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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/29331751/comprehensive-genomic-profiling-of-head-and-neck-squamous-cell-carcinoma-reveals-fgfr1-amplifications-and-tumour-genomic-alterations-burden-as-prognostic-biomarkers-of-survival
#2
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/29330225/genetics-in-endocrinology-genetic-counseling-for-congenital-hypogonadotropic-hypogonadism-and-kallmann-syndrome-new-challenges-in-the-era-of-oligogenism-and-next-generation-sequencing
#3
Luigi Maione, Andrew A Dwyer, Bruno Francou, Anne Guiochon-Mantel, Nadine Binart, Jerome Bouligand, Jacques Young
Congenital hypogonadotropic hypogonadism (CHH) and Kallmann syndrome (KS) are rare, related diseases that prevent normal pubertal development and cause infertility in affected men and women. However, the infertility carries a good prognosis as increasing numbers of patients with CHH/KS are now able to have children through medically assisted procreation. These are genetic diseases that can be transmitted to patients' offspring. Importantly patients and their families should be informed of this risk and given genetic counseling...
January 12, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29329935/tick-borne-pathogen-detection-what-s-new
#4
Alejandro Cabezas-Cruz, Muriel Vayssier-Taussat, Gilbert Greub
Ticks and the pathogens they transmit constitute a growing burden for human and animal health worldwide. Traditionally, tick-borne pathogen detection has been carried out using PCR-based methods that rely in known sequences for specific primers design. This approach matches with the view of a 'single-pathogen' epidemiology. Recent results, however, have stressed the importance of coinfections in pathogen ecology and evolution with impact in pathogen transmission and disease severity. New approaches, including high-throughput technologies, were then used to detect multiple pathogens, but they all need a priori information on the pathogens to search...
January 9, 2018: Microbes and Infection
https://www.readbyqxmd.com/read/29329546/whole-genome-sequencing-of-genotype-vi-newcastle-disease-viruses-from-formalin-fixed-paraffin-embedded-tissues-from-wild-pigeons-reveals-continuous-evolution-and-previously-unrecognized-genetic-diversity-in-the-u-s
#5
Ying He, Tonya L Taylor, Kiril M Dimitrov, Salman L Butt, James B Stanton, Iryna V Goraichuk, Heather Fenton, Rebecca Poulson, Jian Zhang, Corrie C Brown, Hon S Ip, Marcos Isidoro-Ayza, Claudio L Afonso
BACKGROUND: Newcastle disease viruses (NDV) are highly contagious and cause disease in both wild birds and poultry. A pigeon-adapted variant of genotype VI NDV, often termed pigeon paramyxovirus 1, is commonly isolated from columbids in the United States and worldwide. Complete genomic characterization of these genotype VI viruses circulating in wild columbids in the United States is limited, and due to the genetic variability of the virus, failure of rapid diagnostic detection has been reported...
January 12, 2018: Virology Journal
https://www.readbyqxmd.com/read/29329106/genetic-mutations-associated-with-neonatal-diabetes-mellitus-in-omani-patients
#6
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/29328350/helicobacter-pylori-dna-obtained-from-the-stomach-specimens-of-two-17th-century-korean-mummies
#7
Dong Hoon Shin, Chang Seok Oh, Jong Ha Hong, Hyejin Lee, Soong Deok Lee, Eunju Lee
Helicobacter pylori is a bacterium that grows in the stomach mucosal epithelium, and can induce gastric diseases. Although many studies on modern H. pylori genomes have been reported from all over the world, a comprehensive picture of H. pylori is still lacking. Therefore, there is a pressing need to obtain archaeological specimens and to subject the ancient DNA (aDNA) extracted therefrom to analysis. Considering the typically excellent state of preservation of Joseon mummies discovered in Korea, we thus tried to isolate ancient H...
January 12, 2018: Anthropologischer Anzeiger; Bericht über die Biologisch-anthropologische Literatur
https://www.readbyqxmd.com/read/29325452/inherited-cancer-in-the-age-of-next-generation-sequencing
#8
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/29325035/amplicon-based-next-generation-sequencing-of-plasma-cell-free-dna-for-detection-of-driver-and-resistance-mutations-in-advanced-non-small-cell-lung-cancer
#9
N Guibert, Y Hu, N Feeney, Y Kuang, V Plagnol, G Jones, K Howarth, J F Beeler, C P Paweletz, G R Oxnard
Background: Genomic analysis of plasma cell-free DNA is transforming lung cancer care, however available assays are limited by cost, turnaround time, and imperfect accuracy. Here we study amplicon-based plasma next-generation sequencing (NGS), rather than hybrid-capture-based plasma NGS, hypothesizing this would allow sensitive detection and monitoring of driver and resistance mutations in advanced non-small cell lung cancer (NSCLC). Methods: Plasma samples from patients with NSCLC and a known targetable genotype (EGFR, ALK/ROS1 and other rare genotypes) were collected while on therapy and analyzed, blinded to tumor genotype...
