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Results for “genetic test utilization”

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PubMed2001

Periodontal risk assessment, diagnosis and treatment planning.

The prevention and treatment of the periodontal diseases is based on accurate diagnosis, reduction or elimination of causative agents, risk management and correction of the harmful effects of disease. Prominent and confirmed risk factors or risk predictors for periodontitis in adults include smoking, diabetes, race, P. gingivalis, P. intermedia, low education, infrequent dental attendance and genetic influences. Several other specific periodontal bacteria, herpesviruses, increased age, male, sex, depression, race, traumatic occlusion and female osteoporosis in the presence of heavy dental calculus have been shown to be associated with loss of periodontal support and can be considered to be risk indicators of periodontitis. The presence of furcation involvement, tooth mobility, and a parafunctional habit without the use of a biteguard are associated with a poorer periodontal prognosis following periodontal therapy. An accurate diagnosis can only be made by a thorough evaluation of data that have been systematically collected by: 1) patient interview, 2) medical consultation as indicated, 3) clinical periodontal examination, 4) radiographic examination, and 5) laboratory tests as needed. Clinical signs of periodontal disease such as pocket depth, loss of clinical attachment and bone loss are cumulative measures of past disease. They do not provide the dentist with a current assessment of disease activity. In an attempt to improve the ability to predict future disease progression, several types of diagnostic tests have been studied, including host inflammatory products and mediators, enzymes, tissue breakdown products and subgingival temperature. In general, the usefulness of these tests for predicting future disease activity remains to be established in terms of sensitivity, specificity and predictive value. Although microbiological analysis of subgingival plaque is not necessary to diagnose and treat most patients with periodontitis, it is helpful when treating patients with unusual forms of periodontal disease such as early-onset, refractory and rapidly progressive disease. There appears to be a strong genetic component in some types of periodontal disease and genetic testing for disease susceptibility has potential for future use, but more research is needed to determine its utility for use in clinical practice. Treatment of the periodontal diseases may be divided into four phases: systemic, hygienic, corrective and maintenance or supportive periodontal therapy. Regardless of the type of treatment provided, periodontal therapy will fail or will be less effective in the absence of adequate supportive periodontal therapy.

Bacteriological Techniques↗

PubMed1980

An overview of short-term tests for the mutagenic and carcinogenic potential of pesticides.

In the last few years, marked progress has been made in the development of methods for evaluating the mutagenic and carcinogenic potential of pesticide chemicals. The correlation of genetic and related biological activity in short-term tests with carcinogenic activity in whole animals allows the utilization of short-term mutagenicity bioassays to prescreen chemicals for effects related to mutation induction and presumptive carcinogenicity. In addition, bioassays now available can measure directly the chemical transformation of normal cells in culture into cells capable of producing tumors when injected into animals. This paper will review briefly the major types of relevant short-term tests and will develop a rationale for a phased approach to the evaluation of the mutagenic and carcinogenic potential of environmental chemicals. This approach involves the sequential application of bioassays which are organized into a three-level matrix emphasizing first detection, then confirmation, and finally hazard assessment. Chemicals demonstrating positive results in the short-term detection systems and confirmatory bioassays are pursued in higher level whole animal define a negative result. The phased approach should facilitate a cost effective utilization of limited testing resources and provide protection for human health in proportion to the anticipated hazard. Results obtained in evaluating a series of thirty-eight pesticide chemicals according to the phased approach discussed in detail.

Animals↗

PubMedDate not supplied

Characterization of microsatellites in Bambusa arundinacea and cross species amplification in other bamboos.

Microsatellites, tandem repeats of short nucleotide (1-6 bp) sequences, are the DNA marker of choice because of their highly polymorphic, ubiquitous distribution within genome, ease of genotyping through polymerase chain reaction (PCR), selectively neutral, co-dominant and multi allelic nature. Six microsatellites, three polymorphic and three monomorphic, have been characterized for the first time in a bamboo species, Bambusa arudinacea belonging to the family Poaceae. The number of alleles per locus ranges form 2 to 13. Allelic diversity ranges from 0.041 to 0.870. Polymorphic information content (PIC) values for two loci were > 0.3, an indicator of polymorphic allele. Cross species amplification has been tested in other 18 bamboo species. Monomorphic simple sequence repeats (SSRs) have been found to be cross amplified in most of the tested species while polymorphic ones in only three to four species. The utility of the SSR loci in genetic diversity study of B. arundinacea and other cross amplified bamboo species have been discussed.

