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Bioinformatics & pathogenicity prediction

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https://www.readbyqxmd.com/read/28439188/next-generation-sequencing-reveals-high-prevalence-of-brca1-and-brca2-variants-of-unknown-significance-in-early-onset-breast-cancer-in-african-american-women
#1
Luisel Ricks-Santi, J Tyson McDonald, Bert Gold, Michael Dean, Nicole Thompson, Muneer Abbas, Bradford Wilson, Yasmine Kanaan, Tammey J Naab, Georgia Dunston
BACKGROUND: Variants of unknown significance (VUSs) have been identified in BRCA1 and BRCA2 and account for the majority of all identified sequence alterations. Notably, VUSs occur disproportionately in people of African descent hampering breast cancer (BCa) management and prevention efforts in the population. Our study sought to identify and characterize mutations associated with increased risk of BCa at young age. METHODS: In our study, the spectrum of mutations in BRCA1 and BRCA2 was enumerated in a cohort of 31 African American women of early age at onset breast cancer, with a family history of breast or cancer in general and/or with triple negative breast cancer...
2017: Ethnicity & Disease
https://www.readbyqxmd.com/read/28433619/lack-of-pathogenic-mutations-in-sos1-gene-in-phenytoin-induced-gingival-overgrowth-patients
#2
Katia Margiotti, Giulia Pascolini, Federica Consoli, Valentina Guida, Carlo Di Bonaventura, Anna Teresa Giallonardo, Antonio Pizzuti, Alessandro De Luca
OBJECTIVE: Gingival overgrowth is a side effect associated with some distinct classes of drugs, such as anticonvulsants, immunosuppressants, and calcium channel blockers. One of the main drugs associated with gingival overgrowth is the antiepileptic phenytoin, which affects gingival tissues by altering extracellular matrix metabolism. It has been shown that mutation of human SOS1 gene is responsible for a rare hereditary gingival fibromatosis type 1, a benign gingival overgrowth. The aim of the present study is to evaluate the possible contribution of SOS1 mutation to gingival overgrowth-related phenotype...
April 5, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28423643/pole-and-pold1-screening-in-155-patients-with-multiple-polyps-and-early-onset-colorectal-cancer
#3
Clara Esteban-Jurado, David Giménez-Zaragoza, Jenifer Muñoz, Sebastià Franch-Expósito, Miriam Álvarez-Barona, Teresa Ocaña, Miriam Cuatrecasas, Sabela Carballal, María López-Cerón, Maria Marti-Solano, Marcos Díaz-Gay, Tom van Wezel, Antoni Castells, Luis Bujanda, Judith Balmaña, Victoria Gonzalo, Gemma Llort, Clara Ruiz-Ponte, Joaquín Cubiella, Francesc Balaguer, Rosa Aligué, Sergi Castellví-Bel
Germline mutations in POLE and POLD1 have been shown to cause predisposition to colorectal multiple polyposis and a wide range of neoplasms, early-onset colorectal cancer being the most prevalent. In order to find additional mutations affecting the proofreading activity of these polymerases, we sequenced its exonuclease domain in 155 patients with multiple polyps or an early-onset colorectal cancer phenotype without alterations in the known hereditary colorectal cancer genes. Interestingly, none of the previously reported mutations in POLE and POLD1 were found...
March 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28422960/predicting-the-impact-of-lynch-syndrome-causing-missense-mutations-from-structural-calculations
#4
Sofie V Nielsen, Amelie Stein, Alexander B Dinitzen, Elena Papaleo, Michael H Tatham, Esben G Poulsen, Maher M Kassem, Lene J Rasmussen, Kresten Lindorff-Larsen, Rasmus Hartmann-Petersen
Accurate methods to assess the pathogenicity of mutations are needed to fully leverage the possibilities of genome sequencing in diagnosis. Current data-driven and bioinformatics approaches are, however, limited by the large number of new variations found in each newly sequenced genome, and often do not provide direct mechanistic insight. Here we demonstrate, for the first time, that saturation mutagenesis, biophysical modeling and co-variation analysis, performed in silico, can predict the abundance, metabolic stability, and function of proteins inside living cells...
April 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28421333/identification-of-putative-second-genetic-hits-in-schizophrenia-carriers-of-high-risk-copy-number-variants-and-resequencing-in-additional-samples
#5
Julio Rodríguez-López, Beatriz Sobrino, Jorge Amigo, Noa Carrera, Julio Brenlla, Santiago Agra, Eduardo Paz, Ángel Carracedo, Mario Páramo, Manuel Arrojo, Javier Costas
Copy number variants (CNVs) conferring risk of schizophrenia present incomplete penetrance, suggesting the existence of second genetic hits. Identification of second hits may help to find genes with rare variants of susceptibility to schizophrenia. The aim of this work was to search for second hits of moderate/high risk in schizophrenia carriers of risk CNVs and resequencing of the relevant genes in additional samples. To this end, ten patients with risk CNVs at cytobands 15q11.2, 15q11.2-13.1, 16p11.2, or 16p13...
