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https://www.readbyqxmd.com/read/29036683/cr2cancer-a-database-for-chromatin-regulators-in-human-cancer
#1
Beibei Ru, Jianlong Sun, Yin Tong, Ching Ngar Wong, Aditi Chandra, Acacia Tsz So Tang, Larry Ka Yue Chow, Wai Lam Wun, Zarina Levitskaya, Jiangwen Zhang
Chromatin regulators (CRs) can dynamically modulate chromatin architecture to epigenetically regulate gene expression in response to intrinsic and extrinsic signalling cues. Somatic alterations or misexpression of CRs might reprogram the epigenomic landscape of chromatin, which in turn lead to a wide range of common diseases, notably cancer. Here, we present CR2Cancer, a comprehensive annotation and visualization database for CRs in human cancer constructed by high throughput data analysis and literature mining...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036643/glass-assisted-and-standardized-assessment-of-gene-variations-from-sanger-sequence-trace-data
#2
Karol Pal, Vojtech Bystry, Tomas Reigl, Martin Demko, Adam Krejci, Tasoula Touloumenidou, Evangelia Stalika, Boris Tichy, Paolo Ghia, Kostas Stamatopoulos, Sarka Pospisilova, Jitka Malcikova, Nikos Darzentas
Motivation: Sanger sequencing is still being employed for sequence variant detection by many laboratories, especially in a clinical setting. However, chromatogram interpretation often requires manual inspection and in some cases, considerable expertise. Results: We present GLASS, a web-based Sanger sequence trace viewer, editor, aligner and variant caller, built to assist with the assessment of variations in 'curated' or user-provided genes. Critically, it produces a standardized variant output as recommended by the Human Genome Variation Society...
July 13, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036598/global-dna-methylation-analysis-reveals-mir-214-3p-contributes-to-cisplatin-resistance-in-pediatric-intracranial-nongerminomatous-malignant-germ-cell-tumors
#3
Tsung-Han Hsieh, Yun-Ru Liu, Ting-Yu Chang, Muh-Lii Liang, Hsin-Hung Chen, Hsei-Wei Wang, Yun Yen, Tai-Tong Wong
Background: Pediatric central nervous system germ cell tumors (CNSGCTs) are rare and heterogeneous neoplasms, and they can be divided into germinomas and nongerminomatous GCTs (NGGCTs). NGGCTs are further subdivided into mature teratomas and nongerminomatous malignant GCTs (NGMGCTs). Clinical outcomes suggest that NGMGCTs have poor prognosis and survival, and that they require more extensive radiotherapy and adjuvant chemotherapy. However, the mechanisms underlying this difference are still unclear...
October 3, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29036590/tissgdb-tissue-specific-gene-database-in-cancer
#4
Pora Kim, Aekyung Park, Guangchun Han, Hua Sun, Peilin Jia, Zhongming Zhao
Tissue-specific gene expression is critical in understanding biological processes, physiological conditions, and disease. The identification and appropriate use of tissue-specific genes (TissGenes) will provide important insights into disease mechanisms and organ-specific therapeutic targets. To better understand the tissue-specific features for each cancer type and to advance the discovery of clinically relevant genes or mutations, we built TissGDB (Tissue specific Gene DataBase in cancer) available at http://zhaobioinfo...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036588/a-novel-data-structure-to-support-ultra-fast-taxonomic-classification-of-metagenomic-sequences-with-k-mer-signatures
#5
Xinan Liu, Ye Yu, Jinpeng Liu, Corrine F Elliott, Chen Qian, Jinze Liu
Motivation: Metagenomic read classification is a critical step in the identification and quantification of microbial species sampled by high-throughput sequencing. Although many algorithms have been developed to date, they suffer significant memory and/or computational costs. Due to the growing popularity of metagenomic data in both basic science and clinical applications, as well as the increasing volume of data being generated, efficient and accurate algorithms are in high demand. Results: We introduce MetaOthello, a probabilistic hashing classifier for metagenomic sequencing reads...
