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Foodborne pathogens are a significant cause of illness, and infection with Shiga toxin-producing <i>Escherichia coli</i> (STEC) may lead to life-threatening complications. The current methods to identify STEC in meat involve culture-based, molecular, and proteomic assays …
Read PDFLong-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, …
Read PDFMassive parallel sequencing methods, such as exome, genome, and targeted DNA sequencing, have aided molecular diagnosis of genetic diseases in the last 20 years. However, short-read sequencing methods still have several limitations, such inaccurate genome …
Read PDFTelomere length is an important biomarker of organismal aging and cellular replicative potential, but existing measurement methods are limited in resolution and accuracy. Here, we deploy digital telomere measurement (DTM) by nanopore sequencing to understand …
Read PDFThe B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) <i>ETV6::RUNX1</i> translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, …
Read PDFCopy number variations (CNVs) play pivotal roles in disease susceptibility and have been intensively investigated in human disease studies. Long-read sequencing technologies offer opportunities for comprehensive structural variation (SV) detection, and numerous methodologies have been …
Read PDF<h4>Background</h4>Protein-coding genes have been considered the functional part of the genome, although they represent only 2% of the genome. In contrast, more than 90% of the genome produces non-coding RNA (ncRNA), including antisense (AS) genes, …
Read PDFThe study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read …
Read PDFDuring the COVID-19 pandemic, the monitoring of SARS-CoV-2 RNA in wastewater was used to track the evolution and emergence of variant lineages and gauge infection levels in the community, informing appropriate public health responses without …
Read PDF<h4>Summary</h4>The revised WHO guidelines for classifying and grading brain tumors include several copy number variation (CNV) markers. The turnaround time for detecting CNVs and alterations throughout the entire genome is drastically reduced with the customized …
Read PDF<h4>Objective</h4>Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore …
Read PDFThe Long-Read Personalized OncoGenomics (POG) dataset comprises a cohort of 189 patient tumors and 41 matched normal samples sequenced using the Oxford Nanopore Technologies PromethION platform. This dataset from the POG program and the Marathon …
Read PDFCircular extrachromosomal DNA (ecDNA) is a form of oncogene amplification found across cancer types and associated with poor outcome in patients. ecDNA can be structurally complex and can contain rearranged DNA sequences derived from multiple …
Read PDFTandem repeat sequences comprise approximately 8% of the human genome and are linked to more than 50 neurodegenerative disorders. Accurate characterization of disease-associated repeat loci remains resource intensive and often lacks high resolution genotype calls. …
Read PDFThe integration of long-read sequencing technology, such as nanopore sequencing technology [Oxford Nanopore Technologies (ONT)], into routine diagnostic laboratories has the potential to transform bacterial infection diagnostics and improve patient management. Analysis of amplicons from …
Read PDFSince the 1990s, the Pacific oyster <i>Magallana gigas</i> has faced significant mortality, which has been associated with the detection of the Ostreid Herpesvirus type 1 (OsHV-1). Due to the complex genomic architecture and the presence …
Read PDFThird-generation sequencing techniques have become increasingly popular due to their capacity to produce long, high-quality reads. Effective comparative analysis across various samples and sequencing platforms is essential for understanding biological mechanisms and establishing benchmark baselines. …
Read PDFThe rapid advancement of genomic technologies has enabled the production of highly contiguous reference genomes for nonmodel organisms. However, these methods often require exceptionally fresh material containing unfragmented high-molecular-weight nucleic acids. Researchers who preserve field-collected …
Read PDF<h4>Background</h4>Long-read sequencing technology, widely used in research, is proving useful in clinical diagnosis, especially for infectious diseases. Despite recent advances, it hasn't been routinely applied to constitutional human diseases. Long-read sequencing detects intronic variants and …
Read PDFEpitranscriptomics has emerged as a rapidly evolving field that focused on studying post-transcriptional RNA modifications and their role in spatiotemporal regulation of gene expression. N6-methyladenosine (m<sup>6</sup>A) and 5-methylcytosine (m<sup>5</sup>C) represent the most extensively studied modifications …
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