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At least 379 records · Page 21Linked to original sources

PubMed2006

Current evidence on diagnostic accuracy of commercially based nucleic acid amplification tests for the diagnosis of pulmonary tuberculosis.

BACKGROUND: Even though commercial nucleic acid amplification tests (NAATs) have become the most frequently used molecular tests for laboratory diagnosis of pulmonary tuberculosis (TB), published studies report variable estimates of their diagnostic accuracy. We analysed the accuracy of commercial NAATs for the diagnosis of pulmonary TB in smear positive and smear negative respiratory samples using culture as a reference standard. METHODS: English language studies reporting data sufficient for calculating sensitivity and specificity of commercial NAATs on smear positive and/or smear negative respiratory samples were included. Meta-regression was used to analyse associations with reference test quality, the prevalence of TB, sample and test type. Predictive values for different levels of pre-test probability were quantified using Bayes' approach. RESULTS: Sixty three journal articles published between 1995 and 2004 met the inclusion criteria. Pooled sensitivity and specificity were 0.96 and 0.85 among smear positive samples and 0.66 and 0.98 among smear negative samples. The number of culture media used as reference test, the inclusion of bronchial samples, and the TB prevalence were found to influence the reported accuracy. The test type had no effect on the diagnostic odds ratio but seemed to be correlated with sensitivity or specificity, probably via a threshold effect. CONCLUSIONS: Commercial NAATs can be confidently used to exclude TB in patients with smear positive samples in which environmental mycobacteria infection is suspected and to confirm TB in a proportion of smear negative cases. The methodological characteristics of primary studies have a considerable effect on the reported diagnostic accuracy.

Humans↗

PubMedDate not supplied

Laboratory diagnosis of hepatitis C.

In 1989 the hepatitis C virus was cloned, some 20 years after the first suggestion that hepatitis C virus(es) (HCV) existed. Since that time there has been rapid development of serological tests for detection of antibody to HCV and molecular tests for detection, quantitation, and characterization of HCV RNA. The development and performance characteristics of these test methods are reviewed and their implications for diagnosis, prognosis, and monitoring patients on therapy are discussed.

Animals↗

PubMed1991

Genetic control of pattern formation during flower development in Arabidopsis.

Arabidopsis flowers develop from groups of undifferentiated cells on the flank of an inflorescence meristem. The cells in these flower primordia must somehow assess their position within the primordium and differentiate accordingly to produce a flower with a precisely defined pattern of organ types and positions. The molecular mechanisms by which this is accomplished are largely unknown. We are studying a set of genes whose mutations give homeotic phenotypes in Arabidopsis flowers. A genetic model to explain the specification of organ identity by combinatorial action of the products of these homeotic genes is presented, along with several aspects that are not readily addressed by the model. The recent cloning of one of the Arabidopsis homeotic genes, and an additional homeotic gene from Antirrhinum, has provided an opportunity for molecular tests of our genetic model. So far, the molecular data are in accord with the genetic model.

Arabidopsis↗

PubMed2000

Mutation screening for prenatal and presymptomatic diagnosis: cystic fibrosis and haemochromatosis.

UNLABELLED: Hereditary haemochromatosis (HH) and cystic fibrosis (CF) are the most common autosomal recessively inherited disorders in Caucasian populations. In its typical form, CF manifests during the first years of life, while the mean age of onset of organ damage is 54 years in HH. Both disorders can be diagnosed presymptomatically utilising biochemical and/or genetic testing. Since approximately 90% of mid-European HH patients are homozygous for only one specific mutation (C282Y) in the candidate gene for HH, genetic testing is simple and sensitive in HH. In CF, molecular testing is currently hampered by the large number (more than 800) of mutations in the CF transmembrane conductance regulator gene. Several studies have been initiated to investigate the potential benefits and the best time and mode of presymptomatic testing for HH and CF. CONCLUSION: Mutation analysis is widely recommended for presymptomatic diagnosis of cystic fibrosis and hereditary haemochromatosis because of the presumed benefit, although several medical, ethical, social and technical questions warrant further investigations. Prenatal mutation testing is commonly performed for cystic fibrosis but not for hereditary haemochromatosis. Informed consent of tested individuals and the availability of genetic counselling is a prerequisite for any mutation screening approach in either disease.

