Attitudes of families affected by adrenoleukodystrophy toward prenatal diagnosis, presymptomatic and carrier testing, and newborn screening

Families affected by adrenoleukodystrophy (ALD) and adrenomyeloneuropathy (AMN) were surveyed to elicit attitudes toward prenatal, presymptomatic and carrier testing, and newborn screening in order to determine the level of support that these families have for current and future genetic testing protocols. Identifying attitudes toward genetic testing, including newborn screening, is especially important because of new data regarding therapeutic options and the possible addition of ALD to newborn screening regimens. The Kennedy Krieger Institute (KKI) database identified 327 prospective participants. Families that were willing to participate in the study received an anonymous questionnaire for completion. Frequencies were generated using SPSS software for Windows. Questionnaires were returned from 128 families for a response rate of 39%. Sons who were at risk for inheriting the ALD gene would be tested by 93% of respondents, and 89.3% would ideally have this testing performed prenatally or in the newborn period. Eighty-nine percent would test an at-risk daughter and 51.2% would ideally have this testing performed prenatally or shortly after birth. ALD newborn screening for males and females was supported by 90% of respondents. If newborn screening for ALD/AMN commences, or there is a new diagnosis of ALD, genetic professionals need to be prepared to have extensive conversations with families regarding the benefits and limitations of current therapeutic and genetic testing options.     

Parental attitudes toward genetic testing for pediatric deafness

Recent molecular genetic advances have resulted in genetic testing becoming an option for deaf individuals and their families. However, there is little information about the interest in such testing. To investigate this issue, parents with normal hearing who have one or more deaf children were surveyed about their attitudes toward diagnostic, carrier, and prenatal genetic testing for deafness. This population was chosen because it represents the majority of individuals who are encountered in clinical practice, given that 90%-95% of deaf individuals are born to persons with normal hearing. Of 328 surveys distributed, 96 were completed and returned. Of the respondents, 96% recorded a positive attitude toward genetic testing for deafness, including prenatal testing, although none would use this information to terminate an affected pregnancy. All respondents had a poor understanding of genetics, with 98% both incorrectly estimating the recurrence risk of deafness and misunderstanding the concept of inheritance. Notably, these findings were similar in the group who had had genetic testing for their children and in the group who had not, suggesting either that the parents who received genetic testing did not receive genetic counseling or that the counseling was not effective. On the basis of these results, it was concluded that this population is interested in the use of genetic testing and that testing should not be done without first providing formal genetic counseling. Appropriate counseling can help parents to understand the risks, benefits, and limitations of genetic testing.     

Attitudes to genetic testing in families with multiple cases of bipolar disorder

OBJECTIVES: This study assesses interest in genetic testing for gene variations associated with bipolar disorder and associated information needs. METHODS: Two hundred individuals (95 unaffected and 105 affected with either bipolar disorder, schizoaffective disorder--manic type, or recurrent major depression) from families with multiple cases of bipolar disorder were assessed, using mailed, self-administered questionnaires. RESULTS: The percentage of participants reporting interest in genetic testing was associated with the degree of certainty with which any test would indicate the development of bipolar disorder. Interest in genetic testing, given a 25% lifetime risk scenario, was lowest (with 77% of participants indicating interest), and highest for the 100% lifetime risk scenario (92%). Eighty percent of participants indicated interest in genetic testing of their own children; of these 30% reported wanting their children tested at birth, and 33% in early childhood. Forty-one percent of participants reported that they would be interested in preimplantation genetic diagnosis, and 54% in prenatal testing. LIMITATIONS: The possibility of ascertainment bias cannot be ruled out. Interest in hypothetical genetic testing for bipolar disorder may not necessarily translate into actual utilization. CONCLUSIONS: These results indicate that uptake of genetic testing for genotyping for low-risk alleles related to bipolar disorder is likely to be lower than for testing for high-penetrance gene mutations that follow Mendelian inheritance. The discrepancy between the desired age of testing children and the accepted current practice may be a source of distress and conflict for parents and health professionals alike.     

