Third-generation sequencing for genetic disease

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

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

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

BACKGROUND

Thalassemia is one of the most prevalent monogenic disorders in tropical and subtropical regions, imposing significant familial and social burdens on local populations. It is caused by point mutations or structural variations (SVs) in the α- or β-globin gene clusters. Due to the complex structure, full characterization of SVs has always been the focus and difficulty of molecular diagnosis of thalassemia patients.

METHODS

Peripheral blood of a Chinese boy with β-thalassemia intermedia phenotype and his family members were collected. Multiplex ligation dependent probe amplification (MLPA), long-read sequencing (LRS) and Sanger sequencing were used to analyze the variant in this family.

RESULTS

A novel large duplication (αααα280) was identified using LRS technique and validated by Sanger sequencing. Additionally, we conducted a systematic review of known SVs and evaluated the advantages and disadvantages of various methods in analyzing complex SVs.

CONCLUSIONS

Our study identified a novel SV in the α-globin gene cluster and demonstrated that LRS was a superior approach for detecting novel rare SVs. The appropriate use of LRS significantly improves diagnostic accuracy when conventional methods are not capable of completely identifying complex SVs.

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

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

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

Single-molecule sequencing (SMS), a long-read DNA sequencing technology, plays a crucial role in genomics research. However, traditional ultrasonic shearing techniques struggle to efficiently produce DNA fragments ≥10 kbp, limiting the efficiency of SMS library preparation. Here, we developed a zirconia bead-mediated ultrasonic shearing method that enables precise DNA fragmentation through zirconia bead mechanical agitation induced by sonication cavitation. By optimizing parameters such as zirconia bead size, quantity, ultrasonic probe distance, ultrasonic time, water bath temperature, DNA sample volume, and DNA concentration, we obtained target fragments in the 10-20 kbp range. The results demonstrated that this method sheared purified λDNA (48.5 kbp) into fragments averaging 15 kbp within 20 seconds, achieving performance comparable to commercial g-TUBE methods. The method was also successfully applied to human genomic DNA. This simple, rapid and reliable DNA fragmentation method provides an effective solution for SMS library preparation with great potential for molecular detection and diagnostic applications.

Advances in forensic genetics: Exploring the potential of long read sequencing

DNA-based technologies have been used in forensic practice since the mid-1980s. While PCR-based STR genotyping using Capillary Electrophoresis remains the gold standard for generating DNA profiles in routine casework worldwide, the research community is continually seeking alternative methods capable of providing additional information to enhance discrimination power or contribute with new investigative leads. Oxford Nanopore Technologies (ONT) and PacBio third-generation sequencing have revolutionized the field, offering real-time capabilities, single-molecule resolution, and long-read sequencing (LRS). ONT, the pioneer of nanopore sequencing, uses biological nanopores to analyze nucleic acids in real-time. Its devices have revolutionized sequencing and may represent an interesting alternative for forensic research and routine casework, given that it offers unparalleled flexibility in a portable size: it enables sequencing approaches that range widely from PCR-amplified short target regions (e.g., CODIS STRs) to PCR-free whole transcriptome or even ultra-long whole genome sequencing. Despite its higher error rate compared to Illumina sequencing, it can significantly improve accuracy in read alignment against a reference genome or de novo genome assembly. This is achieved by generating long contiguous sequences that correctly assemble repetitive sections and regions with structural variation. Moreover, it allows real-time determination of DNA methylation status from native DNA without the need for bisulfite conversion. LRS enables the analysis of thousands of markers at once, providing phasing information and eliminating the need for multiple assays. This maximizes the information retrieved from a single invaluable sample. In this review, we explore the potential use of LRS in different forensic genetics approaches.

Nanopore-targeted sequencing (NTS) for intracranial tuberculosis: a promising and reliable approach

BACKGROUND

The World Health Organization predicted 10.6 million new tuberculosis cases and 1.5 million deaths in 2022. Tuberculous meningitis, affecting 1% of active TB cases, is challenging to diagnose due to sudden onset, vague symptoms, and limited laboratory tests. Nanopore-targeted sequencing (NTS) is an emerging third-generation sequencing technology known for its sequencing capabilities. We compared its detection efficiency with Xpert, MTB culture, PCR, and AFB smear in cerebrospinal fluid samples to highlight the substantial potential of NTS in detecting intracranial tuberculosis.

METHODS

This study included 122 patients suspected of having intracranial tuberculosis at the Second Hospital of Nanjing in Jiangsu Province, China, between January 2021 and January 2024. The Univariate logistic regression and random forest regression identified risk factors and clinical markers. A chi-square test evaluated diagnostic accuracy for different image types of intracranial tuberculosis.

RESULTS

The research involved 100 patients with intracranial tuberculosis. Among them, 41 had tuberculous meningitis, 27 had cerebral parenchymal tuberculosis, and 32 had mixed intracranial tuberculosis. Besides, 22 patients were diagnosed with other brain conditions. In diagnosing intracranial tuberculosis, NTS demonstrated a sensitivity of 60.0% (95% CI: 49.7-69.5%) and a specificity of 95.5% (95% CI:75.1-99.8%), with an AUC value of 0.78 (95% CI: 0.71 to 0.84), whose overall performance was significantly better than other detection methods. There was no notable difference (P > 0.05) in diagnostic accuracy between NTS and the final diagnosis for intracranial tuberculosis patients with varying imaging types. Furthermore, patients who tested positive had a 31.500 (95% CI: 6.205-575.913) times higher risk of having intracranial tuberculosis compared to those with negative results.

CONCLUSION

Due to its convenience, efficiency, quick turnaround time, and real-time sequencing analysis, NTS might become a promising and reliable method for providing microbiological diagnoses for patients with intracranial tuberculosis and for screening populations at risk.

Advances in Hemoglobinopathies and Thalassemia Evaluation

Hemoglobin (Hb) disorders are among the most prevalent inherited diseases. Despite a limited number of involved genes, these conditions represent a broad clinical and prognostic spectrum. The menu of laboratory tests is extensive. From widely available modalities, for example, complete blood count to rather sophisticated molecular technologies, the investigation of Hb disorders recapitulates an increasing complexity of laboratory workup in other medical fields. This review highlights a current state of biochemical and molecular investigation of Hb disorders and offers a glimpse on technologies that are yet to be fully embraced in clinical practice.

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

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

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

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

High-throughput omics technologies in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic, relapsing intestinal disease. Elucidation of the pathogenic mechanisms of IBD requires high-throughput technologies (HTTs) to effectively obtain and analyze large amounts of data. Recently, HTTs have been widely used in IBD, including genomics, transcriptomics, proteomics, microbiomics, metabolomics and single-cell sequencing. When combined with endoscopy, the application of these technologies can provide an in-depth understanding on the alterations of intestinal microbe diversity and abundance, the abnormalities of signaling pathway-mediated immune responses and functionality, and the evaluation of therapeutic effects, improving the accuracy of early diagnosis and treatment of IBD. This review comprehensively summarizes the development and advancement of HTTs, and also highlights the challenges and future directions of these technologies in IBD research. Although HTTs have made striking breakthrough in IBD, more standardized methods and large-scale dataset processing are still needed to achieve the goal of personalized medicine.