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https://www.readbyqxmd.com/read/28339894/frequency-of-somatic-tp53-mutations-in-combination-with-known-pathogenic-mutations-as-identified-by-next-generation-sequencing
#1
Zahra Shajani-Yi, Francine De Abreu, Jason Peterson, Gregory Tsongalis
No abstract text is available yet for this article.
March 1, 2017: American Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28334876/pdgfrb-gain-of-function-mutations-in-sporadic-infantile-myofibromatosis
#2
Florence A Arts, Raf Sciot, Bénédicte Brichard, Marleen Renard, Audrey de Rocca Serra, Guillaume Dachy, Laura A Noël, Amélie I Velghe, Christine Galant, Maria Debiec-Rychter, An Van Damme, Miikka Vikkula, Raphaël Helaers, Nisha Limaye, Hélène A Poirel, Jean-Baptiste Demoulin
Infantile myofibromatosis is one of the most prevalent soft tissue tumors of infancy and childhood. Multifocal nodules with visceral lesions are associated with a poor prognosis. A few familial cases have been linked to mutations in various genes including PDGFRB. In this study, we sequenced PDGFRB, which encodes a receptor tyrosine kinase, in 16 cases of myofibromatosis or solitary myofibroma. Mutations in the coding sequence of PDGFRB were identified in 6 out of 8 patients with the sporadic multicentric form of the disease and in 1 out of 8 patients with isolated myofibroma...
March 3, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334820/high-resolution-time-course-mapping-of-early-transcriptomic-molecular-and-cellular-phenotypes-in-huntington-s-disease-cag-knock-in-mice-across-multiple-genetic-backgrounds
#3
Seth A Ament, Jocelynn R Pearl, Andrea Grindeland, Jason St Claire, John C Earls, Marina Kovalenko, Tammy Gillis, Jayalakshmi Mysore, James F Gusella, Jong-Min Lee, Seung Kwak, David Howland, Min Young Lee, David Baxter, Kelsey Scherler, Kai Wang, Donald Geman, Jeffrey B Carroll, Marcy E MacDonald, George Carlson, Vanessa C Wheeler, Nathan D Price, Leroy E Hood
Huntington's disease is a dominantly inherited neurodegenerative disease caused by the expansion of a CAG repeat in the HTT gene. In addition to the length of the CAG expansion, factors such as genetic background have been shown to contribute to the age at onset of neurological symptoms. A central challenge in understanding the disease progression that leads from the HD mutation to massive cell death in the striatum is the ability to characterize the subtle and early functional consequences of the CAG expansion longitudinally...
February 27, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334730/examining-the-common-aetiology-of-serous-ovarian-cancers-and-basal-like-breast-cancers-using-double-primaries
#4
Colin B Begg, Megan S Rice, Emily C Zabor, Shelley S Tworoger
BACKGROUND: The somatic molecular profiles of basal-like breast cancers and high-grade serous ovarian cancers share many similarities, leading to the hypothesis that they have similar aetiologies, in which case they should occur together in the same patient more often than expected. METHODS: We identified 545 women with double independent primary cancers of the breast and ovary reported to the California Cancer Registry from 1999 to 2013 and examined the coincidence of subtype combinations...
March 23, 2017: British Journal of Cancer
https://www.readbyqxmd.com/read/28334704/combining-real-time-cold-and-mama-pcr-taqman-techniques-to-detect-and-quantify-r201-gnas-mutations-in-the-mccune-albright-syndrome%C3%A2
#5
Luisa de Sanctis, Ilaria Galliano, Paola Montanari, Patrizia Matarazzo, Daniele Tessaris, Massimiliano Bergallo
BACKGROUND/AIM: The McCune-Albright syndrome (MAS) is a potentially severe disorder hallmarked by fibrous bone dysplasia, café-au-lait skin spots, and endocrine hyperfunction. It is caused by postzygotic activating mutations at the R201 codon of the GNAS gene, leading to a state of somatic mosaicism. Our aim was to improve the mutation detection rate and to quantify the presence of R201 GNAS mutations in different DNA samples from MAS patients. METHODS: Real-time COLD- and MAMA-PCR TaqMan techniques were combined to search for R201 mutations in the DNA of blood or affected tissues from 16 previously molecularly characterized MAS patients, from a further 84 subjects with MAS signs who were R201 negative at RFLP analysis, and from 36 controls...