Colorectal cancer cases and relatives of cases indicate similar willingness to receive and disclose genetic information

Context: Recent developments in genetic testing allow us to detect individuals with inherited susceptibility to some cancers. Genetic testing to identify carriers of cancer-related mutations may help lower risk by encouraging preventive behaviors and surveillance. This study assessed willingness of colon cancer cases and relatives to receive genetic information that may indicate an increased risk for cancer, to whom they would disclose genetic information, and whether receiving genetic test results may influence future prevention behaviors among individuals enrolled in the Seattle Colorectal Cancer Family Registry. Methods: Incident invasive colorectal cancer cases were identified from the Puget Sound Surveillance Epidemiology and End Results (SEER) registry. In 2007, a sequential sample of cases and relatives (n = 147) were asked to respond to a questionnaire addressing study aims. The questionnaire was administered during a baseline or 5-year follow-up interview. Results: Patterns of response to each statement were similar between colorectal cancer cases and relatives. Both colorectal cases (95%) and relatives (95%) reported willingness to receive genetic information. Nearly all participants would tell their doctor the results of a genetic test (99% of cases; 98% of relatives), and all married participants would tell their spouses. Cases (96%) anticipated being slightly more likely than relatives (90%) to change their cancer screening behavior, but this difference was not statistically significant (p = 0.33). Conclusions: A high percentage of both colorectal cancer cases and relatives sampled from the Seattle Colorectal Cancer Family Registry are interested in identifying their genetic status, discussing their genetic status with their family and doctor, and adopting behavioral changes that may reduce cancer risk.     

Professional and personal attitudes about access and confidentiality in the genetic testing of children: a pilot study

The ability to perform predictive genetic testing of children raises ethical concerns regarding whether and when to test and the disclosure of results. Semi-structured interviews with a convenience sample of pediatricians (12) and geneticists (13) were conducted to see how they would react to parental requests for predictive genetic testing of their children, and their attitudes about testing their own children. We also asked about disclosure attitudes and practices for their patients' relatives and within their own families. Respondents would provide predictive genetic testing for most conditions, yet were less likely to seek this information about their own children. Respondents believed it was very important for patients to share some types of genetic information with relatives, and were directive in their counseling about intrafamilial disclosure, especially within their own families. Although respondents would almost never breach patient confidentiality, many would breach confidentiality within their own families. Health care professionals distinguish between their professional and personal roles with regard to issues of access and confidentiality in predictive testing of children. They are willing to provide greater access and more confidentiality for their patients than within their own families.     

遗传密码子研究进展

作为生命信息的基本遗传单位,基因组遗传密码的破译对于人们加深对生命本质的认识具有重要的理论价值和现实意义。目前,遗传密码子的研究重心已由遗传密码子的破译及反常密码子的发现转入到遗传密码子的起源与进化及扩张等研究。遗传密码子的起源与进化是当今基因组学研究的热点命题之一,相关的学说、假设层出不穷,但尚未取得实质性突破。另一方面,无义密码子的再定义及遗传密码的扩张等研究却极大的丰富和发展了遗传密码子的科学内涵,推动了生命科学研究的发展。文章综述了遗传密码子的多态性、起源与进化、无义密码子的再定义及遗传密码的扩张等方面的研究进展,并就其应用价值作了评述,期待为其在基因组学、医学等相关领域的应用研究提供参考。     

Predictors of uptake of obesity genetic testing among affected adults

Given that a large number of candidate genes coding for a tendency toward obesity have been identified and some findings have been replicated, we explored characteristics of those who would be most likely to obtain future genetic testing for this tendency. During a series of focus groups, obese respondents rated their likelihood of obtaining testing under conditions in which either genetically-targeted drug treatment would be available, a positive test would be associated with a prognosis for developing diabetes, or neither of these. Interest in testing was greater given the first two scenarios than the third. Older age and belief that genetics were an important cause of obesity were associated with greater interest. For the first two scenarios, higher educational status was associated with greater interest, while for the third, respondents who said emotional issues caused overweight and those who crash-dieted intermittently were more likely to want genetic testing. Although further research is required to validate these findings, this study is the first published report of respondents’ ratings of likelihood to obtain genetic testing for propensity to obesity, and suggests strong interest in genetic testing among some people, even in the absence of further treatment implications of the test.     

Prions: an evolutionary perspective.

Studies in both prion-due diseases in mammals and some non-Mendelian hereditary processes in yeasts have demonstrated that certain proteins are able to transmit structural information and self-replication. This induces the corresponding conformational changes in other proteins with identical or similar sequences. This ability of proteins may have been very useful during prebiotic chemical evolution, prior to the establishment of the genetic code. During this stage, proteins (proteinoids) must have molded and selected their structural folding units through direct interaction with the environment. The proteinoids that acquired the ability to propagate their conformations (which we refer to as conformons) would have acted as reservoirs and transmitters of a given structural information and hence could have acted as selectors for conformational changes. Despite the great advantage that arose from the establishment of the genetic code, the ability to propagate conformational changes did not necessarily disappear. Depending on the degree of involvement of this capacity in biological evolution, we propose two not mutually exclusive hypotheses: (i) extant prions could be an atavism of ancestral conformons, which would have co-evolved with cells, and (ii) the evolution of conformons would have produced cellular proteins, able to transmit structural information, and, in some cases, participating in certain processes of regulation and epigenesis. Therefore, prions could also be seen as conformons of a conventional infectious agent (or one that co-evolved with it independently) that, after a longer or shorter adaptive period, would have interacted with conformons from the host cells.     

