Search the literature by keyword, topic, or author. Filter to articles with full text available.
1062 results
We present a protocol to achieve a higher depth of long-read sequencing of region(s) of interest in potato cyst nematodes without amplification using a Cas9-based Nanopore enrichment approach. We describe steps for designing high-fidelity guide …
Read PDFOver the last decade CRISPR gene editing has been successfully used to streamline the generation of animal models for biomedical research purposes. However, one limitation to its use is the potential occurrence of on-target mutations …
Read PDF<h4>Background</h4>Fungi are talented producers of secondary metabolites with applications in the pharmaceutical and agrochemical sectors. Aspergillus wentii CBS 141173 has gathered research interest due to its ability to produce high-value norditerpenoid compounds, including anticancer molecules. …
Read PDFTandem repeats (TRs) play important roles in genomic variation and disease risk in humans. Long-read sequencing allows for the accurate characterization of TRs; however, the underlying bioinformatics perspectives remain challenging. We present <i>otter</i> and TREAT: …
Read PDFThe study of the genetic diversity and adaptation mechanisms of the Kazakh apricot (<i>Prunus armeniaca</i> L.) is essential for breeding programs and the conservation of plant genetic resources in arid environments. Despite this species' ecological …
Read PDFThe effect of periodical heatwaves and related thermal stratification in freshwater aquatic ecosystems has been a hot research issue. A large dataset of samples was generated from samples exposed to temporary thermal stratification in mesocosms …
Read PDFBiallelic variants in <i>USH2A</i> are associated with retinitis pigmentosa (RP) and Type 2 Usher Syndrome (USH2), leading to impaired vision and, additionally, hearing loss in the latter. Although the introduction of next-generation sequencing into clinical …
Read PDFThe CYP21A2 gene, mapped to the RCCX module in 6p21.3, is responsible for 21-hydroxylase deficiency (21-HD). In this work, we leveraged Oxford Nanopore Technology (ONT) Long Read sequencing (LRS) to analyze samples from an Argentinian …
Read PDFDinoflagellates are one of the largest groups of marine microalgae and exhibit diverse trophic strategies. Some dinoflagellates can produce secondary metabolites that are known to be toxic, which can lead to ecologically harmful blooms. <i>Amphidinium …
Read PDFExtrachromosomal DNA (ecDNA) is a central mechanism for focal oncogene amplification in cancer, occurring in ∼15% of early-stage cancers and ∼30% of late-stage cancers. ecDNAs drive tumor formation, evolution, and drug resistance by dynamically modulating …
Read PDFUnveiling the potential application of psychrophilic polymerases as candidates for polymerase-nanopore long-read sequencing presents a departure from conventional choices such as thermophilic <i>Bacillus</i> stearothermophilus (Bst) renowned for its limitation in temperature and mesophilic <i>Bacillus subtilis</i> …
Read PDFSomatic structural variations (SVs) represent a critical category of genomic mutations in hepatocellular carcinoma (HCC). However, the accurate identification of somatic SVs using short-read high-throughput sequencing is challenging. Here, we applied long-read nanopore sequencing and …
Read PDFInherited neurological disorders, such as spinocerebellar ataxia (SCA) and fragile X (FraX), are frequently caused by short tandem repeat (STR) expansions. The detection and assessment of STRs is important for diagnostics and prognosis. We tested …
Read PDFLong read sequencing has been widely used to detect structure variations that are not captured by short read sequencing in plant genomic research. In this study, we described an analysis of whole genome re-sequencing of …
Read PDF<h4>Background</h4>Genetic variations linked to changes in gene expression are known as expression quantitative loci (eQTLs). The identification of eQTLs helps to understand the mechanisms governing gene expression. However, prior studies have primarily utilized short-read sequencing …
Read PDFMost microorganisms cannot be cultured in isolation, necessitating sophisticated methods for studying their (eco)physiology. While numerous approaches can probe the activity of given microbes in enrichment cultures, no single technique can render simultaneous data on …
Read PDF<h4>Background</h4>The complex 2 Mb survival motor neuron (SMN) locus on chromosome 5q13, including the spinal muscular atrophy (SMA)-causing gene SMN1 and modifier SMN2, remains incompletely resolved due to numerous segmental duplications. Variation in SMN2 copy …
Read PDF<h4>Introduction</h4>Long-read sequencing (LRS) enables accurate structural variant detection and variant phasing. When a molecular diagnosis is suspected, target enrichment can reduce the cost and duration of sequencing.<h4>Methods</h4>LRS was conducted in five inherited retinal dystrophy (IRD) …
Read PDFWhile several well-established quality control (QC) tools exist for short-read sequencing data, there is a general paucity of computational tools that efficiently deliver comprehensive metrics across a wide range of long-read sequencing data formats, such …
Read PDFThe loading capacity of adeno-associated virus (AAV) vectors is reportedly 4.7-5.0 kb, which limits the size of genes that can be treated with gene therapy. However, the effects of oversized genomes on the integrity of …
Read PDF