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Evaluation of genetic diversity of poplar genotypes by RAPD and AP-PCR analysis.

RAPD (randomly amplified polymorphic DNA) and AP-PCR (arbitrarily primed PCR) were utilized to establish the genetic diversity of 19 Populus genotypes. A set of 40 primers of random sequence was tested, of which 35 exhibited polymorphism. Eighteen primers generated 162 easily detectable bands between 250 and 2,500 base pairs in size, sufficient to distinguish between the genotypes. Similarity measures, cluster and multidimensional scaling analysis were performed to evaluate the RAPD and AP-PCR data. Our study demonstrated that in most instances similarity in the RAPD and AP-PCR banding patterns reflected the relationship due to origin. Nineteen primers gave a species or hybrid-specific pattern. One primer generated a specific pattern in P. euramericana. Ten primers produced specific fragments in VIF (P. alba), 4 primers in KOR (P. pyramidialis x P. berolinensis) and 4 primers in UNA and RAS (P. trichocarpa x P. deltoides). The results of this study demonstrated that RAPD or AP-PCR can be used to distinguish between poplar genotypes.

Genetic Variation↗

Pharmacogenetics: the therapeutic drug monitoring of the future?

Genetic variability in drug response occurs as a result of molecular alterations at the level of drug-metabolising enzymes, drug targets/receptors, and drug transport proteins. In this paper, we discuss the possibility that therapeutic drug monitoring (TDM) in the future will involve not the mere measurement and interpretation of drug concentrations but will include both traditional TDM and pharmacogenetics-oriented TDM. In contrast to traditional TDM, which cannot be performed until after a drug is administered to the patient. pharmacogenetics-oriented TDM can be conducted even before treatment begins. Other advantages of genotyping over traditional TDM include, but are not limited to, the following: (i) it does not require the assumption of steady-state conditions (or patient compliance) for the interpretation of results; (ii) it can often be performed less invasively (with saliva, hair root or buccal swab samples); (iii) it can provide predictive value for multiple drugs [e.g. a number of cytochrome P450 (CYP) 2D6, CYP2C 19 or CYP2C9 substrates] rather than a single drug; (iv) it provides mechanistic, instead of merely descriptive, information; and (v) it is constant over an individual's lifetime (and not influenced by concurrent drug administration, alteration in hormonal levels or disease states). Pharmacogenetic information can be applied a priori for initial dose stratification and identification of cases where certain drugs are simply not effective. However, traditional TDM will still be required for all of the reasons that we use it now. In current clinical practice, pharmacogenetic testing is performed for only a few drugs (e.g. mercaptopurine, thioguanine, azathioprine, trastuzumab and tacrine) and in a limited number of teaching hospitals and specialist academic centres. We propose that other drugs (e.g. warfarin, phenytoin, codeine, oral hypoglycaemics, tricyclic antidepressants, aminoglycosides, digoxin, cyclosporin, cyclophosphamide, ifosfamide, theophylline and clozapine) are potential candidates for pharmacogenetics-oriented TDM. However, prospective studies of phaymacogenetics-oriented TDM must be performed to determine its efficacy and cost effectiveness in optimising therapeutic effects while minimising toxicity. In the future, in addition to targeting a patient's drug concentrations within a therapeutic range, pharmacists are likely to be making dosage recommendations for individual drugs on the basis of the individual patient's genotype. As we enter the era of personalised drug therapy, we will be able to identify not only the best drug to be administered to a particular patient, but also the most effective and safest dosage from the outset of therapy.

Cytochrome P-450 Enzyme System↗

Behavioral and functional analysis of mouse phenotype: SHIRPA, a proposed protocol for comprehensive phenotype assessment.

For an understanding of the aberrant biology seen in mouse mutations and identification of more subtle phenotype variation, there is a need for a full clinical and pathological characterization of the animals. Although there has been some use of sophisticated techniques, the majority of behavioral and functional analyses in mice have been qualitative rather than quantitative in nature. There is, however, no comprehensive routine screening and testing protocol designed to identify and characterize phenotype variation or disorders associated with the mouse genome. We have developed the SHIRPA procedure to characterize the phenotype of mice in three stages. The primary screen utilizes standard methods to provide a behavioral and functional profile by observational assessment. The secondary screen involves a comprehensive behavioral assessment battery and pathological analysis. These protocols provide the framework for a general phenotype assessment that is suitable for a wide range of applications, including the characterization of spontaneous and induced mutants, the analysis of transgenic and gene-targeted phenotypes, and the definition of variation between strains. The tertiary screening stage described is tailored to the assessment of existing or potential models of neurological disease, as well as the assessment of phenotypic variability that may be the result of unknown genetic influences. SHIRPA utilizes standardized protocols for behavioral and functional assessment that provide a sensitive measure for quantifying phenotype expression in the mouse. These paradigms can be refined to test the function of specific neural pathways, which will, in turn, contribute to a greater understanding of neurological disorders.