Arithmetic inside the universal genetic code

The first information system emerged on the earth as primordial version of the genetic code and genetic texts. The natural appearance of arithmetic power in such a linguistic milieu is theoretically possible and practical for producing information systems of extremely high efficiency. In this case, the arithmetic symbols should be incorporated into an alphabet, i.e. the genetic code. A number is the fundamental arithmetic symbol produced by the system of numeration. If the system of numeration were detected inside the genetic code, it would be natural to expect that its purpose is arithmetic calculation e.g., for the sake of control, safety, and precise alteration of the genetic texts. The nucleons of amino acids and the bases of nucleic acids seem most suitable for embodiments of digits. These assumptions were used for the analyzing the genetic code.

The compressed, life-size, and split representation of the Escherichia coli and Euplotes octocarinatus code versions were considered simultaneously. An exact equilibration of the nucleon sums of the amino acid standard blocks and/or side chains was found repeatedly within specified sets of the genetic code. Moreover, the digital notations of the balanced sums acquired, in decimal representation, the unique form 111, 222, …, 999. This form is a consequence of the criterion of divisibility by 037. The criterion could simplify some computing mechanism of a cell if any and facilitate its computational procedure. The cooperative symmetry of the genetic code demonstrates that possibly a zero was invented and used by this mechanism. Such organization of the genetic code could be explained by activities of some hypothetical molecular organelles working as natural biocomputers of digital genetic texts.

It is well known that if mutation replaces an amino acid, the change of hydrophobicity is generally weak, while that of size is strong. The antisymmetrical correlation between the amino acid size and the degeneracy number is known as well. It is shown that these and some other familiar properties may be a physicochemical effect of arithmetic inside the genetic code.

The “frozen accident” model, giving unlimited freedom to the mapping function, could optimally support the appearance of both arithmetic symbols and physicochemical protection inside the genetic code.     

Snapshots of protein folding problem: implications of folding and misfolding studies

Deciphering the code that determines the three-dimensional structure of proteins and the ability to predict the final folded form of a protein is still elusive to molecular biophysists. In the case of several proteins a similar tertiary structure is not accompanied by any significant sequence similarity. The question now remains whether a code beyond the genetic code that describes the arrangement of the amino acid within a three dimensional protein structure. The available data undoubtedly demonstrates that the redundancy of this code must be tremendous. Several techniques such as nuclear magnetic resonance spectroscopy and laser detection techniques, coupled with fast initiation of the folding reaction, can now probe the folding events in milliseconds or even faster and provide highly relevant information. The thermodynamic analysis of the folding process and of kinetic intermediates opens whole new avenue of understanding. Breaking the protein folding code would enable scientists to look at a gene whose function is unknown and predict the three-dimensional structure of the protein it encodes. This would give them a very good idea of what the gene does. In this review we hope to bring together the information available about protein folding with particular emphasis on folding intermediate(s). Additionally, the practical consequences of the solution of the protein folding problem in medicine and biotechnology are also discussed.     

Testing participation in BRCA1/2-positive families: initiator role of index cases

The objectives of this study were to: (1) describe diffusion of information by affected women in whom a mutation has been identified (index cases) to their families and testing participation among high-risk relatives; (2) assess information recall and understanding by index cases and their satisfaction with the testing process; and (3) determine the factors associated with higher/lower testing decision in the family. Thirty index cases completed a self-administered questionnaire assessing their personal and family characteristics and their satisfaction with their own genetic testing process and a telephone interview to evaluate their knowledge about the risk of a genetic predisposition to breast and ovarian cancer, the type and number of close relatives that they informed, and the difficulties that they encountered. Information about breast/ovarian cancer risk and test availability was generally well transmitted (75%), predominantly (88%) to first-degree relatives. In contrast, testing participation was low (15%) and essentially occurred among sisters and daughters. There was a general lack of knowledge despite a high level of satisfaction regarding the information given by the geneticist. Family support and the knowledge of index cases about the risk of transmission of BRCA1/2 mutations by women were found to be positively and significantly associated with the testing decision among first-degree relatives. Difficulties in informing relatives appeared to be related to poor understanding of the information by index cases, as well as fear, and avoidance among close relatives. A major challenge for genetic counseling is to ensure that consulting patients not only receive complete understanding but also understand this information and anticipate the impact of the test result before deciding to take the test.     

