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Results for “Genomic analysis”

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At least 19 recordsLinked to original sources

PubMed1991

Workshop overview: new molecular techniques in genome analysis.

An overview of the application of various molecular techniques to the analysis of genomic DNA is presented. For the analysis of small-scale changes, the polymerase chain reaction (PCR), colony probe hybridization, mismatch hybridization, and denaturing gradient gel electrophoresis (DGGE) are providing information on mutations within prokaryotic and eukaryotic genes. For large-scale changes, fluorescence in situ hybridization (FISH), pulsed-field gel electrophoresis (PFGE), Southern blotting, multiplex PCR, hybridization of linked probes, and restriction enzyme mapping are permitting analysis of genomic alterations that are larger than point mutations but below the resolution of standard cytogenetic analysis. Many of these techniques, either alone or in combination, produce DNA that can be subjected to DNA sequence analysis, which provides the most detailed information regarding genomic changes.

Chromosome Aberrations↗

PubMed2025

Whole-Genome Analysis and Growth-Promoting Mechanism of Klebsiella pneumoniae YMK25 from Maize Rhizobacteria.

Plant growth-promoting rhizobacteria (PGPR) are microorganisms that enhance plant growth through various mechanisms. In the context of global agriculture, which faces fertilizer dependency and environmental pollution, developing eco-friendly microbial fertilizers has become crucial for enhancing agricultural sustainability. To identify highly effective PGPR, we isolated 102 bacterial strains from maize rhizosphere soil using the dilution plating method. The strains were screened for growth-promoting abilities using functional media, resulting in the selection of strain YMK25 for its exceptional capabilities in nitrogen fixation, solubilization of inorganic and organic phosphorus, indole-3-acetic acid (IAA) production, and siderophore production. Strain YMK25 produced IAA at a concentration of 80.49 ± 0.68 μg/mL and exhibited a relative siderophore expression level of 43.68%. Morphological analysis, 16S rDNA gene sequence analysis, and whole-genome sequencing confirmed that strain YMK25 is Klebsiella pneumoniae. Whole-genome analysis revealed a total genome length of 5,115,280 bp, a GC content of 57.61%, and it contained 4746 coding genes. Gene annotation results indicated genes involved in siderophore synthesis, phosphatase activity, and other plant growth-promoting functions, which align with the verified characteristics of strain YMK25. Furthermore, this strain exhibited significant metabolic capabilities. The pot experiment demonstrated that strain YMK25 promotes maize plant growth and assists in nutrient fixation in these plants. In conclusion, strain YMK25 is a high-quality PGPR with substantial potential for application in agricultural production, presenting promise for widespread use in sustainable agriculture.

Klebsiella pneumoniae↗

PubMed2026

LCR-modules: a collection of workflows for cancer genome analysis.

MOTIVATION: The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible analysis of diverse cancer genomics data at scale. The suite comprises 49 Snakemake-based workflows organized into three levels, facilitating tasks from low-level quality control to complex cohort-level analyses. LCR-modules supports various sequencing types and integrates pipelines such as mutation calling, expression quantification, and cohort-level aggregation, ensuring flexibility and reproducibility. LCR-modules represents a significant advancement in genomic data analysis, reducing barriers in reproducibility and scalability and has already been applied to a combination of exomes and genomes from over 10 800 samples. AVAILABILITY: No new data were generated in support of this research. The source code for the LCR-modules is openly available at https://github.com/LCR-BCCRC/lcr-modules.

Software↗

PubMed1991

Applications of the polymerase chain reaction to genome analysis.