July 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036500/glioma-cpg-island-methylator-phenotype-g-cimp-biological-and-clinical-implications
#6
Tathiane M Malta, Camila F de Souza, Thais S Sabedot, Tiago C Silva, Maritza Q S Mosella, Steven N Kalkanis, James Snyder, Ana Valeria B Castro, Houtan Noushmehr
Gliomas are a heterogeneous group of brain tumors with distinct biological and clinical properties. Despite advances in surgical techniques and clinical regimens, treatment of high-grade glioma remains challenging and carries dismal rates of therapeutic success and overall survival. Challenges include the molecular complexity of gliomas, as well as inconsistencies in histopathological grading, resulting in an inaccurate prediction of disease progression and failure in the use of standard therapy. The updated 2016 World Health Organization (WHO) classification of tumors of the central nervous system reflects a refinement of tumor diagnostics by integrating the genotypic and phenotypic features, thereby narrowing the defined subgroups...
September 26, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/29036432/copb2-is-essential-for-embryogenesis-and-hypomorphic-mutations-cause-human-microcephaly
#7
Andrew DiStasio, Ashley Driver, Kristen Sund, Milene Donlin, Ranjith M Muraleedharan, Shabnam Pooya, Beth Kline-Fath, Kenneth M Kaufman, Cynthia A Prows, Elizabeth Schorry, Biplab DasGupta, Rolf W Stottmann
Primary microcephaly is a congenital brain malformation characterized by a head circumference less than three standard deviations below the mean for age and sex and results in moderate to severe mental deficiencies and decreased lifespan. We recently studied two children with primary microcephaly in an otherwise unaffected family. Exome sequencing identified an autosomal recessive mutation leading to an amino acid substitution in a WD40 domain of the highly conserved Coatomer Protein Complex, Subunit Beta 2 (COPB2)...
September 19, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/29036298/myvcf-a-desktop-application-for-high-throughput-mutations-data-management
#8
Alessandro Pietrelli, Luca Valenti
Summary: Next-generation sequencing technologies have become the most powerful tool to discover genetic variants associated with human diseases. Although the dramatic reductions in the costs facilitate the use in the wet-lab and clinics, the huge amount of data generated renders their management by non-expert researchers and physicians extremely difficult. Therefore, there is an urgent need of novel approaches and tools aimed at getting the 'end-users' closer to the sequencing data, facilitating the access by non-bioinformaticians, and to speed-up the functional interpretation of genetic variants...
July 24, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036251/an-adhesive-patch-based-skin-biopsy-device-for-molecular-diagnostics-and-skin-microbiome-studies
#9
Zuxu Yao, Ronald Moy, Talisha Allen, Burkhard Jansen
INTRODUCTION: A number of diagnoses in clinical dermatology are currently histopathologically confirmed and this image recognition-based confirmation generally requires surgical biopsies. The increasing ability of molecular pathology to corroborate or correct a clinical diagnosis based on objective gene expression, mutation analysis, or molecular microbiome data is on the horizon and would be further supported by a tool or procedure to collect samples non-invasively. This study characterizes such a tool in form of a 'bladeless' adhesive patch-based skin biopsy device...
October 1, 2017: Journal of Drugs in Dermatology: JDD
https://www.readbyqxmd.com/read/29036186/the-mgmt-promoter-single-nucleotide-polymorphism-rs1625649-had-prognostic-impact-on-patients-with-mgmt-methylated-glioblastoma
#10
Chih-Yi Hsu, Hsiang-Ling Ho, Shih-Chieh Lin, Tiffany Dai-Hwa Ho, Donald Ming-Tak Ho
Promoter methylation is the most significant mechanism to regulate O6-methylguanine-DNA-methyltransferase (MGMT) expression. Single-nucleotide polymorphisms (SNPs) in the MGMT promoter region may also play a role. The aim of this study was to evaluate the clinical significance of SNPs in the MGMT promoter region of glioblastoma. Genomic DNAs from 118 glioblastomas were collected for polymerase chain reaction (PCR) amplification. Sanger sequencing was used to sequence the MGMT promoter region to detect SNPs...
