Current status of genome-wide association studies in cancer

Genome-wide association studies in cancer have already identified over 150 regions associated with two dozen specific cancers. Already, a handful of multi-cancer susceptibility regions have been uncovered, providing new insights into perhaps common mechanisms of carcinogenesis. For each new susceptibility allele, investigators now face the arduous task of interrogating each region beginning with fine mapping prior to pursuing the biological basis for the direct association of one or more variants. It appears that there may be a significant number of common alleles that contribute to the heritability of a specific cancer. Since each region confers a small contribution to the risk for cancer, it is daunting to consider any single nucleotide polymorphism (SNP) as a clinical test. Since the complex genomic architecture of each cancer differs, additional genotyping and sequence analysis will be required to comprehensively catalog susceptibility alleles followed by the formidable task of understanding the interactions between genetic regions as well as the environment. It will be critical to assess the applicability of genetic tests in specific clinical settings, such as when to perform screening tests with calculable risks (e.g., biopsies or chemoprevention), before incorporating SNPs into clinical practice. To advance the current genomic observations to the clinical venue, new studies will need to be designed to validate the utility of known genetic variants in assessing risk for cancer as well as its outcomes.     

Implications of the human genome initiative for the primary care physician

... Despite the need for physicians to be knowledgeable about and open to advances in genetic technology, little is known about the level of preparedness of primary care physicians to offer new genetic tests. Evidence suggests that several barriers exist to physicians adopting genetic tests. These include lack of knowledge, inability to interpret probabilistic information, low tolerance for uncertainty, negative attitudes about their responsibility for genetic counseling and testing, lack of confidence in their clinical skills, and unfamiliarity with ethical issues raised by testing. This paper will explore some of these barriers in further depth, discuss the ethical impact of physician unpreparedness on both patient care and the diffusion of genetic tests, and describe a study that is currently underway to investigate some of these issues.     

Managing genetic testing: the relative powerlessness of actors in stable practices

Abstract

Genetics is a field in which ethical and social problems have been most pressing. Despite this, new tests often are introduced almost immediately after the isolation of a new gene. Considerations of whether a particular test should be introduced at all seem to have little effect on the development and introduction of new tests. This paper explores how this lack of social and ethical assessment can be understood. In order to do so, the sociohistorical context of clinical genetics and the way in which this practice came about will be analysed in this paper with respect to the Dutch service for clinical genetics. It will be argued that the fragmented way in which tasks and responsibility have become distributed within clinical genetics services has led to a situation in which actors seem to have no control over the introduction of genetic tests.     

The diffusion of new genetic tests for predicting disease.

This paper examines the pathways by which new genetic tests will become available to the public. In view of the scarcity of genetic specialists, the pathway is likely to involve primary care physicians. Other pathways entail state-mandated testing, community-based programs, or testing by laboratories without much involvement of primary care physicians. When testing does become available the "destination" will be either family-centered testing or population-oriented screening. The deterrent to screening will not be the inability to detect disease-causing mutations but the costs and attitudes of providers and the public. When tests are provided primarily to provide information about risks to future children, some people will oppose screening on religious or moral grounds. When there are no inexpensive treatments, some will fear that insurance companies and employers will use tests to deny them health care coverage. Some may not want to know their risks for disorders about which little can be done. For common, multifactorial disorders, genetic tests will have low predictive value. Because of these problems, the decision to be tested, regardless of the destination, requires that "testees" be fully informed and consent to testing. When acceptance rates are low, screening is less likely to be cost-effective; family-centered testing becomes the default destination.     

Improving the prediction of complex diseases by testing for multiple disease-susceptibility genes

Studies have argued that genetic testing will provide limited information for predicting the probability of common diseases, because of the incomplete penetrance of genotypes and the low magnitude of associated risks for the general population. Such studies, however, have usually examined the effect of one gene at time. We argue that disease prediction for common multifactorial diseases is greatly improved by considering multiple predisposing genetic and environmental factors concurrently, provided that the model correctly reflects the underlying disease etiology. We show how likelihood ratios can be used to combine information from several genetic tests to compute the probability of developing a multifactorial disease. To show how concurrent use of multiple genetic tests improves the prediction of a multifactorial disease, we compute likelihood ratios by logistic regression with simulated case-control data for a hypothetical disease influenced by multiple genetic and environmental risk factors. As a practical example, we also apply this approach to venous thrombosis, a multifactorial disease influenced by multiple genetic and nongenetic risk factors. Under reasonable conditions, the concurrent use of multiple genetic tests markedly improves prediction of disease. For example, the concurrent use of a panel of three genetic tests (factor V Leiden, prothrombin variant G20210A, and protein C deficiency) increases the positive predictive value of testing for venous thrombosis at least eightfold. Multiplex genetic testing has the potential to improve the clinical validity of predictive testing for common multifactorial diseases.     

