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https://www.readbyqxmd.com/read/29791457/a-feasibility-study-of-colorectal-cancer-diagnosis-via-circulating-tumor-dna-derived-cnv-detection
#1
Bhuvan Molparia, Glenn Oliveira, Jennifer L Wagner, Emily G Spencer, Ali Torkamani
Circulating tumor DNA (ctDNA) has shown great promise as a biomarker for early detection of cancer. However, due to the low abundance of ctDNA, especially at early stages, it is hard to detect at high accuracies while keeping sequencing costs low. Here we present a pilot stage study to detect large scale somatic copy numbers variations (CNVs), which contribute more molecules to ctDNA signal compared to point mutations, via cell free DNA sequencing. We show that it is possible to detect somatic CNVs in early stage colorectal cancer (CRC) patients and subsequently discriminate them from normal patients...
2018: PloS One
https://www.readbyqxmd.com/read/29791066/application-of-denaturing-capillary-electrophoresis-for-the-detection-of-prognostic-mutations-in-isocitrate-dehydrogenase-1-and-isocitrate-dehydrogenase-2-genes-in-brain-tumors
#2
Lucie Benesova, Barbora Belsanova, Filip Kramar, Tereza Halkova, Vladimir Benes, Marek Minarik
Malignant transformation in gliomas is frequently supplemented by somatic mutations in isocitrate dehydrogenase 1 and isocitrate dehydrogenase 2 genes. It has recently emerged that mutations in these genes are associated with prolonged survival and should be used as prognostic factor in management of brain cancer patients. There are several approaches in use for the detection of isocitrate dehydrogenase 1 and 2 mutations, however, these often exhibit shortcomings such as convoluted protocols with long processing time, complex (and costly) dedicated fluorescent probes and/or high demand on amounts of input DNA...
May 23, 2018: Journal of Separation Science
https://www.readbyqxmd.com/read/29790943/mutalisk-a-web-based-somatic-mutation-analyis-toolkit-for-genomic-transcriptional-and-epigenomic-signatures
#3
Jongkeun Lee, Andy Jinseok Lee, June-Koo Lee, Jongkeun Park, Youngoh Kwon, Seongyeol Park, Hyonho Chun, Young Seok Ju, Dongwan Hong
Somatic genome mutations occur due to combinations of various intrinsic/extrinsic mutational processes and DNA repair mechanisms. Different molecular processes frequently generate different signatures of somatic mutations in their own favored contexts. As a result, the regional somatic mutation rate is dependent on the local DNA sequence, the DNA replication/RNA transcription dynamics and epigenomic chromatin organization landscape in the genome. Here, we propose an online computational framework, termed Mutalisk, which correlates somatic mutations with various genomic, transcriptional and epigenomic features in order to understand mutational processes that contribute to the generation of the mutations...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29789719/selective-vulnerability-of-the-primitive-meningeal-layer-to-prenatal-smo-activation-for-skull-base-meningothelial-meningioma-formation
#4
Julien Boetto, Caroline Apra, Franck Bielle, Matthieu Peyre, Michel Kalamarides
Somatic activating mutations of smoothened (SMO), a component of the embryonic sonic hedgehog (SHH) signaling pathway, are found in 3-5% of grade I meningiomas, most of them corresponding to meningothelial meningiomas located at the anterior skull base. By generating different developmental stage-specific conditional activations in mice, we define a restricted developmental window during which conditional activation of Smo in Prostaglandin D2-synthase-positive mesoderm-derived meningeal layer of the skull base results in meningothelial meningioma formation...
May 22, 2018: Oncogene
https://www.readbyqxmd.com/read/29788737/diagnosis-for-carcinoma-of-unknown-primary-site-with-the-aid-of-simple-pcr-tests-a-single-center-experience
#5
E Suspitsin, G Yanus, E Imyanitov
This study was aimed to incorporate PCR testing in the determination of organ/tissue origin for cancers of unknown primary site (CUP). We developed a PCR panel consisting of 7 expression markers (CDX2, CDH17, SPB, UGRP, MAM, LPB, TG) and 2 genes frequently mutated in cancer (KRAS and BRAF). The expression tests were intentionally interpreted in a non-quantitative way, i.e. classified tumors either as positive or negative expressors. While applying these tests to 135 cancers belonging to 8 common types of adenocarcinomas (AdCa), we observed that this panel was capable to clearly discriminate between gastrointestinal vs...