Age of Onset↗

PubMed1998

Direct spectroscopic detection of molecular dynamics and interactions of the calcium pump and phospholamban.

In order to test molecular models of cardiac calcium transport regulation, we have used spectroscopy to probe the structures, dynamics, and interactions of the Ca pump (Ca-ATPase) and phospholamban (PLB) in cardiac sarcoplasmic reticulum (SR) and in reconstituted membranes. Electron paramagnetic resonance (EPR) and phosphorescence of probes bound to the Ca pump show that the activity of the pump is quite sensitive to its oligomeric interactions. In cardiac SR, PLB aggregates and inhibits the pump, and both effects are reversed by PLB phosphorylation. Previous analyses of PLB's oligomeric state were only in detergent solutions, so we used EPR and fluorescence to determine the oligomeric structure of PLB in its native state in lipid bilayers. Wild-type PLB is primarily oligomeric in the membrane, while the mutant L37A-PLB is monomeric. For both proteins, phosphorylation shifts the dynamic monomer-oligomer equilibrium toward oligomers, and induces a similar structural change, as indicated by tyrosine fluorescence; yet L37A-PLB is more effective than wild-type PLB in inhibiting and aggregating the pump. Fluorescence energy transfer shows that the Ca pump increases the fraction of monomeric PLB, indicating that the pump preferentially binds monomeric PLB. These results support a reciprocal aggregation model for Ca pump regulation, in which the Ca pump is aggregated and inhibited by association with PLB monomers, and phosphorylation of PLB reverses these effects while decreasing the concentration of PLB monomers. To investigate the structure of the PLB pentamer in more detail, we measured the reactivities of cysteine residues in the transmembrane domain of PLB, and recorded EPR spectra of spin labels attached to these sites. These results support an atomic structural model, based on molecular dynamics simulations and mutagenesis studies, in which the PLB pentamer is stabilized by a leucine-isoleucine zipper within the transmembrane domain.

Animals↗

PubMed2005

[Prevalence of human papillomavirus infection in Slovenian women with repeated Pap II smears].

In the detection of precancerous lesions the cervical Papanicolaou smear screening is used in Slovenia and worldwide. Management of patients with repeat abnormal smears (Pap II) represents a great and complex clinical and public health problem. Repeated cytologic examinations are routine procedure in many countries, also in Slovenia, although the sensitivity of Pap smear testing in the detection of cervical intraepithelial neoplasia (CIN) II and III is relatively low. In cases of abnormal squamous cells and mildly dyskaryotic cells the presence of infections with high-risk HPV genotypes is being increasingly used as a complementary method to Pap smear testing. In the study we enrolled 148 cervical samples of women who within two years had three subsequent Pap II smears (abnormal squamous cells or mildly dyskaryotic cells). The prevalence of HPV infections was determined using three molecular tests: Hybrid Capture 2 (hc2) test and two variants of polymerase chain reaction (PCR-PGMY11/PGMY09 and PCR-CPI/CPIIG). HPV infection was detected in 25.7% of women. In women aged < or = 30 years a statistically significant higher prevalence of HPV infections was found (37.8%) than in women aged > 30 years (20.4%). Our findings show that repeat Pap smear as the method of follow-up and detection of precancerous lesions of the observed population do not provide relevant results due to low prevalence of HPV infections in Slovenia, which indirectly indicates low sensitivity and specificity of Pap smear testing. In the detection of HPV infections, molecular methods are thus sensitive screening tests to be used complementary to cytologic tests in women with abnormal squamous cells and mildly dyskaryotic cells.

Adult↗

PubMed2002

Comparison of selection strategies for genetic testing of patients with hereditary nonpolyposis colorectal carcinoma: effectiveness and cost-effectiveness.