The role of genomics in prevention or reducing the impact of congenital malformations

Congenital malformations (CMs) are permanent changes produced by abnormality of development in a body structure during prenatal life. Population based studies place the incidence of major malformations at about 2-3% of all live births. The etiology is mostly due multifactorial inheritance or unknown (50-80%). The continuum and gradual shift from genetics to genomics will offer new possibilities for diagnosis, treatment, prediction and prevention of congenital malformations. Genomics has many tools including pathogenomics, pharmacogenomics, nutrigenomics and bioinformatics. Pathogenomics will help to discover new genes or susceptibility genes and genetic variants with a role in the pathogenesis of CMs. Pharmacogenomics will identify genetic variants affecting the response to drugs and it should be applied to study drug induced birth defects. Nutrigenomics will determine the impact of diet on genome stability and how genotype determines nutritional requirements. Bioinformatics then will collect, store obtained data, which will facilitate analysis of systems biology questions involving relationships between genes, their variants and biological functions. This knowledge should be translated into more sensitive and specific genetic tests.     

Closing the gaps in genetics legislation and policy: a report by the new york state task force on life and the law

The New York State Task Force on Life and the Law, a state bioethical policy commission, recently completed a project addressing the ethical, legal, and social concerns surrounding the predictive uses of genetic testing. Its report, Genetic Testing and Screening in the Age of Genomic Medicine, makes legislative, public policy, and practice recommendations on a host of issues. As part of this project, the Task Force reviewed the current policy and legislative landscapes related to confidentiality protections for genetic information and the use of genetic information by insurers. It also assessed requirements for informed consent to clinical genetic testing and for the use of clinical samples for genetics research. The Task Force considered gaps and unintended consequences of relevant genetic testing legislation and assessed its flexibility to address new uses of genetic testing, such as pharmacogenetic testing, and new ways of offering tests, such as multiplex testing panels. The Task Force also considered the relevance of the pleiotropic characteristic of genes for issues of informed consent to genetic testing and the confidentiality of genetic information. The Task Force's recommendations, presented here, seek to promote the appropriate uses of clinical genetic testing and research while preventing potential harms.     

遗传检测综述

目前,遗传检测正在更多的国家、更广泛的范围内被采用。然而,在中国人们还不大熟悉遗传检测的原理、类型、技术、对社会的益处以及国内或国际是如何对它进行管理的。随着遗传检测的广泛使用,正确的监督显得相当必要。对近年来遗传检测所取得的进展进行了粗略的回顾,这将帮助我们对人类遗传学和分子医学革命的新时代有更多的了解。     

Short-term testing--are we looking at wrong endpoints?

Short-term testing has been performed and interpreted on the basis of correlation between these tests and animal carcinogenicity. This empirical approach has been the only feasible one, due to a lack of knowledge of the actual genetic endpoints of relevance in carcinogenicity. However, the rapidly growing information on genetic alterations actually involved in carcinogenicity and in particular activation of oncogenes, provides facts of basic importance for the strategy of short-term testing. The presently used sets of short-term tests focus on standard genetic endpoints, mainly point mutations and chromosomal aberrations. Little attention has been paid in that connection to other endpoints, which have been shown or suspected to play an important role in carcinogenicity. These endpoints include gene amplification, transpositions, hypomethylation, polygene mutations and recombinogenic effects. Furthermore, indirect effects, for instance via radical generation and an imbalance of the nucleotide pool, may be of great significance for the carcinogenic and cocarcinogenic effects of many chemicals. Modern genetic and molecular technology has opened entirely new prospects for identifying genetic alterations in tumours and in its turn these prospects should be taken advantage of in order to build up more sophisticated batteries of assays, adapted to the genetic endpoints actually demonstrated to be involved in cancer induction. Development of new assay systems in accordance with the elucidation of genetic alterations in carcinogenicity will probably constitute one of the most important areas in genetic toxicology in the future. From a regulatory point of view the prerequisite for a development in this direction will be a flexibility of the handling of questions concerning short-term testing also at a bureaucratic level.     

