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https://www.readbyqxmd.com/read/28453704/genomic-characterization-of-her2-positive-breast-cancer-and-response-to-neoadjuvant-trastuzumab-and-chemotherapy-results-from-the-acosog-z1041-alliance-trial
#1
R Lesurf, O L Griffith, M Griffith, J Hundal, L Trani, M A Watson, R Aft, M J Ellis, D Ota, V J Suman, F Meric-Bernstam, A M Leitch, J C Boughey, G Unzeitig, A U Buzdar, K K Hunt, E R Mardis
Background: HER2 (ERBB2) gene amplification and its corresponding overexpression are present in 15-30% of invasive breast cancers. While HER2-targeted agents are effective treatments, resistance remains a major cause of death. The American College of Surgeons Oncology Group Z1041 trial (NCT00513292) was designed to compare the pathologic complete response (pCR) rate of distinct regimens of neoadjuvant chemotherapy and trastuzumab, but ultimately identified no difference. Patients and methods: In supplement to tissues from 37 Z1041 cases, 11 similarly treated cases were obtained from a single institution study (NCT00353483)...
May 1, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28446605/crispr-cas9-mediated-gene-knockout-screens-and-target-identification-via-whole-genome-sequencing-uncover-host-genes-required-for-picornavirus-infection
#2
Heon Seok Kim, Kyungjin Lee, Sangsu Bae, Jeongbin Park, Chong-Kyo Lee, Meehyein Kim, Eunji Kim, Minju Kim, Seokjoong Kim, Chonsaeng Kim, Jin-Soo Kim
Several groups have used genome-wide libraries of lentiviruses encoding small-guide RNAs (sgRNAs) for genetic screens. In most cases, sgRNA expression cassettes are integrated into cells by using lentiviruses, and target genes are statistically estimated by the readout of sgRNA sequences after targeted sequencing. We present a new virus-free method for human gene-knockout screens using a genome-wide library of CRISPR/Cas9 sgRNAs based on plasmids, and target gene identification via whole-genome sequencing (WGS) confirming authentic mutations rather than statistical estimating through targeted amplicon sequencing...
April 26, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28446577/population-dynamics-of-staphylococcus-aureus-in-cystic-fibrosis-patients-to-determine-transmission-events-utilizing-wgs
#3
Andrea Ankrum, Barry G Hall
Strict infection control practices have been implemented for healthcare visits by Cystic Fibrosis patients in an attempt to prevent transmission of important pathogens. This study used whole genome sequencing (WGS) to determine strain relatedness and assess population dynamics of Staphylococcus aureus isolates from a cohort of CF patients as assessed by strain relatedness. 311 S. aureus isolates were collected from respiratory cultures of 115 CF patients during a 22 month study period. Whole genome sequencing was performed and using SNP analysis, phylogenetic trees were assembled to determine relatedness between isolates...
April 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28446571/a-core-genome-multi-locus-sequence-typing-scheme-for-stable-comparative-analyses-of-campylobacter-jejuni-and-c-coli-human-disease-isolates
#4
Alison J Cody, James E Bray, Keith A Jolley, Noel D McCarthy, C J Maiden Martin
Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterisation methods. Whole genome sequencing (WGS) data enables the improvement of sequence-based typing approaches, such as multi locus sequence typing (MLST), by substantially increasing the number of loci examined...
April 26, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28446055/investigational-drugs-for-nasopharyngeal-carcinoma
#5
Brigette B Y Ma, Edwin P Hui, Anthony T C Chan
Nasopharyngeal carcinoma (NPC) is endemic to Southern China and Asia and is etiologically associated with the Epstein Barr virus (EBV). Whole exome and genome sequencing (WES, WGS) studies of NPC have reported several actionable therapeutic targets, and that the mutational load of NPC maybe comparable to that of squamous head and neck cancer. These unique biological characteristics have been exploited as potential targets and a wide range of investigational drugs are being investigated in clinical trials. Area covered: This review focused on the latest clinical development of the most promising classes of investigational agents in the treatment of advanced NPC...