BACKGROUND: Molecular testing for hereditary nonpolyposis colorectal carcinoma (HNPCC) is becoming standard care and it is cost-effective compared with no genetic testing. However, the best strategy for detection of HNPCC gene carriers is unknown. METHODS: We use a decision analytic model to evaluate the effectiveness and incremental cost-effectiveness of four commonly used testing strategies to detect HNPCC gene carriers. The model starts with a population of colorectal carcinoma (CRC) patients and measures costs, the number of gene carriers detected, and incremental costs per gene carrier detected. RESULTS: We found that germline testing on only those CRC probands who meet the Amsterdam criteria detects the fewest gene carriers and has the lowest cost whereas tumor microsatellite instability (MSI) testing of all CRC patients and families has the highest cost and detects the most gene carriers. When cost-effectiveness is considered, the mixed strategy (MSH2 and MLH1 testing on those who meet the Amsterdam criteria and germline testing for the remainder who meet less stringent modified criteria and are MSI-High) seems superior. The mixed strategy detects 59.6 mutation carriers per 1000 CRC cases and costs much less than the test all strategy, which has an incremental cost-effectiveness of $51,151. The mixed strategy often other strategies and when compared to the Amsterdam strategy, has a cost-effectiveness of only $6441 per gene carrier detected. CONCLUSIONS: It is not very effective to limit genetic testing to only individuals who meet the Amsterdam criteria, as many gene carriers are missed. However, testing all CRC patients for tumor MSI-H, although effective, may be prohibitively expensive. A mixed strategy is the more cost-effective approach.

Adaptor Proteins, Signal Transducing↗

PubMed2000

Prenatal genotyping for the RhD blood group antigen: considerations in developing an accurate test.

Experience performing prenatal genotyping for RHD has shown that consideration must be given to developing a molecular test capable of detecting recombination/gene conversion events involving the RHD and RHCE genes that can lead to erroneous results. Out of 50 prenatal RHD tests performed over the past 5 years, four samples were encountered that gave false-positive results. In only one of the tests, incorrect results were issued to the physician. In the other three instances, the erroneous nature of the test results was revealed through the analysis of multiple regions of the RHD gene and, more importantly, because the mother, and sometimes the father, were tested in parallel with the fetus. In an extension of the observations obtained from the prenatal testing program, a large panel of RhD-negative blood donors were subjected to molecular analysis of the RHD gene. Of 1,183 donors screened, 187 were found to phenotype as RhD negative. Of the 187 donors confirmed RhD negative serologically, 22 (11.8%) were found to retain remnants of the RHD gene that, depending upon the characteristics of the molecular assay performed, could lead to a false-positive result in a genotyping assay. On the basis of the experience presented here, it is recommended that any molecular RHD assay include an analysis of multiple areas of the RHD gene so as to allow for the detection of recombination/gene conversion events between the RHD and RHCE genes. Moreover, it is strongly recommended that the mother (at a minimum) and father be subjected to molecular analysis simultaneously with the fetus to confirm that the known phenotypes of the parent(s) are consistent with their respective genotypes.

Exons↗

PubMed2004

Management of children with infection-associated persistent diarrhea.

Diarrhea is the leading cause of death in children younger than 5 years of age; persistent diarrhea accounts for 30 to 50 percent of those deaths in developing countries. Malnutrition, immunosuppression, young age, and an increase in the preceding diarrhea burdens are risk factors for the development of persistent diarrhea. Although many viruses, bacteria, and parasites can produce persistent diarrhea, enteropathogenic Escherichia coli , enteroaggregative E. coli, Giardia, Cryptosporidium , and Cyclospora are the most important of these agents. With currently available tests, identifying a specific cause usually is difficult. Newer sensitive molecular tests must be used for studying the epidemiology of persistent diarrhea in children. Management includes rehydration, adequate diet, micronutrient supplementation, and antimicrobials. Persistent diarrhea seriously affects nutritional status, growth, and intellectual function. Meeting these challenges is profoundly important, particularly in developing countries.

Anti-Infective Agents↗

PubMed2002

The Scottish molecular genetics consortium--15 years on.

Remarkable advances have been made in recent years in our knowledge of the human genome. Genes for disorders such as Huntington disease, cystic fibrosis and Duchenne muscular dystrophy have been mapped and mutations identified. Simple molecular tests are now available for the diagnosis of these and many other conditions. As a result, in the last 15 years the whole new field of molecular pathology has been introduced to the Health Service of the United Kingdom and now there are nearly 40 diagnostic laboratories offering tests for a wide range of genetic disease. Scotland was at the forefront in the introduction of molecular diagnostics to Clinical Genetics Services and as early as 1985 plans were made to provide laboratories in Aberdeen, Dundee, Edinburgh and Glasgow. The four laboratories, the clinical genetics staff in each centre and the officials of the National Services Division now form the Scottish Molecular Genetics Consortium the objective of which is to provide testing for a wide range of disorders, to introduce new tests as genes are identified and to carry this out in a cooperative and coordinated manner.