The objectives of the Human Genome Project are to create high-resolution genetic and physical maps, and ultimately to determine the complete nucleotide sequence of the human genome. The result of this initiative will be to localize the estimated 50,000-100,000 human genes, and acquire information that will enable development of a better understanding of the relationship between genome structure and function. To achieve these goals, new methodologies that provide more rapid, efficient, and cost effective means of genomic analysis will be required. From both conceptual and practical perspectives, the polymerase chain reaction (PCR) represents a fundamental technology for genome mapping and sequencing. The availability of PCR has allowed definition of a technically credible form that the final composite map of the human genome will take, as described in the sequence-tagged site proposal. Moreover, applications of PCR have provided efficient approaches for identifying, isolating, mapping, and sequencing DNA, many of which are amenable to automation. The versatility and power provided by PCR have encouraged its involvement in almost every aspect of human genome research, with new applications of PCR being developed on a continual basis.

Base Sequence↗

PubMed1991

Genome analysis of adenovirus type 31 strains from immunocompromised and immunocompetent patients.

Adenovirus type 31 (Ad31) was isolated from 15 immunocompromised patients in 12 of whom seroconversion was also recorded. Ad31 infection has a substantial clinical relevance since 8 of 10 with lower respiratory tract infection and 4 of 4 with hepatitis died. Therefore, Ad31 isolates from immunocompetent and immunodeficient hosts were compared by restriction endonuclease analysis. Nine genome types were identified among the 79 Ad31 isolates. Pairwise comparison of comigrating restriction fragments indicated that the genome types could be divided into three genomic clusters. Several Ad31 genome types were isolated from immunocompromised patients, but no highly virulent genome type could be found. A genome type was identified in a child with severe combined immunodeficiency who originally was infected with another genome type. This observation is suggested to have evolutionary implications.

Adenovirus Infections, Human↗

PubMed1992

[Ethical and social issues on the human genome analysis].

The modern technologies for human genome analysis raise a variety of ethical and social questions. The pre-symptomatic diagnostic of diseases of late expression is becoming possible for a rapidly increasing number of situations. The use of that knowledge by employers, insurance companies, schools, and society in general, could lead to discriminations and stigmatizations, in addition to adverse psychological reactions. DNA fingerprinting raises questions of privacy and personal autonomy in its applications to paternity proof, criminal proceedings, and establishment of data banks. The project of the immediate and complete sequencing of the human genome will lead to questions of economical ethics, as well as of access, commercialization and property rights of scientific information and materials obtained. It also favours a reducionistic mentality and international unbalances. The molecular biology of humans, which will follow the complete sequencing of the genome, may foster a rethinking of the concepts of freedom of self-determination (basic for moral responsibility) and of equality. The gene therapy and its possible extension to the betterment of the human species, pose questions of ethical limits to this technology. All these problems will have to be answered in terms of the application of the principle of ethical freedom for self-fulfillment, as a right of the human person, as well as of science and society. Scientific, economic and social interests have to be subordinated to the dignity of the human person.

DNA Fingerprinting↗

PubMed2026

Whole-Genome Analysis Reveals Antimicrobial Resistance and Population Structure of Environmental and Veterinary Acinetobacter baumannii.

Acinetobacter (A.) baumannii is an important multidrug-resistant pathogen increasingly recognized across animal and environmental settings, and carbapenem-resistant A. baumannii (CRAB) is classified as a critical-priority pathogen by the World Health Organization. This study investigated the antimicrobial resistance (AMR) and genomic characteristics of 122 A. baumannii isolates comprising 72 veterinary and 50 environmental isolates collected in Andhra Pradesh, India. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), resistance and virulence gene profiling, multilocus sequence typing (MLST), core-genome analysis, single nucleotide polymorphism (SNP) phylogeny, and pan-genome analysis were performed. Overall, 58.2% of isolates were multidrug-resistant (MDR), and 41.8% were extensively drug-resistant (XDR). Sequence type (ST) 52 predominated among veterinary isolates, whereas ST2 was more frequent among environmental isolates. The presence of carbapenem-resistant isolates along with the ST2 lineage enhances the similarity to clinical A. baumannii. Several intrinsic resistance genes, including blaOXA-23, armA, aph(3″)-Ib, aph(6)-Id, tet(B), mph(E), and msr(E), were more prevalent in the ST2-associated population. Virulence-associated determinants were widely conserved. Core-genome MLST (cgMLST) and core-genome SNP (cgSNP) analyses identified highly related isolates within both lineages, while pairwise SNP differences were 0-7. Pan-genome analysis identified 4204 gene clusters and distinct accessory gene patterns between ST2 and ST52. These findings indicate that resistance gene distribution was closely associated with lineage structure and support integrated genomic surveillance of A. baumannii across animal and environmental reservoirs.

