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Hepatitis B virus (HBV) integration is a key driver of hepatocellular carcinoma (HCC) occurrence and progression; however, its oncogenic mechanisms remain incompletely understood because of limitations in detection methods and sample availability. In this study, …
Read PDFLong-read sequencing boosts alternative splicing analysis but faces technical and computational barriers in single-cell and spatial settings. High Nanopore error rates compromise cell barcode and UMI recovery, while read truncation and misalignment undermine isoform quantification. …
Read PDFCritically ill pediatric patients often have genetic disorders requiring a rapid diagnosis to guide urgent care decisions. Standard genetic testing typically takes weeks and requires multiple tests. Nanopore long-read genome sequencing (LR-GS) delivers genome-wide results …
Read PDFCancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can …
Read PDF<h4>Purpose of review</h4>Long-read sequencing (LRS) has revolutionized pathogen surveillance by enabling real-time, high-fidelity genomic analysis critical for outbreak response. This review synthesizes recent breakthroughs in LRS, evaluating its impact on genomic epidemiology, metagenomics, and public …
Read PDFLong-read sequencing technologies, particularly those from Pacific Biosciences and Oxford Nanopore Technologies, are revolutionizing genome research by providing high-resolution insights into complex and repetitive regions of the human genome that were previously inaccessible. These advances …
Read PDF<h4>Background</h4>Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these …
Read PDFIncontinentia pigmenti (IP) is caused by loss-of-function variants in IKBKG, with molecular genetic diagnosis complicated by a pseudogene. We describe seven individuals from three families with IP but negative clinical genetic testing in whom long-read …
Read PDF<h4>Objective</h4>Fibroblast growth factor 12 (FGF12), a member of the fibroblast homologous factor family, plays a key role in the modulation of voltage-gated sodium (Nav) channels. Pathogenic variants in the FGF12 gene leading to a gain-of-function …
Read PDFPooled sequencing provides a rapid cost-effective approach to assess genetic variation segregating within populations of organisms. However, such studies are typically limited to single nucleotide variants and small indels (≤50 bp), and have not been …
Read PDFTemple syndrome is an imprinting disorder resulting from abnormal genomic or epigenomic aberrations of chromosome 14 including maternal uniparental disomy (matUPD), paternal deletion of 14q32, or aberrant methylation of the imprinting control regions at 14q32. …
Read PDF<h4>Background</h4>Familial adult myoclonic epilepsy (FAME), an autosomal dominant disorder, is characterized by cortical myoclonus and occasional generalized tonic-clonic seizures. To date, intronic pentanucleotide repeat expansions in at least seven genes, including SAMD12, TNRC6A, YEATS2, MARCHF6, …
Read PDFTelomeres protect chromosome ends and their length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many biological fields are interested in understanding its biological significance. Here, we …
Read PDF<h4>Abstract</h4>Hemophilia is an X-linked bleeding disorder caused by defects in the F8 or F9 genes. Given the wide variety of F8 variants, conventional genetic testing typically requires a combination of multiple methods, and detecting rearrangements …
Read PDF<h4>Background</h4>The degree to which alternative RNA splicing influences the function and structure of voltage gated calcium channel (VGCC) splice variants is poorly understood. Here we used long-read RNA-sequencing to catalog rat Cacna1e (Cav2.3) splice variants, …
Read PDF[This corrects the article DOI: 10.3389/fcimb.2025.1517208.].
Read PDFHomologous recombination rearranges genetic information during meiosis, creating new combinations of the genome while also introducing mutations, and influencing GC content. Here we report direct detection of recombination events using highly accurate long-read sequencing from …
Read PDFColorectal cancer (CRC) is driven by a complex spectrum of somatic mutations and structural variants that contribute to tumor heterogeneity and therapy resistance. In this study, we performed a comparative analysis of short-read Illumina and …
Read PDFMalcolmia littorea, a member of the family Brassicaceae, is adapted to coastal and sandy environments and has become a model in studies of reproductive barriers. However, genomic resources for the species are limited. Here, with …
Read PDF<h4>Background</h4>Upper tract urothelial carcinoma (UTUC), including renal pelvic urothelial carcinoma and ureter urothelial carcinoma, accounts for 10% of urothelial carcinoma (UC). Poorer outcomes and different genetic characteristics of UTUC were reported compared to urothelial carcinoma …
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