[Diagnostic tests: Hepatitis C virus genome (HCV RNA)].
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Biomarkers↗
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Results for “Genomic diagnostics”
Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.
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[Biology of infection caused by the dengue virus].
In this review the most important aspects of the biology of the disease caused by the dengue virus are described: the characteristics of the disease, the epidemiology, the vector, the virus (proteins and genome), the diagnostic techniques and the vaccines.
Dengue↗
Characterization of the human aldolase B gene.
The structure of the human gene encoding the aldolase B isozyme has been determined, including the sequence of 14,887 base-pairs. The 5'- and 3'-ends have been determined by S1 mapping. There is a single gene for this enzyme in humans that was determined from the sequence and restriction enzyme digestions of genomic DNA. The gene is 14,500 base-pairs long containing nine exons. In addition, 924 and 208 base-pairs of the 5'- and 3'-flanking region, respectively, have been determined. There is a high degree of conservation of nucleic acid sequence between aldolase B genes of human, rat and chicken. The conservation extends to untranslated and flanking regions, and includes the derived protein structures. In the 5'-flanking region there are several sequence elements that are conserved in vertebrate aldolase B genes in addition to the T-A-T-A and C-C-A-A-T boxes. These sequences may be involved in the co-ordinate and tissue-specific control of expression of this gene. Several possible polymorphic sites were detected in the sequence of the human gene which may be useful for linkage mapping of the human genome and diagnostic analysis of alleles in families with hereditary fructose intolerance.
Animals↗
Statement on the scope of gene patents, research exemption, and licensing of patented gene sequences for diagnostics.
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Base Sequence↗
Genomic Medicine Sweden: Advancing precision medicine at the national level.
High-throughput sequencing has transformed clinical diagnostics of rare diseases (RD), cancer and infectious diseases by enabling the identification of disease-causing genetic alterations and facilitating individualised treatment and care. In response to these advances, Genomic Medicine Sweden (GMS) was established in 2017 as a national collaborative effort to accelerate implementation of genomics-based precision medicine within Sweden's regionally organized, publicly funded healthcare system. GMS brings together the seven university healthcare regions and their associated medical faculties, in collaboration with healthcare regions across Sweden, Science for Life Laboratory, patient organizations, industry and governmental agencies. Activities are coordinated through national disease-specific expert groups, supported by cross-cutting functions in bioinformatics, health economics, ethics, education and patient engagement. At the operational level, seven Genomic Medicine Centres, embedded at university hospitals, develop and deliver harmonised genomic diagnostics nationwide. The National Genomics Platform provides secure infrastructure for large-scale data storage, analysis, and national and international data sharing. Following initial project-based funding, GMS now receives long-term governmental support. This review describes the national implementation of genomic-based precision diagnostics, discusses challenges and lessons learnt, and highlights key milestones across disease areas, including whole-genome sequencing in RD and paediatric cancer, comprehensive genomic profiling of haematological malignancies and solid tumours, pathogen genomics in microbiology, pharmacogenomic testing and emerging applications of polygenic risk scores in complex diseases. Collectively, these efforts have contributed to more than 500,000 genomic tests being performed within Swedish healthcare between 2017 and 2025. Finally, we outline future diagnostic needs and priority areas to ensure sustainable, scalable and equitable access to precision medicine.
Precision Medicine↗
Leveraging clinical intuition to improve accuracy of phenotype-driven prioritization.
PURPOSE: Clinical intuition is commonly incorporated into the differential diagnosis as an assessment of the likelihood of candidate diagnoses based either on the patient population being seen in a specific clinic or on the signs and symptoms of the initial presentation. Algorithms to support diagnostic sequencing in individuals with a suspected rare genetic disease do not yet incorporate intuition and instead assume that each Mendelian disease has an equal pretest probability. METHODS: The LIkelihood Ratio Interpretation of Clinical AbnormaLities (LIRICAL) algorithm calculates the likelihood ratio of clinical manifestations represented by Human Phenotype Ontology terms to rank candidate diagnoses. The initial version of LIRICAL assumed an equal pretest probability for each disease in its calculation of the posttest probability (where the test is diagnostic exome or genome sequencing). We introduce Clinical Intuition for Likelihood Ratios (ClintLR), an extension of the LIRICAL algorithm that boosts the pretest probability of groups of related diseases deemed to be more likely. RESULTS: The average rank of the correct diagnosis in simulations using ClintLR showed a statistically significant improvement over a range of adjustment factors. CONCLUSION: ClintLR successfully encodes clinical intuition to improve ranking of rare diseases in diagnostic sequencing. ClintLR is freely available at https://github.com/TheJacksonLaboratory/ClintLR.
