Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Rapid Genetic Testing”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 397 records · Page 22Linked to original sources
PubMed1994

Rapid genetic characterization of HIV type 1 strains from four World Health Organization-sponsored vaccine evaluation sites using a heteroduplex mobility assay. WHO Network for HIV Isolation and Characterization.

To assist in the preparation for the testing of vaccines against human immunodeficiency virus (HIV) we, as part of the World Health Organization Network for HIV Isolation and Characterization (WHO-NHIC), evaluated the genotypic variation of HIV-1 in cohorts from Brazil, Rwanda, Thailand, and Uganda. Here we report the results from a pilot study of 65 HIV-1-infected individuals. In all cases in which viral envelope gene fragments could be amplified by polymerase chain reaction, subtypes could be assigned using a heteroduplex mobility assay (HMA)1 by comparison with HIV-1 strains representing six HIV-1 envelope subtypes. All subtype classifications matched those found by envelope gene sequencing. Phylogenetic relationships were further clarified by heteroduplex formation between samples within each subtype. A relatively homogeneous subtype E virus population predominated over subtype B viruses in the sample set from Thailand. Viruses from the other countries were also limited to one or two subtypes but were more divergent within each subtype. All samples from Rwanda (13/13) and some from Uganda (3/16) were of subtype A; all Brazilian samples were of subtype B, except for one belonging to subtype C; most samples from Uganda (13/16) clustered with the subtype D. Analysis by HMA is therefore applicable for screening of HIV-1 genotypes in countries under consideration for large-scale vaccine trials. It should be generally useful when samples containing at least one variable genetic locus need to be rapidly classified by genotype and/or analyzed for epidemiological clustering.

AIDS Vaccines↗
PubMed2003

Genetic mapping and QTL analysis of fiber-related traits in cotton ( Gossypium).

Cotton, the leading natural fiber crop, is largely produced by two primary cultivated allotetraploid species known as Upland or American cotton ( Gossypium hirsutum L.) and Pima or Egyptian cotton ( G. barbadense L.). The allotetraploid species diverged from each other and from their diploid progenitors (A or D genome) through selection and domestication after polyploidization. To analyze cotton AD genomes and dissect agronomic traits, we have developed a genetic map in an F2 population derived from interspecific hybrids between G. hirsutum L. cv. Acala-44 and G. barbadense L. cv. Pima S-7. A total of 392 genetic loci, including 333 amplified fragment length polymorphisms (AFLPs), 47 simple sequence repeats (SSRs), and 12 restriction fragment length polymorphisms (RFLPs), were mapped in 42 linkage groups, which span 3,287 cM and cover approximately 70% of the genome. Using chromosomal aneuploid interspecific hybrids and a set of 29 RFLP and SSR framework markers, we assigned 19 linkage groups involving 223 loci to 12 chromosomes. Comparing four pairs of homoeologous chromosomes, we found that with one exception linkage distances in the A-subgenome chromosomes were larger than those in their D-subgenome homoeologues, reflecting higher recombination frequencies and/or larger chromosomes in the A subgenome. Segregation distortion was observed in 30 out of 392 loci mapped in cotton. Moreover, approximately 29% of the RFLPs behaved as dominant loci, which may result from rapid genomic changes. The cotton genetic map was used for quantitative trait loci (QTL) analysis using composite interval mapping and permutation tests. We detected seven QTLs for six fiber-related traits; five of these were distributed among A-subgenome chromosomes, the genome donor of fiber traits. The detection of QTLs in both the A subgenome in this study and the D subgenome in a previous study suggests that fiber-related traits are controlled by the genes in homoeologous genomes, which are subjected to selection and domestication. Some chromosomes contain clusters of QTLs and presumably contribute to the large amount of phenotypic variation that is present for fiber-related traits.

Chromosome Mapping↗
PubMed2005

Clinical evaluation of micro-scale chip-based PCR system for rapid detection of hepatitis B virus.

The polymerase chain reaction (PCR) is widely used to amplify a small amount of DNA in samples for genetic analysis. Rapid and accurate amplification is prerequisite for broad applications including molecular diagnostics of diseases, food safety, and biological warfare tests. We have developed a rapid real-time micro-scale chip-based PCR system, which consists of six individual thermal cycling modules capable of independent control of PCR protocols. The PCR volume is 1 microl and it takes less than 20 min to complete 40 thermal cycles. To test utility of a chip-based PCR system as a molecular diagnostic device, we have conducted the first large-scale clinical evaluation study. Three independent clinical evaluation studies (n = 563) for screening the hepatitis B virus (HBV) infection, the most popular social epidemic disease in Asia, showed an excellent sensitivity, e.g. 94%, and specificity, e.g. 93%, demonstrating micro-scale chip-based PCR can be applied in molecular diagnostics.

