keyword
MENU ▼
Read by QxMD icon Read
search

genotypic sequence

keyword
https://www.readbyqxmd.com/read/28340305/the-clinical-application-of-ngs-based-snp-haplotyping-for-pgd-of-hb-h-disease
#1
Linjun Chen, Zhenyu Diao, Zhipeng Xu, Jianjun Zhou, Guijun Yan, Haixiang Sun
This study investigated the usefulness of next-generation sequencing (NGS)-based single nucleotide polymorphism (SNP) haplotyping for preimplantation genetic diagnosis (PGD) of hemoglobin H (Hb H) disease. Multiple displacement amplification (MDA) was used for whole genome amplification (WGA) of biopsied trophectoderm (TE) cells. Gap-PCR and NGS-based SNP haplotyping was used to distinguish the two genotypes of -α(3.7)/αα and -(SEA)/αα for PGD of Hb H disease. One out of the ten blastocysts (B11) was successfully diagnosed as genotype -α(3...
March 24, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28340175/funresdb-a-web-resource-for-genotypic-susceptibility-testing-of-aspergillus-fumigatus
#2
Michael Weber, Jonas Schaer, Grit Walther, Kerstin Kaerger, Jörg Steinmann, Peter-Michael Rath, Birgit Spiess, Dieter Buchheidt, Axel Hamprecht, Oliver Kurzai
Therapy of invasive aspergillosis is becoming more difficult due to the emergence of azole resistance in Aspergillus fumigatus. A majority of resistant strains carries mutations in the CYP51A gene. Due to a lack of sensitivity of culture-based methods, molecular detection of A. fumigatus has become an important diagnostic tool. We set up the database FunResDB (www.nrz-myk.de/funresdb) to gather all available information about CYP51A-dependent azole resistance from published literature. In summary, the screening resulted in 79 CYP51A variants, which are linked to 59 nonsynonymous mutations...
March 11, 2017: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/28339951/characterization-of-a-hypervirulent-fowl-adenovirus-4-with-the-novel-genotype-newly-prevalent-in-china-and-establishment-of-reproduction-infection-model-of-hydropericardium-syndrome-in-chickens
#3
Q Pan, L Liu, Y Gao, C Liu, X Qi, Y Zhang, Y Wang, K Li, L Gao, X Wang, H Cui
Severe hydropericardium syndrome (HPS) has been present in layers in the northeast of China since June 2015, with mortality rates varying from 30 to 90%. Dead layers had severe hydropericardium with pericardial volumes of 5 to 20 mL, as well as inclusion body hepatitis. Laboratory investigations led to the isolation of a fowl adenovirus strain, HLJFAd15, from the liver tissue of dead layers. Natural deletions of ORF19 and ORF27 were found in this clinical strain by complete genome sequencing, which was identified with the novel genotype recently prevalent in China...
March 4, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339881/genetic-aspects-and-environmental-sources-of-microsporidia-that-infect-the-human-gastrointestinal-tract
#4
Martin F Heyworth
Enterocytozoon bieneusi and Encephalitozoon intestinalis are microsporidia that infect the human gastrointestinal (GI) tract. Each of these microsporidia has been shown to infect various non-human hosts (mammalian and avian), raising the possibility of inter-species transmission, for example, from such hosts to human subjects via waterborne dispersal of microsporidian spores. During the past two decades, genome sequencing has delineated more than 90 genotypes of Ent. bieneusi, and has led to the conclusion that not all the genotypes of this organism infect human subjects...
February 27, 2017: Transactions of the Royal Society of Tropical Medicine and Hygiene
https://www.readbyqxmd.com/read/28339845/expanded-spectrum-%C3%AE-lactamase-producing-escherichia-coli-isolated-from-chickens-with-colibacillosis-in-egypt
#5
D A El-Shazly, S A Nasef, F F Mahmoud, Daniel Jonas
Throughout the world, expanded spectrum β-lactamases (ESBL) are increasing among clinical isolates of Enterobacteriaceae, both in humans and animals. Unfortunately, there is a paucity of data on ESBL or Ampicillin class C β-lactamase (AmpC) in Egypt, although antimicrobial consumption is high in this developing country. This study aims to characterize the resistance mechanisms to expanded spectrum cephalosporins among resistant veterinary Escherichia coli isolates in Egypt. We investigated 50 clinical multi-resistant E...