Genetic Testing↗

PubMed2005

Cytogenetic abnormalities and fragile-X syndrome in Autism Spectrum Disorder.

BACKGROUND: Autism is a behavioral disorder with impaired social interaction, communication, and repetitive and stereotypic behaviors. About 5-10 % of individuals with autism have 'secondary' autism in which an environmental agent, chromosome abnormality, or single gene disorder can be identified. Ninety percent have idiopathic autism and a major gene has not yet been identified. We have assessed the incidence of chromosome abnormalities and Fragile X syndrome in a population of autistic patients referred to our laboratory. METHODS: Data was analyzed from 433 patients with autistic traits tested using chromosome analysis and/or fluorescence in situ hybridization (FISH) and/or molecular testing for fragile X syndrome by Southern and PCR methods. RESULTS: The median age was 4 years. Sex ratio was 4.5 males to 1 female [354:79]. A chromosome (cs) abnormality was found in 14/421 [3.33 %] cases. The aberrations were: 4/14 [28%] supernumerary markers; 4/14 [28%] deletions; 1/14 [7%] duplication; 3/14 [21%] inversions; 2/14 [14%] translocations. FISH was performed on 23 cases for reasons other than to characterize a previously identified cytogenetic abnormality. All 23 cases were negative. Fragile-X testing by Southern blots and PCR analysis found 7/316 [2.2 %] with an abnormal result. The mutations detected were: a full mutation (fM) and abnormal methylation in 3 [43 %], mosaic mutations with partial methylation of variable clinical significance in 3 [43%] and a permutation carrier [14%]. The frequency of chromosome and fragile-X abnormalities appears to be within the range in reported surveys (cs 4.8-1.7%, FRAX 2-4%). Limitations of our retrospective study include paucity of behavioral diagnostic information, and a specific clinical criterion for testing. CONCLUSIONS: Twenty-eight percent of chromosome abnormalities detected in our study were subtle; therefore a high resolution cytogenetic study with a scrutiny of 15q11.2q13, 2q37 and Xp23.3 region should be standard practice when the indication is autism. The higher incidence of mosaic fragile-X mutations with partial methylation compared to FRAXA positive population [50% vs 15-40%] suggests that faint bands and variations in the Southern band pattern may occur in autistic patients.

Autistic Disorder↗

PubMed2005

Mutation detection, interpretation, and applications in the clinical laboratory setting.

Mutation detection plays an increasingly significant role in clinical diagnostic testing, posing formidable challenges for laboratories. The expanding indications for clinical molecular testing and the nuances of interpreting test results are discussed. Methods for screening mutation detection platforms and monitoring assay reliability are presented, and results of platform comparisons are described. The potential for irrevocable medical interventions following a positive mutation analysis is highlighted to stress the imperative for accuracy in mutation detection and vigilance in the clinical arena.

Clinical Laboratory Techniques↗

PubMed1999

Diagnostic yield of the comprehensive assessment of developmental delay/mental retardation in an institute of child neuropsychiatry.

The Consensus Conference of the American College of Medical Genetics has established guidelines regarding the evaluation of patients with mental retardation (MR) [Curry et al., Am. J. Med. Genet. 72:468-477, 1997]. They emphasized the high diagnostic utility of cytogenetic studies and of neuroimaging in certain clinical settings. However, data on the diagnostic yield of these studies in well-characterized populations of individuals with MR are scant. Majnemer and Shevell [J. Pediatr. 127:193-199, 1995] attained a diagnostic yield of 63%. However, this study included only 60 patients and the classification included pathogenetic and causal groups. The Stella Maris Institute has evaluated systematically patients with developmental delay (DD)/MR and performed various laboratory studies and neuroimaging in almost all patients. We report a retrospective analysis of the diagnostic yield of 120 consecutive patients observed at our Institute during the first 6 months of 1996. There were 77 males and 43 females; 47 were mildly delayed (IQ 70-50), 31 were moderately delayed (IQ 50-35), and 42 were severely delayed (IQ 35-20). Diagnostic studies (history, physical examination, standard cytogenetics, fragile X testing, molecular studies, electroencephalography, electromyography, nerve conduction studies, neuroimaging, and metabolic screening tests) yielded a causal diagnosis in 50 (41.6%) and a pathogenetic diagnosis in 47 (39.2%) of the 120 patients. Causal categories included chromosomal abnormalities (14), Fra(X) syndromes (4), known MCA/MR syndromes (19), fetal environmental syndromes (1), neurometabolic (3) disorders, neurocutaneous (3) disorders, hypoxic-ischemic encephalopathy (3), other encephalopathies (1), and congenital bilateral perisylvian syndrome (2). Pathogenetic categories included idiopathic MCA/MR syndromes (35), epileptic syndromes (10), and isolated lissencephaly sequence (2). Diagnostic yield did not differ across categories and degree of DD. Our results, while confirming the diagnostic utility of cytogenetic/molecular genetic, and neuroimaging studies, suggest the usefulness of accurate electroencephalogram recordings, and stress the importance of a thorough physical examination. Referral to a university child neurology and psychiatry service, where a comprehensive assessment with a selected battery of investigations is possible, yields etiologic findings in a high percentage of DD/MR patients, with important implications for management, prognosis and recurrence risk estimate.