Public attitudes toward genetic testing: perceived benefits and objections

The aim of this study was to assess public attitudes toward the availability and use of genetic tests to explore support for genomics developments and to help improve public discussion. Questionnaires to assess the assumed advantages and disadvantages of genetic testing were sent to a representative sample of the Dutch population (n = 1,308; age > or =25 years). The response was 63% (817/1,308). Two groups with extreme scores on a four-item scale were distinguished, representing opponents (n = 248) and supporters (n = 264) of the availability and use of genetic tests. Multiple logistic regression analyses showed that those who were familiar with a genetic disease (odds ratio [OR] 0.54; 95% confidence interval [CI] 0.32-0.89; p = 0.015), those who scored higher on a four-item scale on belief in personal benefits of testing (OR 0.29; 95% CI 0.21-0.40; p < 0.0001), and those who believe that knowledge of the genetic background of disease will help people to live more healthy lives (OR 0.48; 95% CI 0.37-0.62; p < 0.0001), were less likely to be opponents. Those who agreed that genetic testing is tampering with nature (OR 1.63; 95% CI 1.32-2.00; p < 0.0001) were more likely to be opponents. Other variables such as belief in genetic determinism, genetic knowledge, level of education, age, and gender were not significantly associated. These results suggest that in addition to moral acceptability, perceived usefulness is a precondition for supporting genetic testing. It is not expected that more information will necessarily result in more positive attitudes.     

Evaluation of genetic tests for susceptibility to common complex diseases: why, when and how?

Recent research into the human genome has generated a wealth of scientific knowledge and increased both public and professional interest in the concept of personalised medicine. Somewhat unexpectedly, in addition to increasing our understanding about the genetic basis for numerous diseases, these new discoveries have also spawned a burgeoning new industry of ‘consumer genetic testing’. In this paper, we present the principles learnt though the evaluation of tests for single gene disorders and suggest a comparable framework for the evaluation of genetic tests for susceptibility to common complex diseases. Both physicians and the general public will need to be able to assess the claims made by providers of genetic testing services, and ultimately policy-makers will need to decide if and when such tests should be offered through state funded healthcare systems.     

Ethical considerations in the presymptomatic diagnosis of Alzheimer's disease

Research into the human genome has undoubtedly opened up a new perspective in medicine. The ability to identify the cause of specific diseases, especially neurodegenerative diseases, will definitively change the concepts of disease and treatment, while advances such as antibiotic therapy and anesthesia will be relegated to history. However, the arrival of genome medicine poses major bioethical challenges, many of which remain to be resolved. We review the applicability, results and consequences of predictions based on genetic tests for presymptomatic Alzheimer's disease, as well as the dilemmas and contradictions that are already arising as a result of the commercialization of predictive tests for public use with little or no medical supervision. Given that there is currently no effective treatment of Alzheimer?s disease, the greatest challenge and contradiction lies in managing the results of predictive tests. There are no indications for the performance of predictive genetic tests in late or sporadic Alzheimer's disease or for counselling of persons requesting these tests. The PICOGEN program provides a safe, effective, reliable and satisfactory option for persons requesting these tests who meet the inclusion criteria. Currently, caution should be the norm when considering the performance of predictive tests in presymptomatic dementia.     

Genetic counseling in the era of molecular diagnostics

Veterinarians with an interest in theriogenology will often be asked by small animal clients for advice concerning hereditary diseases in their breeds. Many new DNA-based tests for analysis of genetic diseases and traits (e.g. coat color) are now available for use by both breeders and veterinarians. With appropriate interpretation, these tests can be invaluable tools in a breeding program. For example, they can be used to produce animals free of specific diseases, to quickly eliminate a disease from an entire breed, or to select for specific traits in breeding stock. Selection strategies that do not take into account maintaining genetic diversity of the breed may be detrimental and reduce the potential for future improvement.     

Understanding mammalian genetic systems: the challenge of phenotyping in the mouse

Understanding mammalian genetic systems is predicated on the determination of the relationship between genetic variation and phenotype. Several international programmes are under way to deliver mutations in every gene in the mouse genome. The challenge for mouse geneticists is to develop approaches that will provide comprehensive phenotype datasets for these mouse mutant libraries. Several factors are critical to success in this endeavour. It will be important to catalogue assay and environment and where possible to adopt standardised procedures for phenotyping tests along with common environmental conditions to ensure comparable datasets of phenotypes. Moreover, the scale of the task underlines the need to invest in technological development improving both the speed and cost of phenotyping platforms. In addition, it will be necessary to develop new informatics standards that capture the phenotype assay as well as other factors, genetic and environmental, that impinge upon phenotype outcome.     