DNA, Viral↗
PubMed2004

The biological revolution - towards a mechanistic understanding of the impact of diet on cancer risk.

There is strong epidemiological evidence to show that differences in diet explain a significant proportion of the variation in cancer incidence worldwide. However, because of the complex nature of eating behaviour and the chemical heterogeneity of foods, it remains very difficult to ascertain which aspects of diet, in what quantities and over what time-frames are responsible for modifying risk. In addition, there are few dietary intervention studies demonstrating reduction in cancer risk. Much faster progress has been made in understanding the biological basis of cancer. It is now clear that damage to the genome resulting in aberrant expression of genes (principally suppression of tumour suppressor genes (TSGs) and inappropriate expression of oncogenes) is fundamental to tumorigenesis. It is also becoming clear that much of the inter-individual variation in cancer experience is due to differences in the amount of damage experienced and/or the capacity to repair that damage. Both of these processes are influenced strongly by dietary factors and by genetic predisposition (polymorphisms in the requisite genes). It is possible that understanding diet:gene interactions in DNA damage and in repair will not only explain much of the inter-individual variation in risk but also offer opportunities to design better dietary intervention studies aimed at chemoprevention. The Human Genome maps and the SNPs databases, together with the rapid development of tools suitable for investigating genetic and epigenetic changes in small tissue biopsies provide the means to begin to test hypotheses about the mechanisms by which diet influences cancer risk directly in human subjects. This is likely to form a significant component of the emerging science of nutrigenomics.

Anticarcinogenic Agents↗
PubMed2000

The use of phylogenetic data to develop molecular tools for the detection and genotyping of Yam mosaic virus. Potential application in molecular epidemiology.

Molecular detection of Yam mosaic virus (YMV), the most important potyvirus for yam plants (Dioscorea spp.) has been limited by its high genetic diversity. According to recent phylogenetic data, suitable molecular tools were developed for detection and genotyping. A reliable and rapid molecular test is described using single-tube immunocapture (IC)-RT-PCR combining the use of a monoclonal antibody able to recognise all YMV serotypes and primers designed to take into account the whole variability of YMV. Phylogenetic data were then used to develop an uncoupled IC-RT-PCR procedure adapted to the genotyping of the three major phylogenetic groups and the two recombinants implicated in the YMV epidemics in the Caribbean and French Guiana. A third exploitation of phylogenetic data was carried out with the development of a typing test based on the analysis of short nucleotide sequences. The direct sequencing of a 450 nts fragment constituted a reliable complementary typing tool as the resulting information was quite similar to that obtained with sequences of the complete coat protein gene. The approach, consisting in a robust study of YMV variability followed by the use of phylogenetic data to develop reliable detection and genotyping tools, offers new perspectives for powerful molecular epidemiological studies.

Enzyme-Linked Immunosorbent Assay↗
PubMed2000

DNA identification of commercial ginseng samples.

An investigation was performed with the objective of developing a DNA-based protocol for the identification of commercial samples of the herbal compound ginseng. There are currently two major herbal products referred to as ginseng. They are Korean or Chinese ginseng (Panax ginseng) and American ginseng (Panax quinquefolius). The market for ginseng in the United States is estimated to be approximately $300 million annually. Current tests for ginseng species identification rely on expert botanical identification of fresh plant/root specimens or on biochemical characterization of active and marker compounds (e.g., ginsenosides). For the determination of the feasibility of ginseng identification by DNA analysis, a strategy based on the direct DNA sequence analysis of the nuclear ribosomal internal transcribed spacer region was developed. Other genetic tests included sequence analysis of the chloroplast ribulose 1,5-bisphosphate carboxylase large subunit gene and DNA fingerprinting by the rapid amplification of polymorphic DNA technique. To confirm the results, each ginseng sample was identified using high-performance liquid chromatography. All methods were successful in distinguishing American from Korean ginseng. In addition, the protocol was improved for the isolation of genomic and plastid DNA from commercial ginseng preparations by incorporating an impact homogenization step into the standard column chromatography purification procedure.

