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https://www.readbyqxmd.com/read/29334134/a-comprehensive-next-generation-sequencing-assay-for-the-diagnosis-of-epidermolysis-bullosa
#1
Anne W Lucky, Neha Dagaonkar, Karen Lammers, Ammar Husami, Diane Kissell, Kejian Zhang
BACKGROUND: Historically, diagnosis of epidermolysis bullosa has required skin biopsies for electron microscopy, direct immunofluorescence to determine which gene(s) to choose for genetic testing, or both. METHODS: To avoid these invasive tests, we developed a high-throughput next-generation sequencing (NGS)-based diagnostic assay called EBSEQ that allows simultaneous detection of mutations in 21 genes with known roles in epidermolysis bullosa pathogenicity. Mutations are confirmed with traditional Sanger sequencing...
January 15, 2018: Pediatric Dermatology
https://www.readbyqxmd.com/read/29330084/real-time-reverse-transcription-recombinase-polymerase-amplification-assay-for-rapid-detection-of-porcine-epidemic-diarrhea-virus
#2
Jianchang Wang, Ruoxi Zhang, Jinfeng Wang, Qingan Han, Libing Liu, Yanan Li, Wanzhe Yuan
Porcine epidemic diarrhea (PED), which is caused by porcine epidemic diarrhea virus (PEDV), is an acute, highly contagious enteric disease characterized by severe watery diarrhea, vomiting, dehydration, and high mortality in suckling piglets. A real-time reverse-transcription recombinase polymerase amplification assay (RT-RPA) was developed based on the nucleocapsid gene of PEDV. RT-RPA assay was performed at 40 °C for 20 min. The assay could detect both the classical and variant PEDV strains, and there was no cross-reaction with other pathogens tested...
January 9, 2018: Journal of Virological Methods
https://www.readbyqxmd.com/read/29317610/enrichment-of-schizophrenia-heritability-in-both-neuronal-and-glia-cell-regulatory-elements
#3
Katherine E Tansey, Matthew J Hill
Genome-wide association studies have identified over 100 robust risk loci for schizophrenia with thousands of variants mediating genetic heritability, the majority of which reside in non-coding regions. Analytical approaches have shown this heritability is strongly enriched at variants within regulatory elements identified from human post-mortem brain tissue. However, bulk post-mortem brain tissue has a heterogeneous cell composition, making biological interpretations difficult. We sought to refine the cell types mediating schizophrenia heritability by separating neuronal and glial signals using data from: (1) NeuN-sorted post-mortem brain and (2) cell culture systems...
January 10, 2018: Translational Psychiatry
https://www.readbyqxmd.com/read/29288389/principles-and-methods-of-in-silico-prioritization-of-non-coding-regulatory-variants
#4
REVIEW
Phil H Lee, Christian Lee, Xihao Li, Brian Wee, Tushar Dwivedi, Mark Daly
Over a decade of genome-wide association, studies have made great strides toward the detection of genes and genetic mechanisms underlying complex traits. However, the majority of associated loci reside in non-coding regions that are functionally uncharacterized in general. Now, the availability of large-scale tissue and cell type-specific transcriptome and epigenome data enables us to elucidate how non-coding genetic variants can affect gene expressions and are associated with phenotypic changes. Here, we provide an overview of this emerging field in human genomics, summarizing available data resources and state-of-the-art analytic methods to facilitate in-silico prioritization of non-coding regulatory mutations...
December 29, 2017: Human Genetics
https://www.readbyqxmd.com/read/29287113/diffusion-weighted-mri-distinguishes-parkinson-disease-from-the-parkinsonian-variant-of-multiple-system-atrophy-a-systematic-review-and-meta-analysis
#5
Sweta Bajaj, Florian Krismer, Jose-Alberto Palma, Gregor K Wenning, Horacio Kaufmann, Werner Poewe, Klaus Seppi
BACKGROUND: Putaminal diffusivity in brain magnetic resonance diffusion-weighted imaging (DWI) is increased in patients with the parkinsonian variant of multiple system atrophy (MSA-P) compared to Parkinson disease (PD) patients. PURPOSE: We performed a systematic review and meta-analysis to evaluate the diagnostic accuracy of DWI to distinguish MSA-P from PD. METHODS: Studies on DWI were identified through a systematic PubMed and Clarivate Analytics® Web of Science® Core Collection search...
