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https://www.readbyqxmd.com/read/28938736/deep-sequencing-shows-that-oocytes-are-not-prone-to-accumulate-mtdna-heteroplasmic-mutations-during-ovarian-ageing
#1
L Boucret, C Bris, V Seegers, D Goudenège, V Desquiret-Dumas, M Domin-Bernhard, V Ferré-L'Hotellier, P E Bouet, P Descamps, P Reynier, V Procaccio, P May-Panloup
STUDY QUESTION: Does ovarian ageing increase the number of heteroplasmic mitochondrial DNA (mtDNA) point mutations in oocytes? SUMMARY ANSWER: Our results suggest that oocytes are not subject to the accumulation of mtDNA point mutations during ovarian ageing. WHAT IS KNOWN ALREADY: Ageing is associated with the alteration of mtDNA integrity in various tissues. Primary oocytes, present in the ovary since embryonic life, may accumulate mtDNA mutations during the process of ovarian ageing...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938622/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#2
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938601/mutation-profile-based-methods-for-understanding-selection-forces-in-cancer-somatic-mutations-a-comparative-analysis
#3
Zhan Zhou, Yangyun Zou, Gangbiao Liu, Jingqi Zhou, Jingcheng Wu, Shimin Zhao, Zhixi Su, Xun Gu
Human genes exhibit different effects on fitness in cancer and normal cells. Here, we present an evolutionary approach to measure the selection pressure on human genes, using the well-known ratio of the nonsynonymous to synonymous substitution rate in both cancer genomes (CN /CS ) and normal populations (pN /pS ). A new mutation-profile-based method that adopts sample-specific mutation rate profiles instead of conventional substitution models was developed. We found that cancer-specific selection pressure is quite different from the selection pressure at the species and population levels...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938536/integrating-omics-data-and-protein-interaction-networks-to-prioritize-driver-genes-in-cancer
#4
Tiejun Zhang, Di Zhang
Although numerous approaches have been proposed to discern driver from passenger, identification of driver genes remains a critical challenge in the cancer genomics field. Driver genes with low mutated frequency tend to be filtered in cancer research. In addition, the accumulation of different omics data necessitates the development of algorithmic frameworks for nominating putative driver genes. In this study, we presented a novel framework to identify driver genes through integrating multi-omics data such as somatic mutation, gene expression, and copy number alterations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938435/the-role-of-sequential-bmp-signaling-in-directing-human-embryonic-stem-cells-to-bipotential-gonadal-cells
#5
Kirsi Sepponen, Karolina Lundin, Katri Knuus, Pia Väyrynen, Taneli Raivio, Juha S Tapanainen, Timo Tuuri
Context: Human gonads arise as a pair of epithelial ridges on the surface of intermediate mesoderm (IM)-derived mesonephros. Toxic environmental factors and mutations in various genes are known to disturb normal gonadal development, but due to a lack of suitable in vitro models, detailed studies characterizing the molecular basis of the observed defects have not been performed. Objective: Our objective was to establish an in vitro method for studying differentiation of bipotential gonadal progenitors using human embryonic stem cells (hESCs), and to investigate the role of bone morphogenetic protein (BMP) in gonadal differentiation...
August 29, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28937974/high-somatic-mutation-and-neoantigen-burden-are-correlated-with-decreased-progression-free-survival-in-multiple-myeloma
#6
A Miller, Y Asmann, L Cattaneo, E Braggio, J Keats, D Auclair, S Lonial, S J Russell, A K Stewart
Tumor-specific mutations can result in immunogenic neoantigens, both of which have been correlated with responsiveness to immune checkpoint inhibitors in highly mutagenic cancers. However, early results of single-agent checkpoint inhibitors in multiple myeloma (MM) have been underwhelming. Therefore, we sought to understand the relationship between mutation and neoantigen landscape of MM patients and responsiveness to therapies. Somatic mutation burden, neoantigen load, and response to therapy were determined using interim data from the MMRF CoMMpass study (NCT01454297) on 664 MM patients...