Bambusa↗

PubMed2002

Molecular beacons: colorful analysis of nucleic acids.

The completion of the Humane Genome Project has resulted in an exponential rise in the demand for molecular diagnostic assays. To meet this demand, several innovative technologies have become available for performing homogeneous genetic analyses. For this type of assay, special detector probes are necessary. In 1996, Tyagi and Kramer described fluorogenic hairpin-shaped detector probes, called 'molecular beacons', which are extraordinarily specific. Since they characterize alleles by the generation of fluorescent signals, they are perfectly suited for homogeneous genetic analysis. Molecular beacons assays are simple, fast, inexpensive, sensitive, utilize a high-throughput format, enable the testing of many samples simultaneously and allow the detection of a series of different agents in the same assay tube. This review is designed to give the reader a greater understanding of the exciting applications of molecular beacons in DNA, RNA and protein studies.

Color↗

PubMed1989

Peopling of Andean South America.

Archeological, craniometrical, and genetic information is utilized to reconstruct possible migration routes used in the peopling of Andean South America. Special emphasis is given to the elaboration of craniometrical isoline maps and its application in testing models of population displacement based on archeological data. A genetic distance analysis among linguistic groupings complements the conclusions based on archeological and craniometrical information.

Agriculture↗

PubMed1996

Meiotic recombination and germ cell aneuploidy.

Data on human trisomic conceptuses suggest that the extra chromosome commonly has a maternal origin, and the amount and position of crossing-over on nondisjoined chromosomes is commonly altered. These observations may provide important clues to the etiology of human germ cell aneuploidy, especially in regard to evaluating whether environmental factors play a role. There is concordance of effects of environmental agents on fungi, plants, and animals, which suggests that the overall process of meiosis is well conserved and that chemical and physical agents can affect meiotic recombination, leading to aneuploidy. It seems likely that meiosis in humans will fit the general pattern of meiosis in terms of sensitivity to radiation and chemicals. Thus studies on other organisms provide some insight into the procedures necessary for obtaining useful human data. For example, frequencies of spontaneous meiotic recombination are not uniform per physical length in Drosophila, and different regions of a chromosome respond differently to treatment. Treatments that relieve constraints on the distribution of meiotic exchange, without changing greatly the overall frequency of exchange, may increase the number of univalents and give the impression that there are chromosome-specific responses. Recombination studies that monitor one or a few relatively short genetic regions may also give a false impression of the effects of a treatment on recombination. In addition, meiotic mutants in Saccharomyces and Drosophila highlight a number of processes that are important for production of an exchange event and the utility of that event in the proper segregation of both homologues and sisters. They also suggest that tests for pairing at pachytene, chiasmata at diplotene, and genetic crossing-over may give different results.

Aneuploidy↗

PubMed2005

Power and sample size calculations for genetic case/control studies using gene-centric SNP maps: application to human chromosomes 6, 21, and 22 in three populations.

Power and sample size calculations are critical parts of any research design for genetic association. We present a method that utilizes haplotype frequency information and average marker-marker linkage disequilibrium on SNPs typed in and around all genes on a chromosome. The test statistic used is the classic likelihood ratio test applied to haplotypes in case/control populations. Haplotype frequencies are computed through specification of genetic model parameters. Power is determined by computation of the test's non-centrality parameter. Power per gene is computed as a weighted average of the power assuming each haplotype is associated with the trait. We apply our method to genotype data from dense SNP maps across three entire chromosomes (6, 21, and 22) for three different human populations (African-American, Caucasian, Chinese), three different models of disease (additive, dominant, and multiplicative) and two trait allele frequencies (rare, common). We perform a regression analysis using these factors, average marker-marker disequilibrium, and the haplotype diversity across the gene region to determine which factors most significantly affect average power for a gene in our data. Also, as a 'proof of principle' calculation, we perform power and sample size calculations for all genes within 100 kb of the PSORS1 locus (chromosome 6) for a previously published association study of psoriasis. Results of our regression analysis indicate that four highly significant factors that determine average power to detect association are: disease model, average marker-marker disequilibrium, haplotype diversity, and the trait allele frequency. These findings may have important implications for the design of well-powered candidate gene association studies. Our power and sample size calculations for the PSORS1 gene appear consistent with published findings, namely that there is substantial power (>0.99) for most genes within 100 kb of the PSORS1 locus at the 0.01 significance level.

Black or African American↗

PubMed1999

Promoting safe and effective genetic tests in the United States: work of the task force on genetic testing.

