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<h4>Background</h4>Hepatitis B virus (HBV) genomes integrated into human DNA significantly contribute to surface antigen (HBsAg) production and may drive hepatocellular carcinoma (HCC). Long-read sequencing methods like Nanopore offer advantages over short-read next-generation sequencing (NGS) by …
Read PDFHepatocellular carcinoma (HCC) was characterized by a highly complex genome, with structural variations (SVs) playing a significant role in its development. In this study, we employed Oxford Nanopore Technology long-read sequencing in paired tumor and …
Read PDF<h4>Background</h4>Long-read sequencing (LRS) improves genome alignment and facilitates resolving variants in genomic regions of low complexity, making it a promising approach for cancer variant detection and biomarker discovery.<h4>Results</h4>Here, we evaluate the performance of LRS using …
Read PDFDysregulation of alternative splicing - mediated by factors such as RBM20 or SLM2 - can affect proper gene isoform control, disrupting gene isoform homeostasis and underpins severe cardiomyopathy in both animal models and patients. Although …
Read PDFHereditary adult-onset ataxias are a heterogeneous group of phenotypically overlapping conditions, often caused by pathogenic expansions of short tandem repeats. Currently, 18 repeat disorders with a core phenotype of adult-onset ataxia are known. Diagnosis typically …
Read PDFLong-read sequencing improves sensitivity to discover variation in complex repetitive regions, assign parent-of-origin, and distinguish germline from postzygotic mutations. We applied Illumina, Oxford Nanopore Technologies, and PacBio sequencing to discover and validate de novo mutations …
Read PDF<h4>Purpose</h4>CD36 deficiency predisposes to fetal/neonatal alloimmune thrombocytopenia (FNAIT) and platelet transfusion refractoriness (PTR), yet its genetic architecture remains incompletely understood. In particular, the contribution of large structural variants has been difficult to assess using conventional …
Read PDFTandem repeat expansion disorders can be difficult to diagnose when expansions exceed 200 repeats, as standard methods (for example, Southern blot and modified PCR) often fail. We present a Cas9-targeted nanopore sequencing workflow and an …
Read PDFThe European brown hare (Lepus europaeus) is a declining wildlife species of ecological and epidemiological importance, yet its intestinal microbiome remains poorly characterized. Here, Oxford Nanopore long-read sequencing was used to analyse full-length 16S and …
Read PDFLong-read sequencing has enabled comprehensive exploration of human genome at an unprecedented scale, particularly enhancing our understanding of structural variants (SVs). Phasing, a powerful approach for assigning haplotypes to sequencing reads, enables the generation of …
Read PDF<h4>Background</h4>Phlebotomus chinensis is the primary vector of visceral leishmaniasis (VL) in China. However, the lack of a high-quality genome assembly for this species has limited research on its biology, vector-pathogen interactions, and evolutionary adaptations. To …
Read PDFStream-dwelling fishes face diverse hydrological pressures, making the broadly distributed <i>Opsariichthys bidens</i> an ideal model for analyzing adaptive evolution. To elucidate its adaptation to a high-dissolved-oxygen and high-flow-velocity stream environment, a high-quality genome with comprehensive …
Read PDF<h4>Motivation</h4>Long-read sequencing enables complete bacterial genome assemblies, but individual assemblers are imperfect and often produce sequence-level and structural errors. Consensus assembly using Trycycler can improve accuracy, but its lack of automation limits scalability. There is …
Read PDFThe Ural owl (Strix uralensis) is a large member of the Strigidae family and inhabits Eurasian forests from Germany to Japan. However, it faces increased range reduction, particularly at its southwestern distribution edges. Despite being …
Read PDFIndrella ampulla is a polymorphic, brightly colored, forest-dwelling land snail endemic to the Western Ghats of India. Studying and understanding evolutionary processes occurring within this species has remained a challenge largely due to a paucity …
Read PDFWe present a chromosome-level genome assembly and annotation of the hamour, or orange-spotted grouper ( <i>Epinephelus coioides</i>), a high-value and significant teleost fish species across West Indo-Pacific regions of the Middle East, South Africa, and …
Read PDFInvasive species are one of the biggest drivers of species extinction. <i>Ludwigia grandiflora</i> subsp. <i>hexapetala</i> (<i>Lgh</i>) is widely invasive in aquatic ecosystems of Europe, North America, and Japan, and also colonizes emergent freshwater soils, but …
Read PDFAccurate and complete <i>de novo</i> genome assemblies enable variant identification and the discovery of novel genomic features and biological functions. However, <i>de novo</i> assemblies of large and complex genomes remain challenging. Long-read sequencing data, alone …
Read PDF<i>Citrus</i> species are economically and nutritionally vital, with their fruits cultivated globally. Despite the publication of multiple genomes for <i>Citrus</i>, high-quality assemblies that achieve both haplotype resolution and telomere-to-telomere (HR-T2T) continuity remain scarce-pummelo (<i>Citrus maxima</i>) …
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