2017: PloS One
https://www.readbyqxmd.com/read/29035737/rethinking-liquid-biopsy-microfluidic-assays-for-mobile-tumor-cells-in-human-body-fluids
#11
REVIEW
Kuang Hong Neoh, Ayon Ahmed Hassan, Anqi Chen, Yukun Sun, Peng Liu, Kai-Feng Xu, Alice S T Wong, Ray P S Han
Traditionally, liquid biopsy is a blood test involving the harvesting of tumor materials from peripheral blood. Tumor cells from non-blood body fluids have always been clinically available in cytological examinations but limited for use in differential diagnosis due to the low sensitivity of conventional cytopathology. With the recent significant progress in microfluidic and downstream molecular technologies, liquid biopsies have now evolved to include harvesting tumor cells and DNA fragments in all kinds of non-blood body fluids...
October 3, 2017: Biomaterials
https://www.readbyqxmd.com/read/29035424/cyp21a2-mutation-update-comprehensive-analysis-of-databases-and-published-genetic-variants
#12
Leandro Simonetti, Carlos D Bruque, Cecilia S Fernández, Belén Benavides-Mori, Marisol Delea, Jorge E Kolomenski, Lucía D Espeche, Noemí D Buzzalino, Alejandro D Nadra, Liliana Dain
Congenital adrenal hyperplasia (CAH) is a group of autosomal recessive disorders of adrenal steroidogenesis. Disorders in steroid 21-hydroxylation account for over 95% of patients with CAH. Clinically, the 21-hydroxylase deficiency has been classified in a broad spectrum of clinical forms, ranging from severe or classical, to mild late onset or non-classical. Known allelic variants in the disease causing CYP21A2 gene are spread among different sources. Until recently, most variants reported have been identified in the clinical setting, which presumably bias described variants to pathogenic ones, as those found in the CYPAlleles database...
October 16, 2017: Human Mutation
https://www.readbyqxmd.com/read/29035320/personomics-the-missing-link-in-the-evolution-from-precision-medicine-to-personalized-medicine
#13
Roy C Ziegelstein
Clinical practice guidelines have been developed for many common conditions based on data from randomized controlled trials. When medicine is informed solely by clinical practice guidelines, however, the patient is not treated as an individual, but rather a member of a group. Precision medicine, as defined herein, characterizes unique biological characteristics of the individual or of specimens obtained from an individual to tailor diagnostics and therapeutics to a specific patient. These unique biological characteristics are defined by the tools of precision medicine: genomics, proteomics, metabolomics, epigenomics, pharmacogenomics, and other "-omics...
October 16, 2017: Journal of Personalized Medicine
https://www.readbyqxmd.com/read/29035123/physiopathology-and-genetics-in-aspirin-exacerbated-respiratory-disease
#14
Gandhi F Pavón-Romero, Fernando Ramírez-Jiménez, Marco Alejandro Roldán-Alvarez, Luis M Terán, Ramcés Falfán-Valencia
INTRODUCTION: Aspirin-exacerbated respiratory disease (AERD) is a clinical entity characterized by hypersensitivity to aspirin leading to asthma and chronic rhinosinusitis with nasosinusal polyposis. The pathophysiology of the disease involves disruption at the level of arachidonic acid metabolism. Therefore, genetic association studies have been focused on the genes coding this pathway. As other mechanisms involved in the genesis of the disease were elucidated, the corresponding genes were also explored...
October 16, 2017: Experimental Lung Research
https://www.readbyqxmd.com/read/29034262/detection-of-replication-competent-lentivirus-using-a-qpcr-assay-for-vsv-g
#15
Lindsey M Skrdlant, Randall J Armstrong, Brett M Keidaisch, Mario F Lorente, David L DiGiusto
Lentiviral vectors are a common tool used to introduce new and corrected genes into cell therapy products for treatment of human diseases. Although lentiviral vectors are ideal for delivery and stable integration of genes of interest into the host cell genome, they potentially pose risks to human health, such as integration-mediated transformation and generation of a replication competent lentivirus (RCL) capable of infecting non-target cells. In consideration of the latter risk, all cell-based products modified by lentiviral vectors and intended for patient use must be tested for RCL prior to treatment of the patient...
