Bioinformatics from the perspective of the public health laboratory.
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Computational Biology↗
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Overview of bioinformatics and its application to oral genomics.
The "informatics revolution" in both bioinformatics and dental informatics will eventually change the way we practice dentistry. This convergence will play a pivotal role in creating a bridge of opportunity by integrating scientific and clinical specialties to promote the advances in treatment, risk assessment, diagnosis, therapeutics, and oral health-care outcome. Bioinformatics has been an emerging field in the biomedical research community and has been gaining momentum in dental medicine. This area has created a steady stream of large and complex genomic data, which has transformed the way a clinical or basic science researcher approaches genomic research. This application to dental medicine, termed "oral genomics", can aid in the molecular understanding of the genes and proteins, their interactions, pathways, and networks that are responsible for the development and progression of oral diseases and disorders. As the result of the Human Genome Project, new advances have prompted high-throughput technologies, such as DNA microarrays, which have become accepted tools in the biomedical research community. This manuscript reviews the two most commonly used microarray technologies, basic microarray data analysis, and the results from several ongoing oral cancer genomic studies.
Carcinoma, Squamous Cell↗
Individual metabolism should guide agriculture toward foods for improved health and nutrition.
Genomics and bioinformatics have the vast potential to identify genes that cause disease by investigating whole-genome databases. Comparison of an individual's geno-type with a genomic database will allow the prescription of drugs to be tailored to an individual's genotype. This same bioinformatic approach, applied to the study of human metabolites, has the potential to identify and validate targets to improve personalized nutritional health and thus serve to define the added value for the next generation of foods and crops. Advances in high-throughput analytic chemistry and computing technologies make the creation of a vast database of metabolites possible for several subsets of metabolites, including lipids and organic acids. In creating integrative databases of metabolites for bioinformatic investigation, the current concept of measuring single biomarkers must be expanded to 3 dimensions to 1) include a highly comprehensive set of metabolite measurements (a profile) by multiparallel analyses, 2) measure the metabolic profile of individuals over time rather than simply in the fasted state, and 3) integrate these metabolic profiles with genomic, expression, and proteomic databases. Application of the knowledge of individual metabolism will revolutionize the ability of nutrition to deliver health benefits through food in the same way that knowledge of genomics will revolutionize individual treatment of dis-ease with pharmaceuticals.
Biomarkers↗
Military research needs in biomedical informatics.
The 2001 U.S. Army Medical Research and Materiel Command (USAMRMC) Biomedical Informatics Roadmap Meeting was devoted to developing a strategic plan in four focus areas: Hospital and Clinical Informatics, E-Health, Combat Health Informatics, and Bioinformatics and Biomedical Computation. The driving force of this Roadmap Meeting was the recent accelerated pace of change in biomedical informatics in which emerging technologies have the potential to affect significantly the Army research portfolio and investment strategy in these focus areas. The meeting was structured so that the first two days were devoted to presentations from experts in the field, including representatives from the three services, other government agencies, academia, and the private sector, and the morning of the last day was devoted to capturing specific biomedical informatics research needs in the four focus areas. This white paper summarizes the key findings and recommendations and should be a powerful tool for the crafting of future requests for proposals to help align USAMRMC new strategic research investments with new developments and emerging technologies.
Computational Biology↗
PathoSeq-QC: a decision support bioinformatics workflow for robust genomic surveillance.
MOTIVATION: Recommendations on the use of genomics for pathogens surveillance are evidence that high-throughput genomic sequencing plays a key role to fight global health threats. Coupled with bioinformatics and other data types (e.g., epidemiological information), genomics is used to obtain knowledge on health pathogenic threats and insights on their evolution, to monitor pathogens spread, and to evaluate the effectiveness of countermeasures. From a decision-making policy perspective, it is essential to ensure the entire process's quality before relying on analysis results as evidence. Available workflows usually offer quality assessment tools that are primarily focused on the quality of raw NGS reads but often struggle to keep pace with new technologies and threats, and fail to provide a robust consensus on results, necessitating manual evaluation of multiple tool outputs. RESULTS: We present PathoSeq-QC, a bioinformatics decision support workflow developed to improve the trustworthiness of genomic surveillance analyses and conclusions. Designed for SARS-CoV-2, it is suitable for any viral threat. In the specific case of SARS-CoV-2, PathoSeq-QC: (i) evaluates the quality of the raw data; (ii) assesses whether the analysed sample is composed by single or multiple lineages; (iii) produces robust variant calling results via multi-tool comparison; (iv) reports whether the produced data are in support of a recombinant virus, a novel or an already known lineage. The tool is modular, which will allow easy functionalities extension. AVAILABILITY AND IMPLEMENTATION: PathoSeq-QC is a command-line tool written in Python and R. The code is available at https://code.europa.eu/dighealth/pathoseq-qc.
