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At least 19 recordsLinked to original sources
PubMed2024

Application of third-generation sequencing technology for identifying rare α- and β-globin gene variants in a Southeast Chinese region.

BACKGROUND: Third-generation sequencing (TGS) based on long-read technology has been gradually used in identifying thalassemia and hemoglobin (Hb) variants. The aim of the present study was to explore genotype varieties of thalassemia and Hb variants in Quanzhou region of Southeast China by TGS. METHODS: Included in this study were 6,174 subjects with thalassemia traits from Quanzhou region of Southeast China. All of them underwent common thalassemia gene testing using the DNA reverse dot-blot hybridization technology. Subjects who were suspected as rare thalassemia carriers were further subjected to TGS to identify rare or novel α- and β-globin gene variants, and the results were verified by Sanger sequencing and/or gap PCR. RESULTS: Of the 6,174 included subjects, 2,390 (38.71%) were identified as α- and β-globin gene mutation carriers, including 40 carrying rare or novel α- and β-thalassemia mutations. The αCD30(-GAG)α and Hb Lepore-Boston-Washington were first reported in Fujian province Southeast China. Moreover, the βCD15(TGG> TAG), βIVS-II-761, β0-Filipino(~ 45 kb deletion), and Hb Lepore-Quanzhou were first identified in the Chinese population. In addition, 35 cases of Hb variants were detected, the rare Hb variants of Hb Jilin and Hb Beijing were first reported in Fujian province of China. Among them, one case with compound αααanti3.7 and Hb G-Honolulu variants was identified in this study. CONCLUSION: Our findings may provide valuable data for enriching the spectrum of thalassemia and highlight the clinical application value of TGS-based α- and β-globin genetic testing.

Humans↗
PubMed2025

Whole genome study and construction of SHERLOCK detection method for endemic strains of Burkholderia pseudomallei in Hainan based on third-generation sequencing.

UNLABELLED: Burkholderia pseudomallei (Bp) is a gram-negative bacterium found in soil and surface water. It is also the pathogen that causes melioidosis disease in humans and animals. This study aimed to obtain the whole genome sequence of the endemic strain of Bp in Hainan, using third-generation sequencing (TGS) technology, and elucidate the genome structure, function, and genetic evolution. Additionally, the study aimed to achieve rapid and specific identification of these endemic strains using specific high-sensitivity enzymatic reporter unlocking (SHERLOCK) detection technology, providing a new strategy for the early diagnosis of melioidosis. Utilizing the PacBio platform for TGS technology, we completed whole genome sequencing of 16 Bp strains from Hainan. High-precision and complete genome sequences were obtained through quality control and genome assembly of the sequencing data. Additionally, we established a nucleic acid detection technology platform based on SHERLOCK, which could be completed from nucleic acid extraction to result reading within 1-2 hours, demonstrating good sensitivity and specificity (both are 100%). The lateral chromatography strip method does not require special equipment and holds promise as an immediate screening method for the early diagnosis of melioidosis. IMPORTANCE: Melioidosis is a highly pathogenic infectious disease caused by a gram-negative bacterium of Burkholderia pseudomallei (Bp). The traditional gold standard for diagnosing melioidosis is still isolation and culture from clinical samples. Although this method has high specificity, it has low sensitivity and is time-consuming, which often leads to misdiagnosis or missed diagnosis of melioidosis, affecting subsequent treatment. In this study, recombinase polymerase amplification technology and clustered regularly interspaced short palindromic repeats/Cas13a technology were combined to establish the Specific High-sensitivity Enzymatic Reporter Unlocking detection technology, which can achieve rapid and accurate identification of Bp, providing a new method for the early diagnosis of melioidosis.

Burkholderia pseudomallei↗
PubMed2025

Impact of RNA extraction on respiratory microbiome analysis using third-generation sequencing.