Adolescent↗

PubMed2002

Occurrence of newer beta-lactamases in Klebsiella pneumoniae isolates from 24 U.S. hospitals.

Despite the discovery of novel beta-lactamases such as extended-spectrum beta-lactamases (ESBLs), imported AmpC, and carbapenem-hydrolyzing beta-lactamases at least a decade ago, there remains a low level of awareness of their importance and how to detect them. There is a need to increase the levels of awareness of clinical laboratories about the detection of newer beta-lactamases. Therefore, a study was conducted in 2000 to investigate the occurrence of these beta-lactamases in Klebsiella pneumoniae isolates at 24 U.S. medical centers. To enhance the likelihood of detecting imported AmpC and carbapenem-hydrolyzing beta-lactamases, participating laboratories were permitted to include archived strains (1996 to 2000) that were intermediate or resistant to either cefoxitin or imipenem. The beta-lactamase production of 408 isolates positive by screening of 1,123 isolates was investigated by ESBL phenotypic confirmation tests; and for AmpC and carbapenem-hydrolyzing beta-lactamases, three-dimensional tests, isoelectric focusing, beta-lactamase inhibitor studies, spectrophotometric assays, induction assays, and molecular tests were used. ESBL-producing isolates were detected at 18 of the 24 sites (75%), imported AmpC-producing isolates were detected at 10 sites (42%), inducible imported AmpC-producing isolates were detected at 3 sites (12.5%), and a molecular class A carbapenem-hydrolyzing enzyme was detected at 1 site (4%). No class B or D carbapenem-hydrolyzing enzymes were detected. ESBLs and imported AmpC beta-lactamases were detected at a significant number of sites, indicating widespread penetration of these enzymes into U.S. medical institutions. Because these enzymes may significantly affect therapeutic outcomes, it is vital that clinical laboratories be aware of them and be able to detect their occurrence.

Bacterial Proteins↗

PubMed1982

Estimation of molecular weights of membrane proteins in the presence of SDS by low-angle laser light scattering combined with high-performance porous silica gel chromatography. Confirmation of the trimer structure of porin of the E. coli outer membrane.

An assessment study was carried out to evaluate the performance of the low-angle laser light-scattering technique combined with high-performance porous silica gel chromatography in the presence of sodium dodecyl sulfate and precision differential refractometry. It was found that the combined technique is highly promising as a reliable method for determining the molecular weight of a membrane protein solubilized by the surfactant. As a test, molecular weights of porin forming the permeability channel of the outer membrane of E. coli B in an oligomeric form were measured before and after heat treatment, which is known to cause dissociation. The results obtained indicate that the porin oligomer is a trimer with stoichiometric composition.

Chromatography, High Pressure Liquid↗

PubMed2005

Viral infection in the renal transplant recipient.