Genomics↗
Integrated molecular, epidemiological, and bioinformatics perspectives on the Mpox virus: Implications for surveillance and Global Health preparedness.
Mpox has re-emerged as a significant global zoonotic threat, driven mainly by two large waves the 2022 worldwide Clade IIb outbreak and the 2024 Clade Ib epidemic in Central Africa. This review examines the challenges of interpreting this evolving virus from molecular, epidemiological, and bioinformatics perspectives, with a focus on global health workforce preparedness. Clade IIb largely moved through sexual transmission across countries, but Clade Ib has appeared in a wider population-women, children, and individuals infected through household spread without any sexual contact. Early case series suggest that Clade Ib may cause a more severe disease burden, but more research is needed to directly compare severity and fatality rates with Clade IIb due to the limited number of current studies. The review examines the virus's strategies for evading the host's immune defenses throughout its ∼197 kbp genome, including how it disrupts interferon signaling and creates decoy receptors. This review summarizes the clinical findings of PALM007 and STOMP, noting that neither trial achieved its main efficacy endpoint making routine tecovirimat use less compelling-while leaving open whether it helps particular high-risk groups. A further point is that immunity from the MVA-BN vaccine wanes with time, leading to the growing adoption of booster vaccinations. In conclusion, the review calls for a One Health approach pairing genomic tracking with ecological intelligence and including wastewater surveillance to fill existing gaps in knowledge and enhance the global handling of new orthopoxvirus threats.
Animals↗
Building a bioinformatics community of practice through library education programs.
This paper addresses the following questions:What makes the community of practice concept an intriguing framework for developing library services for bioinformatics? What is the campus context and setting? What has been the Health Sciences Library's role in bioinformatics at the University of North Carolina (UNC) Chapel Hill? What are the Health Sciences Library's goals? What services are currently offered? How will these services be evaluated and developed? How can libraries demonstrate their value? Providing library services for an emerging community such as bioinformatics and computational biology presents special challenges for libraries including understanding needs, defining and communicating the library's role, building relationships within the community, preparing staff, and securing funding. Like many academic health sciences libraries, the University of North Carolina (UNC) at Chapel Hill Health Sciences Library is addressing these challenges in the context of its overall mission and goals.
Academic Medical Centers↗
Medical informatics in population health: building Wisconsin's strategic framework for health information technology.
Medicine is increasingly practiced through the application of information sciences. Medical informatics deals with optimal information use within bioinformatics, imaging, clinical, and population health domains. Population health informatics plays an important role in that it critically informs practice in each of the other domains. Proper functioning of health care systems requires an advanced health information network that supports clinical care, personal health management, population health, and research. But this infrastructure does not yet exist in the United States. A number of federal initiatives are underway to address this problem, including the development of a framework for a national health information network and funding for implementation. This network will be facilitated by federal leadership, but public and private partnerships, and state, regional, and local implementation and policy development will play a critical role. In this article, we describe several Wisconsin initiatives that are keys to developing a strategic framework and building the state's electronic health information infrastructure.
Biomedical Technology↗
Detection and characterization of antiviral-resistant viruses during the influenza season of 2024-25.