Animals↗

[How should be the genetic medicine in the near future?].

Massive and systematic information on human genes and genome is accumulating with progress in the Human Genome Project. Information on the genome has the characteristics of a digital signal appropriate for high-throughput handing by computers. Therefore, the field of gene tests has a high affinity to the field of laboratory medicine. In addition, it is important for survival strategy by departments of laboratory medicine that stand on the edge. We have to establish an infrastructure to utilize genome information in clinical medicine while anticipating numerous issues. The following issues need to be addressed in addition to the previous report(Rinsho Byori 50: 156-160, 2002) 1. Integral system for genetic medicine. 2. Center for human germline gene tests. 3. Quality control of human gene tests. 4. Epidemiological data of germline gene tests.

Clinical Laboratory Techniques↗

Barriers to carrier testing for adult cystic fibrosis sibs: the importance of not knowing.

Early experience in centers offering population screening for cystic fibrosis (CF) has shown that few of the public are taking advantage of the offer [Miller, 1993: New Scientist 139:6]. There is similar low utilization among adult CF sibs [Fanos and Johnson, 1993: Am J Hum Genet 53:A51]. The purpose of this study was to identify factors motivating or interfering with the pursuit of carrier testing in adult CF sibs. Eighty-four adult CF sibs and their spouses, drawn from Children's Hospital, Oakland, CA, and Children's Hospital, Boston, MA, were interviewed for about an hour, and qualitative material was coded on various themes. Structural and psychological barriers to the transmission of genetic information were identified: 1) sibs encountered difficulty in obtaining information concerning availability of testing; 2) parental guilt and blame prevents parents from discussing genetic issues with the sib; 3) sibs rarely discuss testing with each other; 4) the CF patient or parent often has difficulty with the implications of the sib seeking carrier testing; 5) family and individual myths about carrier status influence the sib's decision to seek testing; 6) statistical odds have lost meaning in families where the rare has already occurred; 7) the sib fears loss of interpersonal desirability; and 8) carrier status can serve an important function in binding guilt. Remaining unaware of their carrier status may serve significant psychological functions for individuals at risk.

Adolescent↗

Identifying interactions between genes and early environment in the mouse.

Interactions between genetic and early environmental factors are recognized to play a critical role in modulating susceptibility to disease, particularly mental illness. In order to better understand such mechanisms at the molecular level, we have developed a screening paradigm in mice that allows us to test the ability of targeted mutations in candidate genes to modify susceptibility to the long-term effects of different maternal environment. Offspring of genetically identical F1 hybrid dams produced by reciprocal breeding of C57BL/6 and BALB/c parents show alterations in anxiety-related behavior as a consequence of their different maternal environment. Introduction of targeted mutations into these offspring via the father allows for the identification of candidate genes that alter these maternal effects. Our strategy offers several advantages over other methods to study maternal effects, including the use of genetically identical parents, the ability to identify both prenatal and postnatal effects, the straightforward introduction of mutations and its adaptability to high-throughput screening. In order to test the utility of this paradigm to screen candidate genes, we tested for gene-environment interactions involving loss-of-function mutations in the serotonin 1A receptor gene. Our studies demonstrate that early gene-environment interactions can be successfully tested in the mouse. When combined with conditional gene targeting and other molecular genetic techniques available in the mouse, this approach has the potential to identify the molecular mechanisms underlying early gene-environment effects.

Animals↗

Management of complex lipid disorders in a community lipid clinic setting: Implementing a multidisciplinary model.