Aspectos éticos del diagnóstico presintomático de la enfermedad de Alzheimer

Research into the human genome has undoubtedly opened up a new perspective in medicine. The ability to identify the cause of specific diseases, especially neurodegenerative diseases, will definitively change the concepts of disease and treatment, while advances such as antibiotic therapy and anesthesia will be relegated to history. However, the arrival of genome medicine poses major bioethical challenges, many of which remain to be resolved. We review the applicability, results and consequences of predictions based on genetic tests for presymptomatic Alzheimer's disease, as well as the dilemmas and contradictions that are already arising as a result of the commercialization of predictive tests for public use with little or no medical supervision. Given that there is currently no effective treatment of Alzheime?s disease, the greatest challenge and contradiction lies in managing the results of predictive tests. There are no indications for the performance of predictive genetic tests in late or sporadic Alzheimer's disease or for counselling of persons requesting these tests. The PICOGEN program provides a safe, effective, reliable and satisfactory option for persons requesting these tests who meet the inclusion criteria. Currently, caution should be the norm when considering the performance of predictive tests in presymptomatic dementia.     

Pharmacogenetics in Primary Care: The Promise of Personalized Medicine and the Reality of Racial Profiling

Many anticipate that expanding knowledge of genetic variations associated with disease risk and medication response will revolutionize clinical medicine, making possible genetically based Personalized Medicine where health care can be tailored to individuals, based on their genome scans. Pharmacogenetics has received especially strong interest, with many pharmaceutical developers avidly working to identify genetic variations associated with individual differences in drug response. While clinical applications of emerging genetic knowledge are becoming increasingly available, genetic tests for drug selection are not as yet widely accessible, and many primary care clinicians are unprepared to interpret genetic information. We conducted interviews with 58 primary care clinicians, exploring how they integrate emerging pharmacogenetic concepts into their practices. We found that in their current practices, pharmacogenetic innovations have not led to individually tailored treatment, but instead have encouraged use of essentialized racial/ethnic identity as a proxy for genetic heritage. Current manifestations of Personalized Medicine appear to be reinforcing entrenched notions of inherent biological differences between racial groups, and promoting the belief that racial profiling in health care is supported by cutting-edge scientific authority. Our findings raise concern for how pharmacogenetic innovations will actually affect diverse populations, and how unbiased treatment can be assured.     

血小板体外质量评价研究进展

血小板输注是现代医学治疗的一项有效措施,近年来在临床上的应用日益普遍。血小板的临床输注效果与在体外的保存质量密切相关。我们简要介绍目前评价血小板体外质量的主要实验方法和仪器,以及它们在临床使用中的优缺点。     

Beyond consent: ethical and social issues in genetic testing

Informed consent is a vital ethical doctrine in clinical medicine and, through genetic counselling, is being applied to genetic testing. But genetic testing raises issues that transcend the traditional concept of informed consent. Genetic tests are adopted without demonstrable clinical benefit, and the consequences of testing can reach beyond the individual to their families and communities. Understanding the social and cultural context of genetic testing will lead to more informed discussion and debate on these issues.     

Bioethics for clinicians: 14. Ethics and genetics in medicine

Information about a patient''s inherited risk of disease has important ethical and legal implications in clinical practice. Because genetic information is by nature highly personal yet familial, issues of confidentiality arise. Counselling and informed consent before testing are important in view of the social and psychological risks that accompany testing, the complexity of information surrounding testing, and the fact that effective interventions are often not available. Follow-up counselling is also important to help patients integrate test results into their lives and the lives of their relatives. Genetic counselling should be provided by practitioners who have up-to-date knowledge of the genetics of and the tests available for specific diseases, are aware of the social and psychological risks associated with testing, and are able to provide appropriate clinical follow-up. Some physicians may elect to refer patients for genetic counselling and testing. However, it is inevitable that all physicians will be involved in long-term follow-up both by monitoring for disease and by supporting the integration of genetic information into patients'' lives.     

Genetics education for primary-care providers

In an era of growing knowledge about genetics and health, primary-care physicians will have increasing responsibility for evaluating genetic risk and using genetic tests. Although most have little knowledge of genetics, their expertise in the prudent use of technology is relevant to the task. Successful educational programmes will need to forge partnerships between primary care and genetics.