UNLABELLED: During the high severity season of 2024-25, CDC with public health partners sequenced and analyzed genomes of >10,000 influenza viruses for antiviral resistance markers. Available sequence-flagged and representative viruses were tested with antivirals using in vitro assays. In the US, three oseltamivir-resistant A(H3N2) viruses had treatment-emergent neuraminidase (NA) mutations, either E119V or R292K. Oseltamivir-resistant A(H1N1)pdm09 viruses with NA-H275Y were detected in 15 states, albeit at a low frequency (0.53%). They belonged to several phylogenetic groups, with hemagglutinin (HA) subclade D.3.1 combined with either NA subclade D.1 or D.2 being most common. Based on shared sequence data, nearly all H275Y viruses from Australia, Canada, and Chile also belonged to these HA and NA subclades. Conversely, most H275Y viruses (68/81) from China belonged to HA subclade C.1.9 and NA subclade D and shared the permissive mutation R257K. Influenza polymerase acidic (PA) mutations conferring 4- to 92-fold decreased baloxavir susceptibility were detected in nine influenza A viruses. Viruses with PA-I38T showed mild attenuation of replicative fitness in three cell lines. Based on available data, NA-H275Y and PA-I38T viruses were collected from patients with no exposure to antivirals. Baseline susceptibility to all US-approved influenza antivirals remained largely unchanged compared to previous seasons. All swine-origin viruses detected in the US had adamantane resistance-conferring marker, M2-S31N, but remained susceptible to other approved antivirals. Monitoring antiviral susceptibility has substantially improved with increased sequencing capacities and bioinformatic support at public health laboratories. Information gained through influenza surveillance has been used to guide recommendations on antiviral use. IMPORTANCE: Circulation of influenza viruses with reduced susceptibility to antivirals can diminish the usefulness of medications prescribed for influenza. This study informs on the prevalence of drug-resistant influenza viruses in the US during the high severity season of 2024-25. It provides information on susceptibility profile to all approved antiviral medications and on replicative fitness of representative drug-resistant viruses. Most drug-resistant viruses were collected from patients who were not exposed to antivirals indicating their ability to transmit from human to human. Whole-genome sequence (WGS)-based analysis is the cornerstone for surveillance, and numerous laboratories have been utilizing this approach. However, CDC laboratory is the only laboratory in the US conducting phenotypic testing of circulating viruses needed to confirm the outcomes of sequence-based analysis and to identify new molecular markers of resistance. Data gathered through virologic surveillance give much-needed information on drug susceptibility of influenza viruses which are used to guide recommendations on antiviral use.
Antiviral Agents↗
Molecular classification of liver cirrhosis in a rat model by proteomics and bioinformatics.
Liver cirrhosis is a worldwide health problem. Reliable, noninvasive methods for early detection of liver cirrhosis are not available. Using a three-step approach, we classified sera from rats with liver cirrhosis following different treatment insults. The approach consisted of: (i) protein profiling using surface-enhanced laser desorption/ionization (SELDI) technology; (ii) selection of a statistically significant serum biomarker set using machine learning algorithms; and (iii) identification of selected serum biomarkers by peptide sequencing. We generated serum protein profiles from three groups of rats: (i) normal (n=8), (ii) thioacetamide-induced liver cirrhosis (n=22), and (iii) bile duct ligation-induced liver fibrosis (n=5) using a weak cation exchanger surface. Profiling data were further analyzed by a recursive support vector machine algorithm to select a panel of statistically significant biomarkers for class prediction. Sensitivity and specificity of classification using the selected protein marker set were higher than 92%. A consistently down-regulated 3495 Da protein in cirrhosis samples was one of the selected significant biomarkers. This 3495 Da protein was purified on-chip and trypsin digested. Further structural characterization of this biomarkers candidate was done by using cross-platform matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) peptide mass fingerprinting (PMF) and matrix-assisted laser desorption/ionization time of flight/time of flight (MALDI-TOF/TOF) tandem mass spectrometry (MS/MS). Combined data from PMF and MS/MS spectra of two tryptic peptides suggested that this 3495 Da protein shared homology to a histidine-rich glycoprotein. These results demonstrated a novel approach to discovery of new biomarkers for early detection of liver cirrhosis and classification of liver diseases.
Algorithms↗
Toward a unified approach: Considerations for bioinformatic and sequencing activities & data in wastewater surveillance of biologic public health threats.
Genomic technologies such as PCR and next-generation sequencing (NGS) have greatly advanced public health surveillance, especially during COVID-19, by enabling detailed tracking of pathogen spread, origins, and variants. While PCR is vital for targeted detection, falling NGS costs have made large-scale, high-throughput sequencing more feasible, supporting broader pathogen monitoring-including the detection of vaccine escape variants and new strains. Applying NGS to wastewater offers valuable population-level insights but faces challenges such as variable sample complexity, the need for skilled staff, suitable platforms, and robust IT infrastructure. Although there are currently a lot of efforts towards defining guidelines for sampling, analysis, and integrating wastewater data into public health policy, such as the recently published International Cookbook for Wastewater Practitioners, they often lack universal applicability, emphasizing the analytical approaches in favour of the NGS-based approaches. However, standardising protocols for sampling, sequencing, and analysis is crucial to ensure reliable, comparable data across surveillance systems worldwide. Pilot studies and continuous refinement are recommended to overcome implementation hurdles and fully realise the benefits of NGS in wastewater surveillance. This work attempts to outline these challenges and opportunities across the entire wastewater surveillance workflow, from data generation to reporting, and provide some concrete suggestions and considerations across the spectrum of activities. We further highlight that the infrastructure, funding and government-policy context in which surveillance operates acts as an enabling condition for these activities, and that technical standardisation alone is unlikely to deliver durable, comparable surveillance in its absence.
considerations↗
The challenge of ubiquitous computing in health care: technology, concepts and solutions. Findings from the IMIA Yearbook of Medical Informatics 2005.
