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https://www.readbyqxmd.com/read/28422718/validation-and-optimization-of-the-ion-torrent-s5-xl-sequencer-and-oncomine-workflow-for-brca1-and-brca2-genetic-testing
#1
Saeam Shin, Yoonjung Kim, Seoung Chul Oh, Nae Yu, Seung-Tae Lee, Jong Rak Choi, Kyung-A Lee
In this study, we validated the analytical performance of BRCA1/2 sequencing using Ion Torrent's new bench-top sequencer with amplicon panel with optimized bioinformatics pipelines. Using 43 samples that were previously validated by Illumina's MiSeq platform and/or by Sanger sequencing/multiplex ligation-dependent probe amplification, we amplified the target with the Oncomine™ BRCA Research Assay and sequenced on Ion Torrent S5 XL (Thermo Fisher Scientific, Waltham, MA, USA). We compared two bioinformatics pipelines for optimal processing of S5 XL sequence data: the Torrent Suite with a plug-in Torrent Variant Caller (Thermo Fisher Scientific), and commercial NextGENe software (Softgenetics, State College, PA, USA)...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28419775/next-generation-sequencing-mitochondrial-dna-analysis-in-autism-spectrum-disorder
#2
Ashok Patowary, Ryan Nesbitt, Marilyn Archer, Raphael Bernier, Zoran Brkanac
Autism is a complex genetic disorder where both de-novo and inherited genetics factors play a role. Next generation sequencing approaches have been extensively used to identify rare variants associated with autism. To date, all such studies were focused on nuclear genome; thereby leaving the role of mitochondrial DNA (mtDNA) variation in autism unexplored. Recently, analytical tools have been developed to evaluate mtDNA in whole-exome data. We have analyzed the mtDNA sequence derived from whole-exome sequencing in 10 multiplex families...
April 17, 2017: Autism Research: Official Journal of the International Society for Autism Research
https://www.readbyqxmd.com/read/28413748/thiamine-assays-advances-challenges-and-caveats
#3
REVIEW
Katie A Edwards, Nicole Tu-Maung, Krystal Cheng, Binbin Wang, Antje J Baeumner, Clifford E Kraft
Thiamine (vitamin B1) is essential to the health of all living organisms and deficiency has long been associated with diseases in animals such as fish, birds, alligators, and domesticated ruminant mammals. Thiamine is also implicated in several human diseases including Alzheimer's, diabetes, dementia, depression and, most notably, Wernicke-Korsakoff syndrome and Beriberi disease. Yet, highly sensitive and specific detection of thiamine remains an analytical challenge, as pM to nm levels of thiamine need to be detected in environmental and human samples, respectively, various phosphorylated variants need to be discriminated, and rapid on-site detection would be highly desirable...
April 2017: ChemistryOpen
https://www.readbyqxmd.com/read/28404677/comparison-of-two-whole-genome-sequencing-methods-for-analysis-of-three-methicillin-resistant-staphylococcus-aureus-outbreaks
#4
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/28400066/development-of-a-fast-workflow-to-screen-the-charge-variants-of-therapeutic-antibodies
#5
Elsa Wagner-Rousset, Szabolcs Fekete, Laura Morel-Chevillet, Olivier Colas, Nathalie Corvaïa, Sarah Cianférani, Davy Guillarme, Alain Beck
Chemical or enzymatic modifications of therapeutic monoclonal antibodies (mAbs) having high risk towards safety and efficacy are defined as critical quality attributes (CQAs). During therapeutic mAbs process development, a variety of analytical techniques have to be used for the thorough characterization and quantitative monitoring of CQAs. This paper describes the development of a rapid analytical platform to assess and rank charge variants of mAbs. The workflow is first based on a cation exchange chromatography (CEX) comparative analysis of intact IgGs versus F(ab)'2 and Fc sub-domains generated by IdeS digestion...