April 27, 2017: Expert Opinion on Investigational Drugs
https://www.readbyqxmd.com/read/28439300/genetic-variants-of-helicobacter-pylori-type-iv-secretion-system-components-cagl-and-cagi-and-their-association-with-clinical-outcomes
#6
Hirofumi Ogawa, Akira Iwamoto, Toshihito Tanahashi, Rina Okada, Koji Yamamoto, Shin Nishiumi, Masaru Yoshida, Takeshi Azuma
BACKGROUND: Helicobacter pylori infection is associated with risk for chronic gastritis (CG), gastric ulcer (GU), duodenal ulcer (DU), and gastric cancer (GC). The H. pylori Cag type IV secretion system (TFSS) translocates the virulence factor cytotoxin-associated gene A protein into host cells and plays an important role in initiating gastric carcinogenesis. The CagL and CagI proteins are components of the TFSS. The Arg-Gly-Asp (RGD) motif of CagL, and the six most distal C-terminal amino acids (Ser-Lys-Ile-Ile-Val-Lys, and Ser-Lys-Val-Ile-Val-Lys) of CagL and CagI are essential for TFSS adhesion to host cells...
2017: Gut Pathogens
https://www.readbyqxmd.com/read/28437911/investigation-of-third-order-dispersion-of-long-range-surface-plasmon-polariton-waveguides-using-a-hong-ou-mandel-interferometer
#7
Takahide Sakaidani, Ryo Kobayashi, Naoto Namekata, Go Fujii, Daiji Fukuda, Shuichiro Inoue
High-order dispersion of long-range surface-plasmon-polariton waveguides (LR-SPP-WGs) have been investigated using a two-photon interferometer. Since linear and even-ordered dispersions in two-photon interferometry are cancelled out by a nonlocal quantum correlation, odd-ordered dispersions of millimeter-long LR-SPP-WGs are revealed. Even under the highly dispersive condition, the indistinguishability between two photons emerged from LR-SPP-WGs was well preserved. In addition, we demonstrated a strong polarization-selection by the LR-SPP-WGs that leads to the polarization-stable and high-fidelity quantum interference...
April 17, 2017: Optics Express
https://www.readbyqxmd.com/read/28430790/whole-genome-sequencing-suggests-mechanisms-for-22q11-2-deletion-associated-parkinson-s-disease
#8
Nancy J Butcher, Daniele Merico, Mehdi Zarrei, Lucas Ogura, Christian R Marshall, Eva W C Chow, Anthony E Lang, Stephen W Scherer, Anne S Bassett
OBJECTIVES: To investigate disease risk mechanisms of early-onset Parkinson's disease (PD) associated with the recurrent 22q11.2 deletion, a genetic risk factor for early-onset PD. METHODS: In a proof-of-principle study, we used whole-genome sequencing (WGS) to investigate sequence variants in nine adults with 22q11.2DS, three with neuropathologically confirmed early-onset PD and six without PD. Adopting an approach used recently to study schizophrenia in 22q11...
2017: PloS One
https://www.readbyqxmd.com/read/28425484/mycobacterium-tuberculosis-resistance-prediction-and-lineage-classification-from-genome-sequencing-comparison-of-automated-analysis-tools
#9
Viola Schleusener, Claudio U Köser, Patrick Beckert, Stefan Niemann, Silke Feuerriegel
Whole-genome sequencing (WGS) has the potential to accelerate drug-susceptibility testing (DST) to design appropriate regimens for drug-resistant tuberculosis (TB). Several recently developed automated software tools promise to standardize the analysis and interpretation of WGS data. We assessed five tools (CASTB, KvarQ, Mykrobe Predictor TB, PhyResSE, and TBProfiler) with regards to DST and phylogenetic lineage classification, which we compared with phenotypic DST, Sanger sequencing, and traditional typing results for a collection of 91 strains...
