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https://www.readbyqxmd.com/read/29332214/targeted-next-generation-sequencing-in-patients-with-non-syndromic-congenital-heart-disease
#1
Silvia Pulignani, Cecilia Vecoli, Andrea Borghini, Ilenia Foffa, Lamia Ait-Alì, Maria Grazia Andreassi
Congenital heart disease (CHD) is a genetically heterogeneous disease. Targeted next-generation sequencing (NGS) offers a unique opportunity to sequence multiple genes at lower cost and effort compared to Sanger sequencing. We tested a targeted NGS of a specific gene panel in a relatively large population of non-syndromic CHD patients. The patient cohort comprised 68 CHD patients (45 males; 8.3 ± 1.7 years). Amplicon libraries for 16 CHD-strictly related genes were generated using a TruSeq® Custom Amplicon kit (Illumina, CA) and sequenced using the Illumina MiSeq platform...
January 13, 2018: Pediatric Cardiology
https://www.readbyqxmd.com/read/29332125/icg-001-exerts-potent-anticancer-activity-against-uveal-melanoma-cells
#2
Salma Kaochar, Jianrong Dong, Marie Torres, Kimal Rajapakshe, Fotis Nikolos, Christel M Davis, Erik A Ehli, Cristian Coarfa, Nicholas Mitsiades, Vasiliki Poulaki
Purpose: Uveal melanoma (UM) is uniformly refractory to all available systemic chemotherapies, thus creating an urgent need for novel therapeutics. In this study, we investigated the sensitivity of UM cells to ICG-001, a small molecule reported to suppress the Wnt/β-catenin-mediated transcriptional program. Methods: We used a panel of UM cell lines to examine the effects of ICG-001 on cellular proliferation, migration, and gene expression. In vivo efficacy of ICG-001 was evaluated in a UM xenograft model...
January 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29332010/oligogenic-genetic-variation-of-neurodegenerative-disease-genes-in-980-postmortem-human-brains
#3
Michael J Keogh, Wei Wei, Juvid Aryaman, Ian Wilson, Kevin Talbot, Martin R Turner, Chris-Anne McKenzie, Claire Troakes, Johannes Attems, Colin Smith, Safa Al Sarraj, Chris M Morris, Olaf Ansorge, Stuart Pickering-Brown, Nick Jones, James W Ironside, Patrick F Chinnery
BACKGROUND: Several studies suggest that multiple rare genetic variants in genes causing monogenic forms of neurodegenerative disorders interact synergistically to increase disease risk or reduce the age of onset, but these studies have not been validated in large sporadic case series. METHODS: We analysed 980 neuropathologically characterised human brains with Alzheimer's disease (AD), Parkinson's disease-dementia with Lewy bodies (PD-DLB), frontotemporal dementia-amyotrophic lateral sclerosis (FTD-ALS) and age-matched controls...
January 13, 2018: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/29331839/functional-characterization-of-a-novel-herg-variant-in-a-family-with-recurrent-sudden-infant-death-syndrome-retracting-a-genetic-diagnosis
#4
Valentine Sergeev, Frances Perry, Thomas M Roston, Shubhayan Sanatani, Glen F Tibbits, Thomas W Claydon
Long QT syndrome (LQTS) is the most common cardiac ion channelopathy and has been found to be responsible for approximately 10% of sudden infant death syndrome (SIDS) cases. Despite increasing use of broad panels and now whole exome sequencing (WES) in the investigation of SIDS, the probability of identifying a pathogenic mutation in a SIDS victim is low. We report a family-based study who are afflicted by recurrent SIDS in which several members harbor a variant, p.Pro963Thr, in the C-terminal region of the human-ether-a-go-go (hERG) gene, published to be responsible for cases of LQTS type 2...
