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https://www.readbyqxmd.com/read/28339744/determining-the-analytical-specificity-of-pcr-based-assays-for-the-diagnosis-of-ia-what-is-aspergillus
#1
C Oliver Morton, P Lewis White, Rosemary A Barnes, Lena Klingspor, Manuel Cuenca-Estrella, Katrien Lagrou, Stéphane Bretagne, Willem Melchers, Carlo Mengoli, Angela M Caliendo, Massimo Cogliati, Yvette Debets-Ossenkopp, Rebecca Gorton, Ferry Hagen, Catriona Halliday, Petr Hamal, Kathleen Harvey-Wood, Katia Jaton, Gemma Johnson, Sarah Kidd, Martina Lengerova, Cornelia Lass-Florl, Chris Linton, Laurence Millon, C Orla Morrissey, Melinda Paholcsek, Alida Fe Talento, Markus Ruhnke, Birgit Willinger, J Peter Donnelly, Juergen Loeffler
A wide array of PCR tests has been developed to aid the diagnosis of invasive aspergillosis (IA), providing technical diversity but limiting standardisation and acceptance. Methodological recommendations for testing blood samples using PCR exist, based on achieving optimal assay sensitivity to help exclude IA. Conversely, when testing more invasive samples (BAL, biopsy, CSF) emphasis is placed on confirming disease, so analytical specificity is paramount. This multicenter study examined the analytical specificity of PCR methods for detecting IA by blind testing a panel of DNA extracted from a various fungal species to explore the range of Aspergillus species that could be detected, but also potential cross reactivity with other fungal species...
October 7, 2016: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/28339479/mouse-newborn-cells-allow-highly-productive-mouse-cytomegalovirus-replication-constituting-a-novel-convenient-primary-cell-culture-system
#2
Vu Thuy Khanh Le-Trilling, Mirko Trilling
Mammalian cell culture is indispensable for most aspects of current biomedical research. Immortalized cell lines are very convenient, but transforming principles (e.g. oncogenic viruses or their oncogenes) can heavily influence the experimental outcome. Primary cells do not share this apparent disadvantage but are more laborious to generate. Certain viruses (e.g. mouse cytomegalovirus) do not replicate efficiently in most transformed cell lines. In the past, such viruses have been routinely propagated on primary mouse embryonic fibroblasts (MEF) established around day 17 (d17) of gestation...
2017: PloS One
https://www.readbyqxmd.com/read/28338218/evaluation-of-targeted-exome-sequencing-for-28-protein-based-blood-group-systems-including-the-homologous-gene-systems-for-blood-group-genotyping
#3
Elizna M Schoeman, Genghis H Lopez, Eunike C McGowan, Glenda M Millard, Helen O'Brien, Eileen V Roulis, Yew-Wah Liew, Jacqueline R Martin, Kelli A McGrath, Tanya Powley, Robert L Flower, Catherine A Hyland
BACKGROUND: Blood group single nucleotide polymorphism genotyping probes for a limited range of polymorphisms. This study investigated whether massively parallel sequencing (also known as next-generation sequencing), with a targeted exome strategy, provides an extended blood group genotype and the extent to which massively parallel sequencing correctly genotypes in homologous gene systems, such as RH and MNS. STUDY DESIGN AND METHODS: Donor samples (n = 28) that were extensively phenotyped and genotyped using single nucleotide polymorphism typing, were analyzed using the TruSight One Sequencing Panel and MiSeq platform...
