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clinical bioinformatics

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https://www.readbyqxmd.com/read/28453708/towards-a-global-cancer-knowledge-network-dissecting-the-current-international-cancer-genomic-sequencing-landscape
#1
D J Vis, J Lewin, R G Liao, M Mao, F Andre, R L Ward, F Calvo, B T Teh, A A Camargo, B M Knoppers, C L Sawyers, L F A Wessels, M Lawler, L L Siu, E Voest
Background: While next generation sequencing has enhanced our understanding of the biological basis of malignancy, current knowledge on global practices for sequencing cancer samples is limited. To address this deficiency, we developed a survey to provide a snapshot of current sequencing activities globally, identify barriers to data sharing and use this information to develop sustainable solutions for the cancer research community. Methods: A multi-item survey was conducted assessing demographics, clinical data collection, genomic platforms, privacy/ethics concerns, funding sources and data sharing barriers for sequencing initiatives globally...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28453600/whole-exome-sequencing-in-eight-thai-patients-with-leber-congenital-amaurosis-reveals-mutations-in-the-ctnna1-and-cyp4v2-genes
#2
Worapoj Jinda, Todd D Taylor, Yutaka Suzuki, Wanna Thongnoppakhun, Chanin Limwongse, Patcharee Lertrit, Adisak Trinavarat, La-Ongsri Atchaneeyasakul
Purpose: Our goal was to describe the clinical and molecular genetic findings in Thai patients with Leber congenital amaurosis (LCA). Methods: Whole exome sequencing (WES) was performed in eight unrelated patients. All genes responsible for inherited retinal diseases (IRDs) based on RetNet were selected for analysis. Potentially causative variants were filtered through a bioinformatics pipeline and validated using Sanger sequencing. Segregation analysis of the causative genes was performed in family members when available...
April 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28445945/non-small-cell-lung-cancer-associated-microrna-expression-signature-integrated-bioinformatics-analysis-validation-and-clinical-significance
#3
Chunyu Li, Yunhong Yin, Xiao Liu, Xuejiao Xi, Weixiao Xue, Yiqing Qu
Recently, increasing studies of miRNA expression profiling has confirmed that miRNA plays an essential role in non-small cell lung cancer (NSCLC). However, inconsistent or discrepant results exist in these researches. In present study, we performed an integrative analysis of 32 miRNA profiling studies compared the differentially expressed miRNA between NSCLC tissue and non-cancerous lung tissue to identify candidate miRNAs associated with NSCLC. 7 upregulated and 10 downregulated miRNAs were identified as miRNA integrated-signature using Robust Rank Aggregation (RRA) method...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28444906/carbamoyl-phosphate-synthetase-1-deficiency-diagnosed-by-whole-exome-sequencing
#4
Guoqing Zhang, Yulin Chen, Huiqun Ju, Fei Bei, Jing Li, Jian Wang, Jianhua Sun, Jun Bu
BACKGROUND: Carbamoyl Phosphate Synthetase 1 deficiency (CPS1D) is a rare autosomal recessive inborn metabolic disease characterized mainly by hyperammonemia. The fatal nature of CPS1D and its similar symptoms with other urea cycle disorders (UCDs) make its diagnosis difficult, and the molecular diagnosis is hindered due to the large size of the causative gene CPS1. Therefore, the objective of the present study was to investigate the clinical applicability of exome sequencing in molecular diagnosis of CPS1D in Chinese population...
April 26, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28444881/a-three-lncrna-expression-signature-associated-with-the-prognosis-of-gastric-cancer-patients
#5
Peng Song, Bo Jiang, Zhijian Liu, Jie Ding, Song Liu, Wenxian Guan
Long noncoding RNAs (lncRNAs) have emerged as essential players in gene regulation. An ever-increasing number of lncRNAs has been found to be associated with the biogenesis and prognosis of gastric cancer (GC). We aimed to develop an lncRNA signature with prognostic value for survival outcomes of GC. Using an lncRNA mining approach, we analyzed the lncRNA expression profiles of 492 GC patients from the Gene Expression Omnibus (GEO), which consisted of the GSE62254 set (N = 300) and the GSE15459 set (N = 192)...