April 18, 2017: European Archives of Psychiatry and Clinical Neuroscience
https://www.readbyqxmd.com/read/28416776/clinical-value-of-mir-101-3p-and-biological-analysis-of-its-prospective-targets-in-breast-cancer-a-study-based-on-the-cancer-genome-atlas-tcga-and-bioinformatics
#6
Chun-Yao Li, Dan-Dan Xiong, Chun-Qin Huang, Rong-Quan He, Hai-Wei Liang, Deng-Hua Pan, Han-Lin Wang, Yi-Wen Wang, Hua-Wei Zhu, Gang Chen
BACKGROUND MiR-101-3p can promote apoptosis and inhibit proliferation, invasion, and metastasis in breast cancer (BC) cells. However, its mechanisms in BC are not fully understood. Therefore, a comprehensive analysis of the target genes, pathways, and networks of miR-101-3p in BC is necessary. MATERIAL AND METHODS The miR-101 profiles for 781 patients with BC from The Cancer Genome Atlas (TCGA) were analyzed. Gene expression profiling of GSE31397 with miR-101-3p transfected MCF-7 cells and scramble control cells was downloaded from Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) were identified...
April 18, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28391287/identification-of-2-potentially-relevant-gene-mutations-involved-in-strabismus-using-whole-exome-sequencing
#7
Xiangrong Min, Haiying Fan, Guiqiu Zhao, Guixiang Liu
BACKGROUND The etiology of strabismus has a genetic component. Our study aimed to localize the candidate causative gene mutant in a Chinese family with strabismus and to describe its underlying etiology. MATERIAL AND METHODS Genomic DNA was extracted from the affected individual and his parents in a Chinese pedigree with strabismus. The resulting exomes were sequenced by whole-exome sequencing. After variant calling and filtering, the candidate causative gene mutations were selected for the rarity and predicted damaging effect, which complied with the model of recessive disease transmission...
April 9, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/28389359/intronic-variants-of-slc26a4-gene-enhance-splicing-efficiency-in-hybrid-minigene-assay
#8
Rihab Kallel Bouattour, Salima Belguith Maalej, Emna Zouari-Bradai, Mouna Mnif, Mohamed Abid, Hassen Hadj Kacem
The SLC26A4 genomic sequence screening in autoimmune thyroid diseases (AITD) revealed different variants types with possible pathogenic effects. Although intronic variants may have more detrimental effects than those coding, they are poorly explored. Thus, in a first assessment, our bioinformatics analysis of intronic variants predicted a pathogenic effect of c.1002-9A>C, c.1545-5T>G and c.1544+9C>T variants. Validating these variants pathogenicity may provide new clues on the AITD physiopathology...
April 4, 2017: Gene
https://www.readbyqxmd.com/read/28386709/in-silico-analysis-of-five-missense-mutations-in-cyp1b1-gene-in-pakistani-families-affected-with-primary-congenital-glaucoma
#9
Sabika Firasat, Haiba Kaul, Usman Ali Ashfaq, Sobia Idrees
PURPOSE: The purpose of this study was to characterize the five missense mutations in CYP1B1 gene identified in Pakistani families affected with primary congenital glaucoma (PCG) using various bioinformatics and protein modeling tools. METHODS: We previously reported four novel missense mutations in CYP1B1 gene segregating in consanguineous Pakistani families. These mutations were identified by direct sequencing of all coding exons, the exon-intron boundaries and the 5' untranslated region of CYP1B1 using genomic DNA from affected and unaffected family members...
April 6, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28385564/genome-wide-identification-of-microrna-targets-in-the-neglected-disease-pathogens-of-the-genus-echinococcus
#10
Natalia Macchiaroli, Lucas Maldonado, Magdalena Zarowiecki, Marcela Cucher, Maria Ines Gismondi, Laura Kamenetzky, Mara Cecilia Rosenzvit
MicroRNAs (miRNAs), a class of small non-coding RNAs, are key regulators of gene expression at post-transcriptional level and play essential roles in biological processes such as development. MiRNAs silence target mRNAs by binding to complementary sequences in the 3'untranslated regions (3'UTRs). The parasitic helminths of the genus Echinococcus are the causative agents of echinococcosis, a zoonotic neglected disease. In previous work, we performed a comprehensive identification and characterization of Echinococcus miRNAs...
