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PubMed2002

Full-length genome analysis of natural isolates of vesicular stomatitis virus (Indiana 1 serotype) from North, Central and South America.

Most studies on the molecular biology and functional analysis of vesicular stomatitis virus Indiana 1 serotype (VSV-IN1) are based on the only full-length genomic sequence currently deposited in GenBank. This sequence is a composite of several VSV-IN1 laboratory strains passaged extensively in tissue culture over the years and it is not certain that this sequence is representative of strains circulating in nature. We describe here the complete genomic sequence of three natural isolates, each representing a distinct genetic lineage and geographical origin: 98COE (North America), 94GUB (Central America) and 85CLB (South America). Genome structure and organization were conserved, with a 47 nucleotide 3' leader, five viral genes -- N, P, M, G and L -- and a 59 nucleotide 5' trailer. The most conserved gene was N, followed by M, L and G, with the most variable being P. Sequences containing the polyadenylation and transcription stop and start signals were completely conserved among all the viruses studied, but changes were found in the non-transcribed intergenic nucleotides, including the presence of a trinucleotide at the M-G junction of the South American lineage isolate. A 102-189 nucleotide insertion was present in the 5' non-coding region of the G gene only in the viruses within a genetic lineage from northern Central America. These full-length genomic sequences should be useful in designing diagnostic probes and in the interpretation of functional genomic analyses using reverse genetics.

Base Sequence↗

PubMed2001

The complete genome sequence of the lactic acid bacterium Lactococcus lactis ssp. lactis IL1403.

Lactococcus lactis is a nonpathogenic AT-rich gram-positive bacterium closely related to the genus Streptococcus and is the most commonly used cheese starter. It is also the best-characterized lactic acid bacterium. We sequenced the genome of the laboratory strain IL1403, using a novel two-step strategy that comprises diagnostic sequencing of the entire genome and a shotgun polishing step. The genome contains 2,365,589 base pairs and encodes 2310 proteins, including 293 protein-coding genes belonging to six prophages and 43 insertion sequence (IS) elements. Nonrandom distribution of IS elements indicates that the chromosome of the sequenced strain may be a product of recent recombination between two closely related genomes. A complete set of late competence genes is present, indicating the ability of L. lactis to undergo DNA transformation. Genomic sequence revealed new possibilities for fermentation pathways and for aerobic respiration. It also indicated a horizontal transfer of genetic information from Lactococcus to gram-negative enteric bacteria of Salmonella-Escherichia group.

Amino Acids↗

PubMed2026

Artificial intelligence agents and agentic artificial intelligence applied to precision medicine.

Precision medicine seeks to individualise care by integrating multimodal biomedical data, yet most deployed clinical artificial intelligence (AI) remains assistive, providing predictions without managing workflows or adapting autonomously. Agentic AI, built on large language models (LLMs), has emerged as a paradigm characterised by autonomy, goal-directed reasoning, memory, planning and tool use. This review synthesises evidence on agentic AI and LLMs applied to precision medicine, encompassing drug discovery, genomics, oncology, rare disease diagnostics and clinical pharmacology. This review also examines architectural components, recent validation milestones and emerging challenges, including hallucination, sociodemographic bias and evolving regulatory frameworks across the FDA, the EU AI Act and the WHO.

agentic AI↗

PubMed2006

Advancement in characterization of genomic alterations for improved diagnosis, treatment and prognostics in cancer.

Most human cancers are characterized by genetic instabilities. These instabilities manifest themselves as a series of genetic alterations, including discrete mutations and chromosomal aberrations. With the human genome deciphered, high-throughput technologies are rapidly advancing the field to generate genome-wide gene expression and mutation profiles that are highly correlative of biologic and disease phenotypes. While recent advancement in comprehensive genomic characterization presents an unprecedented opportunity for advancing the treatment of cancer, there are still many challenges that need to be overcome before we can fully utilize genomic markers and targets for cancer prediction, diagnostics, treatment and prognostics. This review describes recent advances in comprehensive genomic characterization at the DNA level, and considers some of the challenges that remain for defining the precise genomic portrait of tumors. Potential solutions that may help overcome these challenges are also offered.