Base Sequence↗
PubMed1998

Diagnosis of porphyric syndromes: a practical approach in the era of molecular biology.

For cost-effective diagnosis of porphyric syndromes, a logical stepwise approach is best. If neurovisceral features suggest an acute porphyric syndrome, a rapid screening test for urinary porphobilinogen should be performed. If clinical features suggest a cutaneous porphyria, then for solar urticaria and acute photosensitivity (suggesting protoporphyria) screening tests for increased erythrocytic porphyrins should be done; for vesiculobullous formation (suggesting porphyria cutanea tarda, hereditary coproporphyria, or variegate porphyria) a screening test for urinary porphyrins should be done. Positive screening tests should be confirmed with targeted quantitative testing. Enzymatic assays and DNA-based testing are not usually needed for rapid diagnosis or management of symptomatic subjects, but they are useful for kindred evaluation and genetic counseling.

Acute Disease↗
PubMed2004

Gene genealogy and properties of test statistics of neutrality under population growth.

We consider the Wright-Fisher model with exponential population growth and investigate effects of population growth on the shape of genealogy and the distributions of several test statistics of neutrality. In the limiting case as the population grows rapidly, the rapid-growth-limit genealogy is characterized. We obtained approximate expressions for expectations and variances of test statistics in the rapid-growth-limit genealogy and star genealogy. The distributions in the star genealogy are narrower than those in the cases of the simulated and rapid-growth-limit genealogies. The expectations and variances of the test statistics are monotone decreasing functions of the time length of the expansion, and the higher power of R(2) against population growth is suggested to be due to their smaller variances rather than to change of the expectations. We also investigated by simulation how quickly the distributions of test statistics approach those of the rapid-growth-limit genealogy.

Models, Genetic↗
PubMed2003

Associations of MHC ancestral haplotypes with resistance/susceptibility to AIDS disease development.

We tested the association of MHC ancestral haplotypes with rapid or slow progression to AIDS by comparing their frequencies in the French genetics of resistance/susceptibility to immunodeficiency virus cohort with that reported in a control French population. Seven ancestral haplotypes were identified in the genetics of resistance/susceptibility to immunodeficiency virus cohort with a frequency >1%. The 8.1 (odds ratio (OR) = 3, p = 0.006), 35.1 (OR = 5.7, p = 0.001), and 44.2 (OR = 3.4, p = 0.007) ancestral haplotypes were associated with rapid progression, whereas the 35.2 (OR = 3.6, p = 0.001), 44.1 (OR = 5.4, p < 10(-4)), and 57.1 (OR = 5.8, p < 10(-4)) ancestral haplotypes were associated with slow progression to AIDS. Although the frequency of each ancestral haplotype is low in the population, the OR were quite higher than those previously obtained for single HLA allele associations, with some p values as low as 10(-4). The analysis of the recombinant fragments of these haplotypes allowed the identification of the MHC regions in the 35.1, 35.2, and 44.2 haplotypes associated with rapid progression to AIDS and the MHC regions of the 44.1 and 57.1 haplotypes associated with slow progression to AIDS. Previous studies have identified single HLA alleles associated with disease progression. Our results on recombinant fragments confirm the direct role of HLA-B35 in rapid progression. Associations with HLA-A29 and -B57 might be due to linkage disequilibrium with other causative genes within the MHC region.

Acquired Immunodeficiency Syndrome↗
PubMed2004

[Curriculum reform in dental medicine at the University of Ghent].

The need for dental and oral treatment in the society is constantly changing. Epidemiological studies show that in the rapidly aging population in Western Europe, caries (except for root caries) is declining but more complex periodontal treatment is needed. The number of completely edentulous patients is decreasing. Patients have a longer life expectancy but are medically and psychologically more compromised. Many more patients are at high risk for medical complications. Therefore, a more medical orientation of the dental education is needed. The basic cellular and molecular knowledge in medicine is rapidly expanding. The practical application of this expanded knowledge has been introduced in dentistry such as use of DNA probes, genetic testing, vaccines etc. The graduating dentist should be aware of the scientific progress and be able to apply this technology in his future practice. Therefore, the urgent need was felt to reform the dental education fundamentally and to give it a more medical orientation. Teaching is organised in coherent blocks of lectures covering specific parts of' a discipline and discussing the content from different angles by different lecturers. Basic information (eg. physiology, microscopy, microbiology) is provided in the same block as the clinical and therapeutic information. Preclinical laboratories prepare the student for the clinical phase of a discipline and are not any longer devoted to dental technical laboratory work. More time is given to prosthetic planning, communication with the dental technician and to analyse the biological effects of prosthetic appliances. In the final year a large number of teaching hours is devoted to general medical pathology including physiopathology, dermatology, general head and neck pathology and surgery (ENT, oncology, orthognathic surgery) as well as gerodontology including general medical, psychological and nutritional themes. Finally, clinically the student has a multidisciplinary approach in his diagnosis and treatment of patients. The final aim is train and educated oral physicians.

