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Facultative parthenogenesis and intrapopulation mixed ploidy (where individuals with differing ploidy exist within the same area) are rare in animals. However, these unique characteristics allow opportunities to investigate the relationship between sexual modality and genome …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) represents a leading cause of cancer-associated deaths worldwide, and its development is strongly associated with aberrant RNA processing and metabolic reprogramming. Splicing factor 3B subunit 4 (SF3B4), the core component of the …
Read PDF<h4>Background</h4>Singleton short-read genome sequencing (GS) is increasingly used as a first-line genetic test for childhood neurological disorders (such as intellectual disability, neurodevelopmental delay, motor delay, and hypotonia) with diagnostic yields from 26 to 35%, typically …
Read PDFAAV integration has become an important safety consideration in gene therapy. However, accurately determining integration sites remains challenging due to biases introduced by library preparation methods, sequencing technologies, and bioinformatic pipelines. In this study, we …
Read PDF<h4>Background</h4>Many neurodegenerative diseases are caused by nucleotide repeat expansions, but most expansions, like the C9orf72 'GGGGCC' (G<sub>4</sub>C<sub>2</sub>) repeat that causes approximately 5-7% of all amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) cases, are too …
Read PDFLong-read sequencing technologies are transforming our ability to assemble highly complex genomes. Realizing their full potential is critically reliant on extracting high-quality, high-molecular-weight (HMW) DNA from the organisms of interest. This is especially the case …
Read PDFAccurate and comprehensive characterization of genetic variation is essential for deciphering the genetic basis of diseases and other phenotypes. A vast amount of genetic variation stems from large-scale sequence changes arising from the duplication, deletion, …
Read PDFDespite the high accuracy of short read sequencing (SRS), there are still issues with attaining accurate single nucleotide polymorphism (SNP) genotypes at low sequencing coverage and in highly duplicated genomes due to misalignment. Long read …
Read PDFAdvances in long-read single molecule sequencing have opened new possibilities for 'benchtop' whole-genome sequencing. The Oxford Nanopore Technologies MinION is a portable device that uses nanopore technology that can directly sequence DNA molecules. MinION single …
Read PDF<h4>Background</h4>Poxviruses are large DNA viruses that infect humans and animals. Vaccinia virus (VACV) has been applied as a live vaccine for immunization against smallpox, which was eradicated by 1980 as a result of worldwide vaccination. …
Read PDFPoxvirus adaptation can involve combinations of recombination-driven gene copy number variation and beneficial single nucleotide variants (SNVs) at the same loci. How these distinct mechanisms of genetic diversification might simultaneously facilitate adaptation to host immune …
Read PDFStructural variants (SVs), including duplications, deletions, inversions, translocations, and insertions, play major roles in human phenotypic diversity but remain difficult to detect because of variable size and structural complexity. Optical genome mapping (OGM) uses ultra-high …
Read PDFWith the rapid advancement of sequencing technology, third-generation sequencing, particularly single-molecule real-time sequencing and nanopore sequencing, has opened new avenues for the precise prevention and control of genetic diseases. It offers distinct advantages, including long-read …
Read PDF<h4>Background</h4>Recent advances in single-molecule sequencing techniques, such as Nanopore sequencing, improved read length, increased sequencing throughput, and enabled direct detection of DNA modifications through the analysis of raw signals. These DNA modifications include naturally occurring …
Read PDFTechnological limitations have hindered the large-scale genetic investigation of tandem repeats in disease. We show that long-read sequencing with a single Oxford Nanopore Technologies PromethION flow cell per individual achieves 30× human genome coverage and …
Read PDF<h4>Background</h4>Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have extreme %GC content remains challenging. Long-read, single-molecule …
Read PDFMicrosatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called …
Read PDF<h4>Background</h4>Varicella zoster virus (VZV) is a human pathogenic alphaherpesvirus harboring a relatively large DNA molecule. The VZV transcriptome has already been analyzed by microarray and short-read sequencing analyses. However, both approaches have substantial limitations when …
Read PDF<h4>Background</h4>Preimplantation genetic testing (PGT) has already been applied in patients known to carry chromosomal structural variants to improve the clinical outcome of assisted reproduction. However, conventional molecular techniques are not capable of reliably distinguishing embryos …
Read PDFThe Oxford Nanopore MinION DNA sequencing device can produce large amounts of long sequences, typically several kilobases, within a few hours. This long read capacity was exploited to detect antimicrobial resistance genes (ARGs) in a …
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