March 14, 2018: Neoplasma
https://www.readbyqxmd.com/read/29788099/biomarkers-for-homologous-recombination-deficiency-in-cancer
#6
Michal M Hoppe, Raghav Sundar, David S P Tan, Anand D Jeyasekharan
Defective DNA repair is a common hallmark of cancer. Homologous recombination is a DNA repair pathway of clinical interest due to the sensitivity of homologous recombination-deficient cells to poly-ADP ribose polymerase (PARP) inhibitors. The measurement of homologous recombination deficiency (HRD) in cancer is therefore vital to the appropriate design of clinical trials incorporating PARP inhibitors. However, methods to identify HRD in tumors are varied and controversial. Understanding existing and new methods to measure HRD is important to their appropriate use in clinical trials and practice...
May 18, 2018: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29786783/a-xenograft-model-for-venous-malformation
#7
Jillian Goines, Xian Li, Yuqi Cai, Paula Mobberley-Schuman, Megan Metcalf, Steven J Fishman, Denise M Adams, Adrienne M Hammill, Elisa Boscolo
Vascular malformations are defects caused by the abnormal growth of the vasculature. Among them, venous malformation (VM) is an anomaly characterized by slow-flow vascular lesions with abnormally shaped veins, typically in sponge-like configuration. VMs can expand over years causing disfigurement, obstruction of vital structures, thrombosis, bleeding, and pain. Treatments have been very limited and primarily based on supportive care, compression garments, sclerotherapy, and/or surgical resection. Sirolimus treatment has recently shown efficacy in some patients with complicated vascular anomalies, including VMs...
May 21, 2018: Angiogenesis
https://www.readbyqxmd.com/read/29786075/tp53-gain-of-function-mutation-promotes-inflammation-in-glioblastoma
#8
Seok Won Ham, Hee-Young Jeon, Xiong Jin, Eun-Jung Kim, Jun-Kyum Kim, Yong Jae Shin, Yeri Lee, Se Hoon Kim, Seon Yong Lee, Sunyoung Seo, Min Gi Park, Hye-Mi Kim, Do-Hyun Nam, Hyunggee Kim
Glioblastoma (GBM), the most severe and common brain tumor in adults, is characterized by multiple somatic mutations and aberrant activation of inflammatory responses. Immune cell infiltration and subsequent inflammation cause tumor growth and resistance to therapy. Somatic loss-of-function mutations in the gene encoding tumor suppressor protein p53 (TP53) are frequently observed in various cancers. However, numerous studies suggest that TP53 regulates malignant phenotypes by gain-of-function (GOF) mutations...
May 21, 2018: Cell Death and Differentiation
https://www.readbyqxmd.com/read/29785028/the-reference-epigenome-and-regulatory-chromatin-landscape-of-chronic-lymphocytic-leukemia
#9
Renée Beekman, Vicente Chapaprieta, Núria Russiñol, Roser Vilarrasa-Blasi, Núria Verdaguer-Dot, Joost H A Martens, Martí Duran-Ferrer, Marta Kulis, François Serra, Biola M Javierre, Steven W Wingett, Guillem Clot, Ana C Queirós, Giancarlo Castellano, Julie Blanc, Marta Gut, Angelika Merkel, Simon Heath, Anna Vlasova, Sebastian Ullrich, Emilio Palumbo, Anna Enjuanes, David Martín-García, Sílvia Beà, Magda Pinyol, Marta Aymerich, Romina Royo, Montserrat Puiggros, David Torrents, Avik Datta, Ernesto Lowy, Myrto Kostadima, Maša Roller, Laura Clarke, Paul Flicek, Xabier Agirre, Felipe Prosper, Tycho Baumann, Julio Delgado, Armando López-Guillermo, Peter Fraser, Marie-Laure Yaspo, Roderic Guigó, Reiner Siebert, Marc A Martí-Renom, Xose S Puente, Carlos López-Otín, Ivo Gut, Hendrik G Stunnenberg, Elias Campo, Jose I Martin-Subero
Chronic lymphocytic leukemia (CLL) is a frequent hematological neoplasm in which underlying epigenetic alterations are only partially understood. Here, we analyze the reference epigenome of seven primary CLLs and the regulatory chromatin landscape of 107 primary cases in the context of normal B cell differentiation. We identify that the CLL chromatin landscape is largely influenced by distinct dynamics during normal B cell maturation. Beyond this, we define extensive catalogues of regulatory elements de novo reprogrammed in CLL as a whole and in its major clinico-biological subtypes classified by IGHV somatic hypermutation levels...
