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<h4>Objective</h4>To evaluate the impact of discontinuing contact precautions for vancomycin-resistant enterococci (VRE) on strain and plasmid transmission using long-read whole-genome sequencing (WGS).<h4>Study design</h4>Before-after trial of adults with <i>Enterococcus</i> bloodstream infections pre-(Jan-Oct 2021) and post-(Oct-Dec 2021 …
Read PDFFacultative parthenogenesis and intrapopulation mixed ploidy (where individuals with differing ploidy exist within the same area) are rare in animals. However, these unique characteristics allow opportunities to investigate the relationship between sexual modality and genome …
Read PDFGenome sequencing (GS) has emerged as a transformative tool in the diagnosis of rare diseases with complex phenotypes. This technology uncovers structural, intronic, non-coding, and mitochondrial variants that traditional methods might miss, thereby facilitating the …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) represents a leading cause of cancer-associated deaths worldwide, and its development is strongly associated with aberrant RNA processing and metabolic reprogramming. Splicing factor 3B subunit 4 (SF3B4), the core component of the …
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Read PDF<i>Staphylococcus epidermidis</i> ATCC 12228 was sequenced using a long-read method to generate a complete genome sequence, including some plasmid sequences. Some differences from the previously generated short-read sequence of this nonpathogenic and non-biofilm-forming strain were …
Read PDFThe killer cell immunoglobulin-like receptor (KIR) region of human chromosome 19 contains up to 16 genes for natural killer (NK) cell receptors that recognize human leukocyte antigen (HLA)/peptide complexes and other ligands. The KIR proteins …
Read PDF<h4>Background</h4>Singleton short-read genome sequencing (GS) is increasingly used as a first-line genetic test for childhood neurological disorders (such as intellectual disability, neurodevelopmental delay, motor delay, and hypotonia) with diagnostic yields from 26 to 35%, typically …
Read PDF<h4>Background</h4>Integrating short- and long-read sequencing technologies has become a promising approach for achieving accurate and comprehensive genomic analysis. Although short-read sequencing (Illumina, etc.) offers high base accuracy and cost efficiency, it struggles with structural variant …
Read PDFFrontotemporal dementia represents a group of clinical syndromes characterized by progressive changes in behavior or language that are associated with frontotemporal lobe atrophy. Around 40% of FTD cases are familial, with mutations in <i>MAPT</i> representing …
Read PDFAlthough numerous algorithms have been developed to identify structural variations (SVs) in genomic sequences, there is a dearth of approaches that can be used to evaluate their results. This is significant as the accurate identification …
Read PDFSpeciation is a key driver of biodiversity and understanding its genomic underpinnings can be important for predicting and managing biodiversity. Structural variants (SVs) are large-scale (> 50 bp) changes in the genome and have been …
Read PDFConventional genome mapping-based approaches systematically overlook genetic variation, particularly in regions that substantially differ from the reference. To explore this hidden variation, here we examine unmapped and poorly mapped reads from the genomes of 640 …
Read PDFChronic kidney disease (CKD) represents a significant global health burden, with diverse etiologies and often complex clinical presentations. Among these, a notable subset of CKD patients present without a clear underlying cause despite extensive diagnostic …
Read PDFEquine Juvenile Spinocerebellar Ataxia (EJSCA) is a novel autosomal recessive neurologic disease in Quarter Horses. Affected foals display a progressive proprioceptive ataxia by 1-5 weeks of age, leading to recumbency and necessitating euthanasia. Whole genome …
Read PDFThe model woody plant <i>Populus trichocarpa</i> displays an atypical alkene-diverse wax cuticle likely driven by copy number variation (CNV) of <i>3-ketoacyl-CoA synthases</i> (<i>KCS</i>), which has been difficult to confirm with short-read assemblies. Long-read sequencing enables …
Read PDFPine siskins (Spinus pinus) are irruptive migratory songbirds of biological interest in studies of endocrine regulation, immune function, and behavioral flexibility. Here, we present a chromosome-level reference genome from a female pine siskin, assembled de …
Read PDF<i>Stutzerimonas balearica</i> strain JWOYS.421 was recovered from the shell of a Hong Kong oyster (<i>Magallana hongkongensis</i>) collected from coastal waters in Hong Kong. Its complete genome, a single circular chromosome of 4,405,581 bp (64.80% G+C), …
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