April 26, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28444658/comparing-the-immune-genomic-effects-of-vilazodone-and-paroxetine-in-late-life-depression-a-pilot-study
#6
Harris Eyre, Prabha Siddarth, Natalie Cyr, Hongyu Yang, Steve Cole, Malcolm Forbes, Helen Lavretsky
Vilazodone is a novel antidepressant agent that combines selective serotonin (5-HT) reuptake inhibitor (SSRI) activity and 5-HT(1A) receptor partial agonist activity. A pilot study was conducted to compare vilazodone (novel compound) and paroxetine (gold standard) on antidepressant effects, tolerability, and inflammation and immune modulation. A 12-week, double-blind, randomized clinical trial was conducted with 56 nondemented older adults diagnosed with major depressive disorder (MDD). Between-group differences in mood, tolerability, and safety, as well as genomic markers of inflammation and immune modulation, were examined...
April 25, 2017: Pharmacopsychiatry
https://www.readbyqxmd.com/read/28444231/whole-genome-sequencing-of-7-strains-of-staphylococcus-lugdunensis-allows-identification-of-mobile-genetic-elements
#7
Xavier Argemi, Véronique Martin, Valentin Loux, Sandrine Dahyot, Jérémie Lebeurre, Aurélien Guffroy, Mickael Martin, Aurélie Velay, Daniel Keller, Philippe Riegel, Yves Hansmann, Nicodème Paul, Gilles Prévost
Coagulase negative staphylococci are normal inhabitant of the human skin flora that account for an increasing number of infections, particularly hospital-acquired infections. Staphylococcus lugdunensis has emerged as a most virulent species causing various infections with clinical characteristics close to what clinicians usually observe with Staphylococcus aureus and both bacteria share more than 70% of their genome. Virulence of S. aureus relies on a large repertoire of virulence factors, many of which are encoded on mobile genetic elements...
April 21, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28443461/mir-1202-functions-as-a-tumor-suppressor-in-glioma-cells-by-targeting-rab1a
#8
Yu Quan, Qian Song, Jvbo Wang, Lingyu Zhao, Jian Lv, Shouping Gong
Aberrant expression of microRNAs correlates with the development and progression of human cancers by targeting downstream proteins. MiR-1202 is downregulated in ovarian cancer and clear cell papillary renal cell carcinoma; however, its role in glioma remains unknown. The purpose of this study was to determine the expression and the role of miR-1202 and to elucidate its regulatory mechanism in glioma. We used quantitative real-time polymerase chain reaction to measure miR-1202 expression in both glioma tissues and cell lines...
April 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28443186/general-guidelines-for-biomedical-software-development
#9
REVIEW
Luis Bastiao Silva, Rafael C Jimenez, Niklas Blomberg, José Luis Oliveira
Most bioinformatics tools available today were not written by professional software developers, but by people that wanted to solve their own problems, using computational solutions and spending the minimum time and effort possible, since these were just the means to an end. Consequently, a vast number of software applications are currently available, hindering the task of identifying the utility and quality of each. At the same time, this situation has hindered regular adoption of these tools in clinical practice...
2017: F1000Research
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
#10
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/28438193/pathos-a-decision-support-system-for-reporting-high-throughput-sequencing-of-cancers-in-clinical-diagnostic-laboratories
#11
Kenneth D Doig, Andrew Fellowes, Anthony H Bell, Andrei Seleznev, David Ma, Jason Ellul, Jason Li, Maria A Doyle, Ella R Thompson, Amit Kumar, Luis Lara, Ravikiran Vedururu, Gareth Reid, Thomas Conway, Anthony T Papenfuss, Stephen B Fox
BACKGROUND: The increasing affordability of DNA sequencing has allowed it to be widely deployed in pathology laboratories. However, this has exposed many issues with the analysis and reporting of variants for clinical diagnostic use. Implementing a high-throughput sequencing (NGS) clinical reporting system requires a diverse combination of capabilities, statistical methods to identify variants, global variant databases, a validated bioinformatics pipeline, an auditable laboratory workflow, reproducible clinical assays and quality control monitoring throughout...