2017: PloS One
https://www.readbyqxmd.com/read/29285958/maintaining-consistent-quality-and-clinical-performance-of-biopharmaceuticals
#6
William C Lamanna, Johann Holzmann, Hillel P Cohen, Xinghua Guo, Monika Schweigler, Thomas Stangler, Andreas Seidl, Martin Schiestl
Biopharmaceuticals are large protein based drugs which are heterogeneous by nature due to post translational modifications resulting from cellular production, processing and storage. Changes in the abundance of different variants over time are inherent to biopharmaceuticals due to their sensitivity to subtle process differences and the necessity for regular manufacturing changes. Product variability must thus be carefully controlled to ensure that it does not result in changes in safety or efficacy. Areas Covered: The focus of this manuscript is to provide improved understanding of the science and strategies used to maintain the quality and clinical performance of biopharmaceuticals, including biosimilars, throughout their lifecycle...
December 29, 2017: Expert Opinion on Biological Therapy
https://www.readbyqxmd.com/read/29281255/infrared-spectroscopic-imaging-advances-as-an-analytical-technology-for-biomedical-sciences
#7
Tomasz Wrobel, Rohit Bhargava
Optical chemical imaging seeks to non-destructively acquire spatially resolved chemical information without the use of labels or probes. The combination of vibrational mid-infrared (IR) spectroscopy and microscopy is especially attractive since the fundamental vibrational modes of samples are coincident with optical frequencies, thereby absorbing a large fraction of incident light and providing a strong signal. Modern IR spectroscopic imaging can be traced back nearly 25 years, with the coupling of an IR microscope to an array detector and an interferometer1,2...
December 27, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29279961/assessment-of-mitochondrial-dna-heteroplasmy-detected-on-commercial-panel-using-mps-system-with-artificial-mixture-samples
#8
Sohee Cho, Moon Young Kim, Ji Hyun Lee, Soong Deok Lee
Mitochondrial DNA (mtDNA) heteroplasmy is a potential genetic marker for forensic mtDNA analysis as well as phylogenic studies. Frequency of mtDNA heteroplasmy has been investigated in different populations through massively parallel sequencing (MPS) analysis, revealing various levels of frequency based on different MPS systems. For accurate heteroplasmy identification, it is essential to explore reliable detection threshold on various MPS systems. In addition, software solutions and pipelines need to be evaluated to analyze data effectively...
December 26, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/29276371/normal-theory-two-stage-ml-estimator-when-data-are-missing-at-the-item-level
#9
Victoria Savalei, Mijke Rhemtulla
In many modeling contexts, the variables in the model are linear composites of the raw items measured for each participant; for instance, regression and path analysis models rely on scale scores, and structural equation models often use parcels as indicators of latent constructs. Currently, no analytic estimation method exists to appropriately handle missing data at the item level. Item-level multiple imputation (MI), however, can handle such missing data straightforwardly. In this article, we develop an analytic approach for dealing with item-level missing data-that is, one that obtains a unique set of parameter estimates directly from the incomplete data set and does not require imputations...
August 2017: Journal of Educational and Behavioral Statistics
https://www.readbyqxmd.com/read/29258236/lc-ms-ms-detection-of-karlotoxins-reveals-new-variants-in-strains-of-the-marine-dinoflagellate-karlodinium-veneficum-from-the-ebro-delta-nw-mediterranean
#10
Bernd Krock, Julia A Busch, Urban Tillmann, Francisco García-Camacho, Asterio Sánchez-Mirón, Juan J Gallardo-Rodríguez, Lorenzo López-Rosales, Karl B Andree, Margarita Fernández-Tejedor, Matthias Witt, Allan D Cembella, Allen R Place
A liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed for the detection and quantitation of karlotoxins in the selected reaction monitoring (SRM) mode. This novel method was based upon the analysis of purified karlotoxins (KcTx-1, KmTx-2, 44-oxo-KmTx-2, KmTx-5), one amphidinol (AM-18), and unpurified extracts of bulk cultures of the marine dinoflagellate Karlodinium veneficum strain CCMP2936 from Delaware (Eastern USA), which produces KmTx-1 and KmTx-3. The limit of detection of the SRM method for KmTx-2 was determined as 2...
December 18, 2017: Marine Drugs
https://www.readbyqxmd.com/read/29250767/fast-permutation-tests-and-related-methods-for-association-between-rare-variants-and-binary-outcomes
#11
Arjun Sondhi, Kenneth Martin Rice
In large-scale genetic studies, a primary aim is to test for an association between genetic variants and a disease outcome. The variants of interest are often rare and appear with low frequency among subjects. In this situation, statistical tests based on standard asymptotic results do not adequately control the type I error rate, especially if the case : control ratio is unbalanced. In this article, we propose the use of permutation and approximate unconditional tests for testing association with rare variants...