BACKGROUND: The respiratory microbiome, which comprises bacteria, fungi, and viruses, plays a crucial role in respiratory health and disease. However, its study is limited by the low microbial biomass in respiratory samples and the dominance of host RNA. Metatranscriptomics offers comprehensive insights into active microbial communities and their interactions with the host but requires optimized RNA extraction protocols for robust and unbiased analysis. This study evaluated two RNA extraction kits&#x2014;one employing chemical lysis (CL) and another combining chemical and mechanical lysis (CML)&#x2014;to determine their effectiveness for metatranscriptomic analysis of respiratory samples. RESULTS: The CML protocol significantly increased double-stranded DNA (dsDNA) library yields, leading to higher sequencing read counts for both sample types (p&#x2009;<&#x2009;0.0001). The read length was unaffected by the lysis protocol for the BAL and NPS samples. Taxonomic profiling revealed that CML enhanced the detection of robust microorganisms, such as gram-positive bacteria and fungi, without compromising viral detection. CONCLUSIONS: The CML protocol demonstrated superior recovery of genetic material, particularly for fungi and gram-positive bacteria, making it better suited for comprehensive metatranscriptomic analyses. These findings underscore the need for tailored RNA extraction strategies on the basis of sample type and research objectives. Optimized metatranscriptomic protocols are pivotal for advancing our understanding of the respiratory microbiome and its role in health and disease.

Microbiota↗
PubMed2025

SMART-RNA-Metavirome: a practical RNA metavirome platform compatible with high-throughput sequencing of both short and long reads.

BACKGROUND: The RNA virosphere's extensive diversity and its role in emerging infectious diseases underscore the importance of non-targeted sequencing for identifying unknown or rare pathogens, including co-infections. However, enriching low-abundance viral sequences in RNA metaviromics, particularly in&#xa0;the preparation of cDNA libraries and their compatibility with next-generation sequencing (NGS) and third-generation sequencing (TGS), remains challenging. Therefore, our objective is to develop and systematically assess a practical RNA metavirome methodology specifically tailored for the enrichment of low-abundance viral sequences within samples. METHODS: We developed the SMART-RNA-Metavirome platform, integrating SMART-9n library preparation with NGS and TGS technologies. Total RNA was extracted from two field-collected wild Aedes albopictus pools, along with one laboratory-infected Ae. albopictus pool harboring dengue virus (DENV). This RNA was subjected to reverse transcription using both this optimized protocol and random primer-based methods, followed by high-throughput sequencing on Illumina, Oxford Nanopore, and QitanTech Nanopore technologies. Welch's t-test was employed for comparative analysis of the subsequent RNA metavirome data, specifically to evaluate differences in viral species composition and abundance of viral reads between experimental groups. Furthermore, the effectiveness of this platform was systematically validated via RT-qPCR and SMART-RNA-Metavirome-based Oxford&#xa0;Nanopore sequencing across multiple sample types, including mosquito specimens from DENV-infected Ae. albopictus, serum samples from dengue patients and viral isolates of Japanese encephalitis virus (JEV) and Zika virus (ZIKV). RESULTS: The SMART-RNA-Metavirome platform has been systematically validated to excel in enriching the composition and diversity of the RNA virome (P&#x2009;=&#x2009;0.04), providing sufficient coverage for the complete reconstruction of viral genomes. When employed in the detection of DENV-infected Ae. albopictus, clinical serum samples, and viral isolates of JEV and ZIKV, this technique exhibits a robust correlation with RT-qPCR (r2&#x2009;>&#x2009;0.95). Notably, it demonstrates exceptional sensitivity, ensuring sufficient coverage even in samples of DENV-infected Ae. albopictus with a Ct-value of 35.3, attaining an impressive 99.88% genome coverage. Furthermore, this platform possesses the capability to identify virus species and determine their serotypes. CONCLUSIONS: In our study, the SMART-RNA-Metavirome platform outperforms traditional methods, enriching RNA virome composition and diversity, enabling practical compatibility with both NGS and TGS technologies. It demonstrates significant proficiency in detecting both known and unknown arboviruses, even in low-titer samples such as those from wild mosquitoes and clinical sera. This platform facilitates comprehensive monitoring, risk assessment, and early warning of RNA virus transmissions, enhancing our understanding of RNA virome diversity and ecological patterns.

High-Throughput Nucleotide Sequencing↗
PubMed2025

Allele Level Sequencing of Killer Cell Immunoglobulin-Like Receptor Genes Using Oxford Nanopore Long Read Sequencing.