Belgium↗
PubMed1994

Peroxisomal disorders.

Disorders of peroxisome function result in severe and progressive neurologic deficits. Knowledge of these disorders and their role in neurodegenerative disorders has been growing rapidly over the last 40 years. Noninvasive diagnostic tests can identify all of the peroxisomal disorders, many of them prenatally. The genetic basis of some of these peroxisomal disorders is being established, which will advance understanding of their pathobiology and provide clues for therapeutic interventions.

Adolescent↗
PubMed1994

Alterations of p53 and c-myc in the clonal evolution of malignant lymphoma.

We derived the lymphoma cell lines OCI-Ly 13.1 and OCI-Ly 13.2 from a patient with non-Hodgkin's lymphoma at the time of presentation and during chemotherapy-resistant relapse. These lines were of T-cell phenotype and contained the identical T-cell receptor beta-chain rearrangement, indicating that both lines were members of the same malignant clone. The lines differed in their growth characteristics; OCI-Ly 13.1 grew slowly and required growth factors for colony formation, whereas OCI-Ly 13.2 grew rapidly and formed colonies without addition of growth factors. To test whether or not these biologic differences were associated with specific genetic changes, we evaluated the status of the c-myc and p53 genes of both cell lines. The p53 and c-myc genes of OCI-Ly 13.1 were in germline configuration and produced normal-sized transcripts. The p53 protein expressed in OCI-Ly 13.1 was recognized by the anti-p53 monoclonal antibody, PAb240, indicating a conformation typical of p53 proteins expressed by p53 alleles containing a missense mutation. However, sequencing studies of the entire p53 coding region did not reveal any point mutations. In contrast, the cell line OCI-Ly 13.2 contained structural abnormalities of both the c-myc and p53 genes. In addition, one of the p53 alleles was lost as determined by a cDNA probe for the p53 gene (17p 13.1) and the YNZ22.1 probe (17p 13.3). These changes resulted in the absence of p53 protein and mRNA in OCI-Ly 13.2 as detected by immunoprecipitation and Northern blot analysis, respectively. They may be a reflection of disease progression and may be associated with the altered behavior of the malignant cell population within the patient and in vitro.

Base Sequence↗
PubMed2006

Ethical issues in haemophilia.

Ethical issues surrounding both the lack of global access to care as well as the implementation of advancing technologies, continue to challenge the international haemophilia community. Haemophilia is not given the priority it deserves in most developing countries. Given the heavy burdens of sickness and disease and severe resource constraints, it may not be possible to provide effective treatment to all who suffer from the various 'orphan' diseases. Nevertheless, through joint efforts, some package of effective interventions can be deployed for a significant number of those who are afflicted with 'orphan' diseases. With cost-effective utilization of limited resources, a national standard of care is possible and affordable. Gene-based diagnosis carries attendant ethical concerns whether for clinical testing or for research purposes, even as the list of its potential benefits to the haemophilia community grows rapidly. As large-scale genetic sequencing becomes quicker and cheaper, moving from the research to the clinic, we will face decisions about the implementation of prenatal, neonatal and other screening programs. Such debates will require input from not just the health care professionals but from all stakeholders in the haemophilia community. Finally, long-term therapeutic success gene transfer in small and large animal models raises the question of when and in which patient population the novel therapeutic approach should first be studied in humans with haemophilia. Although gene therapy represents a worthy goal, the central question for the haemophilia community should be whether it wishes to volunteer itself as a model for a much broader set of innovations.

Adult↗
PubMed1981

Genetic influences on locomotor activity in 11-day-old housemice.