September 22, 2017: Blood Cancer Journal
https://www.readbyqxmd.com/read/28933967/aid-biology-a-pathological-and-clinical-perspective
#7
Meenal Choudhary, Anubhav Tamrakar, Amit Kumar Singh, Monika Jain, Ankit Jaiswal, Prashant Kodgire
Activation-induced cytidine deaminase (AID), primarily expressed in activated mature B lymphocytes in germinal centers, is the key factor in adaptive immune response against foreign antigens. AID is responsible for producing high-affinity and high-specificity antibodies against an infectious agent, through the physiological DNA alteration processes of antibody genes by somatic hypermutation (SHM) and class-switch recombination (CSR) and functions by deaminating deoxycytidines (dC) to deoxyuridines (dU), thereby introducing point mutations and double-stranded chromosomal breaks (DSBs)...
September 21, 2017: International Reviews of Immunology
https://www.readbyqxmd.com/read/28933615/role-of-dicer1-in-thyroid-cell-proliferation-and-differentiation
#8
Ricardo Cortez Cardoso Penha, Romina Sepe, Marco De Martino, Francesco Esposito, Simona Pellecchia, Maddalena Raia, Luigi Del Vecchio, Myriam Decaussin-Petrucci, Gabriella De Vita, Luis Felipe Ribeiro Pinto, Alfredo Fusco
DICER1 plays a central role in the biogenesis of microRNAs and it is important for normal development. Altered microRNA expression and DICER1 dysregulation have been described in several types of tumors, including thyroid carcinomas. Recently, our group identified a new somatic mutation (c.5438A>G; E1813G) within DICER1 gene of an unknown function. Herein, we show that DICER1 is overexpressed, at mRNA level, in a significant-relative number of papillary (70%) and anaplastic (42%) thyroid carcinoma samples, whereas is drastically downregulated in all the analyzed human thyroid carcinoma cell lines (TPC-1, BCPAP, FRO and 8505c) in comparison with normal thyroid tissue samples...
September 21, 2017: Cell Cycle
https://www.readbyqxmd.com/read/28933282/molecular-mechanisms-of-epigenetic-regulators-as-activatable-targets-in-cancer-theranostics
#9
Yinglu Li, Zhiming Li, Wei-Guo Zhu
Epigenetics is defined as somatically inheritable changes that are not accompanied by alterations in DNA sequence. Epigenetics encompasses DNA methylation, covalent histone modifications, non-coding RNA as well as nucleosome remodeling. Notably, abnormal epigenetic changes play a critical role in cancer development including malignant transformation, metastasis, prognosis, drug resistance and tumor recurrence, which can provide effective targets for cancer prognosis, diagnosis and therapy. Understanding these changes provide effective means for cancer diagnosis and druggable targets for better clinical applications...
September 20, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28930282/esophageal-cancer-genomic-and-molecular-characterization-stem-cell-compartment-and-clonal-evolution
#10
REVIEW
Ugo Testa, Germana Castelli, Elvira Pelosi
Esophageal cancer (EC) is the eighth most common cancer and is the sixth leading cause of death worldwide. The incidence of histologic subtypes of EC, esophageal adenocarcinoma (EAC) and esophageal squamous carcinoma (ESCC), display considerable geographic variation. EAC arises from metaplastic Barrett's esophagus (BE) in the context of chronic inflammation secondary to exposure to acid and bile. The main risk factors for developing ESCC are cigarette smoking and alcohol consumption. The main somatic genetic abnormalities showed a different genetic landscape in EAC compared to ESCC...
September 14, 2017: Medicines (Basel, Switzerland)
https://www.readbyqxmd.com/read/28929852/the-ethics-of-genome-editing-in-the-clinic-a-dose-of-realism-for-healthcare-leaders
#11
Tania Bubela, Yael Mansour, Dianne Nicol
Genome editing technologies promise therapeutic advances for genetic diseases. We discuss the ethical and societal issues raised by these technologies, including their use in preclinical research, their potential to address mutations in somatic cells, and their potential to make germ line alterations that may be passed to subsequent generations. We call for a proportionate response from health leaders based on a realistic assessment of benefits, risks, and timelines for clinical translation.