The human Killer cell Immunoglobulin-like Receptor (KIR) genes, found on chromosome 19, encode for cell surface protein receptors that, through interaction with their ligand, modulate the action of Natural Killer (NK) cells and some subsets of T lymphocytes. KIR genes exhibit extensive variation through variable gene content, copy number, and allele polymorphism. The combination of KIR genes and their ligands is implicated in various clinical settings including haematopoietic stem cell and solid organ transplant, and infectious disease progression. KIR gene content has been used in the selection of optimal stem cell donors with haplotype variations in recipient and donor giving differential clinical outcomes. With the introduction of massively parallel clonal next generation sequencing and single molecule long read third generation sequencing, allele level determination of KIR genotypes has become feasible. We describe a method for amplicon-based long read sequencing on the Oxford Nanopore Technologies platform that provides largely unambiguous allele level typing of KIR genes. The method was validated using DNA extracted from 48 10th International Histocompatibility Workshop (IHWS) cell lines with previously published allele level KIR genotypes and 176 Western Australian samples previously tested for the presence or absence of KIR genes. Our long-read sequencing method was able to accurately determine KIR alleles with an overall concordance of 97%-99% with the published data. Importantly, phasing ambiguity caused by the inability to phase heterozygous base positions over long stretches of gene sequence was resolved in several samples. Thus, our long read PCR sequencing strategy can be used to determine KIR genotypes at allele resolution level.

Humans↗
PubMed2026

Novel biallelic FSIP2 variants cause male infertility with multiple morphological abnormalities of sperm flagella in humans.

Biallelic variants in fibrous sheath-interacting protein 2 ( FSIP2 ) gene are a known cause of multiple morphological abnormalities of the sperm flagella (MMAF). This study aimed to identify novel FSIP2 variants and evaluate their impact on sperm ultrastructure and intracytoplasmic sperm injection (ICSI) outcomes. Whole-exome sequencing (WES) was employed to screen a cohort of 92 MMAF patients, with candidate variants validated via Sanger sequencing and third-generation sequencing. We identified one homozygous variant in a proband from a consanguineous family and two pairs of compound heterozygous variants in two unrelated, non-consanguineous families. Routine semen analysis demonstrated markedly reduced motility across all probands. Detailed morphological and ultrastructural assessments using Papanicolaou staining, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) demonstrated that approximately 80.0% of spermatozoa exhibited pathological elongation of the mitochondrial sheath in the midpiece. Furthermore, 50.0%-70.0% of spermatozoa displayed fibrous sheath dysplasia or loss in the principal piece. Immunofluorescence assays and Western blotting confirmed that FSIP2 protein localization was disrupted, and the expression of key axonemal assembly factors was dysregulated. Notably, successful pregnancies were achieved via ICSI in the partners of two probands. This study expands the mutational spectrum of FSIP2 in both consanguineous and non-consanguineous populations. Ultrastructural abnormalities, such as mitochondrial sheath elongation and fibrous sheath disassembly, highlight FSIP2 's critical role in flagellar assembly. Clinical results further support ICSI as an effective therapeutic intervention for affected individuals.

Humans↗
PubMed2026

Integrating Next-Generation Sequencing into von Willebrand Disease Diagnostics: Insights from the PCM-EVW-ES Multicenter Project.

Von Willebrand disease (VWD) is the most common inherited bleeding disorder, caused by quantitative or qualitative defects in von Willebrand factor (VWF). Diagnosis is challenging and requires integrating bleeding history, VWF antigen and activity measurements, FVIII assays, and specialized phenotyping. Genetic testing is increasingly recognized as a key component. Here, we review current concepts in VWD diagnostics and highlight the Spanish Clinical and Molecular Profile of von Willebrand Disease (PCM-EVW-ES) project as a model for genomics-enabled precision medicine. PCM-EVW-ES is a multicenter initiative involving 48 hospitals, centralized phenotypic testing, and next-generation sequencing of the VWF coding region, enabling definitive classification in 730 individuals with VWD to date. Harmonized recruitment criteria and standardized workflows improve subtype assignment, uncover complex genotypes, refine genotype-phenotype correlations, and facilitate the identification of asymptomatic carriers. The PCM-EVW-ES variant spectrum highlights recurrent disease-causing variants in Spain and underscores the value of coordinated national registries for variant curation. Building on these data, we propose a diagnostic algorithm in which bleeding assessment and first-line VWF/FVIII assays, combined with, early VWF molecular testing increases diagnostic accuracy and guides targeted second-line investigations to confirm and refine VWD subtype classification. We also outline persisting challenges, including the interpretation of variants of uncertain significance and patients without identifiable pathogenic VWF variants, and future directions integrating third-generation sequencing, expanded gene panels, functional studies, and artificial-intelligence-driven multiomic approaches. Together, these advances illustrate how robust multicenter studies can bridge the gap between complex diagnostics and clinical practice in VWD.

Humans↗
PubMed2026

Mapping Protein Occupancy on DNA with an Unnatural Cytosine Modification.