March 23, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/28334384/the-cancer-paradigms-of-mammalian-regeneration-can-mammals-regenerate-as-amphibians
#6
Rachel Sarig, Eldad Tzahor
Regeneration in mammals is restricted to distinct tissues and occurs mainly by expansion and maturation of resident stem cells. During regeneration, even subtle mutations in the proliferating cells may cause a detrimental effect by eliciting abnormal differentiation or malignant transformation. Indeed, cancer in mammals has been shown to arise through deregulation of stem cells maturation, which often leads to a differentiation block and cell transformation. In contrast, lower organisms such as amphibians retain a remarkable regenerative capacity in various organs, which occurs via de- and re-differentiation of mature cells...
March 15, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28334334/p53-and-its-mutants-on-the-slippery-road-from-stemness-to-carcinogenesis
#7
Alina Molchadsky, Varda Rotter
Normal development, tissue homeostasis and regeneration following injury rely on the proper functions of wide repertoire of stem cells (SCs) persisting during embryonic period and throughout the adult life. Therefore, SCs employ robust mechanisms to preserve their genomic integrity and avoid heritage of mutations to their daughter cells. Importantly, propagation of SCs with faulty DNA as well as dedifferentiation of genomically altered somatic cells may result in derivation of cancer SCs, which are considered to be the driving force of the tumorigenic process...
March 15, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/28333948/epigenomic-annotation-of-noncoding-mutations-identifies-mutated-pathways-in-primary-liver-cancer
#8
Rebecca F Lowdon, Ting Wang
Evidence that noncoding mutation can result in cancer driver events is mounting. However, it is more difficult to assign molecular biological consequences to noncoding mutations than to coding mutations, and a typical cancer genome contains many more noncoding mutations than protein-coding mutations. Accordingly, parsing functional noncoding mutation signal from noise remains an important challenge. Here we use an empirical approach to identify putatively functional noncoding somatic single nucleotide variants (SNVs) from liver cancer genomes...
2017: PloS One
https://www.readbyqxmd.com/read/28330784/vascular-endothelial-growth-factor-vegf-and-vegf-receptor-inhibitors-in-the-treatment-of-renal-cell-carcinomas
#9
REVIEW
Robert Roskoski
One Von Hippel-Lindau (VHL) tumor suppressor gene is lost in most renal cell carcinomas while the nondeleted allele exhibits hypermethylation-induced inactivation or inactivating somatic mutations. As a result of these genetic modifications, there is an increased production of VEGF-A and pro-angiogenic growth factors in this disorder. The important role of angiogenesis in the pathogenesis of renal cell carcinomas and other tumors has focused the attention of investigators on the biology of VEGFs and VEGFR1-3 and to the development of inhibitors of the intricate and multifaceted angiogenic pathways...
March 18, 2017: Pharmacological Research: the Official Journal of the Italian Pharmacological Society
https://www.readbyqxmd.com/read/28329770/antigen-presentation-profiling-reveals-recognition-of-lymphoma-immunoglobulin-neoantigens
#10
Michael S Khodadoust, Niclas Olsson, Lisa E Wagar, Ole A W Haabeth, Binbin Chen, Kavya Swaminathan, Keith Rawson, Chih Long Liu, David Steiner, Peder Lund, Samhita Rao, Lichao Zhang, Caleb Marceau, Henning Stehr, Aaron M Newman, Debra K Czerwinski, Victoria E H Carlton, Martin Moorhead, Malek Faham, Holbrook E Kohrt, Jan Carette, Michael R Green, Mark M Davis, Ronald Levy, Joshua E Elias, Ash A Alizadeh