February 27, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28393407/haemoglobin%C3%A2-a1c-interpretation-more-than-mean-blood-glucose-to-be-considered
#6
W G John
It is more than half a century since Kunkel and Wallenius described the occurrence of 'minor components' in normal adult haemoglobin in the absence of variants [1]; the major fraction of these components was identified as glucose attached to the haemoglobin molecule, and is now termed HbA1c . The importance of this HbA1c did not become fully apparent until 1969 when Rahbar and associates [2] described 'an abnormal fast moving haemoglobin fraction' in the erythrocytes of people with diabetes; hence the relationship of HbA1c to diabetes was established, and within 10 years, methods for measuring this fraction were being introduced into clinical laboratory practice [3]...
April 10, 2017: Diabetic Medicine: a Journal of the British Diabetic Association
https://www.readbyqxmd.com/read/28393384/binomirare-a-robust-test-of-the-association-of-a-rare-variant-with-a-disease-for-pooled-analysis-and-meta-analysis-with-application-to-the-hchs-sol
#7
Tamar Sofer
Most regression-based tests of the association between a low-count variant and a binary outcome do not protect type 1 error, especially when tests are rejected based on a very low significance threshold. Noted exception is the Firth test. However, it was recently shown that in meta-analyzing multiple studies all asymptotic, regression-based tests, including the Firth, may not control type 1 error in some settings, and the Firth test may suffer a substantial loss of power. The problem is exacerbated when the case-control proportions differ between studies...
April 10, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28379786/unbiased-in-depth-characterization-of-cex-fractions-from-a-stressed-monoclonal-antibody-by-mass-spectrometry
#8
François Griaud, Blandine Denefeld, Manuel Lang, Héloïse Hensinger, Peter Haberl, Matthias Berg
Characterization of charge-based variants by mass spectrometry (MS) is required for the analytical development of a new biological entity and its marketing approval by health authorities. However, standard peak-based data analysis approaches are time-consuming and biased towards the detection, identification, and quantification of main variants only. The aim of this study was to characterize in-depth acidic and basic species of a stressed IgG1 monoclonal antibody using comprehensive and unbiased MS data evaluation tools...
April 5, 2017: MAbs
https://www.readbyqxmd.com/read/28374734/-the-isolation-of-organic-compounds-from-hydrosulfuric-mineral-waters-with-the-use-of-the-extractive-freezing-out-technique-with-centrifugation
#9
V N Bekhterev, E A Kabina
The mineral waters, enriched with organic substances find extensive application in balneotherapy. The fast and efficient methods for the identification and quantitative measurement of organic compounds (in the first place, organic acids) in such waters need to be developed for the estimation of their quality and biological activity. AIM: The objective of the present study was to elaborate a gas chromatographic method for the determination of monobasic carbonic acids in sulfide-containing mineral waters by means of extractive freezing-out in combination with the application of the centrifugal forces for the elucidation of the metrological characteristics of the compounds of interest...
2017: Voprosy Kurortologii, Fizioterapii, i Lechebnoĭ Fizicheskoĭ Kultury
https://www.readbyqxmd.com/read/28371718/comparability-study-of-rituximab-originator-and-follow-on-biopharmaceutical
#10
Othman Montacir, Houda Montacir, Murat Eravci, Andreas Springer, Stephan Hinderlich, Amirhossein Saadati, Maria Kristina Parr
Immunglobolin G (IgG)-based biopharmaceuticals are emerging on the pharmaceuticals market due to their high target selectivity in different diseases. In parallel, a growing interest by other companies to produce similar or highly similar follow-on biologics exits, once the patent of blockbuster biotherapeutics is about to expire. In correlation to their complex structure, an analytical challenge is facing the approval of these biosimilars. Health authorities (e.g. FDA and EMA) have issued several guidelines to define critical quality attributes during manufacturing process changes...