Humans↗
Helicobacter pylori--molecular genetics and diagnostic typing.
The genome of H. pylori is 1.68-1.73 Mb in size and contains a relatively low GC content (an average of 32.5 mol%). Physical and genetic maps of five H. pylori strains (NCTC 11637, NCTC 11638, NCTC 11639, UA 802 and UA 861) have been constructed and the complete genome sequence of strain 26695 has been determined. At least 50 genes, some of which play important roles in the physiology and pathogenicity of the bacterium, have been cloned. Marked genomic sequence variability has evolved from stain to strain demonstrated by random arrangement of 17 known genes on the chromosome and frequent mutations within individual genes. Based on such variability, sensitive and efficient molecular tying techniques such ribotyping, AR-PCR, PCR-RFLP, PCR-DNA sequencing and PFGE-RFLP have been developed and widely applied in both epidemiological and clinical studies of this pathogen. Subtypes of vacA (encoding a vacuolating cytotoxin) and the intermediate forms of a pathogenicity island (the cag region) have been identified in different H. pylori strains and these individual vacA subtypes are associated with specific clinical manifestations of H. pylori infection. Further studies on relationships between the genetic diversity and pathogenicity of H. pylori strains would lead to the development of novel and efficient therapeutic strategies for eradication of this microorganism.
Bacterial Typing Techniques↗
Protein array technology. Potential use in medical diagnostics.
The human genome is sequenced, but only a minority of genes have been assigned a function. Whole-genome expression profiling is an important tool for functional genomic studies. Automated technology allows high-throughput gene activity monitoring by analysis of complex expression patterns, resulting in fingerprints of diseased versus normal or developmentally distinct tissues. Differential gene expression can be most efficiently monitored by DNA hybridization on arrays of oligonucleotides or cDNA clones. Starting from high-density filter membranes, cDNA microarrays have recently been devised in chip format. We have shown that the same cDNA libraries can be used for high-throughput protein expression and antibody screening on high-density filters and microarrays. These libraries connect recombinant proteins to clones identified by DNA hybridization or sequencing, hence creating a direct link between gene catalogs and functional catalogs. Microarrays can now be used to go from an individual clone to a specific gene and its protein product. Clone libraries become amenable to database integration including all steps from DNA sequencing to functional assays of gene products.
Diagnosis↗
Genome-wide SNP arrays as a diagnostic tool: clinical description, genetic mapping, and molecular characterization of Salla disease in an Old Order Mennonite population.
An Old Order Mennonite child was evaluated for gross motor delay, truncal ataxia, and slow linear growth. The diagnostic evaluation, which included sub-specialty consultations, neuroimaging, and metabolic testing, was long, costly, and did not yield a diagnosis. Recognition of a similarly affected second cousin prompted a genome-wide homozygosity mapping study using high-density single nucleotide polymorphism (SNP) arrays. SNP genotypes from two affected individuals and their parents were used to localize the disease locus to a 14.9 Mb region on chromosome 6. This region contained 55 genes, including SLC17A5, the gene encoding the lysosomal N-acetylneuraminic acid transport protein. Direct sequencing of SLC17A5 in the proband revealed homozygosity for the 115C --> T (R39C) sequence variant, the common cause of Salla disease in Finland. Three additional affected Mennonite individuals, ages 8 months to 50 years, were subsequently identified by directed molecular genetic testing. This small-scale mapping study was rapid, inexpensive, and analytically simple. In families with shared genetic heritage, genome-wide SNP arrays with relatively high marker density allow disease gene mapping studies to be incorporated into routine diagnostic evaluations.
Agenesis of Corpus Callosum↗
Salivary diagnostics powered by nanotechnologies, proteomics and genomics.