May 21, 2018: Nature Medicine
https://www.readbyqxmd.com/read/29785006/the-era-of-immunogenomics-immunopharmacogenomics
#10
REVIEW
Makda Zewde, Kazuma Kiyotani, Jae-Hyun Park, Hua Fang, Kai Lee Yap, Poh Yin Yew, Houda Alachkar, Taigo Kato, Tu H Mai, Yuji Ikeda, Tatsuo Matsuda, Xiao Liu, Lili Ren, Boya Deng, Makiko Harada, Yusuke Nakamura
Although germline alterations and somatic mutations in disease cells have been extensively analyzed, molecular changes in immune cells associated with disease conditions have not been characterized in depth. It is clear that our immune system has a critical role in various biological and pathological conditions, such as infectious diseases, autoimmune diseases, drug-induced skin and liver toxicity, food allergy, and rejection of transplanted organs. The recent development of cancer immunotherapies, particularly drugs modulating the immune checkpoint molecules, has clearly demonstrated the importance of host immune cells in cancer treatments...
May 21, 2018: Journal of Human Genetics
https://www.readbyqxmd.com/read/29784672/genetic-screening-and-multipotency-in-rhesus-monkey-haploid-neural-progenitor-cells
#11
Haisong Wang, Wenhao Zhang, Jian Yu, Congyu Wu, Qian Gao, Xu Li, Yanni Li, Jinxin Zhang, Yaru Tian, Tao Tan, Weizhi Ji, Luyuan Li, Yang Yu, Ling Shuai
Haploid embryonic stem cells (haESCs) have been extensively applied in forward and reverse genetic screening. However, the mammalian haploid somatic cell line is difficult to achieve because of spontaneous diploidization in differentiation. As a non-human primate species, monkeys are widely used in basic and pre-clinical research in which haploid cells are restricted to ESCs. Here, we report that rhesus monkey haESCs in an optimized culture medium showed naïve-state pluripotency and stable haploidy. This model facilitated the derivation of haploid neural progenitor cells (haNPCs), which maintained haploidy and differentiation potential into neurons and glia for a long period in vitro High-throughput trapping mutations can be efficiently introduced into haNPCs via piggyBac transposons...
May 21, 2018: Development
https://www.readbyqxmd.com/read/29783802/-clinicopathologic-and-molecular-features-of-cribriform-morular-variant-of-papillary-thyroid-carcinoma
#12
X J Cui, H O Zhao, P Su, J Chen, R Y Zhang, Y Pan, X M Ouyang, J Liu, J Q Zhang, Y Yang, R Yang, L Ding, Z Y Liu
Objective: To investigate the clinicopathologic and molecular features of the rare cribriform morular variant of papillary thyroid carcinoma (CMV-PTC). Methods: The clinicopathologic data of 10 patients with CMV-PTC were retrospectively reviewed. Immunohistochemical (IHC) staining was done using LSAB method. DNA sequencing for APC were applied using Sanger method. BRAF V600E mutation was examined using ARMS method. The cytological, morphological, IHC and molecular features were analyzed. Results: All patients were female at an average age of 27 years old...