December 18, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/29246041/testing-the-mutual-information-expansion-of-entropy-with-multivariate-gaussian-distributions
#12
Martin Goethe, Ignacio Fita, J Miguel Rubi
The mutual information expansion (MIE) represents an approximation of the configurational entropy in terms of low-dimensional integrals. It is frequently employed to compute entropies from simulation data of large systems, such as macromolecules, for which brute-force evaluation of the full configurational integral is intractable. Here, we test the validity of MIE for systems consisting of more than m = 100 degrees of freedom (dofs). The dofs are distributed according to multivariate Gaussian distributions which were generated from protein structures using a variant of the anisotropic network model...
December 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29244018/detection-of-novel-betapapillomaviruses-and-gammapapillomaviruses-in-eyebrow-hair-follicles-using-a-single-tube-hanging-droplet-pcr-assay-with-modified-pan-pv-codehop-primers
#13
Diego Chouhy, Boštjan J Kocjan, Jeannette P Staheli, Elisa M Bolatti, Lea Hošnjak, Martin Sagadin, Adriana A Giri, Timothy M Rose, Mario Poljak
A modified pan-PV consensus-degenerate hybrid oligonucleotide primer (CODEHOP) PCR was developed for generic and sensitive detection of a broad-spectrum of human papillomaviruses (HPVs) infecting the cutaneous epithelium. To test the analytical sensitivity of the assay we examined 149 eyebrow hair follicle specimens from immunocompetent male patients. HPV DNA was detected in 60 % (89/149) of analysed eyebrow samples with a total of 48 different HPV sequences, representing 21 previously described HPVs and 27 putative novel HPV types...
December 15, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/29242895/comparison-of-laboratory-developed-tests-and-fda-approved-assays-for-braf-egfr-and-kras-testing
#14
Annette S Kim, Angela N Bartley, Julia A Bridge, Suzanne Kamel-Reid, Alexander J Lazar, Neal I Lindeman, Thomas A Long, Jason D Merker, Alex J Rai, David L Rimm, Paul G Rothberg, Patricia Vasalos, Joel T Moncur
Importance: The debate about the role of the Food and Drug Administration (FDA) in the regulation of laboratory-developed tests (LDTs) has focused attention on the analytical performance of all clinical laboratory testing. This study provides data comparing the performance of LDTs and FDA-approved companion diagnostics (FDA-CDs) in proficiency testing (PT) provided by the College of American Pathologists Molecular Oncology Committee. Objective: To compare the analytical performance of LDTs and FDA-CDs on well-characterized PT samples and to compare the practice characteristics of laboratories using these assays...
December 14, 2017: JAMA Oncology
https://www.readbyqxmd.com/read/29238334/evaluation-of-bronchoalveolar-lavage-fluid-cytokines-as-biomarkers-for-invasive-pulmonary-aspergillosis-in-at-risk-patients
#15
Samuel M Gonçalves, Katrien Lagrou, Cláudia S Rodrigues, Cláudia F Campos, Leticia Bernal-Martínez, Fernando Rodrigues, Ricardo Silvestre, Laura Alcazar-Fuoli, Johan A Maertens, Cristina Cunha, Agostinho Carvalho
Background: Invasive pulmonary aspergillosis (IPA) is an infection that primarily affects immunocompromised hosts, including hematological patients and stem-cell transplant recipients. The diagnosis of IPA remains challenging, making desirable the availability of new specific biomarkers. High-throughput methods now allow us to interrogate the immune system for multiple markers of inflammation with enhanced resolution. Methods: To determine whether a signature of alveolar cytokines could be associated with the development of IPA and used as a diagnostic biomarker, we performed a nested case-control study involving 113 patients at-risk...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29237714/digital-pcr-a-sensitive-and-precise-method-for-kit-d816v-quantification-in-mastocytosis
#16
Georg Greiner, Michael Gurbisz, Franz Ratzinger, Nadine Witzeneder, Ingrid Simonitsch-Klupp, Gerlinde Mitterbauer-Hohendanner, Matthias Mayerhofer, Leonhard Müllauer, Wolfgang R Sperr, Peter Valent, Gregor Hoermann
BACKGROUND: The analytically sensitive detection of KIT D816V in blood and bone marrow is important for diagnosing systemic mastocytosis (SM). Additionally, precise quantification of the KIT D816V variant allele fraction (VAF) is relevant clinically because it helps to predict multilineage involvement and prognosis in cases of advanced SM. Digital PCR (dPCR) is a promising new method for sensitive detection and accurate quantification of somatic mutations. METHODS: We performed a validation study of dPCR for KIT D816V on 302 peripheral blood and bone marrow samples from 156 patients with mastocytosis for comparison with melting curve analysis after peptide nucleic acid-mediated PCR clamping (clamp-PCR) and allele-specific quantitative real-time PCR (qPCR)...