BACKGROUND: Large treatment gaps exist in the management of lipid disorders, and many high-risk patients have factors that complicate management efforts. While lipid clinics exist within academic medical centers, most of these patients are cared for in community settings. OBJECTIVE: To report our experience and results managing challenging and complex lipid disorders in a community-based lipid clinic. METHODS: We established a specialized lipid clinic in a community medical setting, with a focus on patients with management challenges and/or suspicion of a genetic lipid disorder, employing a multidisciplinary approach to optimize patient outcomes, emphasizing appropriate medical therapies and lipid genetic testing in selected patients. Retrospective electronic health record data were collected to analyze patient characteristics, treatment patterns, and lipid results. RESULTS: Over the period 2022 through 2024, 183 patients were seen (mean 63 years, 62% female). The challenging nature of the patient population was highlighted by high rates of statin intolerance (50%), no lipid medical therapy at baseline (50%), and comorbidities (atherosclerotic cardiovascular disease [ASCVD], diabetes, and/or hypertension-61%). Despite this, over a mean follow-up of 9.4&#xa0;&#xb1;&#xa0;7.3 months, we observed a mean low-density lipoprotein cholesterol&#xa0;decrease of 49&#xa0;mg/dL (-24.5%, P&#xa0;<&#xa0;.001), along with significant decreases in total cholesterol and triglycerides. Pathogenic dyslipidemia genetic variants were discovered in 21 patients (of 105 tested). Significant lipid improvements in the whole cohort, as well as multiple subgroups, were associated with greater utilization of combination therapies. CONCLUSION: Patients with complex lipid disorders can be successfully managed within a specialized lipid clinic in community medical settings. Applying such a multidisciplinary model outside of traditional academic medical centers offers the potential to raise the level of lipid management and ASCVD prevention more broadly in larger populations.

Combination medical therapy↗

Familial transmission of alcoholism among nonalcoholics and mild, severe, and dyssocial subtypes of alcoholism.

BACKGROUND: In the field of alcohol studies, there are many typologies attempting to reduce the heterogeneity of expression of this complex disorder to better understand its natural history and etiology. However, few typologies have included empirical assessment of the degree of familial liability. To the extent there is variability in genetic vulnerability to alcoholism, inclusion of measures of this variability in proposed typologies is important to their validity and utility. We test whether the mild, severe, and dyssocial typology distinguished cases of alcohol dependence with high familial liability from those with low familial liability to alcoholism. METHODS: Data came from the National Longitudinal Alcohol Epidemiologic Survey-1992, a household probability sample representative of those 18 years of age and older in the contiguous US Response rate was 92%. Only whites were included here because the typology under study has been successfully applied to this race/ethnic group only. The total number of respondents were 32,447 and included 13,825 men and 18,622 women. Identification of a biological relative as alcoholic was based on the proband's report. All analyses were weighted to adjust for sampling under a multistage stratified design. RESULTS: Familial density of alcoholism (number of alcoholics/number of adult family members) substantially differed by proband alcohol dependence status for both men and women (male probands-nonalcoholics 7%, mild 13%, severe 25%, dyssocial 19%; female probands-nonalcoholics 8%, mild 18%, severe 33%, dyssocial 24%; p <.001). Cross-fostering analysis of the probands with adoptive/stepparents indicated little difference between nonalcoholic and mild alcoholic probands and suggests greater influence of biological parents for severe subtype probands compared to other probands. CONCLUSIONS: These results suggest construct validity for the alcoholism typology as distinguishing subtypes with differing degrees of familial liability to alcoholism. The typology may be useful when employing an extreme comparison strategy in genetic studies of alcohol dependence.

Adult↗

Evaluation of a structural polymorphism in the ankyrin repeat and kinase domain containing 1 (ANKK1) gene and the activation of executive attention networks.

The specificity of genetic effects on brain activation is a central issue in understanding how molecular actions at the synapse relate to anatomic patterns of brain activity. In an effort to understand the basis for the specificity of gene-associated brain activity, we explore a well-studied genetic polymorphism, TaqIA, which lies downstream of the DRD2 gene in the protein-encoding region of a neighboring gene, ANKK1, which is not expressed in the brain. We utilize the attention network test and find that carriers of the A1 allele show gene-associated functional activation in an anatomically specific, dopamine-rich region of the brain comprising the anterior cingulate gyrus, a finding partially consistent with prior data from functional imaging genetics. A review of the patterns of expression for ANKK1 and DRD2 and the extent of linkage disequilibrium between the two genes sheds light on additional criteria for the selection of candidate genes in imaging-genetic studies.

