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https://www.readbyqxmd.com/read/28922838/comparative-genomics-of-a-drug-resistant-pseudomonas-aeruginosa-panel-and-the-challenges-of-antimicrobial-resistance-prediction-from-genomes
#1
J Jeukens, I Kukavica-Ibrulj, J G Emond-Rheault, L Freschi, R C Levesque
Antimicrobial resistance (AMR) is now recognized as a global threat to human health. The accessibility of microbial whole-genome sequencing offers an invaluable opportunity for resistance surveillance via the resistome, i.e. the genes and mutations underlying AMR. Unfortunately, AMR prediction from genomic data remains extremely challenging, especially for species with a large pan-genome. One such organism, for which multidrug-resistant (MDR) isolates are frequently encountered in the clinic, is Pseudomonas aeruginosa...
October 2, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28922774/crop-model-assisted-phenomics-and-genome-wide-association-study-for-climate-adaptation-of-indica-rice-1-phenology
#2
Michael Dingkuhn, Richard Pasco, Julie M Pasuquin, Jean Damo, Jean-Christophe Soulié, Louis-Marie Raboin, Julie Dusserre, Abdoulaye Sow, Baboucarr Manneh, Suchit Shrestha, Alpha Balde, Tobias Kretzschmar
Phenology and time of flowering are crucial determinants of rice adaptation to climate variation. A previous study characterized flowering responses of 203 diverse indica rices (the ORYTAGE panel) to ten environments in Senegal (six sowing dates) and Madagascar (two years and two altitudes) under irrigation in the field. This study used the physiological phenology model RIDEV V2 to heuristically estimate component traits of flowering such as cardinal temperatures (base temperature (Tbase) and optimum temperature), basic vegetative phase, photoperiod sensitivity and cold acclimation, and to conduct a genome-wide association study for these traits using 16 232 anonymous single-nucleotide polymorphism (SNP) markers...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922773/crop-model-assisted-phenomics-and-genome-wide-association-study-for-climate-adaptation-of-indica-rice-2-thermal-stress-and-spikelet-sterility
#3
Michael Dingkuhn, Richard Pasco, Julie Mae Pasuquin, Jean Damo, Jean-Christophe Soulié, Louis-Marie Raboin, Julie Dusserre, Abdoulaye Sow, Baboucarr Manneh, Suchit Shrestha, Tobias Kretzschmar
Low night and high day temperatures during sensitive reproductive stages cause spikelet sterility in rice. Phenotyping of tolerance traits in the field is difficult because of temporal interactions with phenology and organ temperature differing from ambient. Physiological models can be used to separate these effects. A 203-accession indica rice diversity panel was phenotyped for sterility in ten environments in Senegal and Madagascar and climate data were recorded. Here we report on sterility responses while a companion study reported on phenology...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28921573/contralateral-breast-cancers-independent-cancers-or-metastases
#4
Colin B Begg, Irina Ostrovnaya, Felipe C Geyer, Anastasios D Papanastasiou, Charlotte Ky Ng, Rita Sakr, Jonine L Bernstein, Kathleen A Burke, Tari A King, Salvatore Piscuoglio, Audrey Mauguen, Irene Orlow, Britta Weigelt, Venkatraman E Seshan, Monica Morrow, Jorge S Reis-Filho
A cancer in the contralateral breast in a woman with a previous or synchronous breast cancer is typically considered to be an independent primary tumor. Emerging evidence suggests that in a small subset of these cases the second tumor represents a metastasis. We sought to investigate the issue using massively parallel sequencing targeting 254 genes recurrently mutated in breast cancer. We examined the tumor archives at Memorial Sloan Kettering Cancer Center for the period 1995-2006 to identify cases of contralateral breast cancer where surgery for both tumors was performed at the Center...
September 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28918548/tumor-and-serum-dna-methylation-in-women-receiving-preoperative-chemotherapy-with-or-without-vorinostat-in-tbcrc008
#5
Roisin M Connolly, Mary Jo Fackler, Zhe Zhang, Xian C Zhou, Matthew P Goetz, Judy C Boughey, Bridget Walsh, John T Carpenter, Anna Maria Storniolo, Stanley P Watkins, Edward W Gabrielson, Vered Stearns, Saraswati Sukumar
BACKGROUND: Methylated gene markers have shown promise in predicting breast cancer outcomes and treatment response. We evaluated whether baseline and changes in tissue and serum methylation levels would predict pathological complete response (pCR) in patients with HER2-negative early breast cancer undergoing preoperative chemotherapy. METHODS: The TBCRC008 trial investigated pCR following 12 weeks of preoperative carboplatin and albumin-bound paclitaxel + vorinostat/placebo (n = 62)...
