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https://www.readbyqxmd.com/read/29684710/genomic-characterization-of-endemic-salmonella-enterica-serovar-typhimurium-and-salmonella-enterica-serovar-i-4-5-12-i-isolated-in-malaysia
#1
Soo Tein Ngoi, Kien-Pong Yap, Kwai Lin Thong
Salmonella enterica serovar Typhimurium (S. Typhimurium) and the monophasic variant Salmonella I 4,[5],12:i:- are two clinically-important non-typhoidal Salmonella serovars worldwide. However, the genomic information of these two organisms, especially the monophasic variant, is still lacking in Malaysia. The objective of the study was to compare the genomic features of a monophasic variant and two endemic S. Typhimurium strains isolated from humans. All three strains were subjected to whole genome sequencing followed by comparative genomic and phylogenetic analyses...
April 20, 2018: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/29684684/targeted-data-independent-acquisition-for-mass-spectrometric-detection-of-ras-mutations-in-formalin-fixed-paraffin-embedded-tumor-biopsies
#2
Yeoun Jin Kim, Andrew G Chambers, Fabiola Cecchi, Todd Hembrough
Genomic testing for KRAS and NRAS mutations in clinical biopsies of various cancers is routinely performed to predict futility of anti-epidermal growth factor receptor (anti-EGFR) therapies. We hypothesized that RAS mutations could be detected and quantified at the protein level for diagnostic purposes using data-independent acquisition (DIA)-based mass spectrometry in formalin-fixed, paraffin-embedded (FFPE) tumor samples. We developed a targeted DIA assay that surveys the specific mass range of all possible peptides harboring activating mutations in KRAS exon 2...
April 20, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29684080/unexpected-cancer-predisposition-gene-variants-in-cowden-syndrome-and-bannayan-riley-ruvalcaba-syndrome-patients-without-underlying-germline-pten-mutations
#3
Lamis Yehia, Ying Ni, Kaitlin Sesock, Farshad Niazi, Benjamin Fletcher, Hannah JinLian Chen, Thomas LaFramboise, Charis Eng
Patients with heritable cancer syndromes characterized by germline PTEN mutations (termed PTEN hamartoma tumor syndrome, PHTS) benefit from PTEN-enabled cancer risk assessment and clinical management. PTEN-wildtype patients (~50%) remain at increased risk of developing certain cancers. Existence of germline mutations in other known cancer susceptibility genes has not been explored in these patients, with implications for different medical management. We conducted a 4-year multicenter prospective study of incident patients with features of Cowden/Cowden-like (CS/CS-like) and Bannayan-Riley-Ruvalcaba syndromes (BRRS) without PTEN mutations...
April 23, 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29683851/detection-of-numerous-hiv-1-mo-recombinants-in-france
#4
Fabienne De Oliveira, Pierre Cappy, Véronique Lemée, Alice Moisan, Charlotte Pronier, Laurence Bocket, Magali Bouvier-Alias, Marie-Laure Chaix, Elyanne Gault, Odile Morvan, Jean-Dominique Poveda, Véronique Schneider, Marc Wirden, Elodie Alessandri-Gradt, Thomas Mourez, Jean-Christophe Plantier
BACKGROUND: The broad genetic divergence of HIV-1/O relative to HIV-1/M has important implications for diagnosis, monitoring and treatment. Despite this divergence, some HIV-1/M+O dual infections and HIV-1/MO recombinant forms have been reported, mostly in Cameroon, where both groups are prevalent. Here, we describe the characteristics of such infections detected in France in 10 new patients, and discuss their implications for biological and clinical practice, owing to the presence of group O species...
April 19, 2018: AIDS
https://www.readbyqxmd.com/read/29683658/enhanced-biosynthesis-performance-of-heterologous-proteins-in-cho-k1-cells-using-crispr-cas9
#5
Wenpeng Wang, Wenyun Zheng, Fengzhi Hu, Xiujuan He, Dong Wu, Wenliang Zhang, Haipeng Liu, Xingyuan Ma
Chinese hamster ovary (CHO) cells are the famous expression system for industrial production of recombinant proteins, such as therapeutic antibodies. However, there retained still bottlenecks in protein quality and weakness in expression efficiency because of the intrinsic genetic properties of the cell. Here we have enhanced biosynthesis performance of heterologous proteins in CHO-K1 cell using CRISPR-Cas9 by editing the genome precisely with two genes for improving ER microenvironment and reinforcing anti-apoptotic ability...