March 24, 2017: Transfusion
https://www.readbyqxmd.com/read/28337746/thymidylate-synthase-is-functionally-associated-with-zeb1-and-contributes-to-the-epithelial-to-mesenchymal-transition-of-cancer-cells
#4
Aarif Siddiqui, Maria Eleni Vazakidou, Annemarie Schwab, Francesca Napoli, Cristina Fernandez-Molina, Ida Rapa, Marc P Stemmler, Marco Volante, Thomas Brabletz, Paolo Ceppi
Thymidylate synthase (TS) is a fundamental enzyme of nucleotide metabolism and one of the oldest anti-cancer targets. Beginning from the analysis of gene array data from the NCI-60 panel of cancer cell lines, we identified a significant correlation at both gene and protein level between TS and the markers of epithelial-to-mesenchymal transition (EMT), a developmental process that allows cancer cells to acquire features of aggressiveness, like motility and chemoresistance. TS levels were found to be significantly augmented in mesenchymal-like compared to epithelial-like cancer cells, to be regulated by EMT induction, and to negatively correlate with micro-RNAs (miRNAs) usually expressed in epithelial-like cells and known to actively suppress EMT...
March 24, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28333958/targeted-deep-sequencing-of-plasma-circulating-cell-free-dna-reveals-vimentin-and-fibulin-1-as-potential-epigenetic-biomarkers-for-hepatocellular-carcinoma
#5
Reetta Holmila, Athena Sklias, David C Muller, Davide Degli Esposti, Paule Guilloreau, James Mckay, Suleeporn Sangrajrang, Petcharin Srivatanakul, Pierre Hainaut, Philippe Merle, Zdenko Herceg, Andre Nogueira da Costa
Hepatocellular carcinoma (HCC) is the second most common cause of cancer death worldwide, but is still lacking sensitive and specific biomarkers for early diagnosis and prognosis. In this study, we applied targeted massively parallel semiconductor sequencing to assess methylation on a panel of genes (FBLN1, HINT2, LAMC1, LTBP1, LTBP2, PSMA2, PSMA7, PXDN, TGFB1, UBE2L3, VIM and YWHAZ) in plasma circulating cell-free DNA (cfDNA) and to evaluate the potential of these genes as HCC biomarkers in two different series, one from France (42 HCC cases and 42 controls) and one from Thailand (42 HCC cases, 26 chronic liver disease cases and 42 controls)...
2017: PloS One
https://www.readbyqxmd.com/read/28333195/genome-wide-genetic-analyses-highlight-mitogen-activated-protein-kinase-mapk-signaling-in-the-pathogenesis-of-endometriosis
#6
Outi Uimari, Nilufer Rahmioglu, Dale R Nyholt, Katy Vincent, Stacey A Missmer, Christian Becker, Andrew P Morris, Grant W Montgomery, Krina T Zondervan
STUDY QUESTION: Do genome-wide association study (GWAS) data for endometriosis provide insight into novel biological pathways associated with its pathogenesis? SUMMARY ANSWER: GWAS analysis uncovered multiple pathways that are statistically enriched for genetic association signals, analysis of Stage A disease highlighted a novel variant in MAP3K4, while top pathways significantly associated with all endometriosis and Stage A disease included several mitogen-activated protein kinase (MAPK)-related pathways...
February 9, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28332277/sequencing-of-sporadic-attention-deficit-hyperactivity-disorder-adhd-identifies-novel-and-potentially-pathogenic-de-novo-variants-and-excludes-overlap-with-genes-associated-with-autism-spectrum-disorder
#7
Daniel Seung Kim, Amber A Burt, Jane E Ranchalis, Beth Wilmot, Joshua D Smith, Karynne E Patterson, Bradley P Coe, Yatong K Li, Michael J Bamshad, Molly Nikolas, Evan E Eichler, James M Swanson, Joel T Nigg, Deborah A Nickerson, Gail P Jarvik
Attention-Deficit Hyperactivity Disorder (ADHD) has high heritability; however, studies of common variation account for <5% of ADHD variance. Using data from affected participants without a family history of ADHD, we sought to identify de novo variants that could account for sporadic ADHD. Considering a total of 128 families, two analyses were conducted in parallel: first, in 11 unaffected parent/affected proband trios (or quads with the addition of an unaffected sibling) we completed exome sequencing. Six de novo missense variants at highly conserved bases were identified and validated from four of the 11 families: the brain-expressed genes TBC1D9, DAGLA, QARS, CSMD2, TRPM2, and WDR83...
