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Assessing the efficacy of target adaptive sampling long-read sequencing through hereditary cancer patient genomes
Innovations in sequencing technology have led to the discovery of novel mutations that cause inherited diseases. However, many patients with suspected genetic diseases remain undiagnosed. Long-read sequencing technologies are expected to significantly improve the diagnostic …
Read PDFLong-read sequencing reveals two chromosomes and one plasmid in <i>Vibrio</i> sp. strain MAO6 isolated from a Marine Beach in Fukui, Japan
A marine bacterium <i>Vibrio</i> sp. strain MAO6 was isolated from a marine beach in Fukui, Japan. Its complete genome comprises two circular chromosomes (3,418,677 bp and 1,629,627 bp) and one circular plasmid (299,686 bp).
Read PDFEditorial: Long-read sequencing-Pitfalls, benefits and success stories
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Read PDFFully Phased Population-Prevalent East African Cattle BoLA-I Alleles Determined Using PacBio HiFi Long-Read Sequencing Represent Five Novel Specificities With Distinctive Peptide Binding Potential
Due to factors such as lower biosecurity, greater wildlife/farm animal interfaces, and environmental challenges, cattle in sub-Saharan Africa are exposed to more diverse and intensive bacterial, viral and protozoan pathogen challenges than cattle in Europe …
Read PDFClinical application of targeted long read sequencing in prenatal beta-thalassemia testing and genetic counseling
<h4>Background</h4>Beta thalassemia, related to HBB mutation and associated with elevated hemoglobin A2 (HbA2), is an important genetic hemoglobinopathy with high incidences of disease and carrier rates in Singapore. Carrier screening is essential to facilitate prenatal …
Read PDFTargeted long-read sequencing facilitates effective carrier screening for complex monogenic diseases including spinal muscular atrophy, α-/β-thalassemia, 21-hydroxylase deficiency, and fragile-X syndrome
<h4>Background</h4>Next-generation sequencing (NGS) has been applied for carrier screening, effectively reducing the incidence of severe diseases. However, some severe, high-prevalent and complex diseases, including spinal muscular atrophy (SMA), α-/β-thalassemia, 21-hydroxylase deficiency (21-OHD), and fragile-X syndrome …
Read PDFA long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment
In this report, we present OLAF-Seq, a novel strategy to construct a long-read sequencing library such that adjacent fragments are linked with end-terminal duplications. We use the CRISPR-Cas9 nickase enzyme and a pool of multiple …
Read PDFCombined approaches, including long-read sequencing, address the diagnostic challenge of HYDIN in primary ciliary dyskinesia
Primary ciliary dyskinesia (PCD), a disorder of the motile cilia, is now recognised as an underdiagnosed cause of bronchiectasis. Accurate PCD diagnosis comprises clinical assessment, analysis of cilia and the identification of biallelic variants in …
Read PDFEvaluation of Long-Read Sequencing Simulators to Assess Real-World Applications for Food Safety
Shiga toxin-producing <i>Escherichia coli</i> (STEC) and <i>Listeria monocytogenes</i> are routinely responsible for severe foodborne illnesses in the United States. Current identification methods utilized by the U.S. Food Safety Inspection Service require at least four days …
Read PDFSeq2scFv: a toolkit for the comprehensive analysis of display libraries from long-read sequencing platforms
Antibodies have emerged as the leading class of biotherapeutics, yet traditional screening methods face significant time and resource challenges in identifying lead candidates. Integrating high-throughput sequencing with computational approaches marks a pivotal advancement in antibody …
Read PDFCharacterizing <i>PALB2</i> intragenic duplication breakpoints in a triple-negative breast cancer case using long-read sequencing
<h4>Introduction</h4>Accurate identification and characterization of Large Genomic Rearrangements (LGR), especially duplications, are crucial for precise diagnosis and risk assessment. In this report, we characterized an intragenic duplication breakpoint of <i>PALB2</i> to determine its pathogenicity significance.<h4>Methods</h4>A …
Read PDFLong-read sequencing improves the genetic diagnosis of retinitis pigmentosa by identifying an Alu retrotransposon insertion in the EYS gene
<h4>Background</h4>Biallelic variants in EYS are the major cause of autosomal recessive retinitis pigmentosa (arRP) in certain populations, a clinically and genetically heterogeneous disease that may lead to legal blindness. EYS is one of the largest …
Read PDFSex differences in MAGEL2 gene promoter methylation in high functioning autism - trends from a pilot study using nanopore Cas9 targeted long read sequencing
<h4>Background</h4>MAGEL2 is an autism susceptibility gene whose deficiency has been associated with autism-related behaviors in animal models and in syndromic human autism spectrum disorders (ASDs) such as Schaaf-Yang syndrome, but has not been studied in …
Read PDFComparative genomics using long-read sequencing identifies nearly identical TAL effector regions in two <i>Xanthomonas oryzae</i> pv. <i>Oryzae</i> isolates collected from the basmati rice-growing region of Pakistan
The emergence of hostile and novel plant pathogenic strains poses a serious threat to global food security, which renders the strategies for disease management in modern agriculture ineffective. Preventing the consequences of these emerging phytopathogens …
Read PDFGenome Announcement: Draft Genome Assembly of <i>Heterodera humuli</i> Generated Using Long-Read Sequencing
The hop cyst nematode, <i>Heterodera humuli</i>, is the most common plant-parasitic nematode associated with hop worldwide. This study reports the draft genome of <i>H. humuli</i> generated on the PacBio Sequel IIe System with the ultra-low …
Read PDFTradeoffs in alignment and assembly-based methods for structural variant detection with long-read sequencing data
Long-read sequencing offers long contiguous DNA fragments, facilitating diploid genome assembly and structural variant (SV) detection. Efficient and robust algorithms for SV identification are crucial with increasing data availability. Alignment-based methods, favored for their computational …
Read PDFTowards a Long-Read Sequencing Approach for the Molecular Diagnosis of RPGR<sup>ORF15</sup> Genetic Variants
Sequencing of the low-complexity ORF15 exon of RPGR, a gene correlated with retinitis pigmentosa and cone dystrophy, is difficult to achieve with NGS and Sanger sequencing. False results could lead to the inaccurate annotation of …
Read PDFSystematic evaluation of single-cell RNA-seq analyses performance based on long-read sequencing platforms
<h4>Introduction</h4>The rapid development of next-generation sequencing (NGS)-based single-cell RNA sequencing (scRNA-seq) allows for detecting and quantifying gene expression in a high-throughput manner, providing a powerful tool for comprehensively understanding cellular function in various biological processes. …
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