April 23, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29683450/targeted-next-generation-sequencing-and-bioinformatics-pipeline-to-evaluate-genetic-determinants-of-constitutional-disease
#6
Allison A Dilliott, Sali M K Farhan, Mahdi Ghani, Christine Sato, Eric Liang, Ming Zhang, Adam D McIntyre, Henian Cao, Lemuel Racacho, John F Robinson, Michael J Strong, Mario Masellis, Dennis E Bulman, Ekaterina Rogaeva, Anthony Lang, Carmela Tartaglia, Elizabeth Finger, Lorne Zinman, John Turnbull, Morris Freedman, Rick Swartz, Sandra E Black, Robert A Hegele
Next-generation sequencing (NGS) is quickly revolutionizing how research into the genetic determinants of constitutional disease is performed. The technique is highly efficient with millions of sequencing reads being produced in a short time span and at relatively low cost. Specifically, targeted NGS is able to focus investigations to genomic regions of particular interest based on the disease of study. Not only does this further reduce costs and increase the speed of the process, but it lessens the computational burden that often accompanies NGS...
April 4, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29682886/a-common-regulatory-variant-in-slc35b4-influences-the-recurrence-and-survival-of-prostate-cancer
#7
Eric Y Huang, Yu-Jia Chang, Shu-Pin Huang, Victor C Lin, Chia-Cheng Yu, Chao-Yuan Huang, Hsin-Ling Yin, Ta-Yuan Chang, Te-Ling Lu, Bo-Ying Bao
Single nucleotide polymorphisms (SNPs) within the regulatory elements of a gene can alter gene expression, making these SNPs of prime importance for candidate gene association studies. We aimed to determine whether such regulatory variants are associated with clinical outcomes in three cohorts of patients with prostate cancer. We used RegulomeDB to identify potential regulatory variants based on in silico predictions and reviewed genome-wide experimental findings. Overall, 131 putative regulatory SNPs with the highest confidence score on predicted functionality were investigated in two independent localized prostate cancer cohorts totalling 458 patients who underwent radical prostatectomy...
April 23, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29682858/natural-biological-variation-of-white-matter-microstructure-is-accentuated-in-huntington-s-disease
#8
Sarah Gregory, Helen Crawford, Kiran Seunarine, Blair Leavitt, Alexandra Durr, Raymund A C Roos, Rachael I Scahill, Sarah J Tabrizi, Geraint Rees, Douglas Langbehn, Michael Orth
Huntington's disease (HD) is a monogenic neurodegenerative disorder caused by a CAG-repeat expansion in the Huntingtin gene. Presence of this expansion signifies certainty of disease onset, but only partly explains age at which onset occurs. Genome-wide association studies have shown that naturally occurring genetic variability influences HD pathogenesis and disease onset. Investigating the influence of biological traits in the normal population, such as variability in white matter properties, on HD pathogenesis could provide a complementary approach to understanding disease modification...
April 22, 2018: Human Brain Mapping
https://www.readbyqxmd.com/read/29682786/the-evaluation-of-two-genetic-polymorphisms-of-paraoxonase-1-in-patients-with-pulmonary-embolism
#9
Nursah Basol, Nevin Karakus, Asli Yasemen Savas, Kayhan Karakus, İlker Kaya, Serhat Karaman, Serbulent Yigit
BACKGROUND AND OBJECTIVE: Pulmonary embolism (PE) is caused by some genetic factors for more than half patients. Paraoxonase 1 (PON1) has significant anti-oxidative and anti-inflammatory effects. According to our knowledge, there is no study researching the relation between PON 1 gene polymorphisms and PE in the literature. Therefore, it is aimed to research possible impacts of PON 1 Q192R and L55M polymorphisms on PE, considering anti-inflammatory and anti-oxidative effects of PON 1 in Turkish population...
April 22, 2018: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/29682616/human-ccl3l1-copy-number-variation-gene-expression-and-the-role-of-the-ccl3l1-ccr5-axis-in-lung-function
#10
Adeolu B Adewoye, Nick Shrine, Linda Odenthal-Hesse, Samantha Welsh, Anders Malarstig, Scott Jelinsky, Iain Kilty, Martin D Tobin, Edward J Hollox, Louise V Wain
Background: The CCL3L1-CCR5 signaling axis is important in a number of inflammatory responses, including macrophage function, and T-cell-dependent immune responses. Small molecule CCR5 antagonists exist, including the approved antiretroviral drug maraviroc, and therapeutic monoclonal antibodies are in development. Repositioning of drugs and targets into new disease areas can accelerate the availability of new therapies and substantially reduce costs. As it has been shown that drug targets with genetic evidence supporting their involvement in the disease are more likely to be successful in clinical development, using genetic association studies to identify new target repurposing opportunities could be fruitful...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29682505/overview-on-clinical-relevance-of-intra-tumor-heterogeneity
#11
REVIEW
Giorgio Stanta, Serena Bonin
Today, clinical evaluation of tumor heterogeneity is an emergent issue to improve clinical oncology. In particular, intra-tumor heterogeneity (ITH) is closely related to cancer progression, resistance to therapy, and recurrences. It is interconnected with complex molecular mechanisms including spatial and temporal phenomena, which are often peculiar for every single patient. This review tries to describe all the types of ITH including morphohistological ITH, and at the molecular level clonal ITH derived from genomic instability and nonclonal ITH derived from microenvironment interaction...