Adolescent↗

Genetic testing for thrombophilia mutations.

Venous thrombosis is a multicausal disease due to the interaction of genetic and environmental risk factors. Some of the recently discovered genetic risk factors, such as factor V Leiden and prothrombin G20210A mutations, are quite common in the population. Accordingly, laboratory investigation of thrombophilic disorders has expanded to incorporate molecular assays, which unlike functional assays, are unequivocal with no borderline values. When testing for these mutations, specific issues of patient management need to be addressed, such as the duration of anticoagulant therapy, risk stratification for primary or secondary prophylaxis, and family studies. Criteria used to select specific DNA methodologies will center on the issues of cost, automation, speed, reliability, and simplicity. A variety of molecular methods fulfill many but not all of these criteria, whereas the new, semiautomated methodologies of real-time polymerase chain reaction and DNA microarrays offer the potential for widespread application and utility in the future.

Antithrombins↗

A cost-effectiveness analysis of amniocentesis and chorionic villus sampling for prenatal genetic testing.

Amniocentesis and chorionic villus sampling are tests for the prenatal diagnosis of cytogenetic abnormalities. We calculated the incremental costs per abnormal birth averted, and the incremental costs per quality-adjusted outcome, of amniocentesis and chorionic villus sampling performed for the indication of maternal age. Probabilities were obtained from the literature, and direct medical costs from hospital charges deflated to reflect aggregated contracted care reimbursements. Utilities were used to quality-adjust prenatal testing outcomes. Based on costs per abnormal birth averted, at all maternal ages from 30 to 43 years, amniocentesis was more cost-effective than chorionic villus sampling; at ages 44 and 45, chorionic villus sampling was more cost-effective. However, if the anxiety reduction provided by first-trimester diagnosis was equivalent to a 0.2% risk of an abnormal child, chorionic villus sampling was more cost-effective than amniocentesis at all maternal ages. Based on data from the 1988 United States natality cohort, the current policy of testing women aged 35 and older would cost $103,329 and $111,184 per abnormal birth averted for amniocentesis and chorionic villus sampling, respectively. Testing women aged 30 and older would almost double these costs. For either prenatal test, targeting high risk women for testing, and striving for utilization rates of 50% or higher, appeared to be the most cost-effective policy.

Adult↗

Trade-off between gestational age and miscarriage risk of prenatal testing: does it vary according to genetic risk?

It has been generally assumed that as genetic risk rises, so the higher procedure-related miscarriage rates of diagnostic tests done earlier in gestation become more acceptable. To test the hypothesis a decision tree was used, in which the only differences between two tests A and B were that A was carried out earlier in pregnancy and was more likely to cause miscarriage. Over a wide range of rankings for the three outcomes (procedure-related miscarriage of a normal baby, early termination of pregnancy after test A, late termination of pregnancy after test B), the expected utility (relative desirability) of an earlier, but more risky, test was greater at a high (1 in 4) than at a low (1 in 100) genetic risk.

Abortion, Spontaneous↗

Encouraging patients to undergo prenatal genetic counseling before the day of amniocentesis. Its effect on the use of amniocentesis.

The purpose of this study was to determine if encouraging in-depth prenatal genetic counseling before the day of possible genetic amniocentesis affected the use of amniocentesis. Five hundred two patients were referred to our center for prenatal genetic services during a 15-month period. All patients were scheduled for genetic counseling before possible amniocentesis. During the initial three months (group I), patients were routinely scheduled for counseling on the same day of the procedure unless they requested earlier counseling. During the subsequent 12 months (group II), patients were encouraged to undergo counseling before the day of planned amniocentesis, and 48% agreed. When early counseling was encouraged, the use of amniocentesis decreased from 85% (group I) to 73% (group II) (P less than .025). Among patients with advanced maternal age as the only indication for testing (n = 375), utilization of amniocentesis decreased from 93% (group I) to 78% (group II) (P less than .005). A policy of encouraging early prenatal genetic counseling appears to be a significant factor in the use of genetic amniocentesis.

Amniocentesis↗

Structure of breeding programs to capitalize on reproductive technology for genetic improvement.