An 8 X 8 diallel analysis of locomotor activity related to nest return in mice just prior to eye opening indicated a pattern of dominance toward high activity, with little additive genetic variance. Groups of laboratory-reared wild mice did not differ from each other or from the diallel mean, suggesting little relaxation of selection toward rapid nest return during domestication. In contrast to the nest return situation, an eight-strain triple test-cross analysis of locomotion in a test environment unlikely to be encountered by 11-day-old mice indicated only additive genetic variance, with no evidence of dominance for increased activity. When measured in an ecologically relevant environment, the nature of genetic variation appears to change with age in a manner concordant with what one would intuitively assume to be adaptive behavior at each stage of development.

Aging↗
PubMedDate not supplied

Use of provenance tests to predict response to climate change: loblolly pine and Norway spruce.

Provenance tests are often used to determine genetic responses of seed sources to transfer to different climates. This study was undertaken to determine whether provenance tests can be used to predict tree response to rapid climate changes in situ. Data from provenance tests of loblolly pines (Pinus taeda L.), Norway spruce (Picea abies L. Karst) and other southern pines (subsect. AUSTRALES Loud.) were interpreted using regression models to relate growth to temperature variables. Results of different plantings were combined by expressing growth as a percent deviation from the "local" source, and expressing temperature at the source as a deviation from that of the planting site. The results of the loblolly pine and Norway spruce models predicted a loss of about 5 to 10% in height growth below that expected for a genetically adapted seed source, if the average yearly temperature increases by 4 degrees C.

Journal Article↗
PubMed2005

Familial variation in episode frequency in bipolar affective disorder.

OBJECTIVE: Bipolar affective disorder is a familial illness characterized by recurrent episodes of mania and depression, but little is known about the familial nature of episode recurrence or its associated clinical features. The authors analyzed the recurrence frequency of affective episodes (episode frequency), along with associated clinical and demographic variables, in families with at least three members with a major affective disorder. METHOD: Members of 86 families ascertained through probands with bipolar affective disorder who had two or more first-degree relatives with a major affective disorder were interviewed by psychiatrists and assigned an all-sources diagnosis. Data for 407 subjects with a major affective disorder were analyzed. Episode frequency was estimated as the number of episodes of major depression, mania, and hypomania per year of illness. RESULTS: Episode frequency was smoothly distributed over the range of 0.02-20.2 episodes/year. Episode frequency was significantly correlated among relatives (r=0.56, p<0.004). Earlier age at onset, bipolar II disorder, hallucinations or delusions, alcoholism, and suicidal behavior were all more prevalent in the highest than in the lowest quartiles of episode frequency. Female gender and recurrent major depression were more prevalent in the lowest quartile. Panic disorder, substance abuse, and thyroid disease were all unrelated to episode frequency. Subjects with DSM-IV rapid cycling did not differ from other affected subjects for most of the variables tested. CONCLUSIONS: Episode frequency is a highly familial trait in bipolar affective disorder, associated with several indicators of severity, and may be useful in defining clinical subtypes of bipolar affective disorder with greater genetic liability. DSM-IV rapid cycling was not supported by these data as the best predictor of familiality or severity.

Adult↗
PubMed1999

Strain variation in adenovirus serotypes 4 and 7a causing acute respiratory disease.

In order to determine the suitability of vaccine strains established in the 1960s for a new vaccine, a comprehensive study of strain variation of adenovirus serotype 4 (AV 4) and AV 7 was undertaken. A 1,500-bp region of the hexon gene containing the AV neutralization epitopes from prototype, vaccine, and community-acquired strains and from wild-type strains from military personnel that cause acute respiratory disease (ARD) was sequenced and analyzed. The whole hexon gene from prototype strains, vaccine strains, and selected isolates was sequenced. AV 7 and AV 7a were found to have distinct genotypes, and all vaccine and wild-type strains recovered from 1963 to 1997 had the AV 7a genotype. There was no significant strain variation in the neutralization epitopes of the AV 7a genotype over a 42-year period. The evolution of AV 4 was more complex, with continuous genetic drift punctuated by replacement with a new strain. The current strain of AV 4, which has been in circulation since 1995, is significantly different from the AV 4 prototype and the vaccine strains. Genetic differences were confirmed to be antigenic differences by neutralization tests, which define the new strain as an AV 4 variant. A type-specific PCR for AV 4, AV 7/7a, and AV 21 was developed, and this PCR facilitated the rapid identification of isolates from outbreaks of ARD.

Adenovirus Infections, Human↗