Cancer somatic mutations can generate neoantigens that distinguish malignant from normal cells. However, the personalized identification and validation of neoantigens remains a major challenge. Here we discover neoantigens in human mantle-cell lymphomas by using an integrated genomic and proteomic strategy that interrogates tumour antigen peptides presented by major histocompatibility complex (MHC) class I and class II molecules. We applied this approach to systematically characterize MHC ligands from 17 patients...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329761/somatic-mutations-reveal-asymmetric-cellular-dynamics-in-the-early-human-embryo
#11
Young Seok Ju, Inigo Martincorena, Moritz Gerstung, Mia Petljak, Ludmil B Alexandrov, Raheleh Rahbari, David C Wedge, Helen R Davies, Manasa Ramakrishna, Anthony Fullam, Sancha Martin, Christopher Alder, Nikita Patel, Steve Gamble, Sarah O'Meara, Dilip D Giri, Torril Sauer, Sarah E Pinder, Colin A Purdie, Åke Borg, Henk Stunnenberg, Marc van de Vijver, Benita K T Tan, Carlos Caldas, Andrew Tutt, Naoto T Ueno, Laura J van 't Veer, John W M Martens, Christos Sotiriou, Stian Knappskog, Paul N Span, Sunil R Lakhani, Jórunn Erla Eyfjörd, Anne-Lise Børresen-Dale, Andrea Richardson, Alastair M Thompson, Alain Viari, Matthew E Hurles, Serena Nik-Zainal, Peter J Campbell, Michael R Stratton
Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have particular characteristics and effects. Depending on their location in the genome and the proportion of cells they are present in, these mosaic mutations can cause a wide range of genetic disease syndromes and predispose carriers to cancer. They have a high chance of being transmitted to offspring as de novo germline mutations and, in principle, can provide insights into early human embryonic cell lineages and their contributions to adult tissues...
March 22, 2017: Nature
https://www.readbyqxmd.com/read/28329682/the-swi-snf-protein-pbrm1-restrains-vhl-loss-driven-clear-cell-renal-cell-carcinoma
#12
Amrita M Nargund, Can G Pham, Yiyu Dong, Patricia I Wang, Hatice U Osmangeyoglu, Yuchen Xie, Omer Aras, Song Han, Toshinao Oyama, Shugaku Takeda, Chelsea E Ray, Zhenghong Dong, Mathieu Berge, A Ari Hakimi, Sebastien Monette, Carl L Lekaye, Jason A Koutcher, Christina S Leslie, Chad J Creighton, Nils Weinhold, William Lee, Satish K Tickoo, Zhong Wang, Emily H Cheng, James J Hsieh
PBRM1 is the second most commonly mutated gene after VHL in clear cell renal cell carcinoma (ccRCC). However, the biological consequences of PBRM1 mutations for kidney tumorigenesis are unknown. Here, we find that kidney-specific deletion of Vhl and Pbrm1, but not either gene alone, results in bilateral, multifocal, transplantable clear cell kidney cancers. PBRM1 loss amplified the transcriptional outputs of HIF1 and STAT3 incurred by Vhl deficiency. Analysis of mouse and human ccRCC revealed convergence on mTOR activation, representing the third driver event after genetic inactivation of VHL and PBRM1...
March 21, 2017: Cell Reports
https://www.readbyqxmd.com/read/28329645/frequent-somatic-mutations-of-chromatin-remodeling-genes-in-metastatic-cutaneous-squamous-cell-carcinoma
#13
Amanda Ewart Toland
Exome and targeted sequencing studies have identified potential driver mutations for a variety of tumor types. Cutaneous squamous cell carcinoma (cSCC) is one of the most highly mutated cancers but is typically correlated with high survival rates and low rates of metastasis. Nevertheless, metastatic cSCC is a significant health threat; up to 8800 individuals are estimated to die yearly from this disease. As it is difficult to predict which cSCCs are more likely to metastasize, and because there are no targeted therapies specifically designated for metastatic cSCC, we performed exome and targeted sequencing of 18 metastatic and 10 primary cSCCs to identify mutations with potential therapeutic benefit...