April 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28436239/clinical-applications-of-quantitative-proteomics-using-targeted-and-untargeted-data-independent-acquisition-techniques
#12
Jesse G Meyer, Birgit Schilling
While selected/multiple-reaction monitoring (SRM or MRM) is considered the gold standard for quantitative protein measurement, emerging data-independent acquisition (DIA) using high-resolution scans have opened a new dimension of high-throughput, comprehensive quantitative proteomics. These newer methodologies are particularly well suited for discovery of biomarker candidates from human disease samples, and for investigating and understanding human disease pathways. Areas covered: This article reviews the current state of targeted and untargeted DIA mass spectrometry-based proteomic workflows, including SRM, parallel-reaction monitoring (PRM) and untargeted DIA (e...
April 24, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28430657/microrna-signatures-predict-prognosis-of-patients-with-glioblastoma-multiforme-through-the-cancer-genome-atlas
#13
Ying Yuan, Hua Zhang, Xuexia Liu, Zhongming Lu, Guojun Li, Meixia Lu, Xiaofeng Tao
MicroRNAs (miRNAs) play major roles in various biological processes and have been implicated in the pathogenesis and malignant progression of glioblastoma multiforme (GBM). The aim of this study was to assess the predictive values of miRNAs for overall survival (OS) of patients with GBM. MiRNA expression profiles and clinical information of 563 GBM patients were obtained from the Cancer Genome Atlas. The most significantly altered miRNAs were identified and miRNA expression profiles were performed, through principal component analysis, the least absolute shrinkage and selection operator method...
April 6, 2017: Oncotarget
https://www.readbyqxmd.com/read/28430325/identification-of-a-disease-causing-mutation-in-a-chinese-patient-with-retinitis-pigmentosa-by-targeted-next-generation-sequencing
#14
Jianping Xiao, Xueqin Guo, Yong Wang, Mingkun Shao, Xiaoming Wei, Lique Du, Long Li, Yan Sun, Yun Yang
PURPOSE: To identify disease-causing mutations in a Chinese patient with retinitis pigmentosa (RP). METHODS: A detailed clinical examination was performed on the proband. Targeted next-generation sequencing (NGS) combined with bioinformatics analysis was performed on the proband to detect candidate disease-causing mutations. Sanger sequencing was performed on all subjects to confirm the candidate mutations and assess cosegregation within the family. RESULTS: Clinical examinations of the proband showed typical characteristics of RP...
April 14, 2017: European Journal of Ophthalmology
https://www.readbyqxmd.com/read/28429075/toward-personalized-management-in-bladder-cancer-the-promise-of-novel-molecular-taxonomy
#15
REVIEW
Marie-Lisa Eich, Lars Dyrskjøt, George J Netto
Empowered by the recent advances in next generation sequencing and bioinformatics technology, an unprecedented wave of integrated transcriptomic and genomic studies have impacted the field of bladder cancer. These studies not only have confirmed previously charted genetic pathways in bladder cancer development but also have led to the discovery of numerous additional crucial driver genetic alterations. As a result, a novel genomic-based taxonomy is emerging that promises to better define clinically relevant intrinsic subtypes of bladder cancer...