The Task Force on Genetic Testing was created to review genetic testing in the United States and, when necessary, to make recommendations to ensure the development of safe and effective genetic tests. A survey to explore the state of genetic testing was undertaken for the Task Force and completed in early 1995. The survey, as well as literature reports and other information collected for the Task Force, showed problems affecting safety and effectiveness, as defined by the Task Force: validity and utility of predictive tests, laboratory quality, and appropriate use by healthcare providers and consumers. On the basis of these findings, the Task Force made several recommendations to ensure safe and effective genetic testing. The Secretary of Health and Human Services followed up one recommendation by creating the Secretary's Advisory Committee on Genetic Testing. One of its functions will be to implement other recommendations of the Task Force.

Genetic Techniques↗

PubMed1995

Efficient selection of recombinant adenoviruses by vectors that express beta-galactosidase.

Adenovirus serotype 5 vectors which contain the Excherichia coli beta-galactosidase gene driven by the cytomegalovirus immediate-early promoter as a screenable marker have been made and successfully used in the construction of recombinant adenoviruses. The beta-galactosidase gene has been introduced into viruses in which the E3 region is maintained or deleted and in which the cis-acting packaging sequence has been reiterated at the right end of the chromosome. A unique BstBI site has been introduced 3' of the beta-galactosidase gene. Cotransfection of BstBI-digested vector DNA and a plasmid containing the left end of the viral chromosome followed by staining with X-Gal (5-bromo-4-chloro-3-indolyl-beta-D-galactopyranoside) results in clear plaques when overlap recombination has occurred and blue plaques when ligation of the viral arms has occurred within the host cell. The beta-galactosidase-expressing viruses grow to lower titers than do the parental viruses, leading to a relative growth advantage for viruses resulting from overlap recombination. Combined with color selection based on the beta-galactosidase gene, this system permits efficient production and selection of recombinant viruses after cotransfection of BstBI-digested viral DNA with a plasmid including left-end viral sequences and the gene of interest. The beta-galactosidase-expressing viral DNAs were used to construct viruses containing BstBI sites on either side of the cis-acting packaging element as a means of testing their utility.

Adenoviridae↗

PubMed1981

Use of odds of paternity computations in determining the reliability of single exclusions in paternity testing.

In parentage determination with genetic markers the concept of paternity index is used to evaluate the relative likelihood of fathership of an accused male individual. When a battery of genetic tests are performed, the event of inadvertant technical errors or the occurrence of suppressor genes that cause an apparent paternity exclusion of the male concerned reduces this likelihood to zero. However, through a study of statistical properties of the paternity index statistic based on the other genetic systems, it is possible to examine the reliability of one or a few such apparent exclusions. The details of this approach is examined here by analytical methods following the statistical principles of likelihood ratio test procedures. Some illustrative data are also analyzed to show the practical utility of this approach.

Alleles↗

PubMed2003

Current status of preimplantation diagnosis for single gene disorders.

Preimplantation genetic diagnosis (PGD) has become an established procedure for avoiding the birth of affected children with single gene disorders. PGD is performed through polar body or blastomere biopsy, which has no deleterious effect on pre- and post-implantation development. This review describes the most recent developments and current changes in the spectrum of conditions for which PGD has been applied. The most recent applications of PGD include congenital malformations, blood group incompatibility and an increasing number of late onset disorders with genetic predisposition, all of which have not previously been diagnosed using PGD. Despite ethical concerns, PGD has also been used for preselection of unaffected and HLA matched embryos, and recently for preimplantation HLA matching without testing for the causative gene. This extends the practical value of PGD, with its utility being no longer limited to prevention of single gene disorders, by expanding it to treatment of siblings requiring stem cell transplantation.

Fertilization in Vitro↗

PubMed1999

Validation of genetically engineered bioluminescent surfactant resistant bacteria as toxicity assessment tools.