September 15, 2016: Dermatology Online Journal
https://www.readbyqxmd.com/read/28329407/regulatory-requirements-for-genotoxicity-assessment-of-plant-protection-product-active-ingredients-impurities-and-metabolites
#14
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/28328134/somatic-pik3ca-mutations-in-seven-patients-with-pik3ca-related-overgrowth-spectrum
#15
Kit San Yeung, Janice Jing Kun Ip, Chin Pang Chow, Evelyn Yue Ling Kuong, Paul Kwong-Hang Tam, Godfrey Chi-Fung Chan, Brian Hon-Yin Chung
Somatic mutations in PIK3CA cause many overgrowth syndromes that have been recently coined the "PIK3CA-Related Overgrowth Spectrum." Here, we present seven molecularly confirmed patients with PIK3CA-Related Overgrowth Spectrum, including patients with Congenital Lipomatous Overgrowth, Vascular Malformations, Epidermal Nevi, Scoliosis/Skeletal and Spinal syndrome, Klippel-Trenaunay syndrome, lymphatic malformation and two with atypical phenotypes that cannot be classified into existing disease categories. The literature on PIK3CA-Related Overgrowth Spectrum, suggests that PIK3CA c...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28327945/enhancing-knowledge-discovery-from-cancer-genomics-data-with-galaxy
#16
Marco A Albuquerque, Bruno M Grande, Elie J Ritch, Prasath Pararajalingam, Selin Jessa, Martin Krzywinski, Jasleen K Grewal, Sohrab P Shah, Paul C Boutros, Ryan D Morin
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data...
March 9, 2017: GigaScience
https://www.readbyqxmd.com/read/28327901/data-resources-for-the-identification-and-interpretation-of-actionable-mutations-by-clinicians
#17
A Prawira, T J Pugh, T L Stockley, L L Siu
Following initial characterization of the reference human genome, initiatives have evolved worldwide to identify genomic aberrations in cancer with the aim of deriving diagnostic, prognostic and predictive information. However, the functional and clinical relevance of many somatic variants in cancer are presently unknown and there is no consensus definition of "actionability" for genomic aberrancies. Therefore, while robust detection of a variety of genetic aberrations in clinical specimens remains a technical hurdle, the greater challenge lies in the interpretation of these alterations...
January 24, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28325290/rna-guided-crispr-cas9-system-mediated-engineering-of-acute-myeloid-leukemia-mutations
#18
Oliver Brabetz, Vijay Alla, Linus Angenendt, Christoph Schliemann, Wolfgang E Berdel, Maria-Francisca Arteaga, Jan-Henrik Mikesch
Current acute myeloid leukemia (AML) disease models face severe limitations because most of them induce un-physiological gene expressions that do not represent conditions in AML patients and/or depend on external promoters for regulation of gene expression/repression. Furthermore, many AML models are based on reciprocal chromosomal translocations that only reflect the minority of AML patients, whereas more than 50% of patients have a normal karyotype. The majority of AML, however, is driven by somatic mutations...
March 17, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28324028/a-duodenal-sdh-deficient-gastrointestinal-stromal-tumor-in-a-patient-with-a-germline-sdhb-mutation
#19
M S Elston, S Sehgal, M Dray, E Phillips, J V Conaglen, R J Clifton-Bligh, A J Gill
Context: Gastrointestinal Stromal Tumors (GISTs) are mesenchymal tumors of the gastrointestinal tract arising from the interstitial cells of Cajal. Succinate dehydrogenase (SDH) deficient GISTs are a unique class of GIST defined by: loss of immunohistochemical expression of SDHB indicating dysfunction of the mitochondrial complex 2, lack of driver mutations in KIT and PDGFRA, and a distinctive morphology and natural history. To date, all reported SDH-deficient GISTs have arisen in the stomach...
March 15, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28323992/quantification-of-thyroid-cancer-and-multinodular-goiter-risk-in-the-dicer1-syndrome-a-family-based-cohort-study
#20
Nicholas E Khan, Andrew J Bauer, Kris Ann P Schultz, Leslie Doros, Rosamma M Decastro, Alexander Ling, Maya B Lodish, Laura A Harney, Ron G Kase, Ann G Carr, Christopher T Rossi, Amanda Field, Anne K Harris, Gretchen M Williams, Louis P Dehner, Yoav H Messinger, D Ashley Hill, Douglas R Stewart
Context: The risk of thyroid cancer and multinodular goiter (MNG) in the DICER1 syndrome, a rare tumor-predisposition disorder, is unknown. Objective: To quantify the risk of thyroid cancer and MNG in individuals with the DICER1 syndrome. Design: Family-based cohort study. Setting: National Institutes of Health (NIH) Clinical Center (CC). Participants: The National Cancer Institute DICER1 syndrome cohort consisted of 145 individuals with a DICER1 germline mutation and 135 family controls from 48 families...
February 2, 2017: Journal of Clinical Endocrinology and Metabolism
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