December 20, 2017: Forensic Science International
https://www.readbyqxmd.com/read/29331751/comprehensive-genomic-profiling-of-head-and-neck-squamous-cell-carcinoma-reveals-fgfr1-amplifications-and-tumour-genomic-alterations-burden-as-prognostic-biomarkers-of-survival
#5
C Dubot, V Bernard, M P Sablin, S Vacher, W Chemlali, A Schnitzler, G Pierron, K Ait Rais, N Bessoltane, E Jeannot, J Klijanienko, O Mariani, T Jouffroy, V Calugaru, C Hoffmann, M Lesnik, N Badois, F Berger, C Le Tourneau, M Kamal, I Bieche
BACKGROUND: We aimed at identifying deleterious genomic alterations from untreated head and neck squamous cell carcinoma (HNSCC) patients, and assessing their prognostic value. PATIENTS AND METHODS: We retrieved 122 HNSCC patients who underwent primary surgery. Targeted NGS was used to analyse a panel of 100 genes selected among the most frequently altered genes in HNSCC and potential therapeutic targets. We selected only deleterious (activating or inactivating) single nucleotide variations, and copy number variations for analysis...
January 10, 2018: European Journal of Cancer
https://www.readbyqxmd.com/read/29331515/mhc-class-i-loaded-ligands-from-breast-cancer-cell-lines-a-potential-hla-i-typed-antigen-collection
#6
Dmitri V Rozanov, Nikita D Rozanov, Kami Chiotti, Ashok Reddy, Phillip A Wilmarth, Larry L David, Seung W Cha, Sunghee Woo, Pavel Pevzner, Vineet Bafna, Gregory G Burrows, Juha K Rantala, Trevor Levin, Pavana Anur, Katie Johnson-Camacho, Shaadi Tabatabaei, Daniel J Munson, Tullia C Bruno, Jill E Slansky, John W Kappler, Naoto Hirano, Sebastian Boegel, Bernard A Fox, Colt Egelston, Diana L Simons, Grecia Jimenez, Peter P Lee, Joe W Gray, Paul T Spellman
To build a catalog of peptides presented by breast cancer cells, we undertook systematic MHC class I immunoprecipitation followed by elution of MHC class I-loaded peptides in breast cancer cells. We determined the sequence of 3196 MHC class I ligands representing 1921 proteins from a panel of 20 breast cancer cell lines. After removing duplicate peptides, i.e., the same peptide eluted from more than one cell line, the total number of unique peptides was 2740. Of the unique peptides eluted, more than 1750 had been previously identified, and of these, sixteen have been shown to be immunogenic...
January 10, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29329585/involvement-of-hedgehog-pathway-in-early-onset-aggressive-molecular-subtypes-and-metastatic-potential-of-breast-cancer
#7
Syeda Kiran Riaz, Jahangir Sarwar Khan, Syed Tahir Abbas Shah, Fen Wang, Lin Ye, Wen G Jiang, Muhammad Faraz Arshad Malik
BACKGROUND: Dysregulation of hedgehog pathway is observed in numerous cancers. Relevance of hedgehog pathway genes in cancer cohort and inhibition of its downstream effector (GLI1) towards metastasis in cell lines are explored in the study. METHOD: One hundred fifty fresh tumours of breast cancer patients were collected for the study. Based on differential expression, panel of 6 key regulators of the pathway (SHH, DHH, IHH, PTCH1, SMO and GLI1) in microarray datasets were identified...
January 8, 2018: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/29329106/genetic-mutations-associated-with-neonatal-diabetes-mellitus-in-omani-patients
#8
Aisha Al Senani, Nishath Hamza, Hanan Al Azkawi, Manal Al Kharusi, Nashat Al Sukaiti, Maryam Al Badi, Moza Al Yahyai, Matthew Johnson, Elisa De Franco, Sarah Flanagan, Andrew Hattersley, Sian Ellard, Waad-Allah Mula-Abed
BACKGROUND: Neonatal diabetes mellitus (NDM) is a rare disorder worldwide where diabetes is diagnosed in the first 6 months of life. However, Oman has a relatively high incidence of NDM. METHODS: In this study, we investigated the genetic etiologies underlying NDM and their prevalence in Oman. We collected a cohort of 24 NDM patients, with and without genetic diagnosis, referred to our center from 2007 to 2015. All patients without a genetic diagnosis were tested for mutations in 23 NDM-associated genes using a custom-targeted next-generation sequencing (NGS) panel and methylation analysis of the 6q24 locus...