The epigenome provides a dynamic layer of gene regulatory control above the static genetic sequence. DNA base modifications are key epigenetic regulators, predominantly found within CpG contexts in mammalian genomes. Working in tandem with these DNA modifications, chromatin-associated proteins and transcription factors further control gene expression. Given the interplay of these factors, concurrent mapping of DNA base modifications with protein-DNA occupancy can greatly aid in interpreting the epigenome. Existing multimodal mapping methods include the use of DNA methyltransferases to mark accessible, protein-unbound DNA in non-CpG contexts. However, such approaches can either confound readouts with native DNA modifications or constrain users to third-generation sequencing approaches. To circumvent these limitations, we explored the possibility of introducing an unnatural DNA base modification, 5-carboxymethylcytosine, as an alternative label for protein occupancy. Here, we report our efforts to rationally engineer non-CpG-specific DNA methyltransferases to take on neomorphic DNA carboxymethyltransferase (CxMTase) activities. We find that DNA carboxymethylation of cytosines in GpC contexts shows broad compatibility with the most widely used epigenetic detection methods and can be used to reliably report on protein occupancy states. Using this approach, we reveal the single-molecule binding patterns of LexA, a master repressor in the bacterial DNA damage (SOS) response, at its self-regulated and endogenously methylated promoter. We thus show that unnatural DNA modifications can uncover novel biological insights and potentiate new approaches to multimodal epigenetic profiling.

DNA↗
PubMed2026

Improved Genomic Resources for the swordtail cricket, Laupala kohalensis Otte 1994.

Advances in genetic tools such as next and third generation sequencing, paired with a focus on representative clades, provide insight into how processes including adaptation, admixture, and genome structure shape the evolution and maintenance of species. However, our understanding of the genomics of speciation is dominated by systems where ecological adaptations are thought to cause initial barriers to gene exchange. In contrast to other model systems, the 38 species of the genus Laupala constitute a very rapid radiation, where evolution of reproductive barriers and speciation is thought to be driven by sexual selection. Here, with novel PacBio HiFi reads and RNA- and Iso-Seq data, we provide a highly contiguous, chromosome-level genome and markedly improved annotation of the endemic Hawaiian cricket, Laupala kohalensis Otte, 1994. Our new resources advance previous efforts, placing 99% of 47 scaffolds on 7 autosomes and 1 sex chromosome in the 1.67 Gb assembly, with a 98.8% BUSCO score (insecta_db10), N50 of ~268&#xa0;Mb, and L50 of 3. Using a custom repeat library, we estimate the genome to have 46.09% repeat content, and the new annotation includes an increased estimate of 17,670 genes, which coincides with that known from other Orthopterans. Notably, we find a large nuclear DNA segment of mitochondrial origin on chromosome 7. This new resource provides a powerful tool to identify and compare genomic causes of phenotypic diversification in a system characterized by strong signatures of sexual differentiation, representing an underappreciated but potentially widespread cause of speciation.

Hawaii↗
PubMed2025

Protective Effects of HLA-DRB1*08:03 and HLA-DQA1*01:03 Alleles for Alloanti-D Immunisation in the Southern Chinese D-Negative Pregnant Women.

Alloanti-D is still one of the most common causes of severe hemolytic disease of the fetus and newborn in China, as rhesus immunoglobulin (RhIG) prophylaxis is not a routine practice throughout China. HLA plays an important role in the susceptibility to alloimmunisation against red blood cell antigens. This study was designed to identify susceptible and protective HLA alleles for alloanti-D immunisation after pregnancy in the southern Chinese D-negative (D-) pregnant women. In this study, a cohort of 116 true D- pregnant females who had not received prophylactic RhIG prophylaxis, had two or more pregnancies, and did not produce alloanti-D (non-responders group), and 122 true D- pregnant women with alloanti-D immunisation (D responders group), were enrolled. HLA genotyping (HLA-A, -B, -C, -DRB1, -DPA1, -DPB1, -DQA1, and -DQB1) was performed by third generation sequencing with nanopore technology. The phenotypic frequencies of HLA alleles were compared between the D responders group and non-responders group. The results showed that the phenotypic frequencies of HLA-DRB1*08:03 and HLA-DQA1*01:03 alleles in the D responders group were significantly lower than those in the non-responders group: 1.7% versus 13.1% [Odds Ratio (OR): 0.116, 95% CI: 0.026-0.518; pc&#x2009;=&#x2009;0.029] for HLA-DRB1*08:03 allele, and 5.2% versus 18.8% (OR: 0.235, 95% CI: 0.092-0.600, pc&#x2009;=&#x2009;0.019) for HLA-DQA1*01:03 allele. Our findings indicated that the presence of HLA-DRB1*08:03 or HLA-DQA1*01:03 alleles can be considered as a protective factor for alloanti-D immunisation in the southern Chinese D- pregnant women.