OBJECTIVES: To review recent research efforts in the field of ubiquitous computing in health care. To identify current research trends and further challenges for medical informatics. METHODS: Analysis of the contents of the Yearbook on Medical Informatics 2005 of the International Medical Informatics Association (IMIA). RESULTS: The Yearbook of Medical Informatics 2005 includes 34 original papers selected from 22 peer-reviewed scientific journals related to several distinct research areas: health and clinical management, patient records, health information systems, medical signal processing and biomedical imaging, decision support, knowledge representation and management, education and consumer informatics as well as bioinformatics. A special section on ubiquitous health care systems is devoted to recent developments in the application of ubiquitous computing in health care. Besides additional synoptical reviews of each of the sections the Yearbook includes invited reviews concerning E-Health strategies, primary care informatics and wearable healthcare. CONCLUSIONS: Several publications demonstrate the potential of ubiquitous computing to enhance effectiveness of health services delivery and organization. But ubiquitous computing is also a societal challenge, caused by the surrounding but unobtrusive character of this technology. Contributions from nearly all of the established sub-disciplines of medical informatics are demanded to turn the visions of this promising new research field into reality.
Biomedical Technology↗
Metabolomics: building on a century of biochemistry to guide human health.
Medical diagnosis and treatment efficacy will improve significantly when a more personalized system for health assessment is implemented. This system will require diagnostics that provide sufficiently detailed information about the metabolic status of individuals such that assay results will be able to guide food, drug and lifestyle choices to maintain or improve distinct aspects of health without compromising others. Achieving this goal will use the new science of metabolomics - comprehensive metabolic profiling of individuals linked to the biological understanding of human integrative metabolism. Candidate technologies to accomplish this goal are largely available, yet they have not been brought into practice for this purpose. Metabolomic technologies must be sufficiently rapid, accurate and affordable to be routinely accessible to both healthy and acutely ill individuals. The use of metabolomic data to predict the health trajectories of individuals will require bioinformatic tools and quantitative reference databases. These databases containing metabolite profiles from the population must be built, stored and indexed according to metabolic and health status. Building and annotating these databases with the knowledge to predict how a specific metabolic pattern from an individual can be adjusted with diet, drugs and lifestyle to improve health represents a logical application of the biochemistry knowledge that the life sciences have produced over the past 100 years.
Journal Article↗
Medical Imaging Informatics and Medical Informatics: opportunities and constraints. Findings from the IMIA yearbook of Medical Informatics 2002.
OBJECTIVES: The Yearbook of Medical Informatics is published annually by the International Medical Informatics Association (IMIA) and contains a selection of recent excellent papers on medical informatics research (http://www.yearbook.uni-hd.de). The 2002 Yearbook of Medical Informatics took as its theme the topic of Medical Imaging Informatics. In this paper, we will summarize the contributions of medical informatics researchers to the development of medical imaging informatics, discuss challenges and opportunities of imaging informatics, and present the lessons learned from the IMIA Yearbook 2002. RESULTS AND CONCLUSIONS: Medical informatics researchers have contributed to the development of medical imaging methods and systems since the inception of this field approximately 40 years ago. The Yearbook presents selected papers and reviews on this important topic. In addition, as usual, the Yearbook 2002 also contains a variety of papers and reviews on other subjects relevant to medical informatics, such as Bioinformatics, Computer-supported education, Health and clinical management, Health information systems, Knowledge processing and decision support, Patient records, and Signal processing.
Computer-Assisted Instruction↗
Robust replication of associations across patient-mediated and provider-sourced EHR data in the All of Us research program.
