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L1s are repetitive sequences capable of copying themselves into new genomic loci. While L1s are typically repressed by DNA methylation in somatic tissues, they can become reactivated in cancer. Although L1 sequences are highly repetitive, …
Read PDFIdentifying the genetic relatedness of resistant bacterial pathogens in healthcare settings can help identify undetected transmission events and outbreaks. However, current methods are time- and resource-intensive. We evaluated a rapid neighbor typing method paired with …
Read PDFMultidrug-resistant <i>Salmonella</i> has been classified as a pathogen of high priority. However, limited or mixed-quality studies reported multidrug-resistant <i>Salmonella</i> strains from pediatric patients. The study aimed to investigate the prevalence, serotypes, antimicrobial characteristics, and plasmid …
Read PDFRecent advances in bioinstrumentation, such as the development of long-read sequencing, have reignited interest in methods for extracting long, intact nucleic acids from complex samples. One traditional method for this purpose is gel electrophoresis followed …
Read PDFAmerican sloughgrass [Beckmannia syzigachne (Steud.) Fernald] is a problematic annual grass weed in winter wheat fields of China, which causes great loss of wheat yield. A lack of high-quality genome resources has hindered understanding of …
Read PDF<b>Background/Objectives</b>: The Korean Global Antimicrobial Resistance Surveillance System monitors bloodstream <i>Staphylococcus aureus</i> infections by combining antimicrobial susceptibility testing (AST) with conventional polymerase chain reaction (PCR). Considering the clinical significance of methicillin-resistant <i>S. aureus</i> (MRSA), we …
Read PDFThis study presents the first complete mitochondrial genome of <i>Ferula sinkiangensis</i>, a medicinal plant formally recognized in the Chinese Pharmacopoeia since 1977. The assembled mitogenome is 416,958 bp in length, encoding 97 genes, and exhibits …
Read PDFCYP2C19 and CYP2D6 are involved in the hepatic metabolism of approximately 35-40% of clinically used drugs. We conducted an in vivo phenotyping study encompassing 114 Estonian Biobank participants to evaluate the functional impact of rare …
Read PDFTransposable element (TE) variants, the presence or absence of TE sequences such as LINE-1, Alu, SVA, and endogenous retroviruses, are a major source of genomic diversity and play critical roles in human health, evolution, and …
Read PDFBalanced chromosomal rearrangements (BCRs) refer to a type of chromosomal structural variations without chromosomal gains or losses. BCR carriers may experience fertility issues, including a higher risk of infertility, recurrent miscarriages, or having offspring with …
Read PDFDNA conformation may deviate from the classical B-form in ∼13% of the human genome. Non-B DNA regulates many cellular processes; however, its effects on DNA polymerization speed and accuracy have not been investigated genome-wide. Such …
Read PDFComprehensive genomic analysis is essential for advancing our understanding of human genetics and disease. However, short-read sequencing technologies are inherently limited in their ability to resolve highly repetitive, structurally complex, and low-mappability genomic regions, previously …
Read PDFWe present a comprehensive molecular and histopathological characterization of nine patients with mitochondrial myopathy, predominantly manifesting progressive external ophthalmoplegia (PEO), associated with heteroplasmic variants in mitochondrial tRNA genes (mt-tRNA). Among the ten variants identified, four …
Read PDF<h4>Background</h4>The persistent HIV-1 reservoir remains a major barrier to curing HIV-1, underscoring the need for a detailed understanding of its composition to inform targeted interventions.<h4>Methods</h4>Here, we apply the HIV Proviral Unique molecular identifier-mediated Long-read Sequencing …
Read PDFRecombinant adeno-associated virus (rAAVs) vectors are the flagship vehicles for delivering DNA payloads for human gene therapy. However, only a few outstanding therapies have reached the market in the past decade. One reason for the …
Read PDFStructural variants (SVs) are a major type of genetic variation, yet their role in human traits remains largely uncharacterized, primarily due to challenges in genotyping them on a genome-wide scale in large cohorts. Here we …
Read PDFLeveraging new sequencing and omic technologies to enhance the detection of pathogenic variants in known disease genes is a key step toward increasing the likelihood of a precise genetic diagnosis for affected individuals. Short-read sequencing …
Read PDFThe long-read sequencers from Pacific Bioscience (PacBio) and Oxford Nanopore Technologies (ONT) offer the opportunity to phase mutations multiple kilobases apart directly from sequencing reads. In this study, we used long-range PCR with ONT and …
Read PDF<i>Escherichia coli</i> ST131 is a clinical challenge due to its multidrug resistant profile and successful global spread. They are often associated with complicated infections, particularly urinary tract infections (UTIs). Bacteriocins play an important role to …
Read PDFNuclear-embedded mitochondrial DNA segments (NUMT) preserve a record of ongoing mitochondrial-to-nuclear DNA transfer during evolution, with important implications for disease mechanisms and genome organization. Here, we develop a pangenome graph-based NUMT detection approach, achieving a …
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