Acinetobacter baumannii↗

PubMed2026

Comprehensive genomic and computational insights into Brucella suis: pan-genome analysis, evolutionary perspectives, and in-silico vaccine design.

BACKGROUND: Brucella suis is a zoonotic intracellular pathogen responsible for brucellosis, mainly in swine and humans. Although numerous genome sequences are publicly available, an integrative genomic analysis combining pan-genome architecture, structural organization, evolutionary relationships, and vaccine-associated targets remains limited. RESULTS: In this study, we analyzed 91 publicly available B.suis genomes to characterize their pan-genome composition and genomic structure. The pan-genome exhibited an open configuration, indicating continued genomic diversification. A total of 2,146 core genes were identified, representing conserved functions essential for species maintenance, while the accessory genome reflected strain-level variability. Phylogenetic reconstruction based on single-copy orthologs revealed distinct evolutionary clades among the strains. A complementary phylogenetic analysis of pan-genome gene presence-absence patterns further supported clade differentiation and highlighted variation in accessory gene repertoires. Comparative synteny and genome structural analyses demonstrated largely conserved chromosomal organization with localized rearrangements across strains. Screening of the core proteome identified 64 putative antigenic proteins with predicted surface localization and immunogenic properties. Additionally, resistance-associated determinants related to tetracycline and doxycycline were detected in one genome within the dataset. CONCLUSIONS: This comprehensive genomic analysis defines the pan-genome structure, evolutionary relationships, and genome organization of B.suis. The integration of core and pan-genome-based phylogenies provides complementary insights into strain diversification, while the identified conserved antigenic candidates offer a foundation for future experimental validation and rational vaccine development strategies.

Genome, Bacterial↗

PubMed2025

Incorporating Epidemiological Data into the Genomic Analysis of Partially Sampled Infectious Disease Outbreaks.

Pathogen genomic data are increasingly being used to investigate transmission dynamics in infectious disease outbreaks. Combining genomic data with epidemiological data should substantially increase our understanding of outbreaks, but this is highly challenging when the outbreak under study is only partially sampled, so that both genomic and epidemiological data are missing for intermediate links in the transmission chains. Here, we present a new dynamic programming algorithm to perform this task efficiently. We implement this methodology into the well-established TransPhylo framework to reconstruct partially sampled outbreaks using a combination of genomic and epidemiological data. We use simulated datasets to show that including epidemiological data can improve the accuracy of the inferred transmission links compared with inference based on genomic data only. This also allows us to estimate parameters specific to the epidemiological data (such as transmission rates between particular groups), which would otherwise not be possible. We then apply these methods to two real-world examples. First, we use genomic data from an outbreak of tuberculosis in Argentina, for which data was also available on the HIV status of sampled individuals, in order to investigate the role of HIV coinfection in the spread of this tuberculosis outbreak. Second, we use genomic and geographical data from the 2003 epidemic of avian influenza H7N7 in the Netherlands to reconstruct its spatial epidemiology. In both cases, we show that incorporating epidemiological data into the genomic analysis allows us to investigate the role of epidemiological properties in the spread of infectious diseases.

Humans↗

PubMed2025

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.

SUMMARY: Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis, a clonally evolving bacterium with a small accessory genome, as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read versus hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations. AVAILABILITY AND IMPLEMENTATION: Panqc is freely available under an MIT license at https://github.com/maxgmarin/panqc.

Genome, Bacterial↗

PubMed1992

Multilocus markers for mouse genome analysis: PCR amplification based on single primers of arbitrary nucleotide sequence.