The All of Us Research Program is assembling a nationwide cohort with electronic health record (EHR) resources through two complementary pathways: healthcare provider organization (HPO)-sourced EHRs and patient-mediated EHR (PME) contributed through patient portal linkages. The comparative research utility of these two data sources has not been systematically evaluated. Here, we compared PME and HPO EHRs with respect to disease prevalence, phenotype-phenotype associations, and replication of established genotype-phenotype associations using data from 19,703 PME and 373,887 HPO participants. We benchmarked disease prevalence against national estimates, conducted phenome-wide association studies for 10 commonly studied diseases, and tested replication of more than 5000 established genotype-phenotype associations across multiple ancestral groups. Disease prevalence was consistently lower in PME than in HPO, although prevalence of most diseases in both cohorts exceeded national estimates. Both data sources reproduced known phenotype-phenotype associations and showed moderate-to-strong concordance in effect sizes across the phenome. The overall genotype-phenotype replication rate was 49.1% (5399/10,999) in HPO and 5.9% (381/6482) in PME across ancestral groups, with effect sizes strongly correlated among well-powered associations (R = 0.84, P < 0.001). To disentangle the impact of sample size from data quality, we performed 1:1 propensity score matching. After matching, the replication gap in genotype-phenotype associations narrowed from 8.3-fold to 1.3-fold, with equivalent replication rates among adequately powered associations and strongly concordant effect sizes; comorbidity patterns were also consistent across all 10 diseases tested. These findings demonstrate that both data sources are valuable for clinical and genomic research and can inform other cohorts integrating provider-derived and patient-mediated EHRs.
Computational biology and bioinformatics↗
The cost and cost trajectory of genome sequencing and bioinformatics analysis for Indigenous children with suspected rare diseases.
PURPOSE: Indigenous peoples are underrepresented in reference genome libraries. Consequently, rare disease diagnosis may require bespoke bioinformatics analyses of genome sequences. Establishing diagnostic cost is crucial to support policy development for equitable diagnosis of rare diseases. We estimated the cost and cost trajectory of diagnostic genome sequencing and bioinformatics for Indigenous participants with suspected rare diseases. METHODS: We conducted a microcosting study of Indigenous children and their families receiving genome sequencing through Canada's Silent Genomes Project. Invoice data informed the costs of genome sequencing. We conducted a time-and-motion study for bioinformatics analyses, including labor, computing, and data storage costs. RESULTS: With standard bioinformatics, costs ranged from C$3645 (SD: 455) for singletons to C$7402 (SD: 566) for trios. With advanced, bespoke bioinformatics, costs ranged from C$5344 (SD: 634) for singletons to C$9760 (SD: 822) for trios. Genome sequencing was a primary cost driver; however, sequencing costs decreased by 61% over 4 years. Bioinformatics costs ranged from 21.3% to 58.3% of the total costs. The time required for bioinformatics ranged from 71 hours to 215 hours for standard and advanced analyses, respectively. CONCLUSION: Genome sequencing costs decreased over time. Bioinformatics is a significant cost driver, particularly for bespoke analyses arising from nonrepresentative reference libraries.
Humans↗
Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor.
The co-expression of genes coupled to additive probabilistic relationships was used to identify gene sets predictive of the complex biological interactions regulated by ligands of the aryl hydrocarbon receptor ((Italic)Ahr(/Italic)). To maximize the number of possible gene-gene combinations, data sets from murine embryonic kidney, fetal heart, and vascular smooth muscle cells challenged (Italic)in vitro(/Italic) with ligands of the (Italic)Ahr(/Italic) were used to create predictor/training data sets. Biologically relevant gene predictor sets were calculated for (Italic)Ahr(/Italic), cytochrome P450 1B1, insulin-like growth factor-binding protein-5, lysyl oxidase, and osteopontin. Transcript levels were categorized into ternary expressions and target genes selected from the data set and tested for all possible combinations using three gene sets as predictors of transitional level. The goodness of prediction for each set was quantified using a multivariate nonlinear coefficient of determination. Evidence is presented that predictor gene combinations can be effectively used to resolve gene-gene interactions regulated by (Italic)Ahr(/Italic) ligands. (Italic)Key words:(/Italic) aryl hydrocarbon receptor, bioinformatics, gene networks, genomics. (Italic)Environ Health Perspect (/Italic)112:403-412 (2004). [Online 14 January 2004]
Animals↗
In silico methods for evaluating human allergenicity to novel proteins: International Bioinformatics Workshop Meeting Report, 23-24 February 2005.
The ILSI Health and Environmental Sciences Institute (HESI) hosted an expert workshop 22-24 February 2005 in Mallorca, Spain, to review the state-of-the-science for conducting a sequence homology/bioinformatics evaluation in the context of a comprehensive allergenicity assessment for novel proteins, to obtain consensus on the value and role of bioinformatics in evaluating novel proteins, and to discuss the utility and methods of allergen-specific IgE testing in the diagnosis of food allergy. The workshop participants included over forty international experts from academia, industry, and government. The workshop was hosted by the HESI Protein Allergenicity Technical committee, which has established a long-term program whose mission is to advance the scientific understanding of the relevant parameters for characterizing the allergenic potential of novel proteins.
Allergens↗