April 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28420617/application-and-progress-of-high-throughput-sequencing-technologies-in-the-research-of-hereditary-hearing-loss
#10
Wang Cuicui, Yuan Huijun
Hearing loss (HL) is the most common birth defect. Elucidating the genetic basis of hereditary deafness can not only assist diagnosis, provide the basis for genetic counseling and the prevention of deafness, but also bring a deeper understanding of the disease pathogenesis. In the genomic era, high-throughput sequencing technologies, represented by whole genome sequencing (WGS), whole exome sequencing (WES) or target region sequencing, have been widely used in the studies of hereditary HL. Here, we summarize the application and progress of WES and target region sequencing in the research of causative genes and clinical molecular diagnosis of hereditary HL, hoping to be helpful for the development and improvement of clinical genetic diagnosis of deafness in China...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28419202/genomic-characterization-of-usa300-mrsa-to-evaluate-intraclass-transmission-and-recurrence-of-ssti-among-high-risk-military-trainees
#11
Eugene V Millar, Gregory K Rice, Emad M Elassal, Carey D Schlett, Jason W Bennett, Cassie L Redden, Deepika Mor, Natasha N Law, David R Tribble, Theron Hamilton, Michael W Ellis, Kimberly A Bishop-Lilly
Background.: Military trainees are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI). Whole genome sequencing (WGS) can refine our understanding of MRSA transmission and microevolution in congregate settings. Methods.: We conducted a prospective case-control study of SSTI among US Army Infantry trainees at Fort Benning, GA from July 2012-December 2014. We identified clusters of USA300 MRSA SSTI within select training classes and performed WGS on clinical isolates...
April 17, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28412734/whole-genome-sequencing-of-matched-tumor-adjacent-non-tumor-tissues-and-corresponding-normal-blood-samples-of-hepatocellular-carcinoma-patients-revealed-dynamic-changes-of-the-mutations-profiles-during-hepatocarcinogenesis
#12
Ruifang Mao, Jie Liu, Guanfeng Liu, Shanshan Jin, Qingzhong Xue, Liang Ma, Yan Fu, Na Zhao, Jinliang Xing, Lanjuan Li, Yunqing Qiu, Biaoyang Lin
Hepatocellular carcinoma (HCC) has become the third most deadly disease worldwide and HBV is the major factor in Asia and Africa. We conducted 9 WGS (whole genome sequencing) analyses for matched samples of tumor, adjacent non-tumor tissues and normal blood samples of HCC patients from three HBV positive patients. We then validated the mutations identified in a larger cohort of 177 HCC patients. We found that the number of the unique somatic mutations (average of 59,136) in tumor samples is significantly less than that in adjacent non-tumor tissues (average 83, 633)...
February 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/28410368/comprehensive-bioinformatics-analysis-of-mycoplasma-pneumoniae-genomes-to-investigate-underlying-population-structure-and-type-specific-determinants
#13
Maureen H Diaz, Heta P Desai, Shatavia S Morrison, Alvaro J Benitez, Bernard J Wolff, Jason Caravas, Timothy D Read, Deborah Dean, Jonas M Winchell
Mycoplasma pneumoniae is a significant cause of respiratory illness worldwide. Despite a minimal and highly conserved genome, genetic diversity within the species may impact disease. We performed whole genome sequencing (WGS) analysis of 107 M. pneumoniae isolates, including 67 newly sequenced using the Pacific BioSciences RS II and/or Illumina MiSeq sequencing platforms. Comparative genomic analysis of 107 genomes revealed >3,000 single nucleotide polymorphisms (SNPs) in total, including 520 type-specific SNPs...
2017: PloS One
https://www.readbyqxmd.com/read/28407967/molecular-characterization-of-an-unauthorized-genetically-modified-bacillus-subtilis-production-strain-identified-in-a-vitamin-b2-feed-additive
#14
Valentina Paracchini, Mauro Petrillo, Ralf Reiting, Alexandre Angers-Loustau, Daniela Wahler, Andrea Stolz, Birgit Schönig, Anastasia Matthies, Joachim Bendiek, Dominik M Meinel, Sven Pecoraro, Ulrich Busch, Alex Patak, Joachim Kreysa, Lutz Grohmann
Many food and feed additives result from fermentation of genetically modified (GM) microorganisms. For vitamin B2 (riboflavin), GM Bacillus subtilis production strains have been developed and are often used. The presence of neither the GM strain nor its recombinant DNA is allowed for fermentation products placed on the EU market as food or feed additive. A vitamin B2 product (80% feed grade) imported from China was analysed. Viable B. subtilis cells were identified and DNAs of two bacterial isolates (LHL and LGL) were subjected to three whole genome sequencing (WGS) runs with different devices (MiSeq, 454 or HiSeq system)...
