Search Results (1,120)

The date palm (Phoenix dactylifera L.) is a key crop in the arid regions of North Africa and the Middle East, with substantial socioeconomic value. Although multiple genome assemblies have been generated using next-generation sequencing (NGS) technologies, they primarily focus on Middle Eastern cultivars, leaving North African varieties unrepresented. This study aims to address this gap by sequencing and assembling the first genome of a North African date palm using Illumina sequencing technology. We present a draft genome assembly of the elite Tunisian variety Deglet Nour. By comparing it with the Barhee BC4 reference genome, we identify key genetic variants, including single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), potentially associated with ripening processes and fruit quality. This work expands the genomic resources for date palm research, particularly for North African cultivars, and provides new insights into the nucleotide-level variability of the genes linked to key agronomic traits. Full article

Background and Objectives: Autism spectrum disorder (ASD) is a neurodevelopmental disorder that belong to genetic and epigenetic mechanism. Despite the recent advantages in next-generation sequencing (NGS) technology, ASD etiology is still unclear. Materials and Methods: In this study, we tested a customized target genetic panel consisting of 74 genes in a cohort of 53 ASD individuals. The tested panel was designed from the SFARI database. Results: Among 53 patients analyzed using a targeted genetic panel, 102 rare variants were identified, with nine individuals carrying likely pathogenic or pathogenic variants considered genetically “positive.” We identified six de novo variants across five genes (POGZ 2 variants, NCOR1, CHD2, ADNP, and GRIN2B), including two variants of uncertain significance in POGZ p.Thr451Met and NCOR1 p.Glu1137Lys, one likely pathogenic variant in GRIN2B p.Leu714Gln, and three pathogenic variants in POGZ p.Leu775Valfs32, CHD2 p.Thr1108Metfs8, and ADNP p.Pro5Argfs*2. Conclusions: This study presents a comprehensive characterization of the targeted gene panel used for genetic analysis, while critically evaluating its diagnostic limitations within the context of contemporary genomic approaches. A pivotal accomplishment of this study was the ClinVar submission of novel de novo variants which expands the documented mutational spectrum of ASD-associated genes and enhances future diagnostic interpretation. Full article

Evolving technologies available to clinical laboratories and laboratory-related updates to clinical guidelines both drive the need for clinical laboratories to keep their test menu updated and in line with current technological and clinical developments. Our laboratory has developed a targeted Illumina-based amplicon next-generation sequencing (NGS) assay to interrogate the hsp65 and erm(41) genes of Mycobacterium spp. for the purposes of providing species-level ± subspecies-level identification of Mycobacterium spp. organisms in clinical samples and genotypic predictions for inducible macrolide resistance (in the case of M. abscessus complex members). The developed assay demonstrated 100% sensitivity and specificity for M. tuberculosis and M. abscessus complex cultured organisms, 98% ID overall concordance relative to the available reference identification, and a nearly 60% “rescue” rate for primary samples that could not be identified using our previous method. There was 94.6% concordance between genotypic and phenotypic results for inducible macrolide resistance. The developed assay was successfully implemented in our clinical laboratory and has been accredited for clinical use. Full article

Precision medicine is transforming hematologic cancer care by tailoring treatments to individual patient profiles and moving beyond the traditional “one-size-fits-all” model. This review outlines foundational technologies, disease-specific advances, and emerging directions in precision hematology. The field is enabled by molecular profiling techniques, including next-generation sequencing (NGS), whole-exome sequencing (WES), and RNA sequencing (RNA-seq), as well as epigenomic and proteomic analyses. Complementary tools such as liquid biopsy and minimal residual disease (MRD) monitoring have improved diagnosis, risk stratification, and therapeutic decision making. We discuss major molecular targets and personalized strategies across hematologic malignancies: FLT3 and IDH1/2 in acute myeloid leukemia (AML); Philadelphia chromosome–positive and Ph-like subtypes in acute lymphoblastic leukemia (ALL); BCR-ABL1 in chronic myeloid leukemia (CML); TP53 and IGHV mutations in chronic lymphocytic leukemia (CLL); molecular subtypes and immune targets in diffuse large B-cell lymphoma (DLBCL) and other lymphomas; and B-cell maturation antigen (BCMA) in multiple myeloma. Despite significant progress, challenges remain, including high costs, disparities in access, a lack of standardization, and integration barriers in clinical practice. However, advances in single-cell sequencing, spatial transcriptomics, drug repurposing, immunotherapies, pan-cancer trials, precision prevention, and AI-guided algorithms offer promising avenues to refine treatment and improve outcomes. Overcoming these barriers will be critical for ensuring the equitable and widespread implementation of precision medicine in routine hematologic oncology care. Full article