Potential rates of genetic progress are limited by biological constraints, which along with genetic parameters determine the structure of breeding programs to be employed for maximum genetic improvement. The objective here is to determine whether current progeny-testing programs in dairy cattle, which have been dictated and constrained by low female reproductive rates, need to be changed to capitalize on new reproductive technologies and how these changes should be implemented. Many differences between breeding programs diminish when selection on animal model genetic evaluations across all age and population groups is adopted as a strategy. Progeny-testing schemes then evolve toward dispersed open nucleus breeding schemes when multiple ovulation and embryo transfer is used on bull-dams. Nucleus breeding schemes have been advocated to capitalize on embryo transfer technology. In nucleus breeding schemes utilizing high reproductive rates, inbreeding, rather than reproductive rate, poses a limit to genetic progress, and strategies that maximize response to selection while limiting inbreeding need to be employed. One strategy is mating each dam to several sires rather than only one sire. In vitro embryo production techniques can be used to facilitate such mating strategies. Large-scale in vitro embryo production programs, in which large numbers of embryos per female are tested in the commercial population, offer the greatest potential for genetic gain with low rates of inbreeding. Cloning has an impact mainly on methods for dissemination of genetic improvement. Breeding herds, genetically inferior to marketed clones, are needed for continuous genetic gain. Reproductive technologies offer the potential for genetic improvement. Whether new breeding programs require changes in population structure, e.g., by creation of nucleus breeding herds, depends mainly on logistics and on quantity and quality of field information.

Animals↗

Emerging trends in genetic-based medical diagnostics.

Prior to the publication of the sequencing of the human genome in April 2003, approximately 1,000 genetic tests were available for monogenetic diseases, i.e., those diseases that emanate from a single gene. The Human Genome Project (HGP) offers the data needed to elucidate the more difficult polygenetic diseases and genetic predisposition to diseases, and help explain variability in drug response. Microarray technology utilizing HGP data has made it possible to survey a person's genome. The applications of this technology include minimizing drug reactions and deriving cancer prognoses. This article will address the role of genetic testing in diagnosing and predicting disease now and in the near future.

Clinical Laboratory Techniques↗

Characterization of Hafnia alvei by biochemical tests, random amplified polymorphic DNA PCR, and partial sequencing of 16S rRNA gene.

Hafnia alvei strains which possess the attachment-effacement gene (eaeA) may have clinical importance as new diarrhea-causing pathogens and should therefore be differentiated from other H. alvei strains. We characterized diarrheal H. alvei strains, which were positive in the PCR test for the eaeA gene, using biochemical tests not routinely used for identification of members of the family Enterobacteriaceae, and compared them with eaeA-negative strains isolated from different clinical and nonclinical sources to find characteristics useful for identification. Random amplified polymorphic DNA (RAPD)-PCR and partial sequencing of the 16S rRNA gene were utilized to study the genetic diversity of the isolates. The eaeA-positive strains were found to have many characteristic biochemical properties. Negative reactions in the 2-ketogluconate and histidine assimilation tests and a positive reaction in the 3-hydroxybenzoate assimilation test may be useful in routine diagnostics. Nearly identical RAPD-PCR profiles and identical 353-bp fragments of the 16S rRNA genes indicated little genetic diversity among the eaeA-positive strains. The low level of homology (92%) in the partial 16S rRNA genes of eaeA-positive and -negative H. alvei strains raises questions about the taxonomic positioning of eaeA-positive H. alvei.

Base Sequence↗

Bacterial complementation as a means to test enzyme-ligand interactions.

A bacterial complementation assay has been developed for the rapid screening of a large number of compounds to identify those that inhibit an enzyme target for structure-based inhibitor design. The target enzyme is the hypoxanthine phosphoribosyltransferase (HPRT). This enzyme has been proposed as a potential target for inhibitors that may be developed into drugs for the treatment of diseases caused by several parasites. The screening assay utilizes genetically deficient bacteria complemented by active, recombinant enzyme grown in selective medium in microtiter plates. By comparing absorbance measurements of bacteria grown in the presence and absence of test compounds, the effect of the compounds on bacterial growth can be rapidly assayed. IC50 values for inhibition of bacterial growth are a reflection of the ability of the compounds to bind and/or inhibit the recombinant enzyme. We have tested this bacterial complementation screening assay using recombinant HPRT from the parasites. Plasmodium falciparum and Trypanosoma cruzi, as well as the human enzyme. The results of these studies demonstrate that a screening assay using bacterial complement selection can be used to identify compounds that target enzymes and can become an important part of structure-based drug design efforts.

Animals↗