May 8, 2018: Zhonghua Bing Li Xue za Zhi Chinese Journal of Pathology
https://www.readbyqxmd.com/read/29783665/identification-of-novel-somatic-tp53-mutations-in-patients-with-high-grade-serous-ovarian-cancer-hgsoc-using-next-generation-sequencing-ngs
#13
Marica Garziera, Erika Cecchin, Vincenzo Canzonieri, Roberto Sorio, Giorgio Giorda, Simona Scalone, Elena De Mattia, Rossana Roncato, Sara Gagno, Elena Poletto, Loredana Romanato, Franca Sartor, Jerry Polesel, Giuseppe Toffoli
Somatic mutations in TP53 are a hallmark of high-grade serous ovarian cancer (HGSOC), although their prognostic and predictive value as markers is not well defined. Next-generation sequencing (NGS) can identify novel mutations with high sensitivity, that may be repurposed as potential druggable anti-cancer targets and aid in therapeutic decisions. Here, a commercial NGS cancer panel comprising 26 genes, including TP53 , was used to identify new genetic markers of platinum resistance and patient prognosis in a retrospective set of patients diagnosed with epithelial ovarian cancer...
May 18, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29782975/roles-of-germline-jak2-activation-mutation-jak2-v625f-in-the-pathology-of-myeloproliferative-neoplasms
#14
Qing-Yun Wu, Meng-Meng Ma, Lin Fu, Yuan-Yuan Zhu, Yang Liu, Jiang Cao, Ping Zhou, Zhen-Yu Li, Ling-Yu Zeng, Feng Li, Xiao-Yun Wang, Kai-Lin Xu
Janus tyrosine kinase 2 (JAK2) mediates downstream signaling of cytokine receptors in all hematological lineages, constitutively active somatic JAK2 mutations play key roles in the pathology of myeloproliferative neoplasms (MPNs). Recently, germline JAK2 mutations are also associated with triple-negative MPNs. A novel germline mutation JAK2 V625F is reported to be involved in a subset of MPNs patients. However, the pathogenesis of this mutation caused MPN is still unclear. In this study, the homology models of JAK2 V625F showed that the newly formed interaction between F625 and Y613 disrupted the JAK2 JH1-JH2 domain interactions was responsible for its activation, when F625 and Y613 interaction was disrupted, its activity significantly decreased...
May 18, 2018: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/29780774/optimization-to-detect-tp53-mutations-in-circulating-cell-free-tumor-dna-from-patients-with-serous-epithelial-ovarian-cancer
#15
Yu Ran Park, Yong-Man Kim, Shin Wha Lee, Ha Young Lee, Gun Eui Lee, Jong-Eun Lee, Young-Tak Kim
Objective: Circulating cell-free tumor DNA (cfDNA) is the DNA released by apoptotic and necrotic cells of the primary tumor into the blood during the period of tumor development. The cfDNA reflects the genetic and epigenetic alterations of the original tumor. TP53 mutations are a defining feature of high-grade serous ovarian carcinoma. We optimized the methods for detecting TP53 mutations in cfDNA from blood samples. We confirmed the correlation of TP53 mutation in primary ovarian cancer tissue and it in cfDNA using digital polymerase chain reaction (dPCR)...
May 2018: Obstetrics & Gynecology Science
https://www.readbyqxmd.com/read/29780256/the-utilization-of-next-generation-sequencing-to-detect-somatic-mutations-and-predict-clinical-prognosis-of-chinese-non-small-cell-lung-cancer-patients
#16
Liming Cao, Long Long, Min Li, Huaping Yang, Pengbo Deng, Xinru Mao, Jianxing Xiang, Bing Li, Tengfei Zhang, Chengping Hu
Purpose: The development of next-generation sequencing (NGS) has revolutionized the understanding of oncogenesis of multiple types of cancer, including non-small cell lung cancer (NSCLC). However, there has been some debate over the utility of NGS for predicting patient prognosis and determining molecular targeted therapy. Therefore, we sought to demonstrate the numerous applications of NGS in the prognostic predictions and treatment of NSCLC patients. Materials and methods: We performed NGS on either liquid or tissue tumor biopsies obtained from 53 NSCLC patients...
