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Spinal muscular atrophy (SMA) is the second most common fatal genetic disease in infancy. It is caused by deletion or intragenic pathogenic variants of the causative gene SMN1, which degenerates anterior horn motor neurons and …
Read PDFCurrent metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. …
Read PDFLong-read DNA sequencing technologies have been rapidly evolving in recent years, and their ability to assess large and complex regions of the genome makes them ideal for clinical applications in molecular diagnosis and therapy selection, …
Read PDFLong-read genome sequencing (lrGS) is a promising method in genetic diagnostics. Here we investigate the potential of lrGS to detect a disease-associated chromosomal translocation between 17p13 and the 19 centromere. We constructed two sets of …
Read PDFPhlebotomine sand flies are the vectors of leishmaniasis, a neglected tropical disease. High-quality reference genomes are an important tool for understanding the biology and eco-evolutionary dynamics underpinning disease epidemiology. Previous leishmaniasis vector reference sequences were …
Read PDFMassive parallel sequencing methods, such as exome, genome, and targeted DNA sequencing, have aided molecular diagnosis of genetic diseases in the last 20 years. However, short-read sequencing methods still have several limitations, such inaccurate genome …
Read PDFTelomere length is an important biomarker of organismal aging and cellular replicative potential, but existing measurement methods are limited in resolution and accuracy. Here, we deploy digital telomere measurement (DTM) by nanopore sequencing to understand …
Read PDF<h4>Motivation</h4>Long-read sequencing technologies, an attractive solution for many applications, often suffer from higher error rates. Alignment of multiple reads can improve base-calling accuracy, but some applications, e.g. sequencing mutagenized libraries where multiple distinct clones differ …
Read PDFThe B-cell acute lymphoblastic leukemia (ALL) cell line REH, with the t(12;21) <i>ETV6::RUNX1</i> translocation, is known to have a complex karyotype defined by a series of large-scale chromosomal rearrangements. Taken from a 15-yr-old at relapse, …
Read PDFAlterations in the structure and location of telomeres are pivotal in cancer genome evolution. Here, we applied both long-read and short-read genome sequencing to assess telomere repeat-containing structures in cancers and cancer cell lines. Using …
Read PDFThe large-scale heterogeneity of genetic diseases necessitated the deeper examination of nucleotide sequence alterations enhancing the discovery of new targeted drug attack points. The appearance of new sequencing techniques was essential to get more interpretable …
Read PDF<h4>Background</h4>Protein-coding genes have been considered the functional part of the genome, although they represent only 2% of the genome. In contrast, more than 90% of the genome produces non-coding RNA (ncRNA), including antisense (AS) genes, …
Read PDF<h4>Background</h4>21-Hydroxylase deficiency (21-OHD) is caused by mutations in the <i>CYP21A2</i> gene. Due to the complex structure and the high genetic heterogeneity of the <i>CYP21A2</i> gene, genetic testing for 21-OHD is currently facing challenges. Moreover, there …
Read PDFThe study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read …
Read PDFDuring the COVID-19 pandemic, the monitoring of SARS-CoV-2 RNA in wastewater was used to track the evolution and emergence of variant lineages and gauge infection levels in the community, informing appropriate public health responses without …
Read PDFBACKGROUNDCarbapenemase-producing Enterobacterales (CPE) frequently cause nosocomial outbreaks. To investigate these, tracing focused on patients with related CPE strains and spatiotemporal contact (e.g. contact with each other in a room or on a ward during overlapping …
Read PDFObtaining high-quality DNA suitable for long-read sequencing can be difficult for many types of tissues and cells, and it is a key step in current genomic studies. The challenge is even greater when it comes …
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