Bacteria are useful organisms for measuring acute and chronic toxicity. The most popular toxicity tests utilize the inhibition of bioluminescence as an indication of toxicity. An extensive toxicity database on pure chemical compounds has been created using the bioluminescent microorganism, Vibrio fischeri. However, the use of the Microtox assay in applications for environmental samples is not always successful, due to the test organism. Because the genes for bioluminescence have been cloned from V. fischeri, environmentally relevant test strains can be readily constructed. In this study, surfactant-resistant bioluminescent bacterial strains were constructed by transferring a broad host range plasmid containing the bioluminescent genes under the regulation of a constitutive promoter into strains from several bacterial genera. Two test strains, Stenotrophomonas 3664 and Alcaligenes eutrophus 2050, were approximately 400 times more resistant to the nonionic surfactant polyoxyethylene 10 lauryl ether than V. fischeri and are useful for toxicity reduction evaluations of remediation processes which use surfactants for solubilization of hydrophobic pollutants. The use of these strains as alternative test organisms in the Microtox assay was evaluated using nonpolar narcosis as the baseline toxicity mechanisms. The two test strains and V. fischeri indicated linear fits of EC50 values with the octanol/water partition (Kow) for five nonpolar narcotic compounds in acute assays (r2>0.9) with a slope of approximately 1. For all three strains, the y-intercept values were approximately the same, indicating that sensitivity did not vary. These results indicate that the nonpolar narcosis baseline toxicity mechanism may be useful as a general tool to validate the functioning of genetically engineered bioluminescent microorganisms.

Alcaligenes↗

PubMed1996

A model for testing recombinogenic sequences in the mouse germline.

Homologous recombination is a conserved process of genetic exchange generated by homologous pairing of nucleotides. Species diversity and gene evolution are dependent on the outcomes of recombination during germ cell development, yet systems to study mammalian germline recombination, especially those with applications to human genetics, are not well developed. We report on a transgenic mouse system designed to study recombination within test sequences in the male germline utilizing an intron-interrupted lacZ reporter gene. beta-galactosidase positive sperm are detected and quantitated by flow cytometry using fluorogenic substrates. Examination of recombination within a 1.7 kb repeat of test sequences derived from the human glycophorin breakpoint cluster region detects approximately 0.04-0.09% fluorescent sperm. Confirmation that these sperm result from recombination in the germline comes from histochemical staining of testicular cells, examination of spliced mRNA, and PCR analysis of sorted sperm populations. The system is readily adaptable to studies of other sequences reported to have elevated levels of recombination, including those implicated in human genetic disease. Investigations of the molecular basis for genomic instability at specific chromosomal locations may yield important insights into mechanisms of chromosomal loss and rearrangements.

Animals↗

PubMed1997

Leading strand specific spontaneous mutation corrects a quasipalindrome by an intermolecular strand switch mechanism.

Imperfect inverted repeats or quasipalindromes can undergo spontaneous, often complex mutational events that correct them to perfect palindromes. Two models that depend on the quasipalindrome providing a template for a specific mutational event have been described to explain this mutation: an intramolecular and an intermolecular strand switch model. A 17bp quasipalindrome containing a -1 deletion within the chloramphenicol acetyl transferase (CAT) gene in plasmid pJT7 undergoes a spontaneous +1 frameshift mutation that creates a perfect inverted repeat and a Cm(r) phenotype. By analyzing this mutation frequency in two plasmids that contain the CAT gene in either orientation with respect to the origin of replication, we show that the specific frameshift occurs preferentially in the leading strand during DNA replication. Due to the availability and proximity of the lagging strand template as a single strand during replication of the quasipalindrome in the leading but not lagging strand, we suggest that the specificity for the leading strand correction is due to a leading strand specific intermolecular strand switch rather than an intramolecular strand switch. To test this hypothesis, we have designed a genetic selection to detect a leading strand intermolecular strand switch. This selection utilizes asymmetric quasipalindromes, one of which contains two central stop codons. When cloned into the CAT gene in pJT7, reversion to Cm(r) requires inversion of the stop codons and addition of a +1 frameshift to correct the reading frame. The inversion of the central stop codons, which is predicted by an intermolecular but not an intramolecular strand switch, occurs concomitant with the specific correction of the original 17 bp quasipalindrome. Inversion of an asymmetric center can also be demonstrated when not under selective pressure using a quasipalindrome lacking central stop codons. These results are consistent with the correction of a quasipalindrome occurring predominantly by an intermolecular strand switch during replication of the leading strand.

Base Sequence↗

PubMed2005

Development of EST-SSR markers by data mining in three species of shrimp: Litopenaeus vannamei, Litopenaeus stylirostris, and Trachypenaeus birdy.

