The Third-Generation Sequencing Challenge: Novel Insights for the Omic Sciences

Biomolecules, Journal Year: 2024, Volume and Issue: 14(5), P. 568 - 568

Published: May 10, 2024

The understanding of the human genome has been greatly improved by advent next-generation sequencing technologies (NGS). Despite undeniable advantages responsible for their widespread diffusion, these methods have some constraints, mainly related to short read length and need PCR amplification. As a consequence, long-read sequencers, called third-generation (TGS), developed, promising overcome NGS. Starting from first prototype, TGS progressively ameliorated its chemistries improving both base-calling accuracy, as well simultaneously reducing costs/base. Based on premises, is showing potential in many fields, including analysis difficult-to-sequence genomic regions, structural variations detection, RNA expression profiling, DNA methylation study, metagenomic analyses. Protocol standardization development easy-to-use pipelines data will enhance use, also opening way routine applications diagnostic contexts.

Language: Английский

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Large‐Scale Analysis of the Thalassemia Mutation Spectrum in Guizhou Province, Southern China, Using Third‐Generation Sequencing

Clinical Genetics, Journal Year: 2025, Volume and Issue: unknown

Published: March 17, 2025

ABSTRACT This study aimed to comprehensively characterize the molecular spectrum of thalassemia by retrospectively analyzing genetic screening results from a large cohort individuals. Peripheral blood samples were collected 26 047 individuals seeking care at Departments Obstetrics and Gynecology, Pediatrics, Reproductive Medicine, Hematology across multiple regional hospitals in Guizhou Province, China. Thalassemia gene mutations analyzed using targeted third‐generation sequencing (TGS) assess mutation this population. Of cohort, 5099 identified as carriers, yielding an overall carrier rate 19.58%. The rates differed significantly between southern northern regions ( p < 0.001). α‐thalassemia included 40 distinct genotypes, β‐thalassemia comprised 33 cases with concurrent α‐ exhibited 47 unique genotypes. A total 17 gene. showed significant differences when compared other Chinese populations, notable variations within itself. highlights substantial diversity patterns Province. These findings provide valuable insights into distribution genotypes alleles, which can inform counseling prenatal strategies tailored

Language: Английский

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A rapid and efficient zirconia bead-mediated ultrasonic strategy for DNA fragmentation up to 10 kbp

RSC Advances, Journal Year: 2025, Volume and Issue: 15(8), P. 6068 - 6075

Published: Jan. 1, 2025

The scheme of zirconia bead-mediated ultrasonic fragmentation long-stranded DNA.

Language: Английский

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Application value of long-read sequencing in full characterization of thalassemia-associated structural variations: identifying a novel large segmental duplication and literature review

Orphanet Journal of Rare Diseases, Journal Year: 2025, Volume and Issue: 20(1)

Published: April 2, 2025

Abstract Background Thalassemia is one of the most prevalent monogenic disorders in tropical and subtropical regions, imposing significant familial social burdens on local populations. It caused by point mutations or structural variations (SVs) α- β-globin gene clusters. Due to complex structure, full characterization SVs has always been focus difficulty molecular diagnosis thalassemia patients. Methods Peripheral blood a Chinese boy with β-thalassemia intermedia phenotype his family members were collected. Multiplex ligation dependent probe amplification (MLPA), long-read sequencing (LRS) Sanger used analyze variant this family. Results A novel large duplication (αααα 280 ) was identified using LRS technique validated sequencing. Additionally, we conducted systematic review known evaluated advantages disadvantages various methods analyzing SVs. Conclusions Our study SV α-globin cluster demonstrated that superior approach for detecting rare The appropriate use significantly improves diagnostic accuracy when conventional are not capable completely identifying

Language: Английский

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Advances in whole genome sequencing for foodborne pathogens: implications for clinical infectious disease surveillance and public health

Frontiers in Cellular and Infection Microbiology, Journal Year: 2025, Volume and Issue: 15