September 16, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28918154/hot-topic-geographical-distribution-and-strain-diversity-of-lactobacillus-wasatchensis-isolated-from-cheese-with-unwanted-gas-formation
#6
Michele Culumber, Donald J McMahon, Fatih Ortakci, Lauren Montierth, Beatriz Villalba, Jeffery R Broadbent, Craig J Oberg
Lactobacillus wasatchensis, an obligate heterofermentative nonstarter lactic acid bacteria (NSLAB) implicated in causing gas defects in aged cheeses, was originally isolated from an aged Cheddar produced in Logan, Utah. To determine the geographical distribution of this organism, we isolated slow-growing NSLAB from cheeses collected in different regions of the United States, Australia, New Zealand, and Ireland. Seven of the cheeses showed significant gas defects and 12 did not. Nonstarter lactic acid bacteria were isolated from these cheeses on de Man, Rogosa, and Sharpe medium supplemented with ribose, a preferred substrate for Lb...
September 13, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28916716/deregulation-of-microrna-expression-in-purified-t-and-b-lymphocytes-from-patients-with-primary-sj%C3%A3-gren-s-syndrome
#7
Shu-Fang Wang-Renault, Saida Boudaoud, Gaétane Nocturne, Elodie Roche, Nelly Sigrist, Christian Daviaud, Andreas Bugge Tinggaard, Victor Renault, Jean-François Deleuze, Xavier Mariette, Jörg Tost
OBJECTIVE: MicroRNAs (miRNAs) play an important role in the pathogenesis of autoimmune diseases such as primary Sjögren's syndrome (pSS). This study is the first to investigate miRNA expression patterns in purified T and B lymphocytes from patients with pSS using a high-throughput quantitative PCR (qPCR) approach. METHODS: Two independent cohorts of both patients with pSS and controls, one for discovery and one for replication, were included in this study. CD4+ T cells and CD19+ B cells were isolated from peripheral blood mononuclear cells by magnetic microbeads and expression of miRNAs was profiled using the Exiqon Human miRNome panel I analysing 372 miRNAs...
September 15, 2017: Annals of the Rheumatic Diseases
https://www.readbyqxmd.com/read/28916647/the-effect-of-common-inversion-polymorphisms-in-2l-t-and-in-3r-mo-on-patterns-of-transcriptional-variation-in-drosophila-melanogaster
#8
Erik Lavington, Andrew D Kern
Chromosomal inversions are an ubiquitous feature of genetic variation. Theoretical models describe several mechanisms by which inversions can drive adaptation and be maintained as polymorphisms. While inversions have been shown previously to be under selection, or contain genetic variation under selection, the specific phenotypic consequences of inversions leading to their maintenance remain unclear. Here we use genomic sequence and expression data from the Drosophila Genetic Reference Panel to explore the effects of two cosmopolitan inversions, In(2L)t and In(3R)Mo, on patterns of transcriptional variation...
September 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28916377/clinical-and-molecular-characterization-of-two-chinese-patients-with-type-2-congenital-generalized-lipodystrophy
#9
Ruimin Chen, Xin Yuan, Jian Wang, Ying Zhang
BACKGROUND: Type 2 congenital generalized lipodystrophy (CGL2, OMIM 269700) is a rare autosomal recessive disease, characterized by the generalized absence of adipose tissue at birth or in early infancy. Pathogenic variants in BSCL2 gene have been reported to be responsible for CGL2. The aim of this study is to analyze the clinical and genetic characteristics of two Chinese patients with CGL2, and with particular focus on the BSCL2 gene sequence variants. METHODS: Medical history, clinical manifestations, physical examination, laboratory data, and ultrasonography findings were analyzed for the two patients with CGL2...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916321/analysis-of-resistance-genes-in-pan-resistant-myroides-odoratimimus-clinical-strain-pr63039-using-whole-genome-sequencing
#10
Desong Ming, Qing-Qing Chen, Xiao-Tin Chen
To clarify the antibiotic resistance mechanisms of Myroides odoratimimus, pan-resistant M. odoratimimus strain PR63039 was isolated and its genome sequenced and analyzed. Antimicrobial susceptibility testing was conducted using the Kirby-Bauer disk diffusion method, and the Phoenix-100 Automated Microbiology System with a NMIC/ID-4 panel including aminoglycosides, β-lactams, polypeptides, quinolones, sulfonamides, chloramphenicols, and tetracyclines. Single-molecule real-time whole genome sequencing was conducted using the PacBio RSII system, and genome annotation was performed using RAST and IMG ER...