Sudden cardiac death represents an unexpected death for which a strong underlying genetic background has been described. The primary causes are identified in cardiomyopathies and channelopathies, which are heart diseases of the muscle and electrical system, respectively, without coronary artery disease, hypertension, valvular disease, and congenital heart malformations. Genetic variants, especially single nucleotide variants and short insertions/deletions impacting essential myocardial functions, have shown that cardiomyopathies display high heritability. However, genetic heterogeneity, incomplete penetrance, and variable expression may complicate the interpretation of genetic findings, thus delaying the management of seriously at-risk patients. Moreover, recent studies show that the diagnostic yield related to genetic cardiomyopathies ranges from 28 to 40%, raising the need for further research. In this regard, investigating the occurrence of structural variants, especially copy number variants, may be crucial. Based on these considerations, this review aims to provide an overview of copy number variants identified in cardiomyopathies and discuss them, considering diagnostic yield. This review will ultimately address the necessity of incorporating copy number variants into routine genetic testing for cardiomyopathies and channelopathies, a process increasingly enabled by advances in next-generation sequencing technologies. Full article

The genus Salvia L. (Lamiaceae) is characterized by complex taxonomy and controversial phylogeny. This genus includes about a thousand species with worldwide distribution and high ecological, structural, functional and morphological diversity. Because of their high content of essential oils, various Salvia plants are widely used in medicine, as well as in the food, perfume, cosmetic, and paint industries; they also are valuable melliferous resources. The present study reviews the taxonomic history of the genus Salvia and the phylogenetic relationships between the taxa within the subgenera Salvia, Sclarea, and Glutinaria. Among the Salvia species, three basic chromosome numbers, x = 7, x = 8, and x = 11, were most common, although other basic chromosome numbers (x = 6–19) were determined, which was probably due to events of dysploidy, aneupoidy, and/or polyploidy occurring during speciation. Recent molecular cytogenetic studies based on Next Generation Sequencing technologies have clarified the chromosomal organization of several Salvia species. The patterns of chromosome distribution of 45S rDNA, 5S rDNA, and satellite DNAs made it possible to assess their intra- and interspecific chromosome diversity. However, further cytogenetic studies are needed to characterize the chromosomes in the genomes of other Salvia species and specify the genomic relationships among them. Full article

The global prevalence of hepatocellular carcinoma (HCC) is getting worse, leading to an urgent need for improved diagnostic and prognostic strategies. Liquid biopsy, which analyzes circulating tumor cells (CTCs), cell-free DNA (cfDNA), cell-free RNA (cfRNA), and extracellular vesicles (EVs), has emerged as a minimally invasive and promising alternative to traditional tissue biopsy. These biomarkers can be detected using sensitive molecular techniques such as digital PCR, quantitative PCR, methylation-specific assays, immunoaffinity-based CTC isolation, nanoparticle tracking analysis, ELISA, next-generation sequencing, whole-genome sequencing, and whole-exome sequencing. Despite several advantages, liquid biopsy still has challenges like sensitivity, cost-effectiveness, and clinical accessibility. Reports highlight the significance of multi-analyte liquid biopsy panels in enhancing diagnostic sensitivity and specificity. This approach offers a more comprehensive molecular profile of HCC, early detection, and tracking therapeutic treatment, particularly in those cases where single-analyte assays and imaging fail. The technological advancement in the isolation and analysis of CTC, cell-free nucleic acids, and EVs is increasing our understanding of extracting genetic information from HCC tumors and discovering mechanisms of therapeutic resistance. Furthermore, crucial information on tumor-specific transcriptomic and genomic changes can be obtained using cfRNA and cfDNA released into the peripheral blood by tumor cells. This review provides an overview of current liquid biopsy strategies in HCC and their use for early detection, prognosis, and monitoring the effectiveness of HCC therapy. Full article

In recent years, as gene therapy technology has rapidly developed, there has been growing concern that it could be misused by athletes as a means of doping. However, current testing methods for gene doping have a range of limitations and require further improvement. Furthermore, significant progress has been made in the fields of blood storage, next-generation sequencing (NGS), and LabDroid (experimental robots). Against this background, this study was implemented to develop a test method for gene doping using dried blood spot (DBS), NGS, and the LabDroid ”Maholo”. As a first step, recombinant adeno-associated virus containing the human erythropoietin gene (hEPO) was injected into mice to establish a gene doping model. Subsequently, DBS was created using whole blood. Maholo was used to extract DNA from the DBS and to create DNA libraries for NGS. NGS in combination with bioinformatic analysis clearly identified DNA fragments that provided definitive evidence of gene doping in the mouse model, which were absent in the control mouse. To the best of our knowledge, this is the first attempt to use a biological model of hEPO gene doping in conjunction with Maholo, NGS, and DBS. This method should facilitate the further development of gene doping tests. Full article

