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Long-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 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 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 PDF5-Methylcytosine (5mC) is the most common DNA modification in the human genome. Bisulfite conversion combined with short-read sequencing captures this modification at single-nucleotide resolution but introduces PCR duplication bias and limits co-methylation analysis between distant …
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 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 PDFOptimal brain function requires that neurons carry out extensive post-transcriptional RNA processing to produce a vast diversity of transcripts. Accurate reconstruction and quantification of highly processed RNA using standard RNA sequencing approaches is challenging due …
Read PDFMeiotic crossovers rearrange existing genetic variation between homologous chromosomes, profoundly affecting genomic diversity. Crossovers are typically constrained to one to three events per chromosome pair, and their distribution is shaped by chromatin accessibility and DNA …
Read PDFAntibiotic heteroresistance, characterized by rare resistant subpopulations of bacteria within a susceptible main population, is associated with treatment failure and often caused by tandem amplification of resistance genes. Here, we investigated how the distribution of …
Read PDFLong-read sequencing methodologies provide powerful capacity to identify all types of genomic variations in a single test. Long-read platforms such as Oxford Nanopore and PacBio have the potential to revolutionize molecular diagnostics by reaching unparalleled …
Read PDFMetabarcoding is a powerful tool to simultaneously identify multiple taxa within a habitat. However, its application to host-associated microbiomes is challenged by substantial co-amplification of host DNA. Here we developed a host-exclusive primer design workflow, …
Read PDFGiven the increased predictions on interactome size and demand for protein function information, methods for detecting protein-protein interactions remain a significant development area. The all-vs.-all sequencing (AVA-Seq) method utilizes a convergent fusion plasmid design to …
Read PDFAlternative splicing (AS) is a fundamental mechanism governing transcriptomic diversity and cellular identity. Although 293T (human embryonic kidney) and A549 (human lung adenocarcinoma) cell lines are widely used, cell-type-specific splicing dynamics-including responses to receptor overexpression-remain …
Read PDF<h4>Introduction</h4>Faulty DNA repair and epigenetic regulation contribute to neurodegeneration in Alzheimer's disease. Long-read sequencing enables analysis of "dark regions" that are difficult to study via traditional sequencing methodologies.<h4>Methods</h4>Using nanopore whole-genome DNA sequencing of post mortem …
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