September 1, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28407084/comparative-analysis-of-de-novo-assemblers-for-variation-discovery-in-personal-genomes
#15
Shulan Tian, Huihuang Yan, Eric W Klee, Michael Kalmbach, Susan L Slager
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data...
April 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28404681/non-pnca-gene-mutated-but-pyrazinamide-resistant-m-tuberculosis-why-is-that
#16
Jim Werngren, Erik Alm, Mikael Mansjö
Pyrazinamide (PZA) is a key component for the effective treatment of drug susceptible and PZA-susceptible MDR (MDR(PZA-S)) tuberculosis. pncA gene mutations are usually detected in a clear majority (>90%) of the PZA resistant strains but obviously not in all. Rapid and reliable PZA DST is critical whenever PZA will be used in the regimen, not least for the treatment of MDR(PZA-S) TB. In this study, we selected 26 PZA resistant isolates reported to carry a wildtype pncA gene. To confirm resistance, susceptibility testing was repeated to 100 mg/L and 200 mg/L PZA for all the 26 isolates and Sanger sequencing was repeated on the 18 isolates that remained PZA resistant...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28404677/comparison-of-two-whole-genome-sequencing-methods-for-analysis-of-three-methicillin-resistant-staphylococcus-aureus-outbreaks
#17
Scott A Cunningham, Nicholas Chia, Patricio R Jeraldo, Daniel J Quest, Julie A Johnson, Dave J Boxrud, Angela J Taylor, Jun Chen, Gregory D Jenkins, Travis M Drucker, Heidi Nelson, Robin Patel
Whole genome sequencing (WGS) can provide excellent resolution in global and local epidemiological investigations of Staphylococcus aureus outbreaks. A variety of sequencing approaches and analytical tools have been used; it is not clear which is ideal. We compared two WGS strategies and two analytical approaches to the standard method of SmaI restriction digestion pulsed-field gel electrophoresis (PFGE) for typing S. aureus Forty-two S. aureus isolates from three outbreaks and 12 reference isolates were studied...
April 12, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28401899/improved-imputation-accuracy-of-rare-and-low-frequency-variants-using-population-specific-high-coverage-wgs-based-imputation-reference-panel
#18
Mario Mitt, Mart Kals, Kalle Pärn, Stacey B Gabriel, Eric S Lander, Aarno Palotie, Samuli Ripatti, Andrew P Morris, Andres Metspalu, Tõnu Esko, Reedik Mägi, Priit Palta
Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 × ) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28398289/a-high-throughput-molecular-data-resource-for-cutaneous-neurofibromas
#19
Sara J C Gosline, Hubert Weinberg, Pamela Knight, Thomas Yu, Xindi Guo, Nripesh Prasad, Angela Jones, Shristi Shrestha, Braden Boone, Shawn E Levy, Salvatore La Rosa, Justin Guinney, Annette Bakker
Neurofibromatosis type 1 (NF1) is a genetic disorder with a range of clinical manifestations such as widespread growth of benign tumours called neurofibromas, pain, learning disorders, bone deformities, vascular abnormalities and even malignant tumours. With the establishment of the Children's Tumour Foundation biobank, neurofibroma samples can now be collected directly from patients to be analysed by the larger scientific community. This work describes a pilot study to characterize one class of neurofibroma, cutaneous neurofibromas, by molecularly profiling of ~40 cutaneous neurofibromas collected from 11 individual patients...
April 11, 2017: Scientific Data
https://www.readbyqxmd.com/read/28392892/evaluation-of-multiple-approaches-to-identify-genome-wide-polymorphisms-in-closely-related-genotypes-of-sweet-cherry-prunus-avium-l
#20
Seanna Hewitt, Benjamin Kilian, Ramyya Hari, Tyson Koepke, Richard Sharpe, Amit Dhingra
Identification of genetic polymorphisms and subsequent development of molecular markers is important for marker assisted breeding of superior cultivars of economically important species. Sweet cherry (Prunus avium L.) is an economically important non-climacteric tree fruit crop in the Rosaceae family and has undergone a genetic bottleneck due to breeding, resulting in limited genetic diversity in the germplasm that is utilized for breeding new cultivars. Therefore, it is critical to recognize the best platforms for identifying genome-wide polymorphisms that can help identify, and consequently preserve, the diversity in a genetically constrained species...
2017: Computational and Structural Biotechnology Journal
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