Animals↗

PubMed2003

Genome sequencing and comparative genomics of tropical disease pathogens.

The sequencing of eukaryotic genomes has lagged behind sequencing of organisms in the other domains of life, archae and bacteria, primarily due to their greater size and complexity. With recent advances in high-throughput technologies such as robotics and improved computational resources, the number of eukaryotic genome sequencing projects has increased significantly. Among these are a number of sequencing projects of tropical pathogens of medical and veterinary importance, many of which are responsible for causing widespread morbidity and mortality in peoples of developing countries. Uncovering the complete gene complement of these organisms is proving to be of immense value in the development of novel methods of parasite control, such as antiparasitic drugs and vaccines, as well as the development of new diagnostic tools. Combining pathogen genome sequences with the host and vector genome sequences is promising to be a robust method for the identification of host-pathogen interactions. Finally, comparative sequencing of related species, especially of organisms used as model systems in the study of the disease, is beginning to realize its potential in the identification of genes, and the evolutionary forces that shape the genes, that are involved in evasion of the host immune response.

Animals↗

PubMed2026

Conference report: the third Bacterial Genome Sequencing Pan-European Network conference.

The third Bacterial Genome Sequencing Pan-European Network conference, held in Engelberg, Switzerland (12-15 January 2026), brought together experts from six European countries to discuss the implementation of bacterial genome sequencing in clinical microbiology and public health. Key themes included regulatory frameworks (In Vitro Diagnostic Regulation, General Data Protection Regulation), standardization, quality control, data sharing, economic evaluation, and the integration of artificial intelligence and long-read sequencing into diagnostic workflows. Across presentations, panel discussions, and workshops, participants emphasized that successful implementation of genome sequencing requires more than technical capacity: it depends on robust validation, sustainable funding, interoperable data standards, ethical governance, and interdisciplinary collaboration. The meeting highlighted that sequencing should remain question-driven and clinically meaningful, balancing cost, turnaround time, and public health impact. Overall, the conference reinforced the need for coordinated European efforts to advance responsible, standardized, and sustainable genomic surveillance and diagnostics.

bacterial genome sequencing↗

PubMed2026

Hypervirulent Klebsiella pneumoniae ST23 causing pyogenic liver abscess and metastatic endogenous endophthalmitis in Europe: a case report.

INTRODUCTION AND IMPORTANCE: Pyogenic liver abscess (PLA) has traditionally been considered prevalent in Asia. However, its incidence is increasing in Europe. Klebsiella pneumoniae (Kp) has emerged as the leading causative pathogen, and hypervirulent strains pose a higher risk of invasive disease and metastatic complications, such as endogenous endophthalmitis (EE). CASE PRESENTATION: The case describes a 77-year-old woman who presented with fever and right upper quadrant abdominal pain. She was diagnosed with a second episode of PLA within 3 months, caused by Kp. Despite prompt antimicrobial therapy and percutaneous transhepatic drainage, the patient developed acute vision loss in the left eye during hospitalization. Ophthalmologic assessment confirmed EE secondary to bacteremia. Whole-genome sequencing identified the isolate as hypervirulent Kp (hvKp) sequence type 23 (ST23). While the liver abscess resolved following treatment, the patient sustained permanent loss of vision in the affected eye despite aggressive medical and surgical management. CLINICAL DISCUSSION: This case illustrates the invasive nature of hvKp and its potential for recurrence and metastatic complications. Improved recognition through targeted virulence testing is essential to avoid underdiagnosis. CONCLUSION: This case highlights the aggressive nature of hvKp. Early recognition of systemic and ocular symptoms, prompt ophthalmologic evaluation, and timely source control are essential. Optimal management requires multidisciplinary collaboration and the use of molecular diagnostics, including whole-genome sequencing, to identify hypervirulent lineages and support surveillance.