February 23, 2017: Poultry Science
https://www.readbyqxmd.com/read/28339700/a-clinical-perspective-on-the-2016-who-brain-tumor-classification-and-routine-molecular-diagnostics
#6
Martin J van den Bent, Michael Weller, Patrick Y Wen, Johan M Kros, Ken Aldape, Susan Chang
The 2007 World Health Organization (WHO) classification of brain tumors did not use molecular abnormalities as diagnostic criteria. Studies have shown that genotyping allows a better prognostic classification of diffuse glioma with improved treatment selection. This has resulted in a major revision of the WHO classification, which is now for adult diffuse glioma centered around isocitrate dehydrogenase (IDH) and 1p/19q diagnostics. This revised classification is reviewed with a focus on adult brain tumors, and includes a recommendation of genes of which routine testing is clinically useful...
February 21, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28339499/evaluation-of-fusion-protein-cleavage-site-sequences-of-newcastle-disease-virus-in-genotype-matched-vaccines
#7
Shin-Hee Kim, Zongyan Chen, Asuka Yoshida, Anandan Paldurai, Sa Xiao, Siba K Samal
Newcastle disease virus (NDV) causes a devastating poultry disease worldwide. Frequent outbreaks of NDV in chickens vaccinated with conventional live vaccines suggest a need to develop new vaccines that are genetically matched against circulating NDV strains, such as the genotype V virulent strains currently circulating in Mexico and Central America. In this study, a reverse genetics system was developed for the virulent NDV strain Mexico/01/10 strain and used to generate highly attenuated vaccine candidates by individually modifying the cleavage site sequence of fusion (F) protein...
2017: PloS One
https://www.readbyqxmd.com/read/28335006/a-platform-for-functional-assessment-of-large-variant-libraries-in-mammalian-cells
#8
Kenneth A Matreyek, Jason J Stephany, Douglas M Fowler
Sequencing-based, massively parallel genetic assays have revolutionized our ability to quantify the relationship between many genotypes and a phenotype of interest. Unfortunately, variant library expression platforms in mammalian cells are far from ideal, hindering the study of human gene variants in their physiologically relevant cellular contexts. Here, we describe a platform for phenotyping variant libraries in transfectable mammalian cell lines in two steps. First, a landing pad cell line with a genomically integrated, Tet-inducible cassette containing a Bxb1 recombination site is created...
March 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28334939/association-between-tau-deposition-and-antecedent-amyloid-%C3%AE-accumulation-rates-in-normal-and-early-symptomatic-individuals
#9
Duygu Tosun, Susan Landau, Paul S Aisen, Ronald C Petersen, Mark Mintun, William Jagust, Michael W Weiner
A long-term goal of our field is to determine the sequence of pathological events, which ultimately lead to cognitive decline and dementia. In this study, we first assessed the patterns of brain tau tangle accumulation (measured with the positron emission tomography tracer 18F-AV-1451) associated with well-established Alzheimer's disease factors in a cohort including cognitively healthy elderly individuals and individuals at early symptomatic stages of Alzheimer's disease. We then explored highly associated patterns of greater 18F-AV-1451 binding and increased annualized change in cortical amyloid-β plaques measured as florbetapir positron emission tomography binding antecedent to 18F-AV-1451 positron emission tomography scans, and to what extent these multimodal pattern associations explained the variance in cognitive performance and clinical outcome measures, independently and jointly...