Polymerase chain reaction (PCR) based on single primers of arbitrary nucleotide sequence provides a powerful marker system for genome analysis because each primer amplifies multiple products, and cloning, sequencing, and hybridization are not required. We have evaluated this typing system for the mouse by identifying optimal PCR conditions; characterizing effects of GC content, primer length, and multiplexed primers; demonstrating considerable variation among a panel of inbred strains; and establishing linkage for several products. Mg2+, primer, template, and annealing conditions were identified that optimized the number and resolution of amplified products. Primers with 40% GC content failed to amplify products readily, primers with 50% GC content resulted in reasonable amplification, and primers with 60% GC content gave the largest number of well-resolved products. Longer primers did not necessarily amplify more products than shorter primers of the same proportional GC content. Multiplexed primers yielded more products than either primer alone and usually revealed novel variants. A strain survey showed that most strains could be readily distinguished with a modest number of primers. Finally, linkage for seven products was established on five chromosomes. These characteristics establish single primer PCR as a powerful method for mouse genome analysis.

Animals↗

PubMed2026

Assessing the Safety and Probiotic Potential of Bifidobacterium longum subsp. infantis BI45: A Comprehensive Study from Genomic Analysis to Randomized Controlled Clinical Trial in Healthy Adults.

While probiotics are increasingly consumed for health benefits, comprehensive safety assessments, particularly for novel strains, are imperative. This study aimed to conduct a holistic safety and efficacy assessment of Bifidobacterium longum subsp. infantis (B. infantis) BI45, spanning genomic analysis, in vitro tests, In vivo toxicity test, and a clinical trial. The safety of B. infantis BI45 was evaluated through: (1) whole-genome sequencing for antibiotic resistance and virulence genes; (2) in vitro phenotyping (hemolysis, cytotoxicity, gastrointestinal tolerance and antibiotic susceptibility); (3) an acute oral toxicity study in mice; and (4) a randomized, double-blind, placebo-controlled clinical trial. Forty-eight healthy adults were recruited and randomly assigned to receive either B. infantis BI45 or a placebo (n = 24/group) for 8 weeks. Hematological, biochemical, immunological, and gut microbiota parameters were assessed. Genomic analysis identified no transferable antibiotic resistance or virulence genes. In vitro assays confirmed the absence of hemolytic and cytotoxic activity, alongside high gastrointestinal tolerance. Antibiotic susceptibility testing showed that B. infantis BI45 is sensitive to a range of antibiotics. No adverse effects were observed in the murine toxicity study at 2 × 10¹⁰ CFU/kg. Importantly, the clinical intervention revealed no adverse events or significant alterations in hematological, hepatic, or renal function markers in the B. infantis BI45 group, demonstrating an excellent safety profile. Furthermore, B. infantis BI45 supplementation significantly increased serum levels of immunomodulatory markers Immunoglobulin A (IgA) and antimicrobial peptide LL-37 compared to the placebo (p < 0.05) and modulated the gut microbiota by enriching beneficial short-chain fatty acid producers. The multi-tiered evidence demonstrates that B. infantis BI45 is a safe probiotic strain that does not induce adverse reactions in healthy adults. Its consumption positively modulates host immunity and the gut microbiota.Trial Registration Number: NCT06863415 (ClinicalTrials.gov).

Adult↗

PubMed2026

Utility of High-Throughput Genomic Analysis for Genetic Counseling in Large Family with Wilson Disease Carrying a Novel 28-bp ATP7B Splice-Junction Deletion.