Klebsiella pneumoniae↗

PubMed2003

Classification of bladder cancer by microarray expression profiling: towards a general clinical use of microarrays in cancer diagnostics.

At present there are no clinically useful markers available for identifying bladder cancer patients with a high risk of disease recurrence or progression. Thus, identification and tailor-suited treatment, for example radical cystectomy and adjuvant therapy, of patients with a poor prognosis is not possible using current methods. The completion of the Human Genome Project and the simultaneous advances in microarray technology have paved the way for performing systematic, full genome screens for prognostic and diagnostic molecular cancer markers. Furthermore, utilization of microarray technology for identifying clinically relevant subclasses of cancer patients and for discovering new potential drug targets seems promising. This article summarizes some of the clinical aspects of bladder cancer and reviews the potential of using tumor expression profiling for the identification of new molecular cancer markers and drug targets, and for generating disease classifiers and outcome predictors using several key gene markers.

Biomarkers, Tumor↗

PubMed1999

Prader Willi and Angelman syndromes: exemplars of genomic imprinting.

The molecular phenomenon genomic imprinting provides an explanation for why two clinically distinct syndromes share genetic etiologies. Increased understanding of genomic imprinting is affecting diagnostics. Use of improved diagnostic tests can enable early, syndrome-specific, and anticipatory interventions and consequently, improved quality of life; however, these tests are of little use unless clinicians are able to identify at-risk patients. Nurses knowledgeable about Prader Willi and Angelman syndromes and their associated genetic mechanisms can play a significant role in early identification, referral, and intervention of patients with these conditions.

Angelman Syndrome↗

PubMed2026

Respiratory manifestations as clues to inherited metabolic disorders in children: a phenotype-driven diagnostic approach.

UNLABELLED: Inherited metabolic disorders (IMDs) are uncommon but clinically important causes of respiratory morbidity in children. Respiratory involvement may be the first or dominant manifestation, although it may precede, accompany, or follow systemic involvement. Because cough, dyspnea, hypoxemia, recurrent infection, abnormal chest imaging, and ventilatory failure are non-specific, affected children may initially be managed for common respiratory conditions, such as infection, asthma, aspiration, immunodeficiency, or non-metabolic diffuse lung disease, before the underlying IMD is recognized. This narrative mini-review presents a phenotype-driven approach to recognizing IMDs in pediatric respiratory practice. Rather than cataloguing rare disorders by metabolic pathway, it organizes respiratory involvement into practical clinical entry points: diffuse lung disease, pulmonary alveolar proteinosis-like disease, pulmonary vascular disease, recurrent infection or bronchiectasis, upper-airway or thoracic restriction, and neuromuscular respiratory failure and aspiration. For each pattern, we highlight extrapulmonary red flags and first-line biochemical, enzymatic, and genetic tests that may guide early etiological diagnosis. CONCLUSION: Careful recognition of respiratory phenotypes, combined with targeted metabolic and genomic evaluation, may shorten diagnostic delay and allow disease-specific treatment before irreversible pulmonary or neurological injury occurs. WHAT IS KNOWN: • IMDs can involve the respiratory system and may mimic common pediatric respiratory disorders or non-metabolic forms of childhood diffuse lung disease. • Respiratory manifestations may precede, accompany, or follow classical systemic features, and their temporal pattern varies among individual IMDs. WHAT IS NEW: • This mini-review organizes IMD-related respiratory involvement by presenting respiratory phenotype rather than by metabolic pathway. • It links respiratory entry points with extrapulmonary red flags and targeted biochemical, enzymatic, and genetic testing to support earlier diagnosis.

Humans↗

PubMed1995

Direct molecular analysis of myotonic dystrophy in the German population: important considerations in genetic counselling.

