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Filename: drivers/Session_files_driver.php
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Function: strpos
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Robust clinical specimen nucleic acid extraction instrumentation and methods are critical to the performance of downstream molecular diagnostics for the diagnosis of drug-resistant tuberculosis (DR-TB). Currently, there is a high level of interest in sequencing-based solutions for rapid and comprehensive DR-TB testing from primary specimens (i.e., sputum). However, there is no standardized or fully automated sputum extraction system that has been widely implemented for use with Mycobacterium tuberculosis complex-containing sputum specimens. For sequencing-based technologies to be widely adopted in clinical laboratory settings in low- and middle-income countries, automated extraction technologies will be important to enhance scalability and reliability and to standardize performance of the downstream assays. Additionally, the ease of automatic technologies allows for faster uptake in laboratories currently without the expertise or infrastructure to perform manual extractions at the same automated throughput. This work is intended to provide an initial specification comparison of available automated DNA extraction systems that could serve as front-end components for existing and future sequencing approaches and provide the framework for future evaluations.
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http://dx.doi.org/10.1016/j.diagmicrobio.2020.115096 | DOI Listing |
Cell Genom
December 2024
Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA; Cancer Early Detection Advanced Research Institute, Oregon Health & Science University, Portland, OR, USA; Knight Cardiovascular Institute, Oregon Health & Science University, Portland, OR, USA; Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA. Electronic address:
Single-cell methods to assess DNA methylation have not achieved the same level of cell throughput per experiment compared to other modalities, with large-scale datasets requiring extensive automation, time, and other resources. Here, we describe sciMETv3, a combinatorial indexing-based technique that enables atlas-scale libraries to be produced in a single experiment. To reduce the sequencing burden, we demonstrate the compatibility of sciMETv3 with capture techniques to enrich regulatory regions, as well as the ability to leverage enzymatic conversion, which can yield higher library diversity.
View Article and Find Full Text PDFOphthalmology
December 2024
John P. Hussman Institute for Human Genomics, University of Miami, FL; Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, FL.
Purpose: To investigate the association between epigenetic age acceleration and glaucoma progression.
Design: Retrospective cohort study.
Participants: 100 primary open-angle glaucoma (POAG) patients with fast progression and 100 POAG patients with slow progression.
Malar J
December 2024
Institute of Tropical Medicine, Eberhard Karls University of Tübingen, Tübingen, Germany.
Background: Molecular methods play an important role in clinical trials assessing anti-malarial drugs and vaccines, as well as in epidemiological studies aimed at detecting Plasmodium species, especially when dealing with large sample sizes. Molecular techniques are more sensitive and generally have a higher throughput compared to the gold standard microscopy. Further optimization can be achieved with automation of nucleic acid isolation, allowing for rapid and precise extraction.
View Article and Find Full Text PDFJ Am Soc Mass Spectrom
December 2024
Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, 6020 Innsbruck, Austria.
Top-down mass spectrometry (MS) enables comprehensive characterization of modified proteins and nucleic acids and, when native electrospray ionization (ESI) is used, binding site mapping of their complexes with native or therapeutic ligands. However, the high complexity of top-down MS spectra poses a serious challenge to both manual and automated data interpretation, even when the protein, RNA, or DNA sequence and the type of modification or the ligand are known. Here, we introduce FAST MS, a user-friendly software that identifies, assigns and relatively quantifies signals of molecular and fragment ions in MS and MS/MS spectra of biopolymers with known sequence and provides a toolbox for statistical analysis.
View Article and Find Full Text PDFJ Pathol
December 2024
Department of Pathology and Molecular Pathology, University Hospital and University of Zurich, Zurich, Switzerland.
Tumour content plays a pivotal role in directing the bioinformatic analysis of molecular profiles such as copy number variation (CNV). In clinical application, tumour purity estimation (TPE) is achieved either through visual pathological review [conventional pathology (CP)] or the deconvolution of molecular data. While CP provides a direct measurement, it demonstrates modest reproducibility and lacks standardisation.
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