Background/Objectives: Wilson disease (WD) is an autosomal recessive disorder of copper metabolism caused by pathogenic variants in the ATP7B gene. Early diagnosis and appropriate treatment are essential for preventing irreversible complications. This study demonstrated the clinical utility of integrated high-throughput genomic analysis for molecular diagnosis and genetic counseling in a large Thai family affected by WD. Methods: A 32-year-old woman with clinical features suggestive of WD underwent clinical, biochemical, and molecular genetic evaluations, including sequencing of the entire ATP7B gene and SNP microarray. Fluorescent PCR followed by capillary electrophoresis was used for segregation analysis in available family members. SNP microarray analysis and whole-exome sequencing were performed on the proband's husband to identify pathogenic variants in the ATP7B gene and other disease-associated genes for reproductive risk assessment. Results: The proband presented with hepatic dysfunction, Kayser-Fleischer rings, low serum ceruloplasmin, and a family history of fatal liver disease. She also developed progressive weakness, with nerve conduction findings consistent with axonal sensorimotor polyneuropathy predominantly affecting the lower limbs. Sequencing identified a novel homozygous 28-bp splice-junction deletion, c.4022-24_4025del, which disrupted the canonical splice acceptor site at the intron 19/exon 20 boundary and was classified as pathogenic variant. Segregation analysis confirmed carrier status in the proband's father and identified heterozygous carrier or homozygous wild-type status among her living siblings. SNP microarray analysis revealed a 46.7 Mb copy-neutral long contiguous stretch of homozygosity (CN-LCSH) encompassing ATP7B, with CN-LCSH regions accounting for 2.046% of the total autosomal genome. These findings potentially reflected segmental uniparental isodisomy or identity by descent, while the overall homozygosity pattern did not support recent consanguinity. Combined genomic analyses of the proband's husband revealed no pathogenic or likely pathogenic ATP7B variants. Based on the available testing, all offspring are expected to be heterozygous carriers, and the risk of an affected child is considered very low. Conclusions: This study highlights the value of integrated genomic analysis for molecular diagnosis, cascade testing, and reproductive risk counseling. Further functional studies should be conducted to validate their pathogenicity.

ATP7B↗

PubMed2026

Application of qualifying variants for genomic analysis.

MOTIVATION: Qualifying variants (QVs) are genomic alterations selected by defined criteria within analysis pipelines. Although crucial for both research and clinical diagnostics, QVs are often seen as simple filters rather than dynamic elements that influence the entire workflow. In practice these rules are embedded within pipelines, which hinders transparency, audit, and reuse across tools. A unified, portable specification for QV criteria is needed. RESULTS: Our aim is to embed the concept of a "QV" into the genomic analysis vernacular, moving beyond its treatment as a single filtering step. By decoupling QV criteria from pipeline variables and code, the framework enables clearer discussion, application, and reuse. It provides a flexible reference model for integrating QVs into analysis pipelines, improving reproducibility, interpretability, and interdisciplinary communication. Validation across diverse applications confirmed that QV based workflows match conventional methods while offering greater clarity and scalability. AVAILABILITY AND IMPLEMENTATION: The source code and data are accessible at the Zenodo repository https://doi.org/10.5281/zenodo.17414191. Manuscript files are available at https://github.com/DylanLawless/qvApp2025lawless. The QV framework is available under the MIT licence, and the dataset will be maintained for at least two years following publication.

Genomics↗

PubMed2026

Genomic analysis of an Arctic marine Tenacibaculum sp. SM2510 reveals its genetic potential for glutathione utilization.

Glutathione is a key intracellular antioxidant, playing a crucial role in resisting oxidative stress and maintaining cellular redox homeostasis. However, the glutathione metabolic capacity of Tenacibaculum remains poorly characterized. In this study, a Gram-stain-negative bacterium, Tenacibaculum sp. SM2510, was isolated from seawater collected from Kongsfjorden, Svalbard, Norway. Genome sequencing revealed that the strain possesses a single circular chromosome of 2,904,982 bp with a G + C content of 31.44%, encoding 2564 protein-coding genes. Genomic analysis indicates that Tenacibaculum sp. SM2510 may directly take up extracellular oxidized glutathione (GSSG) and reduce it to reduced glutathione (GSH) through a reductive pathway, which potentially allows the strain to alleviate the accumulation of reactive oxygen species (ROS) caused by strong ultraviolet radiation and low temperature in polar environments. Furthermore, genomic analysis predicts that the strain degrades GSH to produce essential life-sustaining substances. In conclusion, these results suggest that Tenacibaculum sp. SM2510 may potentially utilize exogenous glutathione for both antioxidant defense and nutrient acquisition through direct GSH degradation, providing new insights into the environmental adaptive evolution of polar marine bacteria.