March 19, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28369783/utilization-of-sequence-variants-as-biomarkers-to-analyze-population-dynamics-in-cloned-cell-lines
#11
T Jennifer Lin, Kathryn M Beal, Heather S DeGruttola, Steven J Brennan, Lisa A Marzilli, Karin Anderson
The inherent nature of cloned CHO cell lines includes the presence of genetic and phenotypic drift that leads to heterogeneous populations. The genetic heterogeneity exhibited by these cells can be exploited to understand the population dynamics of cloned cell lines. Understanding the interplay between heterogeneity, cell culture conditions and population dynamics will allow for critical assessment of overarching cell line development methods and strategies in terms of population and monoclonality. Sequence variants (SVs) are protein isoforms of the gene-of-interest that contain unintended amino acid substitutions, extensions or truncations that may contribute to heterogeneity...
March 28, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28364486/genetic-basis-of-chronotype-in-humans-insights-from-three-landmark-gwas
#12
David A Kalmbach, Logan D Schneider, Joseph Cheung, Sarah J Bertrand, Thiruchelvam Kariharan, Allan I Pack, Philip R Gehrman
Study Objectives: Chronotype, or diurnal preference, refers to behavioral manifestations of the endogenous circadian system that governs preferred timing of sleep and wake. As variations in circadian timing and system perturbations are linked to disease development, the fundamental biology of chronotype has received attention for its role in the regulation and dysregulation of sleep and related illnesses. Family studies indicate that chronotype is a heritable trait, thus directing attention toward its genetic basis...
February 1, 2017: Sleep
https://www.readbyqxmd.com/read/28358272/evaluation-of-rapid-post-mortem-test-kits-for-bovine-spongiform-encephalopathy-bse-screening-in-japan-their-analytical-sensitivity-to-atypical-bse-prions
#13
Ken'ichi Hagiwara, Yoshifumi Iwamaru, Naoko Tabeta, Takashi Yokoyama, Minoru Tobiume
A classical type of bovine spongiform encephalopathy (C-BSE), recognized in 1987, had a large impact on public health due to its zoonotic link to variant Creutzfeldt-Jakob disease by the human consumption of dietary products contaminated with the C-BSE prion. Thus, a number of countries implemented BSE surveillance using rapid post-mortem test kits that were approved for detection of the C-BSE prion in the cattle brain. However, as atypical BSE (L- and H-BSE) cases emerged in subsequent years, the efficacy of the kits for the detection of atypical BSE prions became a matter of concern...
March 4, 2017: Prion
https://www.readbyqxmd.com/read/28357155/analytical-and-clinical-validity-study-of-firststepdx-plus-a-chromosomal-microarray-optimized-for-patients-with-neurodevelopmental-conditions
#14
Charles Hensel, Rena Vanzo, Megan Martin, Sean Dixon, Christophe Lambert, Brynn Levy, Lesa Nelson, Andy Peiffer, Karen S Ho, Patricia Rushton, Moises Serrano, Sarah South, Kenneth Ward, Edward Wassman
INTRODUCTION: Chromosomal microarray analysis (CMA) is recognized as the first-tier test in the genetic evaluation of children with developmental delays, intellectual disabilities, congenital anomalies and autism spectrum disorders of unknown etiology. ARRAY DESIGN: To optimize detection of clinically relevant copy number variants associated with these conditions, we designed a whole-genome microarray, FirstStep(Dx) PLUS (FSDX). A set of 88,435 custom probes was added to the Affymetrix CytoScanHD platform targeting genomic regions strongly associated with these conditions...
February 27, 2017: PLoS Currents
https://www.readbyqxmd.com/read/28356564/combined-pituitary-hormone-deficiency-due-to-gross-deletions-in-the-pou1f1-pit-1-and-prop1-genes
#15
Eleonore Bertko, Jürgen Klammt, Petra Dusatkova, Mithat Bahceci, Nazli Gonc, Louise Ten Have, Nurgun Kandemir, Georg Mansmann, Barbora Obermannova, Wilma Oostdijk, Heike Pfäffle, Denise Rockstroh-Lippold, Marina Schlicke, Alpaslan Kemal Tuzcu, Roland Pfäffle
Pituitary development depends on a complex cascade of interacting transcription factors and signaling molecules. Lesions in this cascade lead to isolated or combined pituitary hormone deficiency (CPHD). The aim of this study was to identify copy number variants (CNVs) in genes known to cause CPHD and to determine their structure. We analyzed 70 CPHD patients from 64 families. Deletions were found in three Turkish families and one family from northern Iraq. In one family we identified a 4.96 kb deletion that comprises the first two exons of POU1F1...