March 17, 2017: Brain: a Journal of Neurology
https://www.readbyqxmd.com/read/28334874/efficient-cnv-breakpoint-analysis-reveals-unexpected-structural-complexity-and-correlation-of-dosage-sensitive-genes-with-clinical-severity-in-genomic-disorders
#10
Ling Zhang, Jingmin Wang, Cheng Zhang, Dongxiao Li, Claudia M B Carvalho, Haoran Ji, Jianqiu Xiao, Ye Wu, Weichen Zhou, Hongyan Wang, Li Jin, Yang Luo, Xiru Wu, James R Lupski, Feng Zhang, Yuwu Jiang
Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders...
March 14, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334784/testing-the-ret-and-sema3d-genetic-interaction-in-mouse-enteric-nervous-system-development
#11
Ashish Kapoor, Dallas R Auer, Dongwon Lee, Sumantra Chatterjee, Aravinda Chakravarti
For most multigenic disorders, clinical manifestation (penetrance) and presentation (expressivity) are likely to be an outcome of genetic interaction between multiple susceptibility genes. Here, using gene knockouts in mice we evaluated genetic interaction between loss of Ret and loss of Sema3d, two Hirschsprung disease susceptibility genes. We intercrossed Ret and Sema3d double null heterozygotes to generate mice with the nine possible genotypes and assessed survival by counting various genotypes, myenteric plexus presence by acetylcholinesterase staining and embryonic day 12...
March 7, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28334725/predominance-of-g9p-4-rotavirus-from-children-with-acute-gastroenteritis-in-northwestern-mexico
#12
Leticia Felix-Valenzuela, Dora Patricia Cooley-García, Manuel Alberto Cano-Rangel, Maria de Los Angeles Durazo-Arvizu, Veronica Mata-Haro
In Mexico, group A rotavirus (RVA) infections remain the most common cause of severe dehydrating diarrhea in children. This study was conducted to examine the circulating RVA strains in the northwest region of Mexico. RVA strains collected from stool samples of children were genotyped, and their partial sequences were analyzed. RT-PCR of the VP4 and VP7 genes showed the partial G9P[4] genotype in all the samples. Sequencing and phylogenetic analysis of the partial VP7 gene amplicons of 10 strains showed that they clustered in the RVA G9 lineage III, and 7 of them showed 100% identity with the reference strain LB1562, which was collected in the USA 2 years earlier...
March 23, 2017: Intervirology
https://www.readbyqxmd.com/read/28334390/seqarray-a-storage-efficient-high-performance-data-format-for-wgs-variant-calls
#13
Xiuwen Zheng, Stephanie M Gogarten, Michael Lawrence, Adrienne Stilp, Matthew P Conomos, Bruce S Weir, Cathy Laurie, David Levine
Motivation: Whole-genome sequencing (WGS) data is being generated at an unprecedented rate. Analysis of WGS data requires a flexible data format to store the different types of DNA variation. Variant call format (VCF) is a general text-based format developed to store variant genotypes and their annotations. However, VCF files are large and data retrieval is relatively slow. Here we introduce a new WGS variant data format implemented in the R/Bioconductor package "SeqArray" for storing variant calls in an arrayoriented manner which provides the same capabilities as VCF, but with multiple high compression options and data access using high-performance parallel computing...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334373/estimating-error-models-for-whole-genome-sequencing-using-mixtures-of-dirichlet-multinomial-distributions
#14
Steven H Wu, Rachel S Schwartz, David J Winter, Donald F Conrad, Reed A Cartwright
Motivation: Accurate identification of genotypes is an essential part of the analysis of genomic data, including in identification of sequence polymorphisms, linking mutations with disease, and determining mutation rates. Biological and technical processes that adversely affect genotyping include copy-numbervariation, paralogous sequences, library preparation, sequencing error, and reference-mapping biases, among others. Results: We modeled the read depth for all data as a mixture of Dirichlet-multinomial distributions, resulting in significant improvements over previously used models...