The role of financial factors in acceptance of clinical BRCA genetic testing

Many women who are offered BRCA genetic testing by genetics professionals do not have the test, possibly for financial reasons. We explored financial factors implicated in non-uptake of BRCA testing in women who had received genetic counseling in a clinical setting. Specifically, we described financial factors (affordability, health insurance, other) involved with BRCA testing; compared nonfinancial factors (disease, sociodemographic, risk assessment) in women who did not have BRCA testing (nontesters) with women who had the test (testers); showed associations of financial and nonfinancial factors with BRCA testing; and identified predictors of non-uptake of BRCA testing. The sample of 100 women (64 nontesters and 36 testers) completed an anonymous mailed survey on financial factors; 52 of the nontesters answered questions about nonfinancial factors. Testers had significantly better affordability and insurance coverage (p < 0.001), more diagnoses of breast or ovarian cancer (p < 0.05) and higher rates of receiving post-counseling risk estimates (p < 0.05), than nontesters. Non-uptake was 5.5-fold more likely in women that could not afford full or partial payment for the test and was 15.5-fold more likely in women that did not recall receiving risk estimates post-counseling. For many women having risk factors for breast/ovarian cancer, affordability of BRCA testing and insurance coverage for the test remain problematic. Post-counseling reminders of risk estimates may contribute to uptake of testing.     

Allowing for missing parents in genetic studies of case-parent triads

In earlier work, my colleagues and I described a log-linear model for genetic data from triads composed of affected probands and their parents. This model allows detection of and discrimination between effects of an inherited haplotype versus effects of the maternal haplotype, which presumably would be mediated by prenatal factors. Like the transmission disequilibrium test (TDT), the likelihood-ratio test (LRT) based on this model is not sensitive to associations that are due to genetic admixture. When used as a method for testing for linkage disequilibrium, the LRT can be regarded as an alternative to the TDT. When one or both parents are missing, the resulting incomplete triad must be discarded to ensure validity of the TDT, thereby sacrificing information. By contrast, when the problem is set in a likelihood framework, the expectation-maximization algorithm allows the incomplete triads to contribute their information to the LRT without invalidation of the analysis. Simulations demonstrate that much of the lost statistical power can be recaptured by means of this missing-data technique. In fact, power is reasonably good even when no triad is complete-for example, when a study is designed to include only mothers of cases. Information from siblings also can be incorporated to further improve the statistical power when genetic data from parents or probands are missing.     

The Level and Landscape of Optimization in the Origin of the Genetic Code

We consider a model of the origin of genetic code organization incorporating the biosynthetic relationships between amino acids and their physicochemical properties. We study the behavior of the genetic code in the set of codes subject both to biosynthetic constraints and to the constraint that the biosynthetic classes of amino acids must occupy only their own codon domain, as observed in the genetic code. Therefore, this set contains the smallest number of elements ever analyzed in similar studies. Under these conditions and if, as predicted by physicochemical postulates, the amino acid properties played a fundamental role in genetic code organization, it can be expected that the code must display an extremely high level of optimization. This prediction is not supported by our analysis, which indicates, for instance, a minimization percentage of only 80%. These observations can therefore be more easily explained by the coevolution theory of genetic code origin, which postulates a role that is important but not fundamental for the amino acid properties in the structuring of the code. We have also investigated the shape of the optimization landscape that might have arisen during genetic code origin. Here, too, the results seem to favor the coevolution theory because, for instance, the fact that only a few amino acid exchanges would have been sufficient to transform the genetic code (which is not a local minimum) into a much better optimized code, and that such exchanges did not actually take place, seems to suggest that, for instance, the reduction of translation errors was not the main adaptive theme structuring the genetic code.     

Psychiatrists' attitudes regarding genetic testing and patient safeguards: a preliminary study

AIMS: A probability sample of U.S. psychiatrists (n = 93) was invited to complete a mail survey regarding the likely impact of genetic testing on psychiatry; the clinical utility of pharmacogenetic, diagnostic, and susceptibility genetic testing; and 14 proposed ethical and legal safeguards for clinical genetic testing. RESULTS: Forty-five psychiatrists participated in the survey (response rate = 48%). The majority (80% and 60%, respectively) believed that genetic testing would benefit many psychiatric patients and would dramatically change the way psychiatry is practiced. Many psychiatrists (73-85%) also stated that pharmacogenetic, diagnostic, and susceptibility tests for common psychiatric disorders would be somewhat useful or extremely useful in the clinical setting. Nearly all (98-100%) believed that psychiatrists should obtain informed consent before genetic testing, should keep test results confidential, should provide pre- and posttest counseling, and should demonstrate competence in interpreting test results. Nearly all (96-100%) supported laws and regulations to prevent discrimination based on genetic test results and to protect consumers from misleading advertisements for testing. Ninety-one percent endorsed restrictions on the sale of genetic tests directly to consumers. CONCLUSIONS: This probability sample of U.S. psychiatrists expressed a strongly positive view of genetic testing in psychiatry, while voicing nearly unanimous support for seven ethical and legal safeguards.     