2018: OncoTargets and Therapy
https://www.readbyqxmd.com/read/29779918/tracking-tumor-biology-with-radiomics-a-systematic-review-utilizing-a-radiomics-quality-score
#17
REVIEW
Sebastian Sanduleanu, Henry C Woodruff, Evelyn E C de Jong, Janna E van Timmeren, Arthur Jochems, Ludwig Dubois, Philippe Lambin
INTRODUCTION: In this review we describe recent developments in the field of radiomics along with current relevant literature linking it to tumor biology. We furthermore explore the methodologic quality of these studies with our in-house radiomics quality scoring (RQS) tool. Finally, we offer our vision on necessary future steps for the development of stable radiomic features and their links to tumor biology. METHODS: Two authors (S.S. and H.W.) independently performed a thorough systematic literature search and outcome extraction to identify relevant studies published in MEDLINE/PubMed (National Center for Biotechnology Information, NCBI), EMBASE (Ovid) and Web of Science (WoS)...
May 18, 2018: Radiotherapy and Oncology: Journal of the European Society for Therapeutic Radiology and Oncology
https://www.readbyqxmd.com/read/29779891/fixation-and-spread-of-somatic-mutations-in-adult-human-colonic-epithelium
#18
Anna M Nicholson, Cora Olpe, Alice Hoyle, Ann-Sofie Thorsen, Teja Rus, Mathilde Colombé, Roxanne Brunton-Sim, Richard Kemp, Kate Marks, Phil Quirke, Shalini Malhotra, Rogier Ten Hoopen, Ashraf Ibrahim, Cecilia Lindskog, Meagan B Myers, Barbara Parsons, Simon Tavaré, Mark Wilkinson, Edward Morrissey, Douglas J Winton
We investigated the means and timing by which mutations become fixed in the human colonic epithelium by visualizing somatic clones and mathematical inference. Fixation requires two sequential steps. First, one of approximately seven active stem cells residing within each colonic crypt has to be mutated. Second, the mutated stem cell has to replace neighbors to populate the entire crypt in a process that takes several years. Subsequent clonal expansion due to crypt fission is infrequent for neutral mutations (around 0...
May 11, 2018: Cell Stem Cell
https://www.readbyqxmd.com/read/29778488/the-2016-bernard-sachs-lecture-timing-in-morphogenesis-and-genetic-gradients-during-normal-development-and-in-malformations-of-the-nervous-system
#19
REVIEW
Harvey B Sarnat
Nervous system development is quadradimensional. Both normal ontogenesis and developmental malformations are explained in the context of the fourth dimension, timing. Timing of the onset of either the genetic expression of a mutation or an epigenetic event that may be teratogenic is primordial in determining morphogenesis and the forms of malformations with their functional consequences. Multiple genotypes may cause similar phenotypes or a single genotype with different degrees of retained normal genetic expression may result in variable phenotypes...
March 30, 2018: Pediatric Neurology
https://www.readbyqxmd.com/read/29778426/germline-cytoskeletal-and-extra-cellular-matrix-related-single-nucleotide-variations-associated-with-distinct-cancer-survival-rates
#20
Shayan Falasiri, Tasnif Rahman, Yaping N Tu, Timothy J Fawcett, George Blanck
BACKGROUND: Human mutagenesis has a large stochastic component. Thus, large coding regions, especially cytoskeletal and extra-cellular matrix protein (CECMP) coding regions are particularly vulnerable to mutations. Recent results have verified a high level of somatic mutations in the CECMP coding regions in the cancer genome atlas (TCGA), and a relatively common occurrence of germline, deleterious mutations in the TCGA breast cancer dataset. METHODS: The objective of this study was to determine the correlations of CECMP coding region, germline nucleotide variations with both overall survival (OS) and disease-free survival (DFS)...
May 17, 2018: Gene
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