March 22, 2017: American Journal of Medical Genetics. Part B, Neuropsychiatric Genetics
https://www.readbyqxmd.com/read/28331560/introducing-crucial-protein-panel-of-gastric-adenocarcinoma-disease
#8
Mostafa Rezaei-Tavirani, Majid Rezaei-Tavirani, Vahid Mansouri, Seyed Mohammad Mahdavi, Reza Valizadeh, Mohammad Rostami-Nejad, Mohammad Reza Zali
AIM: Since interactome analysis of diseases can provide candidate biomarker panel related to the diseases, in this research, protein-protein interaction (PPI) network analysis is used to introduce the involved crucial proteins in Gastric adenocarcinoma (GA). BACKGROUND: Gastric adenocarcinoma (GA) is the most common type of stomach cancer. There is no efficient diagnostic molecular method for GA. METHOD: Applying Cytoscape software 3.4.0 and String Database, the PPI network was constructed for 200 genes...
2017: Gastroenterology and Hepatology From Bed to Bench
https://www.readbyqxmd.com/read/28330790/outcomes-of-diagnostic-exome-sequencing-in-patients-with-diagnosed-or-suspected-autism-spectrum-disorders
#9
Mari Rossi, Dima El-Khechen, Mary Helen Black, Kelly D Farwell Hagman, Sha Tang, Zöe Powis
BACKGROUND: Exome sequencing has recently been proved to be a successful diagnostic method for complex neurodevelopmental disorders. However, the diagnostic yield of exome sequencing for autism spectrum disorders has not been extensively evaluated in large cohorts to date. MATERIALS AND METHODS: We performed diagnostic exome sequencing in a cohort of 163 individuals with autism spectrum disorder (66.3%) or autistic features (33.7%). RESULTS: The diagnostic yield observed in patients in our cohort was 25...
February 8, 2017: Pediatric Neurology
https://www.readbyqxmd.com/read/28328508/hapiso-an-accurate-method-for-the-haplotype-specific-isoforms-reconstruction-from-long-single-molecule-reads
#10
Serghei Mangul, Harry Taegyun Yang, Farhad Hormozdiari, Alex Dainis, Elizabeth Tseng, Euan A Ashley, Alex Zelikovsky, Eleazar Eskin
Sequencing of RNA provides the possibility to study an individual's transcriptome landscape and determine allelic expression ratios. Single-molecule protocols generate multi-kilobase reads longer than most transcripts allowing sequencing of complete haplotype isoforms. This allows partitioning the reads into two parental haplotypes. While the read length of the single-molecule protocols is long, the relatively high error rate limits the ability to accurately detect the genetic variants and assemble them into the haplotype-specific isoforms...
March 17, 2017: IEEE Transactions on Nanobioscience
https://www.readbyqxmd.com/read/28328162/predictive-model-for-inflammation-grades-of-chronic-hepatitis-b-large-scale-analysis-of-clinical-parameters-and-gene-expressions
#11
Weichen Zhou, Yanyun Ma, Jun Zhang, Jingyi Hu, Menghan Zhang, Yi Wang, Yi Li, Lijun Wu, Yida Pan, Yitong Zhang, Xiaonan Zhang, Xinxin Zhang, Zhanqing Zhang, Jiming Zhang, Hai Li, Lungen Lu, Li Jin, Jiucun Wang, Zhenghong Yuan, Jie Liu
BACKGROUND: Liver biopsy is the gold standard to assess pathological features (e.g. inflammation grades) for hepatitis B virus infected patients, although it's invasive and traumatic; meanwhile, several gene profiles of chronic hepatitis B (CHB) have been separately described in relatively small HBV-infected samples. We aimed to analyze correlations among inflammation grades, gene expressions and clinical parameters (serum alanine amino transaminase, aspartate amino transaminase, and HBV-DNA) in large-scale CHB samples, and to predict inflammation grades by using clinical parameters and/or gene expressions...
