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<h4>Background</h4>Long-read sequencing technologies enable resolution of structural variants (SV) and long-range genome assembly, but require high molecular weight (HMW) DNA of both high quantity and quality to produce optimal sequencing results. New DNA extraction methods …
Read PDFAcartia tonsa is a calanoid copepod with a cosmopolitan distribution. Its ecological relevance makes it a useful bioindicator organism for assessing the toxicity of various compounds. However, transcriptomic assemblies of A. tonsa using long-read technologies …
Read PDFApproximately half of high-grade serous ovarian carcinomas (HGSOCs) demonstrate homologous recombination deficiency (HRD) with characteristic genomic rearrangements. However, the impact of HRD on centromeres and transposable elements remains largely unexplored in HGSOC since conventional short-read …
Read PDFThe encyrtid wasp <i>Ixodiphagus hookeri</i> (Hymenoptera: Encyrtidae) predates on a broad range of tick species, including the important disease vectors of the <i>Ixodes ricinus</i> complex. This wasp is a promising candidate for the biological control …
Read PDF<h4>Objective</h4>Variants in PRKN and PINK1 are the leading cause of early-onset autosomal recessive Parkinson's disease, yet many cases remain genetically unresolved. We previously identified a 7 megabases complex structural variant in a pair of monozygotic …
Read PDFThe human Killer cell Immunoglobulin-like Receptor (KIR) genes, found on chromosome 19, encode for cell surface protein receptors that, through interaction with their ligand, modulate the action of Natural Killer (NK) cells and some subsets …
Read PDFThough short read high-throughput sequencing, commonly known as Next-Generation Sequencing (NGS), has revolutionized genomics and genetic testing, there is no single genetic test that can accurately detect single nucleotide variants (SNVs), small insertions/deletions (indels), complex …
Read PDFOne of the challenges in clinical genetics for rare diseases and personalized medicine is evaluating isoform alterations arising from heterozygous putative splicing variants at the allele level. Our aim was to analyze these variants by …
Read PDFCancer initiation occurs when a cell acquires and accumulates mutations in genes involved in the regulation of cell processes: each cell division throughout a person's life introduces novel mutations in the cells' DNA and under …
Read PDF<h4>Background</h4>Imprinted genes are expressed in a parental-origin-specific manner. The imprinted regions including imprinted genes have differentially methylated regions (DMRs) with different 5-methylcytosine (5mC) patterns for CpGs on each parental allele, and DMRs function as imprinting …
Read PDFThe emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the terrestrial microbial genome catalogue has been challenging due to the enormous complexity of these …
Read PDFHigh-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with the complete genome reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing …
Read PDF<h4>Background</h4>Coffin-Siris Syndrome 8 (CSS8; MIM# 618362) is a rare neurodevelopmental disorder caused by heterozygous variants in the SMARCC2 gene. Patients with CSS8 present with variable phenotypic presentations, with speech abnormalities, behavioral issues, hypotonia, and dysmorphic …
Read PDFWe present a comprehensive gene fusion (GF) detection and analysis workflow that combines targeted panel-based and whole-transcriptome long-read sequencing. We first adapted libraries from the short-read CHOP Cancer Fusion Panel, which targets 119 oncogenes commonly …
Read PDF<h4>Background</h4>Non-invasive urine tests for bladder cancer (BC) could reduce dependence on flexible cystoscopy for diagnosis and surveillance. Most recent developments in urine testing are based on targeted detection of genomic and/or epigenomic markers. We hypothesised …
Read PDF<h4>Purpose</h4>To investigate the sensitivity and specificity of herpes virus detection by nanopore metagenomic analysis (NMA) compared with multiplex polymerase chain reaction (mPCR)-positive and -negative controls.<h4>Methods</h4>This study included 43 patients with uveitis who had been screened …
Read PDF<i>Achillea</i> species, commonly referred to as yarrow, belong to the family Asteraceae and are typically perennial, outbreeding plants used in traditional medicine. The genus <i>Achillea</i> has undergone hybridization and polyploidization events, resulting in phylogenetically complex …
Read PDFFriedreich's ataxia (FRDA) is an autosomal recessive neurodegenerative disorder characterized by ataxia, sensory loss and pyramidal signs. While the majority of FRDA cases are caused by biallelic GAA trinucleotide repeat expansions in intron 1 of …
Read PDF<h4>Background</h4>Even though alternative RNA splicing was discovered nearly 50 years ago (1977), we still understand very little about most isoforms arising from a single gene, including in which tissues they are expressed and if their …
Read PDFHepatitis 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, …
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