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CpG methylation, a key epigenetic mark involved in gene regulation, development, and other biological processes, is commonly analyzed using Whole-Genome Bisulfite Sequencing (WGBS). However, bisulfite treatment causes significant DNA degradation. Enzymatic Methyl-seq (EM-seq) offers a …
Read PDFThe evolution of the virulence and antibiotic resistance of staphylococci, important opportunistic pathogens, is strongly determined by their mobilome, which can spread by phage virions or small-headed particles resulting from the hijacking of helper phage …
Read PDF<h4>Background</h4>A subset of developmental disorders (DD) is characterized by disease-specific genome-wide methylation changes. These episignatures inform on the underlying pathogenic mechanisms and can be used to assess the pathogenicity of genomic variants as well as …
Read PDFBrain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in …
Read PDF<h4>Background</h4>Despite the widespread use of Multiplex Ligation-dependent Probe Amplification (MLPA) and Next-Generation Sequencing (NGS) in Duchenne/Becker Muscular Dystrophy (DMD/BMD), these methods have limitations when dealing with complex genetic backgrounds. Long-Read Sequencing (LRS), an emerging technology …
Read PDFNOD-like receptors (NLRs) are intracellular immune receptors that detect pathogen-associated cues and trigger defence mechanisms, including regulated cell death. In filamentous fungi, some NLRs mediate heterokaryon incompatibility, a self-/non-self-recognition process that prevents the vegetative fusion …
Read PDFThe effects of sample multiplexing on the detection sensitivity of antimicrobial resistance genes (ARGs) and pathogenic bacteria in metagenomic sequencing remain underexplored in newer sequencing technologies such as Oxford Nanopore Technologies (ONT), despite its critical …
Read PDFA requirement of any foodborne pathogen testing method is that it only detects live bacteria. Ethidium monoazide (EMA) and propidium monoazide (PMA) are dyes that penetrate the membranes of dead cells and form cross-linkages in …
Read PDF<h4>Purpose</h4>The purpose is to develop a preimplantation genetic testing (PGT) method for α-thalassemia in one reaction, without requiring a proband, using targeted long-range polymerase chain reaction (LR-PCR) followed by long-read sequencing (LRS).<h4>Methods</h4>We developed a targeted …
Read PDF<h4>Background</h4>In the context of increasing antimicrobial resistance (AMR), whole-genome sequencing (WGS) of bacteria is considered a highly accurate and comprehensive surveillance method for detecting and tracking the spread of resistant pathogens. Two primary sequencing technologies …
Read PDFMultiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system (CNS), characterized by neuroinflammation and neurodegeneration. Emerging evidence links gut microbiota dysbiosis to immune dysregulation and MS progression. While extensive research has …
Read PDFCRISPR/Cas9 genome editing holds promise for precise genetic modifications, yet off-target effects remain a concern-particularly in gene families with high sequence similarity. In this study, we present a computational framework for analyzing editing specificity and …
Read PDFOxford Nanopore Technologies (ONT) long-read sequencing (LRS) has emerged as a promising genomic analysis tool, yet comprehensive benchmarks with established platforms across diverse datasets remain limited. This study aimed to benchmark LRS performance against Illumina …
Read PDF<h4>Background</h4>Multidrug-resistant organisms (MDRO) pose a significant threat to public health worldwide. The ability to identify antimicrobial resistance determinants, to assess changes in molecular types, and to detect transmission are essential for surveillance and infection prevention …
Read PDFWith ongoing improvements in the detection of complex genomic and epigenomic variations, long-read sequencing (LRS) technologies could serve as a unified platform for clinical genetic testing, particularly in rare disease settings, where nearly half of …
Read PDFChinese red steppe cattle, a highly developed breed for their meat and milk, are not well known about the formation mechanisms for high-quality beef. Furthermore, many fundamental investigations of cattle are hampered by deficient full-length …
Read PDF<h4>Motivation</h4>Quality control of sequencing data is the first step in many sequencing workflows. Short- and long-read sequencing technologies have many commonalities with regard to quality control. Several quality control programs exist; however, none possess a …
Read PDFLong-read sequencing (LRS) was introduced as the third generation of next-generation sequencing technologies with a high accuracy rate in genomic variant identification for some of its platforms. Due to the structural complexity of many pharmacogenes, …
Read PDF<h4>Background</h4>Increasing resistance to broad-spectrum beta-lactams and carbapenems is a significant concern in healthcare settings. This study aimed to determine the prevalence of intestinal carriage of extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant Enterobacterales (CRE) in a tertiary …
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