September 12, 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28915228/analysis-of-the-genes-involved-in-mendelian-forms-of-low-renin-hypertension-in-chinese-early-onset-hypertensive-patients
#11
Kai Liu, Fang Qin, Xiaolu Sun, Yang Zhang, Jizheng Wang, Yajie Wu, Wenjun Ma, Wei Wang, Xueyi Wu, Ying Qin, Huimin Zhang, Xianliang Zhou, Haiying Wu, Rutai Hui, Yubao Zou, Xiongjing Jiang, Lei Song
BACKGROUND: The study aimed to analyze genes involved in Mendelian forms of low-renin hypertension in Chinese early-onset hypertensive patients. METHODS: A panel of nine genes, namely SCNN1B, SCNN1G, WNK1, WNK4, KLHL3, CUL3, nuclear receptor subfamily 3, group C (NR3C)1, NR3C2, and HSD11B2 were screened by targeted resequencing in 260 Chinese early-onset hypertensive patients. Additionally, exon 13 of both SCNN1B and SCNN1G was sequenced in an independent cohort of 506 Chinese early-onset hypertensive patients...
September 14, 2017: Journal of Hypertension
https://www.readbyqxmd.com/read/28914754/investigation-of-antimicrobial-peptide-genes-associated-with-fungus-and-insect-resistance-in-maize
#12
Joseph Noonan, William Paul Williams, Xueyan Shan
Antimicrobial peptides (AMPs) are small defense proteins present in various organisms. Major groups of AMPs include beta-barrelin, hevein, knottin, lipid transfer protein (LTP), thionin, defensin, snakin, and cyclotide. Most plant AMPs involve host plant resistance to pathogens such as fungi, viruses, and bacteria, whereas a few plant AMPs from the cyclotide family carry insecticidal functions. In this research, a genome-wide investigation on antimicrobial peptide genes in maize genome was conducted. AMPs previously identified from various plant species were used as query sequences for maize genome data mining...
September 15, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28914269/looking-beyond-the-exome-a-phenotype-first-approach-to-molecular-diagnostic-resolution-in-rare-and-undiagnosed-diseases
#13
Loren D M Pena, Yong-Hui Jiang, Kelly Schoch, Rebecca C Spillmann, Nicole Walley, Nicholas Stong, Sarah Rapisardo Horn, Jennifer A Sullivan, Allyn McConkie-Rosell, Sujay Kansagra, Edward C Smith, Mays El-Dairi, Jane Bellet, Martha Ann Keels, Joan Jasien, Peter G Kranz, Richard Noel, Shashi K Nagaraj, Robert K Lark, Daniel S G Wechsler, Daniela Del Gaudio, Marco L Leung, Laura G Hendon, Collette C Parker, Kelly L Jones, David B Goldstein, Vandana Shashi
PurposeTo describe examples of missed pathogenic variants on whole-exome sequencing (WES) and the importance of deep phenotyping for further diagnostic testing.MethodsGuided by phenotypic information, three children with negative WES underwent targeted single-gene testing.ResultsIndividual 1 had a clinical diagnosis consistent with infantile systemic hyalinosis, although WES and a next-generation sequencing (NGS)-based ANTXR2 test were negative. Sanger sequencing of ANTXR2 revealed a homozygous single base pair insertion, previously missed by the WES variant caller software...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28914263/coexistent-genetic-alterations-involving-alk-ret-ros1-or-met-in-15-cases-of-lung-adenocarcinoma
#14
Zhenya Tang, Jianjun Zhang, Xinyan Lu, Wei Wang, Hui Chen, Melissa K Robinson, Joanne Cheng, Guilin Tang, L Jeffrey Medeiros
In lung cancer, targetable activating alterations in cancer genes, such as EGFR, ALK, RET, ROS1 and MET, are usually mutually exclusive. Rare lung cancer cases with coexistent alterations of EGFR and ALK or EGFR mutations with RET or ROS1 rearrangements have been reported. In this study, we report 15 patients (3 men and 12 women; 14 Caucasians and 1 African American) with ages ranging from 43 to 81 years (median 60 years) with lung adenocarcinoma in which coexistent alterations of two cancer-associated genes, including ALK, ROS1, or RET rearrangement or MET amplification were present...
September 15, 2017: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/28913935/induction-of-cancer-cell-stemness-by-depletion-of-macrohistone-h2a1-in-hepatocellular-carcinoma
#15
Oriana Lo Re, Caterina Fusilli, Francesca Rappa, Matthias Van Haele, Julien Douet, Jana Pindjakova, Sura Wanessa Rocha, Illar Pata, Barbora Valčíková, Stjepan Uldrijan, Raymond S Yeung, Christina Alves Peixoto, Tania Roskams, Marcus Buschbeck, Tommaso Mazza, Manlio Vinciguerra
Hepatocellular carcinomas (HCC) contain a sub-population of cancer stem cells (CSCs), which exhibit stem-cell like features and are responsible for tumor relapse, metastasis, and chemoresistance. The development of effective treatments for HCC will depend on a molecular-level understanding of the specific pathways driving CSC emergence and stemness. MacroH2A1 is a variant of the histone H2A and an epigenetic regulator of stem cell function, where it promotes differentiation and, conversely, acts as a barrier to somatic cell reprogramming...