May 2017: Healthcare Management Forum
https://www.readbyqxmd.com/read/28928742/a-streamlined-approach-to-antibody-novel-germline-allele-prediction-and-validation
#12
Ben S Wendel, Chenfeng He, Peter D Crompton, Susan K Pierce, Ning Jiang
Advancements in high-throughput sequencing and molecular identifier-based error correction have opened the door to antibody repertoire sequencing with single mutation precision, increasing both the breadth and depth of immune response characterization. However, improvements in sequencing technology cannot resolve one key aspect of antibody repertoire sequencing accuracy: the possibility of undocumented novel germline alleles. Somatic hypermutation (SHM) calling requires a reference germline sequence, and the antibody variable region gene alleles collected by the IMGT database, although large in number, are not comprehensive...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28927463/towards-precision-medicine-discovering-novel-gynecological-cancer-biomarkers-and-pathways-using-linked-data
#13
Alokkumar Jha, Yasar Khan, Muntazir Mehdi, Md Rezaul Karim, Qaiser Mehmood, Achille Zappa, Dietrich Rebholz-Schuhmann, Ratnesh Sahay
BACKGROUND: Next Generation Sequencing (NGS) is playing a key role in therapeutic decision making for the cancer prognosis and treatment. The NGS technologies are producing a massive amount of sequencing datasets. Often, these datasets are published from the isolated and different sequencing facilities. Consequently, the process of sharing and aggregating multisite sequencing datasets are thwarted by issues such as the need to discover relevant data from different sources, built scalable repositories, the automation of data linkage, the volume of the data, efficient querying mechanism, and information rich intuitive visualisation...
September 19, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28927462/generation-of-special-autosomal-dominant-polycystic-kidney-disease-ipscs-with-the-capability-of-functional-kidney-like-cell-differentiation
#14
Jiahui Huang, Shumin Zhou, Xin Niu, Bin Hu, Qing Li, Feng Zhang, Xue Zhang, Xiujuan Cai, Yuanlei Lou, Fen Liu, Chenming Xu, Yang Wang
BACKGROUND: Human induced pluripotent stem cells (iPSCs) have been verified as a powerful cell model for the study of pathogenesis in hereditary disease. Autosomal dominant polycystic kidney disease (ADPKD) is caused by mutations of PKD or non-PKD genes. The pathogenesis of ADPKD remains unexplored because of the lack of a true human cell model. METHODS: Six ADPKD patients and four healthy individuals were recruited as donors of somatic cells from a Chinese ADPKD family without mutations of the PKD genes but carrying SAMSN1 gene deletion...
September 19, 2017: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/28927094/genomic-markers-of-ovarian-adenocarcinoma-and-its-relevancy-to-the-effectiveness-of-chemotherapy
#15
Monika Englert-Golon, Bartosz Burchardt, Bartlomiej Budny, Szymon Dębicki, Blanka Majchrzycka, Elzbieta Wrotkowska, Piotr Jasiński, Katarzyna Ziemnicka, Radosław Słopień, Marek Ruchała, Stefan Sajdak
Ovarian cancer is the eighth most common cancer and the seventh highest cause of cancer-associated mortality in women worldwide. It is the second highest cause of mortality among female reproductive malignancies. The current standard first-line treatment for advanced ovarian cancer includes a combination of surgical debulking and standard systemic platinum-based chemotherapy with carboplatin and paclitaxel. Although a deeper understanding of this disease has been attained, relapse occurs in 70% of patients 18 months subsequent to the first-line treatment...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28926605/assessment-of-common-somatic-mutations-of-egfr-kras-braf-nras-in-pulmonary-non-small-cell-carcinoma-using-iplex%C3%A2-hs-a-new-highly-sensitive-assay-for-the-massarray%C3%A2-system
#16
Bobbie C Sutton, Ryan T Birse, Kevin Maggert, Tammy Ray, Jessica Hobbs, Amobi Ezenekwe, Jason Kazmierczak, Michael Mosko, Joan Kish, Andrew Bullock, Zonggao Shi, M Sharon Stack, Darryl Irwin
Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and navigational biopsy, as well as thin needle core biopsies. As many lung cancer patients have late stage disease and other comorbidities that make open surgical procedures hazardous, the least invasive biopsy technique with the highest potential specimen yield is now the preferred first diagnostic study...