Potato early dying disease complex (PED) leads to premature senescence and rapid decline in potato plants. Unlike potato wilt caused solely by Verticillium species, PED symptoms are more severe due to the synergistic effects of multiple pathogens, including root-lesion nematodes, fungi such as Colletotrichum and Fusarium, and soft-rot bacteria. To investigate the microbiome responsible for PED, soil and stem samples from healthy-looking and symptomatic plants were analyzed using amplicon-targeted next-generation sequencing (Illumina MiSeq and PacBio technologies). Samples were collected from four locations in New Brunswick, Canada from fields previously rotated with barley or oat. Comparative analysis of the bacterial, fungal, and eukaryotic diversity in soil samples showed minimal differences, with only bacterial alpha diversity influenced by the plant health status. Verticillium dahliae was abundant in all soil samples, and its abundance was significantly higher in the stems of diseased plants. Additional fungal species implicated in PED, including Plectosphaerella cucumerina, Colletotrichum coccodes, Botrytis sp., and Alternaria alternata, were also identified in the stems. This study highlights the complex, plant-associated microbial interactions underlying PED and provides a foundation for microbiome-informed disease management strategies. Full article

With rapid advances in image-generative AI, interest has grown in applying these technologies across diverse domains. While current models excel at producing high-quality final images, they rarely model the intermediate stages of the drawing process. This study proposes a drawing support system that leverages generative AI to sequentially generate and modify images during the drawing process. To train the system, we constructed a custom dataset of time-series drawing images, which are typically unavailable in existing AI models. We developed an encoder–decoder model based on convolutional neural networks to predict the next frame from a current input image. To address error accumulation during recursive generation, we introduced a noise-augmented training method, incorporating noisy images into the dataset. Experimental results show that standard training suffers from image degradation over time, while the noise-augmented approach significantly improves stability and quality throughout the sequence. Averaged across all generated frames, the noise-augmented training achieved a PSNR of 20.48, SSIM of 0.81, and LPIPS of 0.13. As a benchmark, we compared this approach to PredRNN, a representative temporal model, which achieved a PSNR of 24.05, SSIM of 0.88, and LPIPS of 0.08. These results demonstrate the effectiveness of noise-augmented learning while also highlighting potential performance gains using temporal architectures. PredRNN also required more computation, with 6.41 M parameters and a 0.188 s inference time per sequence, compared to 5.20 M and 0.005 s for our model. Furthermore, in a sample-level analysis of 10 final images, the proposed model outperformed PredRNN in three cases across all metrics, suggesting its robustness in certain sequences despite architectural simplicity. Future directions include using more advanced models such as Variational Autoencoders and diffusion models, and enhancing consistency in long-term sequences. Our work confirms the feasibility of generating interactive drawing sequences using AI and sets the foundation for more robust and creative drawing support tools. Full article

Millipedes (Diplopoda) are crucial decomposers in soil ecosystems, as they play a vital role in organic matter degradation while also holding potential as bioindicators of environmental health. This study deciphered the complete mitogenomes of four millipede species (Diplopoda: Spirostreptida and Spirobolida) using next-generation sequencing technology, thus revealing evolutionary relationships among diplopod taxa and characterizing mitochondrial genomic features. The full mitochondrial sequences of Agaricogonopus acrotrifoliolatus, Bilingulus sinicus, Paraspirobolus lucifugus, and Trigoniulus corallinus, ranged in size from 14,906 to 15,879 bp, with each containing 37 typical genes and one D-loop region. Notably, the D-loop regions of A. acrotrifoliolatus and B. sinicus were positioned atypically, thus indicating structural rearrangements. A nucleotide composition analysis revealed pronounced AT-skews, with tRNA sequences exhibiting the highest A+T content. Ka/Ks ratios demonstrated that the ND5 gene experienced the weakest purifying selection pressure, thus suggesting its potential role in adaptive evolution. The results of the phylogenetic analysis showed genetic relationships between the three orders of ((Julida, Spirostreptida), Spirobolida), which was inconsistent with the previous conclusion regarding the three orders, obtained through morphological studies: ((Julida, Spirobolida), Spirostreptida). These findings highlight the role of the mitochondrial genome in resolving phylogenetic conflicts and provide important insights for further studies on millipedes. Full article