Tenacibaculum↗

PubMed1991

[Genome analysis--current status of knowledge and future perspectives].

The rapid recent progress in molecular biology has placed the complete analysis of the human genome near at hand. This analysis of the human genome is not only restricted to the mapping, i.e. the localization of the genes on the chromosomes, but also involves the complete sequence analysis of the human DNA. Combined with increasingly sophisticated techniques which demand less and less amounts of material, the high resolution genome maps and the availability of a growing set of human genes will also expand the spectrum of possible future applications. Like in other fields these new technological developments will generate problems of social, ethical and legal nature. Therefore it seems absolutely essential not only to advance further technical developments and methodological improvements, but also to integrate these developments within a broad open discussion about their intended and unintended consequences.

Chromosome Aberrations↗

PubMed1992

The new approaches to whole genome analysis of bacteria.

A range of recombinant DNA techniques now enables whole genome analysis of any bacterium to be carried out without recourse to the classical means of bacterial genetic exchange. Using enzymes which cut infrequently, such as SpeI, combined with pulsed field gel electrophoresis, a physical map of ordered fragments can be constructed. By means of cloned fragments of known genes or oligonucleotides synthesized using data from DNA or protein sequence banks, the location of individual genes on this map can be determined. We have used these techniques to study whole genome structure in three species of Pseudomonas: P. aeruginosa, P. putida and P. solanacearum.

Chromosome Mapping↗

PubMed2026

Genomic Analysis and Clinical Correlation of Non-Small Cell Lung Cancer with Special Reference to Brain Metastasis.

BACKGROUND: Next-generation sequencing (NGS) has improved genomic analysis depth in precision oncology. This study analyzed genomic biomarker testing in stage IV NSCLC, focusing on brain metastasis and clinicopathological correlations. OBJECTIVE: To study molecular markers and clinicopathological correlations in stage IV NSCLC patients, with and without brain metastasis. METHODS: A total of 169 stage IV NSCLC patients were studied from April 2023 to May 2025. Demographic data, clinical presentations, and mutation analyses were assessed using NGS on tissue blocks or liquid biopsies. RESULTS: Among 169 patients, 41.42% (n = 70) had brain metastasis (NSCLC-BM), while 58.58% (n = 99) had no brain metastasis (mNSCLC). Median ages were 51.5 and 56 years, respectively. Adenocarcinoma comprised 95.27% (n = 161) of cases. The cerebral hemisphere was the most common intracranial metastatic site, while skeletal involvement was the most common extracranial site. Headache was the predominant neurological symptom. EGFR mutations were the most common overall. EGFR > TP53 > ALK > other mutations were observed in NSCLC-BM, while EGFR > TP53 > KRAS > other mutations were seen in mNSCLC. Mutation analysis stratified by smoking history (χ²(1) = 1.347, p = 0.245) and sex (χ²(1) = 0.0302, p = 0.862) was not statistically significant. The benefit of gefitinib plus chemotherapy in EGFR exon 19 and exon 21 L858R mutations was greater in mNSCLC (log-rank χ²(1) = 10.813, p = 0.001) than in NSCLC-BM (log-rank χ²(1) = 3.100, p = 0.078). Median survival was 11 months (95% CI: 7.506-14.494) for NSCLC-BM versus 21 months (95% CI: 8.365-33.635) for mNSCLC, with a statistically significant difference (log-rank χ²(1) = 8.639, p = 0.003). CONCLUSION: NSCLC-BM showed higher genomic biomarker enrichment (80% vs. 68.68%) but poorer outcomes than mNSCLC. EGFR was the most common targetable mutation, followed by ALK in NSCLC-BM and KRAS in mNSCLC.

Humans↗