March 16, 2018: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/29034210/biomarkers-for-response-of-melanoma-patients-to-immune-checkpoint-inhibitors-a-systematic-review
#16
Charissa A C Jessurun, Julien A M Vos, Jacqueline Limpens, Rosalie M Luiten
BACKGROUND: Immune checkpoint inhibitors (ICIs), targeting CTLA-4 or PD-1 molecules, have shown impressive therapeutic results. However, only 20-40% of advanced melanoma patients have durable responses to ICI, and these positive effects must be balanced against severe off-target immune toxicity and high costs. This urges the development of predictive biomarkers for ICI response to select patients with likely clinical benefit from treatment. Although many candidate biomarkers exist, a systematic overview of biomarkers and their usefulness is lacking...
2017: Frontiers in Oncology
https://www.readbyqxmd.com/read/29034124/multi-provincial-salmonellosis-outbreak-related-to-newly-hatched-chicks-and-poults-a-genomics-perspective
#17
Matthew A Croxen, Kimberley A Macdonald, Matthew Walker, Nancy deWith, Erin Zabek, Christy Peterson, Aleisha Reimer, Linda Chui, Lorelee Tschetter, Linda Hoang, Robin K King
BACKGROUND: A multi-provincial outbreak of Salmonella enterica serovar Enteritidis was linked to newly hatched chicks and poults from a single hatchery during the spring of 2015. In total, there were 61 human cases that were epidemiologically confirmed to be linked to the chicks and poults and the outbreak was deemed to have ended in the summer of 2015. METHODS: PulseNet Canada, in coordination with the affected provinces, used genome sequencing of human and agricultural Salmonella Enteritidis isolates to aid in the epidemiological investigation, while also using traditional typing methods such as phagetyping and pulsed-field gel electrophoresis (PFGE)...
August 9, 2017: PLoS Currents
https://www.readbyqxmd.com/read/29033918/dna-sequence-based-typing-of-the-cronobacter-genus-using-mlst-crispr-cas-array-and-capsular-profiling
#18
Pauline Ogrodzki, Stephen J Forsythe
The Cronobacter genus is composed of seven species, within which a number of pathovars have been described. The most notable infections by Cronobacter spp. are of infants through the consumption of contaminated infant formula. The description of the genus has greatly improved in recent years through DNA sequencing techniques, and this has led to a robust means of identification. However some species are highly clonal and this limits the ability to discriminate between unrelated strains by some methods of genotyping...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29033570/atypical-depression-current-perspectives
#19
REVIEW
Dorota Łojko, Janusz K Rybakowski
The history and present status of the definition, prevalence, neurobiology, and treatment of atypical depression (AD) is presented. The concept of AD has evolved through the years, and currently, in Diagnostic and Statistical Manual of Mental Disorders (DSM), Fifth Edition, the specifier of depressive episode with atypical feature is present for both diagnostic groups, that is, depressive disorders and bipolar and related disorders. This specifier includes mood reactivity, hyperphagia, hypersomnia, leaden paralysis, and interpersonal rejection sensitivity...
2017: Neuropsychiatric Disease and Treatment
https://www.readbyqxmd.com/read/29033451/dasatinib-and-azacitidine-followed-by-haploidentical-stem-cell-transplant-for-chronic-myeloid-leukemia-with-evolving-myelodysplasia-a-case-report-and-review-of-treatment-options
#20
Fabian Lang, Lydia Wunderle, Heike Pfeifer, Susanne Schnittger, Gesine Bug, Oliver G Ottmann
BACKGROUND CML presenting with a variant Philadelphia translocation, atypical BCR-ABL transcript, additional chromosomal aberrations, and evolving MDS is uncommon and therapeutically challenging. The prognostic significance of these genetic findings is uncertain, even as singular aberrations, with nearly no data on management and outcome when they coexist. MDS evolving during the course of CML may be either treatment-associated or an independently coexisting disease, and is generally considered to have an inferior prognosis...
October 16, 2017: American Journal of Case Reports
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