2018: Frontiers in Medicine
https://www.readbyqxmd.com/read/29682330/yes-associated-protein-yap-in-pancreatic-cancer-at-the-epicenter-of-a-targetable-signaling-network-associated-with-patient-survival
#12
Enrique Rozengurt, James Sinnett-Smith, Guido Eibl
Pancreatic ductal adenocarcinoma (PDAC) is generally a fatal disease with no efficacious treatment modalities. Elucidation of signaling mechanisms that will lead to the identification of novel targets for therapy and chemoprevention is urgently needed. Here, we review the role of Yes-associated protein (YAP) and WW-domain-containing Transcriptional co-Activator with a PDZ-binding motif (TAZ) in the development of PDAC. These oncogenic proteins are at the center of a signaling network that involves multiple upstream signals and downstream YAP-regulated genes...
2018: Signal Transduction and Targeted Therapy
https://www.readbyqxmd.com/read/29682217/leptin-signaling-axis-specifically-associates-with-clinical-prognosis-and-is-multifunctional-in-regulating-cancer-progression
#13
REVIEW
Tsung-Chieh Lin, Kuan-Wei Huang, Chia-Wei Liu, Yu-Chan Chang, Wei-Ming Lin, Tse-Yen Yang, Michael Hsiao
Leptin is a peptide hormone that has been characterized as the ligand of leptin receptor ( LEPR ). The observation of leptin secretion and leptin receptor expression beyond the normal tissues suggests the potentially critical roles other than its physiological function. In addition to the original function in controlling appetite and energy expenditure, leptin-mediated signaling axis through leptin receptor is multifunctional which plays role in the regulation toward broad types of cancer. Emerging evidences has indicated leptin's function in promoting several processes which are relevant to cancer progression including cell proliferation, metastasis, angiogenesis and drug resistance...
March 30, 2018: Oncotarget
https://www.readbyqxmd.com/read/29682207/racial-differences-in-endometrial-cancer-molecular-portraits-in-the-cancer-genome-atlas
#14
David S Guttery, Kevin Blighe, Konstantinos Polymeros, R Paul Symonds, Salvador Macip, Esther L Moss
Endometrial cancer (EC) is now the most prevalent gynaecological malignancy in the Western world. Black or African American women (BoAA) have double the mortality of Caucasian women, and their tumours tend to be of higher grade. Despite these disparities, little is known regarding the mutational landscape of EC between races. Hence, we wished to investigate the molecular features of ECs within The Cancer Genome Atlas (TCGA) dataset by racial groupings. In total 374 Caucasian, 109 BoAA and 20 Asian patients were included in the analysis...
March 30, 2018: Oncotarget
https://www.readbyqxmd.com/read/29682206/copy-number-changes-at-8p11-12-predict-adverse-clinical-outcome-and-chemo-and-radiotherapy-response-in-breast-cancer
#15
Cathy B Moelans, Caroline M G van Maldegem, Elsken van der Wall, Paul J van Diest
Purpose: The short arm of chromosome 8 (8p) is a frequent target of loss of heterozygosity (LOH) in cancer, and 8p LOH is commonly associated with a more aggressive tumor phenotype. The 8p11-12 region is a recurrent breakpoint area characterized by a sharp decrease in gains/amplifications and increase in allelic loss towards 8pter. However, the clustering of genomic aberrations in this region, even in the absence of proximal amplifications or distal LOH, suggests that the 8p11-12 region could play a pivotal role in oncogenesis...
March 30, 2018: Oncotarget
https://www.readbyqxmd.com/read/29682192/-atm-rb1-mutations-predict-shorter-overall-survival-in-urothelial-cancer
#16
Ming Yin, Petros Grivas, Hamid Emamekhoo, Prateek Mendiratta, Siraj Ali, JoAnn Hsu, Monali Vasekar, Joseph J Drabick, Sumanta Pal, Monika Joshi
Background: Mutations of DNA repair genes, e.g. ATM/RB1 , are frequently found in urothelial cancer (UC) and have been associated with better response to cisplatin-based chemotherapy. Further external validation of the prognostic value of ATM/RB1 mutations in UC can inform clinical decision making and trial designs. Results: In the discovery dataset, ATM/RB1 mutations were present in 24% of patients and were associated with shorter OS (adjusted HR 2.67, 95% CI, 1...