Molecular testing in renal cell carcinoma (RCC) has allowed for a better understanding of the biology of both sporadic and hereditary diseases, where genetic testing is currently recommended in the guidelines for a select population with risk factors. Historically, screening, surveillance, and management decisions were based solely on clinicopathologic data; however, we now know that molecular profiling can enhance decision making, altering the treatment plan, approach, or selection of systemic therapy and enhancing the delivery of precision oncologic care. Advances and the increasing availability of next-generation sequencing technologies have improved the identification of germline and somatic variants in key RCC-associated genes. Given the molecular heterogeneity of RCC, these modern methods can identify unique genetic events that occur in a single individual, allowing for distinction between a metachronous tumor from metastases. Separate four-tier systems have been proposed to categorize germline and somatic variants according to their clinical significance, which should be highlighted. Additionally, emerging technologies, such as liquid biopsy, show potential for enhancing precision oncology in RCC. With this said, challenges, such as variant interpretation, ethical considerations, and accessibility, persist. This review examines the molecularly defined RCC, genetic testing methodologies currently available, their current clinical applications, limitations, and future directions. Full article

Haplotype phasing refers to determining the haplotype sequences inherited from each parent in a diploid organism. It is a critical process for various downstream analyses, and numerous haplotype phasing methods for genomic single nucleotide polymorphisms (SNPs) have been developed. Allele-specific (AS) expression and alternative splicing play key roles in diverse biological processes. AS studies usually focus more on exonic SNPs, and multiple phased SNPs need to be combined to obtain better inferences. In this paper, we introduce an alignment-free algorithm HPTAS for haplotype phasing in AS studies. Instead of using sequence alignment to count the number of reads covering SNPs, HPTAS constructs a mapping structure from transcriptome annotations and SNPs and employs a k-mer-based approach to derive phasing counts from RNA-seq data. Using both next-generation sequencing (NGS) and the third-generation sequencing (TGS) NA12878 RNA-seq data and comparing with the most advanced algorithm in the field, we have demonstrated that HPTAS achieves high phasing accuracy and performance and that transcriptome data indeed facilitates the phasing of exonic SNPs. With the continued advancement of sequencing technology and the improvement in transcriptome annotations, HPTAS may serve as a foundation for future haplotype phasing methods. Full article

Oral squamous cell carcinoma (OSCC), a major subtype of head and neck squamous cell carcinoma (HNSCC), is a significant global health burden owing to its late-stage diagnosis and poor prognosis. Recent advancements in molecular biology, genomics, and imaging have transformed the landscape of OSCC diagnosis and treatment. This review provides a comprehensive synthesis of early molecular diagnostic strategies, including biomarker discovery using next-generation sequencing, liquid biopsy, and salivary exosomal microRNAs. In addition, we highlight the emerging role of non-invasive optical imaging technologies and their clinical integration for improved surgical precision and early lesion detection. This review also discusses evolving therapeutic approaches, including immunotherapy, neoadjuvant chemotherapy, and patient-centered multimodal regimens tailored through molecular profiling. We emphasized balancing therapeutic efficacy with the quality of life in patients undergoing chemoradiotherapy. The convergence of multi-omics, artificial intelligence, and precision medicine holds promise for revolutionizing early detection and personalized treatment of OSCC, ultimately improving patient survival and clinical outcomes. Full article

The increasing burden of cancer globally necessitates innovative approaches for diagnosis, prognosis, and treatment. This article explores the transformative impact of genomics and artificial intelligence (AI) in precision oncology, addressing how their convergence is reshaping cancer care and its challenges. Methods: This review synthesizes current research on the applications of genomics, including next-generation sequencing, and AI, such as machine learning and deep learning, across the cancer care continuum. It examines their roles in identifying genetic variants, assessing cancer risk, guiding targeted therapies and immunotherapy, predicting treatment response, and enabling early detection through liquid biopsies. Results: Genomics and AI are revolutionizing oncology by enabling personalized treatment strategies, improving early detection, and overcoming drug resistance. AI enhances the interpretation of complex genomic data, facilitates drug repurposing, and accelerates the development of novel therapeutics. However, challenges remain regarding data standardization, interpretability, bias in AI algorithms, and ethical considerations. Conclusions: The integration of genomics and AI holds immense potential to advance precision oncology, offering more effective, equitable, and sustainable cancer care. Addressing current challenges and fostering interdisciplinary training will be crucial to fully harness these technologies and redefine oncology practice. Full article