April 3, 2017: Molecular and Biochemical Parasitology
https://www.readbyqxmd.com/read/28352270/the-immune-epitope-database-and-analysis-resource-in-epitope-discovery-and-synthetic-vaccine-design
#11
REVIEW
Ward Fleri, Sinu Paul, Sandeep Kumar Dhanda, Swapnil Mahajan, Xiaojun Xu, Bjoern Peters, Alessandro Sette
The task of epitope discovery and vaccine design is increasingly reliant on bioinformatics analytic tools and access to depositories of curated data relevant to immune reactions and specific pathogens. The Immune Epitope Database and Analysis Resource (IEDB) was indeed created to assist biomedical researchers in the development of new vaccines, diagnostics, and therapeutics. The Analysis Resource is freely available to all researchers and provides access to a variety of epitope analysis and prediction tools...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28314727/transcriptomic-analyses-elucidate-adaptive-differences-of-closely-related-strains-of-p-aeruginosa-in-fuel
#12
Thusitha S Gunasekera, Loryn L Bowen, Carol E Zhou, Susan C Howard-Byerly, William S Foley, Richard C Striebich, Larry C Dugan, Oscar N Ruiz
Pseudomonas aeruginosa can utilize hydrocarbons, but different strains have varying degrees of adaptation despite their highly conserved genome. P. aeruginosa ATCC 33988 is highly adapted to hydrocarbons while strain PAO1, a human pathogen, is less-adapted and degrades jet fuel at a slower rate than does ATCC 33988. We investigated fuel specific transcriptomic differences between these strains in order to ascertain the underling mechanisms utilized by the adapted strain to proliferate in fuel. During growth in fuel, the genes related to alkane degradation, heat-shock response, membrane proteins, efflux pumps and several novel genes were upregulated in ATCC 33988...
March 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28299517/characterization-and-complete-genome-sequence-analysis-of-a-novel-virulent-siphoviridae-phage-against-staphylococcus-aureus-isolated-from-bovine-mastitis-in-xinjiang-china
#13
Qian Zhang, Shaozhen Xing, Qiang Sun, Guangqian Pei, Shi Cheng, Yannan Liu, Xiaoping An, Xianglilan Zhang, Yonggang Qu, Yigang Tong
Bovine mastitis is one of the most costly diseases in dairy cows worldwide. It can be caused by over 150 different microorganisms, where Staphylococcus aureus is the most frequently isolated and a major pathogen responsible for heavy economic losses in dairy industry. Although antibiotic therapy is most widely used, alternative treatments are necessary due to the increasing antibiotic resistance. Using phage for pathogen control is a promising tool in the fight against antibiotic resistance. Mainly using high-throughput sequencing, bioinformatics and our proposed phage termini identification method, we have isolated and characterized a novel virulent phage, designated as vB_SauS_IMEP5, from manure collected from dairy farms in Shihezi, Xinjiang, China, for use as a biocontrol agent against Staphylococcus aureus infections...
March 15, 2017: Virus Genes
https://www.readbyqxmd.com/read/28297664/coupling-between-protein-stability-and-catalytic-activity-determines-pathogenicity-of-g6pd-variants
#14
Anna D Cunningham, Alexandre Colavin, Kerwyn Casey Huang, Daria Mochly-Rosen
G6PD deficiency, an enzymopathy affecting 7% of the world population, is caused by over 160 identified amino acid variants in glucose-6-phosphate dehydrogenase (G6PD). The clinical presentation of G6PD deficiency is diverse, likely due to the broad distribution of variants across the protein and the potential for multidimensional biochemical effects. In this study, we use bioinformatic and biochemical analyses to interpret the relationship between G6PD variants and their clinical phenotype. Using structural information and statistical analyses of known G6PD variants, we predict the molecular phenotype of five uncharacterized variants from a reference population database...
March 14, 2017: Cell Reports
https://www.readbyqxmd.com/read/28288890/abdominal-aortic-aneurysm-associated-microrna-516a-5p-regulates-expressions-of-methylenetetrahydrofolate-reductase-matrix-metalloproteinase-2-and-tissue-inhibitor-of-matrix-metalloproteinase-1-in-human-abdominal-aortic-vascular-smooth-muscle-cells
#15
Crystal Yin Tung Chan, Bernice Lai Yee Cheuk, Stephen Wing Keung Cheng
BACKGROUND: MicroRNAs (miRNAs or miRs) have been highlighted to be involved in abdominal aortic aneurysm (AAA) with the emergence of recent miRNA microarray profiling studies. miR-516a-5p has been shown to be significantly overexpressed in vascular smooth muscle cells (VSMCs) from human AAA tissues from our previous microarray study, suggesting its crucial association with AAA. In addition, further bioinformatics analysis predicted methylenetetrahydrofolate reductase (MTHFR), which regulates homocysteine (Hcy) metabolism and is proposed to be a risk gene for AAA formation and to be the downregulation target of miR-516a-5p...