Humans↗
PubMed2026

Whole-genome characterization of seven multidrug-resistant Neisseria gonorrhoeae isolates from a single tertiary center in Beijing.

BACKGROUND: To characterize the whole-genome features of Neisseria gonorrhoeae clinical isolates collected from a tertiary medical institution in Beijing, with a focus on the genomic basis of ceftriaxone non-susceptibility and multidrug resistance. METHODS: Clinical isolates were collected from April 2023 to November 2024. Of 14 collected isolates, seven were successfully subcultured after revival and included in subsequent analyses. Minimum inhibitory concentrations (MICs) were determined by the Etest method. Whole-genome data were obtained using a combination of second- and third-generation sequencing technologies. The isolates were combined with global and Chinese reference datasets to construct a core-genome single-nucleotide polymorphism (core-SNP) phylogenetic tree. Chromosomal resistance-associated mutations and plasmid characteristics were subsequently analyzed. RESULTS: The seven isolates displayed genomic diversity at the whole-genome level. Four isolates (8087, 8423, 8461, and 8801) carried penA 60.001 and belonged to distinct sequence types, including ST7365, ST8123, and ST7367. One additional isolate (8726) carried penA 273.001; both alleles encode PBP2 proteins sharing the core substitutions A311V, I312M, V316T, and T483S. All five isolates were non-susceptible to ceftriaxone (MIC 0.25-0.5&#x202f;mg/L). Ceftriaxone non-susceptibility was associated with the co-occurrence of mutations at core penA positions and additional mutations in porB and ponA, with an mtrR mutation present in one isolate. Plasmid collinearity analysis revealed that several multidrug-resistant isolates simultaneously harbored an intact conjugative plasmid and an African-type resistance plasmid carrying bla TEM-1. CONCLUSION: The multidrug-resistant phenotype of Neisseria gonorrhoeae results from the co-existence of chromosomal multi-locus mutations and resistance plasmids. The penA 60.001 isolates in this study did not originate from a single source. This allele appeared in multiple local clonal lineages. This pattern is consistent with horizontal gene transfer of this resistance determinant into multiple endemic lineages.

Neisseria gonorrhoeae↗
PubMed2026

Third-generation whole-genome sequencing reveals the role of CNTNAP2 as a tumor suppressor gene in high-risk neuroblastomas.

BACKGROUND: Neuroblastoma is a common and aggressive pediatric sympathetic nervous system tumor. Genomic structural variants (SVs) contribute substantially to neuroblastoma, yet remain under-characterized in high-risk neuroblastomas. We aimed to elucidate neuroblastoma pathogenesis using third-generation whole-genome sequence high-risk cases to identify driver aberrations and explore potential therapeutic strategies. METHODS: We analyzed third-generation whole-genome sequencing data of 20 high-risk neuroblastoma samples and combined the findings with those obtained from the analysis of clinical samples, in vitro models, and public datasets. RESULTS: The contactin-associated protein-like 2 (CNTNAP2) gene was observed to be frequently aberrated because of structural variants in high-risk neuroblastoma samples. CNTNAP2 expression was significantly correlated with favorable histology and could be used to predict prognosis using clinical samples and neuroblastoma datasets. Overexpression and knockdown experiments and transcriptomic analysis revealed that CNTNAP2 was primarily involved in neuronal differentiation and axon guidance pathways; moreover, CNTNAP2 was required for neuroblastoma differentiation and affected cancer stemness. Immunoprecipitation and mass spectrometry revealed that CNTNAP2 interacted with cytoskeletal proteins like drebrin 1 (DBN1) and myosin-heavy chain 9 (MYH9). CNTNAP2 dynamically reorganises actin and microtubules for DBN1-mediated neuronal differentiation. CNTNAP2 also reduces CTNNB1 transcription and &#x3b2;-catenin pathway activation by inhibiting MYH9 nuclear translocation. CNTNAP2 overexpression in neuroblastoma cell lines resulted in cell cycle arrest, decreased cell proliferation and metastasis. CONCLUSIONS: The recurrent loss of CNTNAP2 in neuroblastoma contributes to an aggressive phenotype by impairing neuronal differentiation and increasing cancer stemness. These findings may serve as a foundation for developing therapeutic strategies to overcome barriers to differentiation.

Humans↗