Myotonic dystrophy (DM) is associated with the expansion and instability of a trinucleotide (CTG) repeat at the DM locus on chromosome 19. Direct genomic analysis in the German population was carried out on 18 DM families, six families with equivocal diagnosis, 69 subjects with equivocal clinical diagnosis, and 100 controls using the polymerase chain reaction (PCR) and a refined Southern protocol. In the majority of the cases molecular analysis confirmed the clinical diagnosis. These included seven cases of congenital DM (CDM) with widely differing gene expansions and instabilities. In most DM families the expanded fragment became larger in successive generations, but we also identified four families with contractions and two families that showed stability of the enlarged fragment during transmission. In four clinically defined DM patients we were unable to detect enlarged CTG repeats. Sequencing of each exon of the DM gene in two of these patients failed to show any mutations. Our cases have important implications for genetic counselling of DM families, highlighting both the diagnostic value of direct genomic analysis and its limitations.

Adult↗

PubMedDate not supplied

Direct detection of Bordetella pertussis and Bordetella parapertussis: comparison of polymerase chain reaction and culture.

We evaluated the diagnostic performance of a genomic DNA amplification method for Bordetella pertussis and Bordetella parapertussis compared with culture isolation. Aliquots from B. pertussis and B. parapertussis cultures were added to sterile physiological saline or sterile distilled water to give bacterial suspensions of 10(8) cells/ml and serial dilutions were prepared. Suspensions in physiological saline were cultured on charcoal agar medium; bacterial growth was observed up to dilutions of 10(-7). Suspensions in distilled water were subjected to DNA extraction and nested polymerase chain reaction (PCR) was performed on the extracts; the PCR was positive up to dilutions of 10(-8) for B. pertussis and 10(-9) for B. parapertussis. Since the efficacy of culture isolation, regarded as the standard for the detection of B. pertussis and B. parapertussis, declines after the first stage of pertussis or with prior vaccination or antibiotic therapy, PCR, although not yet standardized, may provide an alternative diagnostic tool.

Bacterial Typing Techniques↗

PubMed2003

The high road to success: how investing in ethics enhances corporate objectives.

There is a growing gap between the tidal wave of information emerging from the Human Genome Project and other molecular biology initiatives, and the clinical research needed to transform these discoveries into new diagnostics and therapeutics. While genomics-based technologies are being rapidly integrated into pharmaceutical R&D, many steps in the experimental process are still reliant on traditional surrogate model systems whose predictive power about human disease is incomplete or inaccurate. There is a growing trend underway in the research community to introduce actual human disease understanding as early as possible into discovery, thereby improving accuracy of results throughout the R&D continuum. Such an approach (known as clinical genomics: the large scale study of genes in the context of actual human disease) requires the availability of large quantities of ethically and legally sourced, high-quality human tissues with associated clinical information.Heretofore, no source could meet all of these requirements. Ardais Corporation was the first to address this need by pioneering a systematized, standardized network for the collection, processing, dissemination and research application of human tissue and associated clinical information, all of which rest on the highest ethical standards. Based on a novel model of collaboration between industry and the academic/medical community, Ardais has created procedures, structures, technologies, and information tools that collectively compromise a new paradigm in the application of human disease to biomedical research. Ardais now serves as a clinical genomics resource to dozens of academic researchers and biopharmaceutical companies, providing products and services to accelerate and improve drug discovery and development.

Advisory Committees↗

PubMed1992

Differentiation of potyviruses and their strains by hybridization with the 3' non-coding region of the viral genome.