March 10, 2017: Annals of Vascular Surgery
https://www.readbyqxmd.com/read/28284182/the-prediction-of-a-pathogenesis-related-secretome-of-puccinia-helianthi-through-high-throughput-transcriptome-analysis
#16
Lan Jing, Dandan Guo, Wenjie Hu, Xiaofan Niu
BACKGROUND: Many plant pathogen secretory proteins are known to be elicitors or pathogenic factors,which play an important role in the host-pathogen interaction process. Bioinformatics approaches make possible the large scale prediction and analysis of secretory proteins from the Puccinia helianthi transcriptome. The internet-based software SignalP v4.1, TargetP v1.01, Big-PI predictor, TMHMM v2.0 and ProtComp v9.0 were utilized to predict the signal peptides and the signal peptide-dependent secreted proteins among the 35,286 ORFs of the P...
March 11, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28280605/next-generation-sequencing-identifies-interactome-signatures-in-relapsed-and-refractory-metastatic-colorectal-cancer
#17
Benny Johnson, Laurence Cooke, Daruka Mahadevan
BACKGROUND: In the management of metastatic colorectal cancer (mCRC), KRAS, NRAS and BRAF mutational status individualizes therapeutic options and identify a cohort of patients (pts) with an aggressive clinical course. We hypothesized that relapsed and refractory mCRC pts develop unique mutational signatures that may guide therapy, predict for a response and highlight key signaling pathways important for clinical decision making. METHODS: Relapsed and refractory mCRC pts (N=32) were molecularly profiled utilizing commercially available next generation sequencing (NGS) platforms...
February 2017: Journal of Gastrointestinal Oncology
https://www.readbyqxmd.com/read/28260060/bioinformatics-analysis-on-the-differentiation-of-bone-mesenchymal-stem-cells-into-osteoblasts-and-adipocytes
#18
Xiaoyuan Xu, He Jiang, Xingnuan Li, Ping Wu, Jianyun Liu, Tao Wang, Xiaoou Zhou, Jianjun Xiong, Weidong Li
The present study aimed to screen several differentially expressed genes (DEGs) and differentially expressed microRNAs (miRNAs) for two types of mesenchymal stem cell (MSC) differentiation. Bone morphogenetic protein 6 (BMP‑6) and dexamethasone were used to induce MSCs towards osteoblastic differentiation or adipocytic differentiation. The t‑test in the Bioconductor bioinformatics software tool was used to screen DEGs and differentially expressed miRNAs in the two samples. Subsequent gene ontology (GO) and pathway analyses on the DEGs were performed using the GO and Kyoto Encyclopedia of Genes and Genomes databases, respectively; potential target genes for the screened miRNAs were predicted using the TargetScan database...
April 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28259674/assessment-of-the-potential-utility-of-different-regions-of-streptococcus-uberis-adhesion-molecule-suam-for-mastitis-subunit-vaccine-development
#19
Melina Soledad Perrig, Carolina Veaute, María Sol Renna, Nazarena Pujato, Luis Calvinho, Iván Marcipar, María Sol Barbagelata
Streptococcus uberis is one of the most prevalent pathogens causing clinical and subclinical mastitis worldwide. Among bacterial factors involved in intramammary infections caused by this organism, S. uberis adhesion molecule (SUAM) is one of the main virulence factors identified. This molecule is involved in S. uberis internalization to mammary epithelial cells through lactoferrin (Lf) binding. The objective of this study was to evaluate SUAM properties as a potential subunit vaccine component for prevention of S...
March 1, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28242707/oligomeric-lipoprotein-pelc-guides-pel-polysaccharide-export-across-the-outer-membrane-of-pseudomonas-aeruginosa
#20
Lindsey S Marmont, Jacquelyn D Rich, John C Whitney, Gregory B Whitfield, Henrik Almblad, Howard Robinson, Matthew R Parsek, Joe J Harrison, P Lynne Howell
Secreted polysaccharides are important functional and structural components of bacterial biofilms. The opportunistic pathogen Pseudomonas aeruginosa produces the cationic exopolysaccharide Pel, which protects bacteria from aminoglycoside antibiotics and contributes to biofilm architecture through ionic interactions with extracellular DNA. A bioinformatics analysis of genome databases suggests that gene clusters for Pel biosynthesis are present in >125 bacterial species, yet little is known about how this biofilm exopolysaccharide is synthesized and exported from the cell...
March 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
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