunohistochemical-evaluation-of-mismatch-repair-proteins-in-colorectal-carcinoma-the-aifeg-gipad-proposal
#9
A Remo, M Fassan, G Lanza
Microsatellite instability (MSI) is a hypermutable phenotype that usually arises from either a germline mutation in components of the mismatch repair (MMR) machinery (i.e. hMLH1, MSH2, MSH6 and PMS2) in patients with Lynch syndrome (LS) or somatic hypermethylation of the hMLH1 promoter in sporadic carcinomas. In all colorectal cancers (CRC) is possible to identify the MMR deficiency through protein expression by immunoistochemistry (IHC). Recently, the predictive role of MMR deficiency in reduced chemotherapy benefit and the introduction of universal screening for Lynch syndrome suggest to include MMR testing into routine clinical practice...
September 2016: Pathologica
https://www.readbyqxmd.com/read/28137276/towards-standardization-of-next-generation-sequencing-of-ffpe-samples-for-clinical-oncology-intrinsic-obstacles-and-possible-solutions
#10
Maxim Ivanov, Konstantin Laktionov, Valery Breder, Polina Chernenko, Ekaterina Novikova, Ekaterina Telysheva, Sergey Musienko, Ancha Baranova, Vladislav Mileyko
BACKGROUND: Next generation sequencing has a potential to revolutionize the management of cancer patients within the framework of precision oncology. Nevertheless, lack of standardization decelerated entering of the technology into the clinical testing space. Here we dissected a number of common problems of NGS diagnostics in oncology and introduced ways they can be resolved. METHODS: DNA was extracted from 26 formalin fixed paraffin embedded (FFPE) specimens and processed with the TrueSeq Amplicon Cancer Panel (Illumina Inc, San Diego, California) targeting 48 cancer-related genes and sequenced in single run...
January 31, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/28068873/patterns-of-treatment-failure-in-anaplastic-thyroid-carcinoma
#11
Sarika N Rao, Mark Zafereo, Ramona Dadu, Naifa L Busaidy, Kenneth Hess, Gilbert J Cote, Michelle D Williams, William N William, Vlad Sandulache, Neil Gross, G Brandon Gunn, Charles Lu, Renata Ferrarotto, Stephen Y Lai, Maria E Cabanillas
BACKGROUND: Anaplastic thyroid cancer (ATC) is one of the most lethal forms of cancer with a high mortality rate. Current guidelines support surgery for resectable ATC followed by external beam radiation therapy (EBRT) with or without chemotherapy. Treatment for those who are unresectable is palliative. Our goal was to examine first-line therapies as well as the role of genomic profiling in an effort better understand how to approach ATC. METHODS: This is a retrospective study of ATC patients who were seen at our institution from January 2013 to October 2015...
May 2017: Thyroid: Official Journal of the American Thyroid Association
https://www.readbyqxmd.com/read/27931835/management-of-patients-with-recurrent-advanced-cervical-cancer-beyond-first-line-platinum-regimens-where-do-we-stand-a-literature-review
#12
REVIEW
Stergios Boussios, Esmeralda Seraj, George Zarkavelis, Dimitrios Petrakis, Aristomenes Kollas, Aikaterini Kafantari, Abraam Assi, Konstantina Tatsi, Nicholas Pavlidis, George Pentheroudakis
BACKGROUND: Cervical cancer is the fourth most common cancer affecting women worldwide. Despite advances in screening and human papillomavirus (HPV) vaccination, a significant number of women present with or develop advanced disease. Palliative platinum-based chemotherapy (CT) is the standard first-line treatment for metastatic/recurrent cervical cancer. The prognosis remains poor and effective second line options are urgently needed. METHODS: We searched the English-language medical literature as well as relevant guideline databases, published from January 1981 to December 2015 and identified publications related to cervical cancer and its therapies...
December 2016: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/27899194/strategies-for-clinical-implementation-of-screening-for-hereditary-cancer-syndromes
#13
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
#14
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...
November 4, 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
#15
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
#16
REVIEW
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...
January 2017: 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
#17
REVIEW
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...
June 2017: 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
#18
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
#19
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
#20
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
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