We report on the data mining of publicly available Litopenaeus vannamei expressed sequence tags (ESTs) to generate simple sequence repeat (SSRs) markers and on their transferability between related Penaeid shrimp species. Repeat motifs were found in 3.8% of the evaluated ESTs at a frequency of one repeat every 7.8 kb of sequence data. A total of 206 primer pairs were designed, and 112 loci were amplified with the highest success in L. vannamei. A high percentage (69%) of EST-SSRs were transferable within the genus Litopenaeus. More than half of the amplified products were polymorphic in a small testing panel of L. vannamei. Evaluation of those primers in a larger testing panel showed that 72% of the markers fit Hardy-Weinberg equilibrium, which shows their utility for population genetic analysis. Additionally, a set of 26 of the EST-SSRs were evaluated for Mendelian segregation. A high percentage of monomorphic markers (46%) proved to be polymorphic by singles-stranded conformational polymorphism analysis. Because of the high number of ESTs available in public databases, a data mining approach similar to the one outlined here might yield high numbers of SSR markers in many animal taxa.

Animals↗

PubMed2000

Selective pressure by antibiotic use in livestock.

Selective pressure exerted by the use of antibiotics as growth promoters in food animals appears to have created large reservoirs of transferable antibiotic resistance in these ecosystems. This first became evident for oxytetracycline and later for the streptothricin antibiotic nurseothricin, for which a transfer of relevant resistance determinants (sat genes) to bacterial pathogens of humans was demonstrated. With the emergence of glycopeptide resistance in Enterococcus faecium outside hospitals, a large reservoir of transferable resistance (vanA gene cluster) was identified in animal husbandry due to the use of avoparcin as feed additive. The spread of resistance, which reaches the human enterococcal flora via meat products, is probably due to the dissemination of the vanA gene cluster integrated into different conjugative plasmids among a variety of different strains. Streptogramin resistance associated with the resistance genes vatA and vatG has been found in E. faecium of animal and of clinical origin. Because virginiamycin has been used as growth promoter in animals but streptogramins have been used infrequently in human medicine, this again suggests an animal origin of resistance. Since the use of avoparcin ended, a decline in the rates of glycopeptide-resistant E. faecium (GREF) from animals and humans in the community has been recorded. This supports the ban of antibacterial growth promoters that might interfere with human chemotherapy that has been introduced in European Union countries.

Animals↗

PubMed1986

Comparative effects of dietary protein and cholesterol-fat content on genetically lean and obese pigs.

Interactions of a high fat-high cholesterol diet with low and high dietary protein levels were tested in genetically obese and lean growing pigs. Sixty-four growing swine (32 obese and 32 lean) were utilized in a 9-wk experiment in which four diets were fed in a 2 X 2 factorial arrangement with two levels of plant protein (8 and 16%) and two levels of fat and cholesterol (0 added or 11% beef tallow-3% dried egg yolk added). Daily gain and gain-to-feed ratio were significantly reduced by low protein (P less than 0.01) and increased by high fat-high cholesterol. Obese pigs gained weight faster than lean pigs but were less efficient in feed utilization (P less than 0.02) except when consuming low protein diets (P less than 0.001). Plasma cholesterol was increased by low protein (P less than 0.01) and by high fat-high cholesterol (P less than 0.02); highest values were in pigs fed low protein-high fat-high cholesterol. Lean pigs showed a greater rise than obese pigs in plasma cholesterol when fed low protein diets, reflecting a higher dietary protein requirement for lean pigs as indicated by plasma total protein, albumin and urea nitrogen (urea-N) responses to diet. Percentage of aortic surface area stained by Sudan IV tended to be higher in lean than in obese pigs but the difference was not statistically significant (P less than 0.25). The data show the hypercholesterolemic effect of dietary protein restriction in growing swine and establish that genetic differences related to body composition and quantitative protein requirement affect the response.

Animals↗

PubMed1986

A current genotoxicity database for heterocyclic thermic food mutagens. I. Genetically relevant endpoints.

Cooking, heat processing, or pyrolysis of protein-rich foods induce the formation of a series of structurally related heterocyclic aromatic bases that have been found to be mutagens. The primary genetic assay utilized to detect and isolate these mutagens has been the his reversion assay in Salmonella typhimurium. The classification and nomenclature of these chemicals is revised to reflect recent advances. The findings of short-term tests for genetic injury that have been applied to these agents are presented in a systematic way. Cell-free, bacterial, mammalian cell culture, and in vivo systems are included. Major results, the mutagens tested, and key references are presented in tabular form, with text commentary. Integrated conclusions on the state of current knowledge of the genetic toxicity of thermic food mutagens are presented. Areas in need of further research are defined. Finally, an outline is presented of a suggested path leading to the determination whether normal methods of food preparation and processing constitute a human health hazard.

Animals↗