March 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334284/genomic-diversity-guides-conservation-strategies-among-rare-terrestrial-orchid-species-when-taxonomy-remains-uncertain
#15
Collin W Ahrens, Megan A Supple, Nicola C Aitken, David J Cantrill, Justin O Borevitz, Elizabeth A James
Background and Aims: Species are often used as the unit for conservation, but may not be suitable for species complexes where taxa are difficult to distinguish. Under such circumstances, it may be more appropriate to consider species groups or populations as evolutionarily significant units (ESUs). A population genomic approach was employed to investigate the diversity within and among closely related species to create a more robust, lineage-specific conservation strategy for a nationally endangered terrestrial orchid and its relatives from south-eastern Australia...
March 15, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28334237/dna-compass-a-secure-client-side-site-for-navigating-personal-genetic-information
#16
Charles Curnin, Assaf Gordon, Yaniv Erlich
Motivation: Millions of individuals have access to raw genomic data using direct-to-consumer companies. The advent of large-scale sequencing projects, such as the Precision Medicine Initiative, will further increase the number of individuals with access to their own genomic information. However, querying genomic data requires a computer terminal and computational skill to analyze the data - an impediment for the general public. Results: DNA Compass is a website designed to empower the public by enabling simple navigation of personal genomic data...
March 11, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334117/a-generalized-association-test-based-on-u-statistics
#17
Changshuai Wei, Qing Lu
Motivation: Second generation sequencing technologies are being increasingly used for genetic association studies, where the main research interest is to identify sets of genetic variants that contribute to various phenotypes. The phenotype can be univariate disease status, multivariate responses and even high-dimensional outcomes. Considering the genotype and phenotype as two complex objects, this also poses a general statistical problem of testing association between complex objects...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28334108/fast-admixture-analysis-and-population-tree-estimation-for-snp-and-ngs-data
#18
Yu Jade Cheng, Thomas Mailund, Rasmus Nielsen
Structure methods are highly used population genetic methods for classifying individuals in a sample fractionally into discrete ancestry components. We introduce a new optimization algorithm for the classical STRUCTURE model in a maximum likelihood framework. Using analyses of real data we show that the new method finds solutions with higher likelihoods than the state-of-the-art method inthe same computational time. The optimization algorithm is also applicable to models based on genotype likelihoods, that can account for the uncertainty in genotype-calling associated with Next Generation Sequencing (NGS) data...
February 17, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28333944/mechanisms-of-glycosylase-induced-genomic-instability
#19
Daniel E Eyler, Kylie A Burnham, Thomas E Wilson, Patrick J O'Brien
Human alkyladenine DNA glycosylase (AAG) initiates base excision repair (BER) to guard against mutations by excising alkylated and deaminated purines. Counterintuitively, increased expression of AAG has been implicated in increased rates of spontaneous mutation in microsatellite repeats. This microsatellite mutator phenotype is consistent with a model in which AAG excises bulged (unpaired) bases, altering repeat length. To directly test the role of base excision in AAG-induced mutagenesis, we conducted mutation accumulation experiments in yeast overexpressing different variants of AAG and detected mutations via high-depth genome resequencing...
2017: PloS One
https://www.readbyqxmd.com/read/28333340/evaluation-of-the-new-genotype-ntm-dr-kit-for-the-molecular-detection-of-antimicrobial-resistance-in-non-tuberculous-mycobacteria
#20
Faiza Mougari, Jade Loiseau, Nicolas Veziris, Christine Bernard, Béatrice Bercot, Wladimir Sougakoff, Vincent Jarlier, Laurent Raskine, Emmanuelle Cambau
Objectives: Non-tuberculous mycobacteria (NTM) are emerging pathogens causing difficult-to-treat infections. We tested a new assay (GenoType NTM-DR) that detects natural and acquired resistance mechanisms to macrolides and aminoglycosides in frequently isolated NTM species. Methods: Performance was assessed on 102 isolates including reference strains [16 Mycobacterium avium , 10 Mycobacterium intracellulare , 8 Mycobacterium chimaera , 15 Mycobacterium chelonae and 53 Mycobacterium abscessus (including subsp...
February 28, 2017: Journal of Antimicrobial Chemotherapy
keyword
keyword
43250
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"