BACKGROUND: The ability to monitor health status, disease onset and progression, and treatment outcome through noninvasive means is a highly desirable goal in health care promotion and delivery. Oral fluid is a perfect medium to be explored for health and disease surveillance. METHODS: Two prerequisites exist before the goal of salivary diagnostics can be achieved: identification of specific biomarkers associated with a health or disease state and the development of technologies that can discriminate between the biomarkers. A recent initiative of the National Institute of Dental and Craniofacial Research has created a roadmap to achieve these goals through the use of oral fluids as the diagnostic medium to scrutinize the health and/or disease status of patients. This is an ideal opportunity to optimize state-of-the-art saliva-based biosensors for salivary biomarkers that discriminate between diseases. RESULTS: Seven technology groups are developing point-of-care salivary diagnostic technologies. Three groups are working together toward deciphering the salivary proteome. CONCLUSION: These collective efforts and the convergence of salivary diagnostic technologies and the salivary proteome will present unparalleled opportunities to explore the diagnostic potential of saliva for oral and systemic diseases.
Biomarkers↗
Commercial molecular diagnostics in the U.S.: The Human Genome Project to the clinical laboratory.
Molecular diagnosis is the detection of pathogenic mutations in DNA and RNA samples to aid in detection, diagnosis, subclassification, prognosis, and monitoring response to therapy. Principles underlying nucleic-based diagnosis originate from localization, identification, and characterization of genes responsible for human disease. Clinical molecular genetics is now part of the mainstream of medical care in the United States. All commercial clinical reference laboratories now have a molecular genetic diagnostic unit, many of which are in contractual agreement with third party payers to provide services. Gene discovery provides valuable insight into the mechanisms of disease processes and gene-based markers will enable clinicians to study disease predisposition, as well as improved methods for diagnoses, prognosis, and monitoring of therapy. The broad range of mutation spectrum and type performed in the clinical laboratory requires the use of multiple technologies rather than a single typing platform. Platform choice depends on such diverse factors as local expertise, test volume, economies of scale, R&D budget, and royalties. Test validation is a major hurdle and positive control samples are often not readily available. Oversight and the regulatory environment for clinical molecular genetics laboratories in the United States are evolving rapidly. Several government agencies and private organizations are currently involved in revision of specific laboratory standards, including the Secretary's Advisory Committee on Genetic Testing (SACGT), Food and Drug Administration (FDA), Center for Disease Control (CDC), College of American Pathologists (CAP), American College of Medical Genetics (ACMG), and the individual states.
DNA Mutational Analysis↗
The human genome project and the future of diagnostics, treatment, and prevention.
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DNA Mutational Analysis↗
Comparative genomics in the fight against tuberculosis: diagnostics, epidemiology, and BCG vaccination.
Although the causative agent of tuberculosis, Mycobacterium tuberculosis, has been known for some 120 years, the disease continues to plague humanity. In 1998, the sequencing of M. tuberculosis H37Rv enabled tuberculosis researchers to draw comparisons between it and other species of the closely-related M. tuberculosis complex, including bacillus Calmette-Guerin (BCG), the vaccine administered to prevent human tuberculosis. These efforts have uncovered genomic variability that potentially encodes the discrepant phenotypes displayed by species. Due to the infrequency of single nucleotide polymorphisms (SNPs) and other modes of genomic change, large sequence polymorphisms (LSPs) have presented themselves as the most obvious form of genomic variability among species. This review discusses genomic polymorphism among species of the M. tuberculosis complex as revealed through comparative genomics. Attention is drawn towards the impact of comparative genomics in generating several exciting hypotheses towards diagnosis, epidemiology, and prevention of tuberculosis disease.
BCG Vaccine↗
Expression of multiple gamma-glutamyltransferase genes in man.
In clinical and pharmacological laboratories, the assay for gamma-glutamyltransferase (GGT) activity is an important diagnostic test, but one with high biological variability. Although the human genome contains multiple GGT genomic sequences, the diagnostic tests generally assume that only a single GGT gene is active. In the current study, segments encompassing parts of seven different potential human GGT genes have been molecularly cloned. Based on sequence determination of exons within these distinct genomic clones, oligonucleotide primers were designed which would prime and PCR-amplify putative mRNA of all seven potential GGT genes, if expressed. Gene-specific oligonucleotide probes were then utilized to assay the transcriptional status of the seven possible GGT genes in a wide variety of human RNAs. Our results show that a single GGT gene exhibits ubiquitous expression in all RNAs tested, including those from fetal and adult liver. A surprisingly large number of four additional GGT genes is expressed in man. Interestingly, these novel GGT genes are expressed in a tissue-restricted manner, which suggests that their corresponding gene products exhibit distinct functions in these specific tissues.