March 30, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28356196/facile-preparation-of-fibrin-coated-open-tubular-column-for-characterization-of-monoclonal-antibody-variants-by-capillary-electrochromatography
#16
Xue Xiao, Wentao Wang, Yamin Zhang, Li Jia
Monoclonal antibodies (mAbs) are one of the most promising classes of therapeutic protein biopharmaceuticals. However, the complexity of mAbs poses a daunting analytical challenge for heterogeneity characterization of mAbs. In this study, inspired by blood coagulation, we adopted a fibrin coating as a novel stationary phase in open tubular (OT) column for the separation of the mAbs variants by capillary electrochromatography. The fibrin coating was prepared by in situ polymerization of fibrin in the presence of thrombin as a catalyst inside a fused-silica capillary...
March 16, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28347285/whole-exome-sequencing-and-digital-pcr-identified-a-novel-compound-heterozygous-mutation-in-the-nphp1-gene-in-a-case-of-joubert-syndrome-and-related-disorders
#17
Shingo Koyama, Hidenori Sato, Manabu Wada, Toru Kawanami, Mitsuru Emi, Takeo Kato
BACKGROUND: Joubert syndrome and related disorders (JSRD) is a clinically and genetically heterogeneous condition with autosomal recessive or X-linked inheritance, which share a distinctive neuroradiological hallmark, the so-called molar tooth sign. JSRD is classified into six clinical subtypes based on associated variable multiorgan involvement. To date, 21 causative genes have been identified in JSRD, which makes genetic diagnosis difficult. CASE PRESENTATION: We report here a case of a 28-year-old Japanese woman diagnosed with JS with oculorenal defects with a novel compound heterozygous mutation (p...
March 27, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28344774/the-dockstore-enabling-modular-community-focused-sharing-of-docker-based-genomics-tools-and-workflows
#18
Brian D O'Connor, Denis Yuen, Vincent Chung, Andrew G Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing...
2017: F1000Research
https://www.readbyqxmd.com/read/28344655/interactions-among-cox-2-gpiiia-and-p2y1-variants-are-associated-with-aspirin-responsiveness-and-adverse-events-in-patients-with-ischemic-stroke
#19
Xingyang Yi, Zhao Han, Qiang Zhou, Jing Lin, Chun Wang
BACKGROUND: The effect of gene variants and their interactions on response to aspirin and clinical adverse outcomes after an acute ischemic stroke (IS) is not fully understood. The aim of this study was to investigate the association of aspirin-relevant gene variants and their interactions with clinical adverse outcomes in IS patients taking aspirin. METHODS: A total of 14 variants from six genes encoding COX enzymes (COX-1, COX-2), platelet membrane receptors (TXAS1, P2Y1, P2Y12) and glycoprotein receptor (GPIIIa) were examined in 850 acute IS patients...
March 2017: Therapeutic Advances in Neurological Disorders
https://www.readbyqxmd.com/read/28344127/replicated-association-between-the-european-gwas-locus-rs10503253-at-csmd1-and-schizophrenia-in-asian-population
#20
Weiqing Liu, Fang Liu, Xiufeng Xu, Yan Bai
Schizophrenia is one of the most severe mental disorders with significant heritability. Recent genetic association studies including genome-wide association studies (GWAS) have identified multiple common variants conferring risk of schizophrenia. An intronic SNP within CSMD1, rs10503253, is one of the top risk SNPs for schizophrenia in Europeans discovered through large GWAS. However, whether rs10503253 is also a risk SNP for schizophrenia in other populations, such as Asians, is still unknown. To answer this question, we examined the association of rs10503253 with schizophrenia in a total of 7514 schizophrenia patients, 9058 healthy controls and 1115 nuclear families originated from Asia using a meta-analytic approach...
March 24, 2017: Neuroscience Letters
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