March 30, 2018: Oncotarget
https://www.readbyqxmd.com/read/29681852/genotypic-and-phenotypic-factors-influencing-drug-response-in-mexican-patients-with-type-2-diabetes-mellitus
#17
Hector E Sanchez-Ibarra, Luisa M Reyes-Cortes, Xian-Li Jiang, Claudia M Luna-Aguirre, Dionicio Aguirre-Trevino, Ivan A Morales-Alvarado, Rafael B Leon-Cachon, Fernando Lavalle-Gonzalez, Faruck Morcos, Hugo A Barrera-Saldaña
The treatment of Type 2 Diabetes Mellitus (T2DM) consists primarily of oral antidiabetic drugs (OADs) that stimulate insulin secretion, such as sulfonylureas (SUs) and reduce hepatic glucose production (e.g., biguanides), among others. The marked inter-individual differences among T2DM patients' response to these drugs have become an issue on prescribing and dosing efficiently. In this study, fourteen polymorphisms selected from Genome-wide association studies (GWAS) were screened in 495 T2DM Mexican patients previously treated with OADs to find the relationship between the presence of these polymorphisms and response to the OADs...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29681821/genomic-profiling-of-two-histologically-distinct-rare-urothelial-cancers-in-a-clinical-setting-to-identify-potential-therapeutic-options-for-treatment-and-management-of-disease
#18
Andrew N Hesse, William Fabricius, Christian A Thomas, Ramesh Gaindh, Robert Christman, Pavalan Selvam, Matthew Prego, Gregory Lewis, Jasmina Uvalic, Daniel Bergeron, Shelbi Burns, Bridgette Sisson, Kevin Kelly, Jens Rueter, Honey V Reddi
Molecular profiling of urothelial cancers for therapeutic and prognostic potential has been very limited due to the absence of cancer-specific targeted therapies. We describe here 2 clinical cases with a histological diagnosis of an invasive sarcomatoid and a poorly differentiated carcinoma favoring urothelial with some neuroendocrine differentiation, two of the rarer types of urothelial cancers, which were evaluated for mutations in 212 genes for single-nucleotide variants and copy-number variants and 53 genes for fusions associated with solid tumors...
January 2018: Case Reports in Oncology
https://www.readbyqxmd.com/read/29681620/recontacting-or-not-recontacting-a-survey-of-current-practices-in-clinical-genetics-centres-in-europe
#19
Fabio Sirchia, Daniele Carrieri, Sandi Dheensa, Caroline Benjamin, Hülya Kayserili, Christophe Cordier, Carla G van El, Peter D Turnpenny, Bela Melegh, Álvaro Mendes, Tanya F Halbersma-Konings, Irene M van Langen, Anneke M Lucassen, Angus J Clarke, Francesca Forzano, Susan E Kelly
Advances in genomic medicine are improving diagnosis and treatment of some health conditions, and the question of whether former patients should be recontacted is therefore timely. The issue of recontacting is becoming more important with increased integration of genomics in 'mainstream' medicine. Empirical evidence is needed to advance the discussion over whether and how recontacting should be implemented. We administered a web-based survey to genetic services in European countries to collect information about existing infrastructures and practices relevant to recontacting patients...
April 23, 2018: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/29681544/dissecting-the-contributions-of-cooperating-gene-mutations-to-cancer-phenotypes-and-drug-responses-with-patient-derived-ipscs
#20
Chan-Jung Chang, Andriana G Kotini, Malgorzata Olszewska, Maria Georgomanoli, Julie Teruya-Feldstein, Henrik Sperber, Roberto Sanchez, Robert DeVita, Timothy J Martins, Omar Abdel-Wahab, Robert K Bradley, Eirini P Papapetrou
Connecting specific cancer genotypes with phenotypes and drug responses constitutes the central premise of precision oncology but is hindered by the genetic complexity and heterogeneity of primary cancer cells. Here, we use patient-derived induced pluripotent stem cells (iPSCs) and CRISPR/Cas9 genome editing to dissect the individual contributions of two recurrent genetic lesions, the splicing factor SRSF2 P95L mutation and the chromosome 7q deletion, to the development of myeloid malignancy. Using a comprehensive panel of isogenic iPSCs-with none, one, or both genetic lesions-we characterize their relative phenotypic contributions and identify drug sensitivities specific to each one through a candidate drug approach and an unbiased large-scale small-molecule screen...
April 17, 2018: Stem Cell Reports
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