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Cancer is a multifaceted disease arising from numerous genomic aberrations that have been identified as a result of advancements in sequencing technologies. While next-generation sequencing (NGS), which uses short reads, has transformed cancer research and …
Read PDFStructural variations (SV) are common in the cancer genome and play critical roles in regulating tumorigenesis. In the past decades, many SVs have been detected through analyses of whole-genome sequencing (WGS) data generated mainly by …
Read PDFCpG 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 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 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 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 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 PDFNasopharyngeal carcinoma (NPC) is prevalent in Southeast Asia, particularly in Indonesia. Despite advances in treatment, patients with advanced NPC face poor outcomes. Examining the NPC mutational landscape is crucial for understanding its biology and enable …
Read PDFLake Balaton, a large shallow freshwater lake in Hungary, exhibits diverse bacterioplankton communities influenced by various environmental factors. This study aims to evaluate the bacterial diversity in Lake Balaton using the long-read approach to 16 …
Read PDFSporothrix spp. are dimorphic fungi capable of undergoing morphological changes in response to temperature variations. The genus Sporothrix includes the species S. schenckii sensu stricto, S. brasiliensis, S. globosa, and S. luriei that cause sporotrichosis, …
Read PDF<h4>Purpose</h4>Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.<h4>Methods</h4>Thirteen mock samples comprised …
Read PDFAccurate detection of somatic structural variants (SVs) and somatic copy number aberrations (SCNAs) is critical to study the mutational processes underpinning cancer evolution. Here we describe SAVANA, an algorithm designed to detect somatic SVs and …
Read PDF<h4>Background</h4>Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder with characteristic clinical features such as overgrowth and macroglossia. Hypermethylation of the H19/IGF2:IG-differentially methylated region (H19-DMR) is identified in 5% of BWS patients. Although defects in the OCT4/SOX2 …
Read PDFHuman papillomaviral (HPV) integrations into host human genome, a frequently observed event in HPV associated cervical cancer, are currently mapped through expensive Whole Genome sequencing (WGS) or RNA sequencing (RNA-seq) methodologies. This study aims to …
Read PDF<h4>Objective</h4>The hereditary spastic-ataxia spectrum disorders are a group of disabling neurological diseases. The traditional genetic testing pathway is complex, multistep and leaves many cases unsolved. We aim to streamline and improve this process using long-read …
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