Nucleic acid hybridization with the 3' non-coding region of the potyvirus genome as the probe was shown to be a relatively simple means of distinguishing between distinct potyviruses and their strains. Comparisons of the nucleotide sequences of potyvirus genomes (ignoring gaps) showed that the degree of identity between equivalent genes of strains was greater than 96%, while between distinct potyviruses the identity ranged from 42% to 65%, suggesting that any extended sequence could be considered representative of the whole genome and be suitable as a diagnostic probe. The comparisons however, also revealed that some parts of the genome, but not the 3' non-coding region, had local regions of high sequence identity that could lead to cross-hybridization between distinct potyviruses. For this reason, and because its location immediately upstream of the poly(A) tail makes it the most accessible region for the purpose of cloning and sequencing, the 3' non-coding sequence should be most suitable for use as a diagnostic probe. Successful hybridizations (using radiolabeled, polymerase chain reaction-amplified 3' non-coding sequences) have been achieved by probing recombinant clones, purified potyviral RNA, partially purified total RNA from infected plants, and a crude extract of infected plant tissue. The method has been used to support the proposals that watermelon mosaic virus 2 and soybean mosaic virus-N are both strains of the same virus, and to discriminate between several isolates previously believed to be strains of sugarcane mosaic virus. The method should have wide application as a means of differentiating distinct potyviruses from strains.

Blotting, Southern↗

PubMed2026

Proteomics identify disease-associated variants in patients with rare diseases undiagnosed after genome sequencing.

Despite the introduction of genome sequencing (GS) for rare disease diagnostics, a genetic cause is not identified in most patients. Here, we explored the potential of proteomics to improve the diagnostic yield in 424 patients with rare diseases from the 100,000 Genomes Project (100kGP) without a genetic diagnosis. Serum proteomic profiling was performed using the Olink Explore 1536 assay (N = 1463 proteins). For 13 patients without genetic diagnoses, detection of lower serum protein "outliers" (z-score < -2) led to confirmed genetic diagnoses by resolving variants of uncertain significance or prioritizing genes for targeted GS reanalysis. For 23 additional patients without genetic diagnoses (64% of findings), we identified candidate gene-disease links and variants through convergent evidence from lower protein outliers and variants ranked through the variant prioritization tool Exomiser. For example, we identified a candidate heterozygous missense variant [Genome Aggregation Database (gnomAD) minor allele frequency = 0.006%] in tyrosine kinase with immunoglobulin-like and epidermal growth factor homology domains 1 (TIE1) that was only present in a patient with lower TIE1 serum abundance (z-score = -5.12) and their father, both of whom were affected by the same monogenic cardiac disorder, but in no other individuals from the 100kGP. Missense (52.5%) and splice region (27.5%) variants accounted for most diagnostic or candidate variants prioritized. This proof-of-principle study demonstrated that serum proteomics can support rare disease diagnosis and identify disease-causing genes in patients undiagnosed after GS, although successful implementation will likely depend on tissue specificity of protein expression, detectability in blood, proteomic platform coverage, and sensitivity.

Humans↗

PubMed2006

Natural language processing and visualization in the molecular imaging domain.

Molecular imaging is at the crossroads of genomic sciences and medical imaging. Information within the molecular imaging literature could be used to link to genomic and imaging information resources and to organize and index images in a way that is potentially useful to researchers. A number of natural language processing (NLP) systems are available to automatically extract information from genomic literature. One existing NLP system, known as BioMedLEE, automatically extracts biological information consisting of biomolecular substances and phenotypic data. This paper focuses on the adaptation, evaluation, and application of BioMedLEE to the molecular imaging domain. In order to adapt BioMedLEE for this domain, we extend an existing molecular imaging terminology and incorporate it into BioMedLEE. BioMedLEE's performance is assessed with a formal evaluation study. The system's performance, measured as recall and precision, is 0.74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information.

Animals↗

PubMed2006

The potential of comparative genomic hybridization as a tool in the differential diagnosis of matrix-producing bone lesions.

Matrix-producing bone lesions consist of a wide variety of benign and malignant conditions. With respect to morphology, an overlap exists between benign and malignant bone tumors that causes difficulties in the final determination of the tumor. This study was conducted to show the potential of comparative genomic hybridization as a tool in the differential diagnosis of matrix-producing bone lesions. Thirty benign bone tumors were evaluated by conventional comparative genomic hybridization. To test its diagnostic reliability, 5 additional cases were analyzed, all with differential diagnostic difficulties related to morphology and radiology. All were ultimately diagnosed as malignant sarcomas, and unbalanced alterations were detected. In contrast benign tumors or tumor-like lesions did not reveal any chromosomal alterations. Comparative genomic hybridization is a useful adjunct in the complicated differential diagnostic algorithms of matrix-producing bone tumors.