April 21, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/28428751/identification-of-nf-%C3%AE%C2%BAb-as-determinant-of-posttraumatic-stress-disorder-and-its-inhibition-by-the-chinese-herbal-remedy-free-and-easy-wanderer
#16
Chunlan Hong, Anja Schüffler, Ulrich Kauhl, Jingming Cao, Ching-Fen Wu, Till Opatz, Eckhard Thines, Thomas Efferth
Posttraumatic stress disorder (PTSD) is a mental disorder developing after exposure to traumatic events. Although psychotherapy reveals some therapeutic effectiveness, clinically sustainable cure is still uncertain. Some Chinese herbal formulae are reported to work well clinically against mental diseases in Asian countries, but the safety and their mode of action are still unclear. In this study, we investigated the mechanisms of Chinese remedy free and easy wanderer (FAEW) on PTSD. We used a reverse pharmacology approach combining clinical data to search for mechanisms of PTSD with subsequent in vitro verification and bioinformatics techniques as follows: (1) by analyzing microarray-based transcriptome-wide mRNA expression profiling of PTSD patients; (2) by investigating the effect of FAEW and the antidepressant control drug fluoxetine on the transcription factor NF-κB using reporter cell assays and western blotting; (3) by performing molecular docking and literature data mining based on phytochemical constituents of FAEW...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28428271/master-transcriptional-regulators-in-cancer-discovery-via-reverse-engineering-approaches-and-subsequent-validation
#17
REVIEW
Bruce Moran, Arman Rahman, Katja Palonen, Fiona T Lanigan, William M Gallagher
Reverse engineering of transcriptional networks using gene expression data enables identification of genes that underpin the development and progression of different cancers. Methods to this end have been available for over a decade and, with a critical mass of transcriptomic data in the oncology arena having been reached, they are ever more applicable. Extensive and complex networks can be distilled into a small set of key master transcriptional regulators (MTR), genes that are very highly connected and have been shown to be involved in processes of known importance in disease...
April 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28426096/managing-the-sequence-specificity-of-antisense-oligonucleotides-in-drug-discovery
#18
Peter H Hagedorn, Bo R Hansen, Troels Koch, Morten Lindow
All drugs perturb the expression of many genes in the cells that are exposed to them. These gene expression changes can be divided into effects resulting from engaging the intended target and effects resulting from engaging unintended targets. For antisense oligonucleotides, developments in bioinformatics algorithms, and the quality of sequence databases, allow oligonucleotide sequences to be analyzed computationally, in terms of the predictability of their interactions with intended and unintended RNA targets...
March 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28424670/azathioprine-mercaptopurine-and-5-aminosalicylic-acid-affect-the-growth-of-ibd-associated-campylobacter-species-and-other-enteric-microbes
#19
Fang Liu, Rena Ma, Stephen M Riordan, Michael C Grimm, Lu Liu, Yiming Wang, Li Zhang
Campylobacter concisus is a bacterium that is associated with inflammatory bowel disease (IBD). Immunosuppressive drugs including azathioprine (AZA) and mercaptopurine (MP), and anti-inflammatory drug such as 5-aminosalicylic acid (5-ASA) are commonly used to treat patients with IBD. This study aimed to examine the effects of AZA, MP, and 5-ASA on the growth of IBD-associated bacterial species and to identify bacterial enzymes involved in immunosuppressive drug metabolism. A total of 15 bacterial strains of five species including 11 C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28423715/a-functional-variant-at-the-mirna-binding-site-in-hmgb1-gene-is-associated-with-risk-of-oral-squamous-cell-carcinoma
#20
Chiao-Wen Lin, Ying-Erh Chou, Chia-Ming Yeh, Shun-Fa Yang, Chun-Yi Chuang, Yu-Fan Liu
Oral squamous cell carcinoma (OSCC) is a common malignancy that has been causally associated with both hereditary and acquired factors. The high mobility group box 1 (HMGB1) gene plays an important role as a DNA chaperone to help maintain nuclear homeostasis. Altered expression of HMGB1 has been implicated in a wide range of pathological processes, including inflammation and cancer. The present study explores the impact of HMGB1 gene polymorphisms, combined with environmental risks regarding susceptibility to oral tumorigenesis...
March 11, 2017: Oncotarget
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