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Multiple primary cancers (MPC) refer to the occurrence of two or more independent primary malignant tumors in the same patient, either simultaneously or metachronously. Their clinical diagnosis and differential diagnosis are challenging, treatment strategies are …
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Read PDFNucleotide sequences in the FASTQ or BAM format are widely shared, yet derived from platform-specific raw data outputs that differ across sequencing platforms. In Oxford Nanopore Technologies (ONT) sequencing, raw signal data contain valuable biological …
Read PDFLablab purpureus (L.) Sweet, a resilient tropical legume critical for sustainable agriculture, is prized for its adaptability, nutritional richness, and drought tolerance. Here, we present the first telomere-to-telomere (T2T) genome assembly of Lablab purpureus (L.) …
Read PDF<h4>Background</h4>Clear cell renal cell carcinoma (ccRCC) is the most common subtype of kidney cancer and is marked by pronounced intra-tumoural heterogeneity that complicates therapeutic response. Patient-derived organoids offer a physiologically relevant model to capture this …
Read PDF<h4>Background</h4>The genus <i>Betta</i> (family Osphronemidae) comprises over 70 species, many of which are endemic to Southeast Asia and highly vulnerable to habitat loss. While <i>Betta splendens</i> is well studied due to its importance in the …
Read PDF<h4>Introduction</h4>Whole genome sequencing (WGS) is a valuable tool in surveillance of antimicrobial resistance (AMR). However, the technology faces several implementation challenges in low-resource settings. While advances in Oxford Nanopore Technologies (ONT) field sequencing have enabled …
Read PDF<h4>Background and purpose</h4>Metabolic disorders, which are estimated to include approximately 1,500 distinct conditions such as urea cycle disorders, lysosomal storage diseases, and mitochondrial dysfunctions, pose a significant clinical challenge due to their genetic heterogeneity and …
Read PDFWhole-genome sequencing (WGS) is an invaluable tool that enables high-resolution genotyping to precisely identify bacterial strains. It is particularly significant for highly pathogenic bacteria such as <i>Streptococcus pneumoniae</i>, a worldwide leading cause of mortality and …
Read PDFNanopore sequencing enables real-time, long-read analysis by processing raw signals as they are produced. A key step, segmentation of signals into events, is typically handled algorithmically, struggling in noisy regions. We present Campolina, a first …
Read PDF<h4>Background</h4>Nanopore sequencing is currently one of the leading third-generation sequencing technologies on the market and is gaining popularity among researchers. Due to its long-read capabilities, full-length 16S rRNA gene metabarcoding using Oxford Nanopore Technologies (ONT) …
Read PDFIn recent years, the field of shotgun metagenomics has witnessed remarkable advancements, primarily driven by the development and refinement of next-generation sequencing technologies, particularly long-read sequencing platforms such as Nanopore and PacBio. These platforms have …
Read PDFMicrobial cell-free DNA (mcfDNA) enables rapid and sensitive pathogen detection via direct plasma-sequencing. Here, we present a fast, cost-effective mcfDNA multiplex workflow to complement or improve the sensitivity of microbiological diagnostics for systemic and focal …
Read PDF<h4>Background</h4>Over the years, there has been growing interest in epigenetics, where nucleotide modifications are increasingly recognized for their roles in health and disease. Understanding methylation patterns at the nucleotide level has become pivotal for advancing …
Read PDFThe vaginal microbiota is a dynamic ecosystem that plays a central role in women's reproductive health, with Lactobacillus species typically dominating in healthy individuals. Disruptions to this microbiota can lead to dysbiosis, increasing susceptibility to …
Read PDFHuman papillomavirus 16 (HPV16) drives precursor cervical lesions that often progress to cervical cancer (CC). Variation within the HPV16 genome has been associated with CC risk. Here, we developed an affordable and portable amplicon-based long-read …
Read PDF<b>Objectives.</b> <i>Vibrio cholerae</i> remains a significant public health threat in Africa, with antimicrobial resistance (AMR) complicating treatment. This study leverages whole-genome sequencing (WGS) of <i>V. cholerae</i> isolates from Côte d'Ivoire, Ghana, Zambia and South Africa …
Read PDFNanoPrePro is a streamlined read preprocessor specifically designed for high precision in identifying full-length reads from Oxford Nanopore Technology (ONT) transcriptomic sequencing results, achieved through the precise identification of adapters/primers. However, the preprocessing of ONT …
Read PDFCarpoglyphus lactis is a globally distributed stored-product pest mite that inflicts substantial damage on dried fruits, grains, and other preserved commodities. However, the absence of high-quality genomic resources has long constrained insights into its biology …
Read PDFOxford Nanopore Technologies (ONT) stands at the forefront of third-generation sequencing, utilizing a nanopore sequencing approach to achieve high-throughput DNA and RNA sequencing. This technology offers several key advantages, including real-time data generation, portability, and …
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