Attitude toward genetic testing for cancer risk in Istanbul

To identify attitudes toward genetic testing, and the effects of this information on decisions regarding issues such as pregnancy, abortion, and prophylactic surgery, several subsets of the Turkish population were surveyed in hospital settings. Individuals (n = 179) chosen arbitrarily from four different subsets of a Turkish population were asked to participate in a confidential 23-question survey. Survey participants were familiar with the concept of cancer being a familial disease (85.5%), and 84.7% of them expressed interest in genetic testing to determine cancer risk, 83.9% would have their fetuses tested for such cancer risk, 65.1% would terminate their pregnancies, 92.2% would have their children tested if they were determined to have an increased cancer risk, 71.9% would agree to undergo prophylactic oophorectomy or orchiectomy and 67.6% would have mastectomy/prostatectomy should there be an increased cancer risk to these organs. It appears that at least the sampled segment of a Turkish population is willing to undergo genetic testing to determine if they are at increased risk for cancer. The feasibility and acceptance of genetic testing and the influence of education and genetic counseling in the Turkish people should further be evaluated with a larger stratified sample of the population.     

On How Many Fundamental Kinds of Cells are Present on Earth: Looking for Phylogenetic Traits that Would Allow the Identification of the Primary Lines of Descent

The phylogenetic analyses as far as the identification of the number of domains of life is concerned have not reached a clear conclusion. In the attempt to improve this circumstance, I introduce the concept that the amino acids codified in the genetic code might be of markers with outstanding phylogenetic power. In particular, I hypothesise the existence of a biosphere populated, for instance, by three groups of organisms having different genetic codes because codifying at least a different amino acid. Evidently, these amino acids would mark the proteins that are present in the three groups of organisms in an unambiguous way. Therefore, in essence, this mark would not be other than the one that we usually try to make in the phylogenetic analyses in which we transform the protein sequences in phylogenetic trees, for the purpose to identify, for example, the domains of life. Indeed, this mark would allow to classify proteins without performing phylogenetic analyses because proteins belonging to a group of organisms would be recognisable as marked in a natural way by at least a different amino acid among the diverse groups of organisms. This conceptualisation answers the question of how many fundamental kinds of cells have evolved from the Last Universal Common Ancestor (LUCA), as the genetic code has unique proprieties that make the codified amino acids excellent phylogenetic markers. The presence of the formyl-methionine only in proteins of bacteria would mark them and would identify these as domain of life. On the other hand, the presence of pyrrolysine in the genetic code of the euryarchaeota would identify them such as another fundamental kind of cell evolved from the LUCA. Overall, the phylogenetic distribution of formyl-methionine and pyrrolysine would identify at least two domains of life—Bacteria and Archaea—but their number might be actually four; that is to say, Bacteria, Euryarchaeota, archeobacteria that are not euryarchaeota and Eukarya. The usually accepted domains of life represented by Bacteria, Archaea and Eukarya are not compatible with the phylogenetic distribution of these two amino acids and therefore this last classification might be mistaken.     

The effect of species models on estimates of within-lineage variation in integration

Species may be modeled as comprised of individuals, populations or a virtual code. A virtual code can be understood as general potential that appears as actualization within specific environmental, both internal and external, contexts. These general potentials form a capacity to network that allows potentials to be expressed and offers robustness through its interconnections. In the present work, the degree of within-lineage variation in integration was not strongly model-dependent. However, the relationships among model-dependent estimates of such variation and within-lineage phyletic variation were not equal. The strongest relationship was between within-lineage variation in integration, when species were modeled as a virtual code, and within-lineage phyletic variation. The second strongest, and only other statistically significant relationship, was between variation in integration when species were modeled as a virtual code and as a collection of populations. The last result argues for a strong ontogenetic and micro-environmental effect on the expression of features in an individual. If species were a virtual code they would evolve by incorporation of all attributes, ontogenetic, environmental and genetic into that code until it becomes unstable and bifurcates. Species as a virtual code, an approach that explicitly incorporates developmental change into evolution, is a non-material representation of species as a complex information system, incorporating, if we refer to mathematical analysis, both the real and the imaginary. If one wished to stress the material, this study could be seen as empirical documentation of species as information systems.