January 9, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29324814/comprehensive-molecular-profiling-of-advanced-metastatic-olfactory-neuroblastomas
#10
Jasmina Topcagic, Rebecca Feldman, Anatole Ghazalpour, Jeffrey Swensen, Zoran Gatalica, Semir Vranic
Olfactory neuroblastoma (ONB) is a rare, locally aggressive, malignant neoplasm originating in the olfactory epithelium in the nasal vault. The recurrence rate of ONB remains high and there are no specific treatment guidelines for recurrent/metastatic ONBs. This study retrospectively evaluated 23 ONB samples profiled at Caris Life Sciences (Phoenix, Arizona) using DNA sequencing (Sanger/NGS [Illumina], n = 15) and gene fusions (Archer FusionPlex, n = 6), whole genome RNA microarray (HumanHT-12 v4 beadChip, Illumina, n = 4), gene copy number assays (chromogenic and fluorescent in situ hybridization), and immunohistochemistry...
2018: PloS One
https://www.readbyqxmd.com/read/29324655/evaluation-of-an-accelerated-workflow-for-surveillance-of-esbl-ctx-m-producing-escherichia-coli-using-amplicon-based-next-generation-sequencing-and-automated-analysis
#11
Nilay Peker, John W A Rossen, Ruud H Deurenberg, Paula C Langereis, Erwin G C Raangs, Jan A Kluytmans, Alexander W Friedrich, Jacobien Veenemans, Bhanu Sinha
Outbreak management of extended spectrum β-lactamase (ESBL)-producing pathogens requires rapid and accurate diagnosis. However, conventional screening is slow and labor-intensive. The vast majority of the screened samples are negative and detection of non-outbreak-related resistant micro-organisms often complicates outbreak management. In a CTX-M-15-producing Escherichia coli outbreak, 149 fecal samples and rectal eSwabs were collected by a cross-sectional survey in a Dutch nursing home. Samples were processed by routine diagnostic methods...
January 11, 2018: Microorganisms
https://www.readbyqxmd.com/read/29323541/development-of-a-targeted-next-generation-sequencing-assay-to-detect-diagnostically-relevant-mutations-of-jak2-calr-and-mpl-in-myeloproliferative-neoplasms
#12
Thomas Frawley, Cathal P O'Brien, Eibhlin Conneally, Elisabeth Vandenberghe, Melanie Percy, Stephen E Langabeer, Karl Haslam
BACKGROUND: The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of these mutations has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for these mutations in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms...
January 11, 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29321868/global-mtdna-genetic-structure-and-hypothesized-invasion-history-of-a-major-pest-of-citrus-diaphorina-citri-hemiptera-liviidae
#13
Yufa Luo, Ingi Agnarsson
The Asian citrus psyllid Diaphorina citri Kuwayama is a key pest of citrus as the vector of the bacterium causing the "huanglongbing" disease (HLB). To assess the global mtDNA population genetic structure, and possible dispersal history of the pest, we investigated genetic variation at the COI gene collating newly collected samples with all previously published data. Our dataset consists of 356 colonies from 106 geographic sites worldwide. High haplotype diversity (H-mean = 0.702 ± 0.017), low nucleotide diversity (π-mean = 0...
January 2018: Ecology and Evolution
https://www.readbyqxmd.com/read/29321057/influenza-a-virus-infection-impacts-systemic-microbiota-dynamics-and-causes-quantitative-enteric-dysbiosis
#14
Soner Yildiz, Béryl Mazel-Sanchez, Matheswaran Kandasamy, Balaji Manicassamy, Mirco Schmolke
BACKGROUND: Microbiota integrity is essential for a growing number of physiological processes. Consequently, disruption of microbiota homeostasis correlates with a variety of pathological states. Importantly, commensal microbiota provide a shield against invading bacterial pathogens, probably by direct competition. The impact of viral infections on host microbiota composition and dynamics is poorly understood. Influenza A viruses (IAV) are common respiratory pathogens causing acute infections...
January 10, 2018: Microbiome
https://www.readbyqxmd.com/read/29316893/frequency-of-sca8-sca10-sca12-sca36-fxtas-and-c9orf72-repeat-expansions-in-sca-patients-negative-for-the-most-common-sca-subtypes
#15
Gülsah Aydin, Gabriele Dekomien, Sabine Hoffjan, Wanda Maria Gerding, Jörg T Epplen, Larissa Arning
BACKGROUND: Spinocerebellar ataxia (SCA) subtypes are often caused by expansions in non-coding regions of genes like SCA8, SCA10, SCA12 and SCA36. Other ataxias are known to be associated with repeat expansions such as fragile X-associated tremor ataxia syndrome (FXTAS) or expansions in the C9orf72 gene. When no mutation has been identified in the aforementioned genes next-generation sequencing (NGS)-based diagnostics may also be applied. In order to define an optimal diagnostic strategy, more information about the frequency and phenotypic characteristics of rare repeat expansion disorders associated with ataxia should be at hand...