Published: April 28, 2025

Foodborne outbreaks affecting millions of people worldwide are a significant and growing global health threat, exacerbated by the emergence new increasingly virulent foodborne pathogens. Traditional methods detecting these outbreaks, including culture-based techniques, serotyping molecular such as real-time PCR, still widely used. However, approaches often lack precision resolution required to definitively trace source an outbreak distinguish between closely related strains Whole genome sequencing (WGS) has emerged revolutionary tool in investigations, providing high-resolution, comprehensive genetic data that allows accurate species identification strain differentiation. WGS also facilitates detection virulence antimicrobial resistance (AMR) genes, critical insight into potential pathogenicity, treatment/control options risks spreading This capability enhances surveillance, tracing risk assessment, making integrated component public surveillance systems. Despite its advantages, widespread implementation faces several pressing challenges, high costs, need for specialized bioinformatics expertise, limited computational infrastructure resource-constrained settings, standardization data-sharing frameworks across regulatory agencies. Addressing barriers is crucial maximizing impact on disease surveillance. Even so, emerging vital food safety health, become gold standard been recognized authorities USA, European Union, Australia China, example. review highlights role

Language: Английский

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High-throughput omics technologies in inflammatory bowel disease

Clinica Chimica Acta, Journal Year: 2024, Volume and Issue: 555, P. 117828 - 117828

Published: Feb. 13, 2024

Language: Английский

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A novel growth-friendly system alleviates pulmonary dysplasia in early-onset scoliosis combined with thoracic insufficiency syndrome: Radiological, pathological, and transcriptomic assessments

Heliyon, Journal Year: 2024, Volume and Issue: 10(6), P. e27887 - e27887

Published: March 1, 2024

BackgroundThe posterior procedure utilizing growth-friendly techniques is the golden standard for patients with early-onset scoliosis combined thoracic insufficiency syndrome (EOS + TIS). Pulmonary hypoplasia main cause of dying prematurely in EOS TIS. This study assessed therapeutic impact a novel system on pulmonary development piglet's TIS model.MethodsThe animal period lasts 12 weeks, which construction was performed at 0–8 and implantation applied 8–12 weeks. During procedure, X-rays CT were to observe scoliosis, thorax, lungs. After pathological changes lung tissue using HE IHC staining. RNA-seq characterized system-associated differentially expressed genes (DEGs) validated RT-qPCR, western blotting, IHC.ResultsImplantation increased body weight, length, total volume, as well decreased coronal sagittal Cobb angles model. It also ameliorated TIS-induced thickening alveolar wall, spaces, number diameter. In tissue, 790 DEGs identified, they mainly involved regulation immune, inflammatory, calcium transport, vascular development. Among these DEGs, BDKRB1, THBS1, DUSP1, IDO1, SPINK5 hub genes, their differential expression consistent results tissues.ConclusionThe has mitigated We further elucidate molecular mechanisms underlying amelioration hypoplasia.

Language: Английский

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Advances in Hemoglobinopathies and Thalassemia Evaluation

Clinics in Laboratory Medicine, Journal Year: 2024, Volume and Issue: 44(3), P. 441 - 453

Published: June 5, 2024

Language: Английский

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From haystack to high precision: advanced sequencing methods to unraveling circulating tumor DNA mutations

Frontiers in Molecular Biosciences, Journal Year: 2024, Volume and Issue: 11

Published: Aug. 6, 2024

Identifying mutations in cancer-associated genes to guide patient treatments is essential for precision medicine. Circulating tumor DNA (ctDNA) offers valuable insights early cancer detection, treatment assessment, and surveillance. However, a key issue ctDNA analysis from the bloodstream choice of technique with adequate sensitivity identify low frequent molecular changes. Next-generation sequencing (NGS) technology, evolving parallel long-read capabilities, enhances mutation analysis. In present review, we describe different NGS approaches identifying mutation, discussing challenges standardized methodologies, cost, specificity, clinical context, bioinformatics expertise optimal application.

Language: Английский

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Zirconia Bead-Mediated Ultrasonic Fragmentation Method of Long-Stranded DNA

Published: Jan. 1, 2024

Language: Английский

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