Amino Acid Sequence↗
Denaturing gradient gel electrophoresis and direct sequencing of PCR amplified genomic DNA: a rapid and reliable diagnostic approach to beta thalassaemia.
The analysis of polymerase chain reaction (PCR)-amplified beta-globin DNA with allele-specific oligonucleotide (ASO) probes reveals a very heterogeneous spectrum of beta-thalassaemia in the Netherlands. However about 20% of the beta-thalassemia mutations cannot be identified with this approach. The combination of specific amplification of certain regions of the beta-globin gene with denaturing gradient gel electrophoresis (DGGE) allowed us to rapidly localize several of these mutations to specific regions of the gene, which were again amplified and directly sequenced. We believe that the combination of DGGE and the direct sequence determination of PCR amplified genomic DNA represents a valid alternative to the 'ASO probes' approach, especially in countries where a very heterogeneous spectrum of beta-thalassaemia mutations occurs.
Base Sequence↗
Draft versus finished sequence data for DNA and protein diagnostic signature development.
Sequencing pathogen genomes is costly, demanding careful allocation of limited sequencing resources. We built a computational Sequencing Analysis Pipeline (SAP) to guide decisions regarding the amount of genomic sequencing necessary to develop high-quality diagnostic DNA and protein signatures. SAP uses simulations to estimate the number of target genomes and close phylogenetic relatives (near neighbors or NNs) to sequence. We use SAP to assess whether draft data are sufficient or finished sequencing is required using Marburg and variola virus sequences. Simulations indicate that intermediate to high-quality draft with error rates of 10(-3)-10(-5) (approximately 8x coverage) of target organisms is suitable for DNA signature prediction. Low-quality draft with error rates of approximately 1% (3x to 6x coverage) of target isolates is inadequate for DNA signature prediction, although low-quality draft of NNs is sufficient, as long as the target genomes are of high quality. For protein signature prediction, sequencing errors in target genomes substantially reduce the detection of amino acid sequence conservation, even if the draft is of high quality. In summary, high-quality draft of target and low-quality draft of NNs appears to be a cost-effective investment for DNA signature prediction, but may lead to underestimation of predicted protein signatures.
Computational Biology↗
MEMS-based sample preparation for molecular diagnostics.
Completion of the Human Genome Project is driving the rapid development of molecular diagnostics in the laboratory. To accelerate the penetration of genetic tests and other nucleic acid-based tests into clinical markets, simple, compact, automatic sample-preparation systems for molecular diagnostics must be developed. Microelectromechanical systems (MEMS) is a promising approach for the development of automated sample preparation for the clinical laboratory or point-of-care setting. This review discusses MEMS-based components that could be applied to the different stages of the sample-preparation process such as cell separation, nucleic acid purification, and nucleic acid amplification. Examples of functional component integration are given. Issues discussed include partitioning of functions between the instrument and disposable unit, methods of propulsion of fluids and particles, vapor and liquid barriers, and sample size. Although further evaluation and development are needed to provide practical solutions to some of these issues, we conclude that MEMS-based components might contribute to some components in a sample-preparation system consisting of modular instruments and disposable units, but will not provide a generic or a totally integrated solution.
DNA, Bacterial↗
General colorimetric method for DNA diagnostics allowing direct solid-phase genomic sequencing of the positive samples.
A system for rapid colorimetric detection of specific genome DNA fragments amplified by the polymerase chain reaction (PCR) is described that has been designed to allow direct solid-phase sequencing of positive samples. The amplified material is immobilized on magnetic beads by using the biotin streptavidin system. An Escherichia coli lac operator DNA sequence is incorporated in the amplified material during the second step of a nested primer procedure. This 21-base-pair sequence is used for a general colorimetric detection with a fusion protein consisting of the E. coli Lac repressor and beta-galactosidase. Positive samples can be treated subsequently with alkali to obtain a single-stranded DNA template suitable for direct genomic sequencing. This method to detect immobilized amplified nucleic acids (DIANA) is well adapted for automated or semiautomated clinical assays. Here, we show that it can be used to detect and sequence Chlamydia trachomatis genomic DNA in clinical samples.
Amino Acid Sequence↗