January 9, 2018: BMC Neurology
https://www.readbyqxmd.com/read/29316364/more-than-150-novel-variants-of-hla-class-i-genes-detected-in-german-stem-cell-donor-registry-and-ucla-international-cell-exchange-samples
#16
Vera Balz, Stefan Krause, Johannes Fischer, Jürgen Enczmann
High throughput analysis using amplicon-based next-generation sequencing (NGS) of HLA class I genes in samples of registered stem cell donors of the German Stem Cell Donor Registry Düsseldorf revealed 151 novel variants. In addition, 4 new variants were identified in well-defined samples obtained from the UCLA International Cell Exchange program. New alleles included 37 HLA-A, 57 HLA-B, and 61 HLA-C variant alleles. All variants were confirmed by NGS of HLA-A, HLA-B, and HLA-C genes including the respective 5´ and 3´ untranslated regions as well as Sanger sequence analysis...
January 8, 2018: HLA
https://www.readbyqxmd.com/read/29316359/whole-exome-sequencing-diagnoses-the-first-fetal-case-of-bainbridge-ropers-syndrome-presenting-as-pontocerebellar-hypoplasia-type-1
#17
Séverine Bacrot, Charlotte Mechler, Naima Talhi, Dominique Martin-Coignard, Philippe Roth, Caroline Michot, Amale Ichkou, Olivier Alibeu, Patrick Nitschke, Sophie Thomas, Michel Vekemans, Férechté Razavi, Lucile Boutaud, Tania Attie-Bitach
BACKGROUND: Bainbridge-Ropers syndrome (BRPS) is a recently identified severe disorder characterized by failure to thrive, facial dysmorphism, and severe developmental delay, caused by de novo dominant loss of function mutation in the ASXL3 gene. CASE: We report here the first case of prenatal BRPS in a fetus presenting with arthrogryposis on ultrasound and for pontocerebellar hypoplasia type 1 (PCH1) following neuropathological examination. The diagnosis was done by whole exome sequencing that identified a novel de novo ASXL3 mutation...
January 8, 2018: Birth Defects Research
https://www.readbyqxmd.com/read/29314756/sorting-specimen-rich-invertebrate-samples-with-cost-effective-ngs-barcodes-validating-a-reverse-workflow-for-specimen-processing
#18
Wendy Y Wang, Amrita Srivathsan, Maosheng Foo, Seiki Yamane, Rudolf Meier
Biologists frequently sort specimen-rich samples to species. This process is daunting when based on morphology, and disadvantageous if performed using molecular methods that destroy vouchers (e.g., metabarcoding). An alternative is barcoding every specimen in a bulk sample and then presorting the specimens using DNA barcodes, thus mitigating downstream morphological work on presorted units. Such a "reverse workflow" is too expensive using Sanger sequencing, but we here demonstrate that is feasible with an NGS barcoding pipeline that allows for cost-effective high throughput generation of short specimen-specific barcodes (313 bp of COI; lab cost <$0...
January 5, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29310573/association-of-rs662799-in-apoa5-with-cad-in-chinese-han-population
#19
Hua Chen, Shifang Ding, Mi Zhou, Xiayin Wu, Xi Liu, Yun Wu, Dechao Liu
BACKGROUND: CAD (Coronary Artery Disease) is a complex disease that influenced by various environmental and genetic factors. Previous studies have found many single nucleotide polymorphisms (SNPs) associated with the risk of CAD occurrence. However, the results are inconsistent. In this study, we aim to investigate genetic etiology in Chinese Han population by analysis of 7 SNPs in lipid metabolism pathway that previously has been reported to be associated with CAD. METHODS: A total of 631 samples were used in this study, including 435 CAD cases and 196 normal healthy controls...
January 8, 2018: BMC Cardiovascular Disorders
https://www.readbyqxmd.com/read/29309945/brca1-brca2-germline-mutation-carriers-and-sporadic-pancreatic-adenocarcinoma
#20
Alex B Blair, Vincent P Groot, Georgios Gemenetzis, Jishu Wei, John L Cameron, Matthew J Weiss, Michael Goggins, Christopher L Wolfgang, Jun Yu, Jin He
BACKGROUND: The outcomes of sporadic pancreatic adenocarcinoma (PDAC) patients with germline mutations of BRCA1/BRCA2 remains unclear. The prognostic significance of BRCA1/BRCA2 mutations on survival is not well established. STUDY DESIGN: We performed targeted next-generation sequencing (NGS) to identify BRCA1/BRCA2 germline mutations in resected sporadic PDAC cases from 2000-2015. Germline BRCA mutation-carriers were matched by age and tumor location to those with BRCA1/BRCA2 wild-type genes from our institutional database...
January 5, 2018: Journal of the American College of Surgeons
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