January 12, 2018: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/29328443/-retracted-effects-of-cyclin-e-gene-silencing-on-the-proliferation-of-esophageal-cancer-cell-lines-ec9706-eca109-and-kyse30
#9
Na Wang, Min Li, Wen-Qiao Zang, Yun-Yun Ma, Yuan-Yuan Wang, Guo-Qiang Zhao
Subsequently to the publication of this article, an interested reader drew to our attention the fact that the six panels shown in Fig. 6 shared several areas of identity among them. Following an internal investigation, a laboratory technician, who was responsible for editing the pictures, admitted that the data as presented in the figure had been manipulated after having mislaid some of the original data. The corresponding author of the article takes responsibility for this oversight, and therefore the paper is to be retracted from publication...
January 9, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29327707/appendiceal-goblet-cell-carcinoids-and-adenocarcinomas-ex-goblet-cell-carcinoid-are-genetically-distinct-from-primary-colorectal-type-adenocarcinoma-of-the-appendix
#10
Moritz Jesinghaus, Björn Konukiewitz, Sebastian Foersch, Albrecht Stenzinger, Katja Steiger, Alexander Muckenhuber, Claudia Groß, Martin Mollenhauer, Wilfried Roth, Sönke Detlefsen, Wilko Weichert, Günter Klöppel, Nicole Pfarr, Anna Melissa Schlitter
The appendix gives rise to goblet cell carcinoids, which represent special carcinomas with distinct biological and histological features. Their genetic background and molecular relationship to colorectal adenocarcinoma is largely unknown. We therefore performed a next-generation sequencing analysis of 25 appendiceal carcinomas including 11 goblet cell carcinoids, 7 adenocarcinomas ex-goblet cell carcinoid, and 7 primary colorectal-type adenocarcinomas, using a modified Colorectal Cancer specific Panel comprising 32 genes linked to colorectal and neuroendocrine tumorigenesis...
January 12, 2018: Modern Pathology: An Official Journal of the United States and Canadian Academy of Pathology, Inc
https://www.readbyqxmd.com/read/29325965/genome-wide-association-mapping-for-seed-protein-and-oil-contents-using-a-large-panel-of-soybean-accessions
#11
Dongmei Li, Xue Zhao, Yingpeng Han, Wenbin Li, Futi Xie
Soybean is globally cultivated primarily for its protein and oil. The protein and oil contents of the seeds are quantitatively inherited traits determined by the interaction of numerous genes. In order to gain a better understanding of the molecular foundation of soybean protein and oil content for the marker-assisted selection (MAS) of high quality traits, a population of 185 soybean germplasms was evaluated to identify the quantitative trait loci (QTLs) associated with the seed protein and oil contents. Using specific length amplified fragment sequencing (SLAF-seq) technology, a total of 12,072 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0...
January 8, 2018: Genomics
https://www.readbyqxmd.com/read/29325778/nonstructural-proteins-nsp2tf-and-nsp2n-of-porcine-reproductive-and-respiratory-syndrome-virus-prrsv-play-important-roles-in-suppressing-host-innate-immune-responses
#12
Y Li, P Shang, D Shyu, C Carrillo, P Naraghi-Arani, Crystal J Jaing, G J Renukaradhya, A E Firth, E J Snijder, Y Fang
Recently, we identified a unique -2/-1 ribosomal frameshift mechanism in PRRSV, which yields two truncated forms of nonstructural protein (nsp) 2 variants, nsp2TF and nsp2N. Here, in vitro expression of individual PRRSV nsp2TF and nsp2N demonstrated their ability to suppress cellular innate immune responses in transfected cells. Two recombinant viruses were further analyzed, in which either nsp2TF was C-terminally truncated (vKO1) or expression of both nsp2TF and nsp2N was knocked out (vKO2). Host cellular mRNA profiling showed that a panel of cellular immune genes, in particular those involved in innate immunity, was upregulated in cells infected with vKO1 and vKO2...