March 22, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28328141/a-590-kb-deletion-caused-by-non-allelic-homologous-recombination-between-two-line-1-elements-in-a-patient-with-mesomelia-synostosis-syndrome
#12
Tomohiro Kohmoto, Takuya Naruto, Miki Watanabe, Yuji Fujita, Sae Ujiro, Nana Okamoto, Hideaki Horikawa, Kiyoshi Masuda, Issei Imoto
Mesomelia-synostoses syndrome (MSS) is a rare, autosomal-dominant, syndromal osteochondrodysplasia characterized by mesomelic limb shortening, acral synostoses, and multiple congenital malformations due to a non-recurrent deletion at 8q13 that always encompasses two coding-genes, SULF1 and SLCO5A1. To date, five unrelated patients have been reported worldwide, and MMS was previously proposed to not be a genomic disorder associated with deletions recurring from non-allelic homologous recombination (NAHR) in at least two analyzed cases...
April 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28327786/polymorphisms-in-genes-tlr1-2-and-4-are-associated-with-differential-cytokine-and-chemokine-serum-production-in-patients-with-leprosy
#13
Nadja de Lima Santana, Jamile Leão Rêgo, Joyce Moura Oliveira, Lucas Frederico de Almeida, Marcos Braz, Lídia Maria Medeiros Machado, Paulo Roberto Lima Machado, Léa Cristina Castellucci
BACKGROUND: Leprosy or hansen's disease is a spectral disease whose clinical forms mostly depends on host's immune and genetic factors. Different Toll-like receptors (TLR) variants have been described associated with leprosy, but with some lack of replication across different populations. OBJECTIVES: To evaluate the role of polymorphisms in genes TLR1, TLR2 and TLR4 and susceptibility to leprosy in a genetic case control study; to verify the association between genotypes of these markers and the immunological profile in the serum of patients with leprosy...
April 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28327201/detecting-gene-signature-activation-in-breast-cancer-in-an-absolute-single-patient-manner
#14
E R Paquet, R Lesurf, A Tofigh, V Dumeaux, M T Hallett
BACKGROUND: The ability to reliably identify the state (activated, repressed, or latent) of any molecular process in the tumor of a patient from an individual whole-genome gene expression profile obtained from microarray or RNA sequencing (RNA-seq) promises important clinical utility. Unfortunately, all previous bioinformatics tools are only applicable in large and diverse panels of patients, or are limited to a single specific pathway/process (e.g. proliferation). METHODS: Using a panel of 4510 whole-genome gene expression profiles from 10 different studies we built and selected models predicting the activation status of a compendium of 1733 different biological processes...
March 21, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28324944/biclustering-strategies-for-genetic-marker-selection-in-gynecologic-tumor-cell-lines
#15
A Alevyzaki, S Sfakianakis, E S Bei, E Obermayr, R Zeillinger, D Fotiadis, M Zervakis
Over the past few decades great interest has been focused on cell lines derived from tumors, because of their usability as models to understand the biology of cancer. At the same time, advanced technologies such as DNA-microarrays have been broadly used to study the expression level of thousands of genes in primary tumors or cancer cell lines in a single experiment. Results from microarray analysis approaches have provided valuable insights into the underlying biology and proven useful for tumor classification, prognostication and prediction...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28324281/detection-of-minimal-residual-disease-in-childhood-b-acute-lymphoblastic-leukemia-by-4-color-flowcytometry
#16
Ahmad Baraka, Laila M Sherief, Naglaa M Kamal, Shereen El Shorbagy
Monitoring of minimal residual disease (MRD) is currently considered the most powerful predictor of outcome in acute lymphoblastic leukemia (ALL). Achievement of a negative MRD state assessed by multicolor flowcytometry (MFC) is an important predictor of disease-free survival (DFS) and overall survival (OS) in ALL patients. We sought to determine whether panels of antibodies combination are more suitable for detection of MRD in Childhood ALL. Eighty-four (84) patients with ALL (B-lineage subtype) were enrolled in this study...