Adolescent↗

PubMed2004

[Myiasis caused by Oestridae: serological and molecular diagnosis].

Myiasis-causing Oestridae (bot flies) infect several animal species world-wide, from palaearctic to subtropical/tropical areas. Oestrids affect livestock production causing abortion, reduced milk production, losses in weight and fertility, poor hide quality and an impairment of the host's immune system. In the last few years much research has been carried out on the immunology of these infestations, in order to acquire efficient and reliable diagnostic serological tools; the genome of the different species of Oestridae has been studied to further their molecular identification, taxonomy and phylogenesis. The immunodiagnostic methods for many myiasis causing Oestrids have proven to be a viable alternative to the clinical parasitological examination or the post-mortem examination. Numerous serological tests have been developed for the diagnosis of bovine hypodermosis caused by Hypoderma bovis and Hypoderma lineatum, and ELISAs using larval hypodermin C as the antigen are currently used on serum, individual and pooled milk samples to detect the presence of circulating anti-Hypoderma antibodies. In Italy the best period to sample the animals is November-January, since it is in this period that the antibody kinetics of the animals reaches a peak. Recently the efficacy of the ELISA test on pasteurized milk samples has been demonstrated, allowing the diagnosis of bovine hypodermosis also in areas where there is no information on the presence of the disease and the sampling of the animals is laborious. The cross-reactivity between Przhevalskiana silenus antigens and anti-Hypoderma antibodies led to assessing the usefulness of a simple and cost-effective ELISA for the diagnosis of goat warble fly infection. In particular, it has been demonstrated that infected goats display an antibody peak in November-December in blood and milk, thus making this period suitable for sampling. Although no extensive data is available on the immunology of sheep and goat oestrosis caused by Oestrus ovis, the efficacy of ELISA has been demonstrated by correlating serological results with clinical post-mortem examinations. No immunological techniques are currently used to diagnose gasterophilosis of equids and only one study reports the efficacy of ELISA for detecting anti-Gasterophilus antibodies in infected equids. Several studies have been conducted into the molecular characterization of the mitochondrial DNA (mtDNA)--in particular of the gene encoding for the cytochrome oxidase I (COI)--for many free-living and parasitic arthropods for diagnostic, taxonomic and phylogenetic purposes. As regards Oestridae causing myiasis, the first study features a PCR-RFLP assay of the most common Italian species (i.e. H. bovis, H. lineatum, Gasterophilus intestinalis, P. silenus, O. ovis), which showed clear genetic differences among the genera examined, but no inter-specific variation between the two species of Hypoderma considered. The molecular characterization of the most variable region of the COI gene (encoding for the region from E4 to the terminal COOH) was able to clearly differentiate H. bovis and H. lineatum. The E4-COOH region of the COI gene has been characterized for 18 oestrid species and from a taxonomical point of view, molecular data confirm the morphological classification, with the examined species divided into four subfamilies. New insights have also been gained on the molecular differentiation of the most common species of Hypoderma (i.e. H. bovis, H. lineatum, Hypoderma actaeon, Hypoderma diana and Hypoderma tarandi) and, in particular, the restriction enzyme BfaI, provides a diagnostic profile that can be used to simultaneously differentiate all the species examined. The characterization of the E4-COOH COI gene and the hypervariable region of the gene encoding for the ribosomal Isu revealed the identity of Hypoderma sinense as a new species, infecting cattle and yaks in China. Finally, the molecular analysis of the same mitochondrial and ribosomal regions showed that P. silenus, Przhevalskiana aegagri and Przhevalskiana crossii are morphotypes of the same species.

Animals↗