January 8, 2018: Virology
https://www.readbyqxmd.com/read/29325612/genetics-of-parkinson-disease
#13
Aloysius Domingo, Christine Klein
An understanding of the genetic etiology of Parkinson disease (PD) has become imperative for the modern-day neurologist. Although genetic forms cause only a minority of PD, the disease mechanisms they elucidate advance the understanding of idiopathic cases. Moreover, recently identified susceptibility variants contribute to complex-etiology PD and broaden the contribution of genetics beyond familial and early-onset cases. Dominantly inherited monogenic forms mimic idiopathic PD and are caused by mutations or copy number variations of SNCA, LRRK2, and VPS35...
2018: Handbook of Clinical Neurology
https://www.readbyqxmd.com/read/29325452/inherited-cancer-in-the-age-of-next-generation-sequencing
#14
Kristin S Price, Ashley Svenson, Elisabeth King, Kaylene Ready, Gabriel A Lazarin
Next-generation sequencing (NGS) technology has led to the ability to test for multiple cancer susceptibility genes simultaneously without significantly increasing cost or turnaround time. With growing usage of multigene testing for inherited cancer, ongoing education for nurses and other health-care providers about hereditary cancer screening is imperative to ensure appropriate testing candidate identification, test selection, and posttest management. The purpose of this review article is to (1) provide an overview of how NGS works to detect germline mutations, (2) summarize the benefits and limitations of multigene panel testing, (3) describe risk categories of cancer susceptibility genes, and (4) highlight the counseling considerations for patients pursuing multigene testing...
January 1, 2018: Biological Research for Nursing
https://www.readbyqxmd.com/read/29324546/applying-precision-medicine-to-ovarian-cancer-proof-of-principle-for-a-molecular-second-look
#15
Melissa Schwartz, Olga Camacho-Vanegas, Ashley M Wood, Matthew Dashkoff, Courtney Whitelock, Timothy T Harkins, Carmel J Cohen, Ann Marie Beddoe, Peter Dottino, John A Martignetti
OBJECTIVES: The objectives of this study were to assess if targeted investigation for tumor-specific mutations by ultradeep DNA sequencing of peritoneal washes of ovarian cancer patients after primary surgical debulking and chemotherapy, and clinically diagnosed as disease free, provides a more sensitive and specific method to assess actual treatment response and tailor future therapy and to compare this "molecular second look" with conventional cytology and histopathology-based findings...