March 21, 2017: International Journal of Hematology
https://www.readbyqxmd.com/read/28323214/immunological-interactions-between-piscine-orthoreovirus-and-salmonid-alphavirus-infections-in-atlantic-salmon
#17
Magnus Vikan Røsæg, Morten Lund, Ingvild Berg Nyman, Turhan Markussen, Vidar Aspehaug, Hilde Sindre, Maria Krudtaa Dahle, Espen Rimstad
Heart and skeletal muscle inflammation (HSMI) and pancreas disease (PD) cause substantial losses in Atlantic salmon (Salmo salar) aquaculture. The respective causative agents, Piscine orthoreovirus (PRV) and Salmonid alphavirus (SAV), are widespread and often concurrently present in farmed salmon. An experimental infection in Atlantic salmon was conducted to study the interaction between the two viruses, including the immunological mechanisms involved. The co-infected fish were infected with PRV four or ten weeks before they were infected with SAV...
March 18, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28322587/development-and-validation-of-targeted-next-generation-sequencing-panels-for-detection-of-germline-variants-in-inherited-diseases
#18
Avni Santani, Jill Murrell, Birgit Funke, Zhenming Yu, Madhuri Hegde, Rong Mao, Andrea Ferreira-Gonzalez, Karl V Voelkerding, Karen E Weck
CONTEXT: - The number of targeted next-generation sequencing (NGS) panels for genetic diseases offered by clinical laboratories is rapidly increasing. Before an NGS-based test is implemented in a clinical laboratory, appropriate validation studies are needed to determine the performance characteristics of the test. OBJECTIVE: - To provide examples of assay design and validation of targeted NGS gene panels for the detection of germline variants associated with inherited disorders...
March 21, 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28321828/genome-wide-association-analysis-tracks-bacterial-leaf-blight-resistance-loci-in-rice-diverse-germplasm
#19
Christine Jade Dilla-Ermita, Erwin Tandayu, Venice Margarette Juanillas, Jeffrey Detras, Dennis Nicuh Lozada, Maria Stefanie Dwiyanti, Casiana Vera Cruz, Edwige Gaby Nkouaya Mbanjo, Edna Ardales, Maria Genaleen Diaz, Merlyn Mendioro, Michael J Thomson, Tobias Kretzschmar
BACKGROUND: A range of resistance loci against different races of Xanthomonas oryzae pv. oryzae (Xoo), the pathogen causing bacterial blight (BB) disease of rice, have been discovered and characterized. Several have been deployed in modern varieties, however, due to rapid evolution of Xoo, a number have already become ineffective. The continuous "arms race" between Xoo and rice makes it imperative to discover new resistance loci to enable durable deployment of multiple resistance genes in modern breeding lines...
December 2017: Rice
https://www.readbyqxmd.com/read/28319827/immunophenotypical-characterization-of-canine-mesenchymal-stem-cells-from-perivisceral-and-subcutaneous-adipose-tissue-by-a-species-specific-panel-of-antibodies
#20
Ana Ivanovska, Stefano Grolli, Paolo Borghetti, Francesca Ravanetti, Virna Conti, Elena De Angelis, Francesca Macchi, Roberto Ramoni, Paolo Martelli, Ferdinando Gazza, Antonio Cacchioli
Immunophenotypical characterization of mesenchymal stem cells is fundamental for the design and execution of sound experimental and clinical studies. The scarce availability of species-specific antibodies for canine antigens has hampered the immunophenotypical characterization of canine mesenchymal stem cells (MSC). The aim of this study was to select a panel of species-specific direct antibodies readily useful for canine mesenchymal stem cells characterization. They were isolated from perivisceral and subcutaneous adipose tissue samples collected during regular surgeries from 8 dogs...
February 27, 2017: Research in Veterinary Science
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