December 13, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/29235198/substrate-interaction-defects-in-histidyl-trna-synthetase-linked-to-dominant-axonal-peripheral-neuropathy
#17
Jamie A Abbott, Rebecca Meyer-Schuman, Vincenzo Lupo, Shawna Feely, Inès Mademan, Stephanie N Oprescu, Laurie B Griffin, M Antonia Alberti, Carlos Casasnovas, Sharon Aharoni, Lina Basel-Vanagaite, Stephan Züchner, Peter De Jonghe, Jonathan Baets, Michael E Shy, Carmen Espinós, Borries Demeler, Anthony Antonellis, Christopher Francklyn
Histidyl-tRNA synthetase (HARS) ligates histidine to cognate tRNA molecules, which is required for protein translation. Mutations in HARS cause the dominant axonal peripheral neuropathy Charcot Marie-Tooth disease type 2W (CMT2W); however, the precise molecular mechanism remains undefined. Here, we investigated three HARS missense mutations associated with CMT2W (p.Tyr330Cys, p.Ser356Asn, and p.Val155Gly). The three mutations localize to the HARS catalytic domain and failed to complement deletion of the yeast ortholog (HTS1)...
December 12, 2017: Human Mutation
https://www.readbyqxmd.com/read/29232607/simultaneous-uplc-ms-ms-analysis-of-two-stable-isotope-labeled-versions-of-sucrose-in-mouse-plasma-and-brain-samples-as-markers-of-blood-brain-barrier-permeability-and-brain-vascular-space
#18
Ekram Ahmed Chowdhury, Faleh Alqahtani, Raktima Bhattacharya, Reza Mehvar, Ulrich Bickel
Blood Brain Barrier (BBB) permeability is frequently compromised in the course of diseases affecting the central nervous system (CNS). Sucrose is a low molecular weight, hydrophilic marker with slow permeability at the naive BBB and therefore one of the widely used indicators of barrier integrity. Our laboratory recently developed a highly sensitive UPLC-MS/MS method for stable isotope labeled [13C12]sucrose in biological matrices. Correction of total brain concentration for contribution of intravascular space is required in such experiments in order to accurately measure BBB permeability, and it is often accomplished by vascular perfusion with buffer solutions prior to brain sampling...
December 6, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29228562/clinical-mutational-profiling-of-1006-lung-cancers-by-next-generation-sequencing
#19
Peter B Illei, Deborah Belchis, Li-Hui Tseng, Doreen Nguyen, Federico De Marchi, Lisa Haley, Stacy Riel, Katie Beierl, Gang Zheng, Julie R Brahmer, Frederic B Askin, Christopher D Gocke, James R Eshleman, Patrick M Forde, Ming-Tseh Lin
Analysis of lung adenocarcinomas for actionable mutations has become standard of care. Here, we report our experience using next generation sequencing (NGS) to examine AKT1, BRAF, EGFR, ERBB2, KRAS, NRAS, and PIK3CA genes in 1006 non-small cell lung cancers in a clinical diagnostic setting. NGS demonstrated high sensitivity. Among 760 mutations detected, the variant allele frequency (VAF) was 2-5% in 33 (4.3%) mutations and 2-10% in 101 (13%) mutations. A single bioinformatics pipeline using Torrent Variant Caller, however, missed a variety of EGFR mutations...
November 14, 2017: Oncotarget
https://www.readbyqxmd.com/read/29225697/comparative-evaluation-of-populus-variants-total-sugar-release-and-structural-features-following-pretreatment-and-digestion-by-two-distinct-biological-systems
#20
Vanessa A Thomas, Ninad Kothari, Samarthya Bhagia, Hannah Akinosho, Mi Li, Yunqiao Pu, Chang Geun Yoo, Sivakumar Pattathil, Michael G Hahn, Arthur J Raguaskas, Charles E Wyman, Rajeev Kumar
Background: Populus natural variants have been shown to realize a broad range of sugar yields during saccharification, however, the structural features responsible for higher sugar release from natural variants are not clear. In addition, the sugar release patterns resulting from digestion with two distinct biological systems, fungal enzymes and Clostridium thermocellum, have yet to be evaluated and compared. This study evaluates the effect of structural features of three natural variant Populus lines, which includes the line BESC standard, with respect to the overall process of sugar release for two different biological systems...
2017: Biotechnology for Biofuels
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