January 10, 2018: International Journal of Gynecological Cancer
https://www.readbyqxmd.com/read/29323230/developing-an-in-silico-minimum-inhibitory-concentration-panel-test-for-klebsiella-pneumoniae
#16
Marcus Nguyen, Thomas Brettin, S Wesley Long, James M Musser, Randall J Olsen, Robert Olson, Maulik Shukla, Rick L Stevens, Fangfang Xia, Hyunseung Yoo, James J Davis
Antimicrobial resistant infections are a serious public health threat worldwide. Whole genome sequencing approaches to rapidly identify pathogens and predict antibiotic resistance phenotypes are becoming more feasible and may offer a way to reduce clinical test turnaround times compared to conventional culture-based methods, and in turn, improve patient outcomes. In this study, we use whole genome sequence data from 1668 clinical isolates of Klebsiella pneumoniae to develop a XGBoost-based machine learning model that accurately predicts minimum inhibitory concentrations (MICs) for 20 antibiotics...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322836/activation-studies-with-amines-and-amino-acids-of-the-%C3%AE-carbonic-anhydrase-encoded-by-the-rv3273-gene-from-the-pathogenic-bacterium-mycobacterium-tuberculosis
#17
Andrea Angeli, Sonia Del Prete, Sameh M Osman, Fatmah A S Alasmary, Zeid AlOthman, William A Donald, Clemente Capasso, Claudiu T Supuran
The activation of a β-class carbonic anhydrase (CAs, EC 4.2.1.1) from Mycobacterium tuberculosis, encoded by the gene Rv3273 (mtCA 3), was investigated using a panel of natural and non-natural amino acids and amines. mtCA 3 was effectively activated by D-DOPA, L-Trp, dopamine and serotonin, with KAs ranging between 8.98 and 12.1 µM. L-His and D-Tyr showed medium potency activating effects, with KAs in the range of 17.6-18.2 µM, whereas other amines and amino acids were relatively ineffective activators, with KAs in the range of 28...
December 2018: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/29322237/genome-wide-association-study-of-cold-tolerance-of-chinese-indica-rice-varieties-at-the-bud-burst-stage
#18
Mengchen Zhang, Jing Ye, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, Xinghua Wei, Yaolong Yang
A region containing three genes on chromosome 1 of indica rice was associated with cold tolerance at the bud burst stage; these results may be useful for breeding cold-tolerant lines. Low temperature at the bud burst stage is one of the major abiotic stresses limiting rice growth, especially in regions where rice seeds are sown directly. In this study, we investigated cold tolerance of rice at the bud burst stage and conducted a genome-wide association study (GWAS) based on the 5K rice array of 249 indica rice varieties widely distributed in China...
January 10, 2018: Plant Cell Reports
https://www.readbyqxmd.com/read/29321952/fasciculation-and-elongation-zeta-1-protein-fez1-interacts-with-the-retinoic-acid-receptor-and-participates-in-transcriptional-regulation-of-the-hoxb4-gene
#19
Mariana Bertini Teixeira, Ana Carolina M Figueira, Ariane S Furlan, Bruno Aquino, Marcos R Alborghetti, Adriana F Paes Leme, Li-Na Wei, Jörg Kobarg
Fasciculation and elongation zeta-1 (FEZ1) protein is involved in axon outgrowth and is highly expressed in the brain. It has multiple interaction partners, with functions varying from the regulation of neuronal development and intracellular transport mechanisms to transcription regulation. One of its interactors is retinoic acid receptor (RAR), which is activated by retinoic acid and controls many target genes and physiological process. Based on previous evidence suggesting a possible nuclear role for FEZ1, we wanted to deepen our understanding of this function by addressing the FEZ1-RAR interaction...
January 2018: FEBS Open Bio
https://www.readbyqxmd.com/read/29321870/contrasting-genetic-metrics-and-patterns-among-naturalized-rainbow-trout-oncorhynchus-mykiss-in-two-patagonian-lakes-differentially-impacted-by-trout-aquaculture
#20
Cristian B Canales-Aguirre, Lisa W Seeb, James E Seeb, María I Cádiz, Selim S Musleh, Ivan Arismendi, Gonzalo Gajardo, Ricardo Galleguillos, Daniel Gomez-Uchida
Different pathways of propagation and dispersal of non-native species into new environments may have contrasting demographic and genetic impacts on established populations. Repeated introductions of rainbow trout (Oncorhynchus mykiss) to Chile in South America, initially through stocking and later through aquaculture escapes, provide a unique setting to contrast these two pathways. Using a panel of single nucleotide polymorphisms, we found contrasting genetic metrics and patterns among naturalized trout in Lake Llanquihue, Chile's largest producer of salmonid smolts for nearly 50 years, and Lake Todos Los Santos (TLS), a reference lake where aquaculture has been prohibited by law...
January 2018: Ecology and Evolution
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