Viruses are among the most common causes of opportunistic infection after transplantation and the most important. The risk for viral infection is a function of the specific virus encountered, the intensity of immune suppression used to prevent graft rejection, and other host factors governing susceptibility. Viral infection, both symptomatic and asymptomatic, causes the "direct effects" of invasive disease and "indirect effects," including immune suppression predisposing to other opportunistic infections and oncogenesis. Rapid and sensitive microbiologic assays for many of the common viruses after transplantation have replaced, for the most part, serologic testing and in vitro cultures for the diagnosis of infection. Furthermore, quantitative molecular tests allow the individualization of antiviral therapies for prevention and treatment of infection. This advance is most prominent in the management of cytomegalovirus, Epstein-Barr, hepatitis B, and hepatitis C viruses. Diagnostic advances have not been accompanied by the development of specific and nontoxic anti-viral agents or effective antiviral vaccines. Vaccines, where available, should be given to patients as early as possible and well in advance of transplantation to optimize the immune response. Studies of viral latency, reactivation, and the cellular effects of viral infection will provide clues for future strategies in prevention and treatment of viral infections.

Acute Disease↗

PubMed1995

Transgenic models of HIV-1.

Transgenic technology has been very successful at providing insights into possible processes involved in HIV-induced pathogenesis. The availability of these small animal models for the study of HIV-related syndromes including KS, epidermal proliferative lesions, HIV-associated nephropathy, AIDS-related growth failure and cachexia may well facilitate the development of novel therapies for these complications. Other phenotypes created in mice, such as cataracts and hepatic cancer [59], may not have human analogies but may still provide insight into pathogenesis. Thus, transgenic models have already provided resources to study many manifestations of AIDS and others are likely to be developed. The optimal strategy for designing future transgenic animals, however, is less clear. No transgenic mouse model has been generated to date that will provide an avenue for vaccine development. This advance awaits the further discovery of the host factors that facilitate the virus replicative cycle in humans and a better understanding of these pathways in the mouse. For the development of molecular-based therapy, however, the currently available models may well be adequate to test molecular inhibitors of transcription [7,60,61] and post-transcriptional processing of viral mRNA [62]. Whether single or multigenic constructs under the control of the LTR are better or worse for this purpose is a debatable issue. Transgenic technology may yet make an additional contribution to the development of molecular therapy for AIDS. The best method of demonstrating that a gene therapeutic strategy is safe to administer to patients has not been determined. By introducing potentially therapeutic constructs into mice as transgenes, their safety can be assessed in many different cell types in vivo, analogous to toxicological testing in rodents for systemically administered drugs. Thus, transgenic technology has already provided insights into the pathogenesis of HIV-1. While it has not yet proven its utility for vaccine development, transgenic technology holds the promise of being an active participant in the development of both safe and effective gene therapy approaches for the treatment of AIDS.

AIDS Dementia Complex↗

PubMed2001

Automation of laboratory testing for infectious diseases using the polymerase chain reaction-- our past, our present, our future.

While it is an extremely powerful and versatile assay method, polymerase chain reaction (PCR) can be a labor-intensive process. Since the advent of commercial test kits from Roche and the semi-automated microwell Amplicor system, PCR has become an increasingly useful and widespread clinical tool. However, more widespread acceptance of molecular testing will depend upon automation that allows molecular assays to enter the routine clinical laboratory. The forces driving the need for automated PCR are the requirements for diagnosis and treatment of chronic viral diseases, economic pressures to develop more automated and less expensive test procedures similar to those in the clinical chemistry laboratories, and a shortage in many areas of qualified laboratory personnel trained in the types of manual procedures used in past decades. The automated Roche COBAS AMPLICOR system has automated the amplification and detection process. Specimen preparation remains the most labor-intensive part of the PCR testing process, accounting for the majority of the hands-on-time in most of the assays. A new automated specimen preparation system, the COBAS AmpliPrep, was evaluated. The system automatically releases the target nucleic acid, captures the target with specific oligonucleotide probes, which become attached to magnetic beads via a biotin-streptavidin binding reaction. Once attached to the beads, the target is purified and concentrated automatically. Results of 298 qualitative and 57 quantitative samples representing a wide range of virus concentrations analyzed after the COBAS AmpliPrep and manual specimen preparation methods, showed that there was no significant difference in qualitative or quantitative hepatitis C virus (HCV) assay performance, respectively. The AmpliPrep instrument decreased the time required to prepare serum or plasma samples for HCV PCR to under 1 min per sample. This was a decrease of 76% compared to the manual specimen preparation method. Systems that can analyze more samples with higher throughput and that can answer more questions about the nature of the microbes that we can presently only detect and quantitate will be needed in the future.

Hepacivirus↗