September 15, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28913558/only-setbp1-hotspot-mutations-are-associated-with-refractory-disease-in-myeloid-malignancies
#16
Nils Winkelmann, Vivien Schäfer, Jenny Rinke, Alexander Kaiser, Philipp Ernst, Sebastian Scholl, Andreas Hochhaus, Thomas Ernst
INTRODUCTION: SETBP1 mutations have been established as a diagnostic marker in myeloid malignancies and are associated with inferior survival. Since there is limited data on their clinical impact and stability during disease progression, we sought to investigate the relationship between SETBP1 mutations and disease evolution. METHODS: Bidirectional Sanger sequencing of the SETBP1 gene was performed for 442 unselected patients with World Health Organization (WHO) defined myeloid disorders...
September 14, 2017: Journal of Cancer Research and Clinical Oncology
https://www.readbyqxmd.com/read/28912962/gene-panel-sequencing-in-brazilian-patients-with-retinitis-pigmentosa
#17
Kárita Antunes Costa, Mariana Vallim Salles, Chris Whitebirch, John Chiang, Juliana Maria Ferraz Sallum
BACKGROUND: Retinal dystrophies constitute a group of diseases characterized by clinical variability and pronounced genetic heterogeneity. Retinitis pigmentosa is the most common subtype of hereditary retinal dystrophy and is characterized by a progressive loss of peripheral field vision (Tunnel Vision), eventual loss of central vision, and progressive night blindness. The characteristics of the fundus changes include bone-spicule formations, attenuated blood vessels, reduced and/or abnormal electroretinograms, changes in structure imaged by optical coherence tomography, and subjective changes in visual function...
2017: International Journal of Retina and Vitreous
https://www.readbyqxmd.com/read/28912180/dilated-cardiomyopathy-genetic-determinants-and-mechanisms
#18
REVIEW
Elizabeth M McNally, Luisa Mestroni
Nonischemic dilated cardiomyopathy (DCM) often has a genetic pathogenesis. Because of the large number of genes and alleles attributed to DCM, comprehensive genetic testing encompasses ever-increasing gene panels. Genetic diagnosis can help predict prognosis, especially with regard to arrhythmia risk for certain subtypes. Moreover, cascade genetic testing in family members can identify those who are at risk or with early stage disease, offering the opportunity for early intervention. This review will address diagnosis and management of DCM, including the role of genetic evaluation...
September 15, 2017: Circulation Research
https://www.readbyqxmd.com/read/28912070/recombinant-influenza-h7-hemagglutinin-containing-cfllc-minidomain-in-the-transmembrane-domain-showed-enhanced-cross-protection-in-mice
#19
Yang Wang, Yun Zhang, Jialing Wu, Ying Lin, Zhihui Wu, Ying Wei, Xiaona Wei, Jianru Qin, Chunyi Xue, George Dacai Liu, Yongchang Cao
Since February 2013, H7N9 influenza virus, causing human infections with high mortality in China, has been a potential pandemic threat. The H7N9 viruses are found to diverge into distinct genotypes as other influenza viruses; thus a vaccine that can provide sufficient cross-protection against different genotypes of H7N9 viruses is urgently needed. Our previous studies demonstrated that the HA-based structural design approach by introducing a CFLLC minidomain into transmembrane domain (TM) of H1, H5 or H9 hemagglutinin (HA) proteins by replacing with H3 subtype HA TM could enhance their cross-protection...
September 11, 2017: Virus Research
https://www.readbyqxmd.com/read/28911263/potential-role-of-oct4-in-leukemogenesis
#20
Tiphanie Picot, Sanae Kesr, Yuenv Wu, Carmen Aanei, Pascale Flandrin-Gresta, Sylvie Tondeur, Emmanuelle Tavernier, Eric Wattel, Denis Guyotat, Lydia Campos
Embryonic stem cells typically show properties of long term self-renewal and lack of differentiation. When appropriately stimulated, they are able to differentiate into all cell lineages, and lose their self-renewal characteristics. These properties are controlled by a series of genes encoding several transcription factors including OCT4, the product of POU5F1 gene. OCT4 is expressed in germ-cell tumors, but also aberrantly in cancers developing in differentiated tissues. In a previous study, we observed a high expression of OCT4 in acute myeloid cell lines and primary cells, regardless of the Acute Myeloid Leukemia subtype...
September 14, 2017: Stem Cells and Development
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