2017: PloS One
https://www.readbyqxmd.com/read/28925398/functional-significance-and-therapeutic-implication-of-ring-type-e3-ligases-in-colorectal-cancer
#17
REVIEW
L Liu, C C Wong, B Gong, J Yu
Accumulative studies revealed that E3 ubiquitin ligases have important roles in colorectal carcinogenesis. The pathogenic mechanisms of colorectal cancer (CRC) initiation and progression are complex and heterogeneous, involving somatic mutations, abnormal gene fusion, deletion or amplification and epigenetic alteration, which may cause aberrant expression or altered function of E3 ligases in CRC. Defects of E3 ligases have been reported to be involved in the molecular etiology and pathogenesis of CRC. The aberrant expressed E3 ligases can function as either oncogenes or tumor suppressors depending on ubiquiting target substrates in CRC...
September 18, 2017: Oncogene
https://www.readbyqxmd.com/read/28923911/how-ribosomes-translate-cancer
#18
REVIEW
Sergey O Sulima, Isabel J F Hofman, Kim De Keersmaecker, Jonathan D Dinman
A wealth of novel findings, including congenital ribosomal mutations in ribosomopathies and somatic ribosomal mutations in various cancers, have significantly increased our understanding of the relevance of ribosomes in oncogenesis. Here, we explore the growing list of mechanisms by which the ribosome is involved in carcinogenesis-from the hijacking of ribosomes by oncogenic factors and dysregulated translational control, to the effects of mutations in ribosomal components on cellular metabolism. Of clinical importance, the recent success of RNA polymerase inhibitors highlights the dependence on "onco-ribosomes" as an Achilles' heel of cancer cells and a promising target for further therapeutic intervention...
September 18, 2017: Cancer Discovery
https://www.readbyqxmd.com/read/28923673/monogenic-autoinflammatory-diseases-general-concepts-and-presentation-in-adult-patients
#19
REVIEW
José Hernández-Rodríguez, Estíbaliz Ruiz-Ortiz, Jordi Yagüe
Monogenic autoinflammatory diseases (AIFD) are rare disorders characterized by an uncontrolled increase of the systemic inflammatory response, which is caused by mutations in genes involved in inflammatory pathways. Over the last few years, new genes and proteins responsible for new monogenic AIFD have been identified and a substantial improvement in their treatment has been achieved. Monogenic AIFD manifestations typically begin during childhood, but they can also occur in adults. Compared to pediatric patients, adults usually present with a less severe disease and fewer long-term complications...
September 15, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/28923495/crispr-cas9-engineering-of-adult-mouse-liver-demonstrates-that-the-dnajb1-prkaca-gene-fusion-is-sufficient-to-induce-tumors-resembling-fibrolamellar-hepatocellular-carcinoma
#20
Lars H Engelholm, Anjum Riaz, Denise Serra, Frederik Dagnæs-Hansen, Jens V Johansen, Eric Santoni-Rugiu, Steen H Hansen, Francesco Niola, Morten Frödin
BACKGROUND & AIMS: Fibrolamellar hepatocellular carcinoma (FL-HCC) is a primary liver cancer that predominantly affects young adults with no underlying liver disease. A somatic, 400 Kb deletion on chromosome 19 that fuses part of the DnaJ heat shock protein family (Hsp40) member B1 gene (DNAJB1) to the protein kinase cAMP-activated catalytic subunit alpha gene (PRKACA) has been repeatedly identified in patients with FL-HCC. However, the DNAJB1-PRKACA gene fusion has not been shown to induce liver tumorigenesis...
September 15, 2017: Gastroenterology
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