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Nasopharyngeal carcinoma (NPC) is prevalent in Southeast Asia, particularly in Indonesia. Despite advances in treatment, patients with advanced NPC face poor outcomes. Examining the NPC mutational landscape is crucial for understanding its biology and enable …
Read PDF<h4>Background</h4>The gene C9orf72 harbors a non-coding hexanucleotide repeat expansion known to cause amyotrophic lateral sclerosis and frontotemporal dementia. While previous studies have estimated the length of this repeat expansion in multiple tissues, technological limitations have …
Read PDFAll forms of genetic variation originate from new mutations, making it crucial to understand their rates and mechanisms. Here, we use long-read sequencing from Pacific Biosciences (PacBio) to investigate de novo mutations that accumulated in …
Read PDFThe characterization of soil mite (Acari) communities traditionally follows morphological identifications of specimens extracted from soil, which is a highly laborious and time-consuming process. Metabarcoding has become an increasingly utilized approach for species identification from …
Read PDFLake Balaton, a large shallow freshwater lake in Hungary, exhibits diverse bacterioplankton communities influenced by various environmental factors. This study aims to evaluate the bacterial diversity in Lake Balaton using the long-read approach to 16 …
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Read PDFSporothrix spp. are dimorphic fungi capable of undergoing morphological changes in response to temperature variations. The genus Sporothrix includes the species S. schenckii sensu stricto, S. brasiliensis, S. globosa, and S. luriei that cause sporotrichosis, …
Read PDF<h4>Purpose</h4>Recent improvements in Nanopore sequencing chemistry has made it a promising platform for long-read 16S rRNA sequencing. This study evaluated its clinical utility in a nationwide collaboration coordinated by Genomic Medicine Sweden.<h4>Methods</h4>Thirteen mock samples comprised …
Read PDFAccurate detection of somatic structural variants (SVs) and somatic copy number aberrations (SCNAs) is critical to study the mutational processes underpinning cancer evolution. Here we describe SAVANA, an algorithm designed to detect somatic SVs and …
Read PDFLong-read sequencing (LRS) technologies have revolutionized transcriptomic research by enabling the comprehensive sequencing of full-length transcripts. Using these technologies, researchers have reported tens of thousands of novel transcripts, even in well-annotated genomes, while developing new …
Read PDF<h4>Background</h4>Congenital adrenal hyperplasia (CAH) is an autosomal recessive disorder primarily caused by defects in adrenal steroidogenesis. Conventional genetic methods struggle to resolve complex structural variations and pseudogene interference in key genes like <i>CYP21A2</i>. Our study …
Read PDFHuman papillomaviral (HPV) integrations into host human genome, a frequently observed event in HPV associated cervical cancer, are currently mapped through expensive Whole Genome sequencing (WGS) or RNA sequencing (RNA-seq) methodologies. This study aims to …
Read PDFFamilial Adult Myoclonic Epilepsy type 3 (FAME3) is a rare autosomal dominant disorder characterized by cortical tremor and epilepsy, caused by a noncoding pentanucleotide repeat expansion (TTTTA/TTTCA)<sub>n</sub> in the MARCHF6 gene. Conventional genetic testing often …
Read PDF<h4>Objective</h4>The hereditary spastic-ataxia spectrum disorders are a group of disabling neurological diseases. The traditional genetic testing pathway is complex, multistep and leaves many cases unsolved. We aim to streamline and improve this process using long-read …
Read PDFComparative genomic studies of Marek's disease virus (MDV) have suggested that attenuated and virulent strains share >98% sequence identity. However, these estimates fail to account for variation in regions of the MDV genome harboring tandem …
Read PDF<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 PDFHere, we present a protocol that identifies and classifies structurally diverse variants of msp1, msp2, glurp, and csp in Plasmodium falciparum using an amplicon-based long-read sequencing platform. We describe steps for PCR barcoding, PacBio circular …
Read PDF<h4>Background</h4>Adrenocortical hyperplasia is an autosomal recessive disorder characterized by congenital metabolic dysfunction, resulting in endocrine disturbances and abnormal sexual development (such as female masculinity), requiring lifelong hormonal therapy. Notably, non-classical congenital adrenal hyperplasia (NCCAH) exhibits …
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 PDFWith the increasing interest in whole genome sequencing of eukaryotes, it is becoming evident that selecting the most suitable high molecular weight DNA extraction method is crucial for maximizing the benefits of long-read technologies. However, …
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