On being “actionable”: clinical sequencing and the emerging contours of a regime of genomic medicine in oncology

This article explores commercial, academic, and national initiatives aimed at using sequencing technologies to generate “actionable” genomic results that can be applied to the clinical management of oncology patients. We argue that the term “actionable” is not merely a buzzword, but signals the emergence of a distinctive sociotechnical regime of genomic medicine in oncology. Unlike other regimes of genomic medicine that are organized around assessing and managing inherited risk for developing cancer (e.g. BRCA testing), actionable regimes aim to generate predictive relationships between genetic information and drug therapies, thereby generating new kinds of clinical actions. We explore how these genomic results are made actionable by articulating them with existing clinical routines, clinical trials, regulatory regimes, and health care systems; and in turn, how clinical sequencing programs have begun to reconfigure knowledge and practices in oncology. Actionability regimes confirm the emergence of bio-clinical decision-making in oncology, whereby the articulation of molecular hypotheses and experimental therapeutics become central to patient care.     

Knowledge of genetics among residents in obstetrics and gynecology.

A supervised genetics examination was administered to 76 obstetrics and gynecology (ob/gyn) residents from 15 different institutions in the Philadelphia area. The questions were specifically designed to be applicable to obstetrical practice. Overall, the mean score was 69% (range 32%-88%). Using the nonparametric Mann-Whitney rank sum test, we found that the 25 residents from institutions with an obstetrics-gynecology-genetics (OGG) program, coordinated by an obstetrician/gynecologist board certified in clinical genetics, had statistically significant higher scores than the remaining 51 residents from institutions without an OGG program (77% vs. 65%, respectively; P < .001). This study demonstrates that knowledge of genetics among residents in ob/gyn is deficient, especially among residents at institutions without OGG programs. Special efforts should be made to provide genetics education to these individuals. We propose that more obstetricians be encouraged to pursue postgraduate training in genetics in light of the rapid development of medical genetics; its application to prenatal screening, diagnosis, and counseling; the anticipated utilization of genetics services; and the need for educational initiatives geared toward ob/gyn patients.     

Impulsive culling of a structured population on two patches

We consider a model for a creature inhabiting two patches between which migration may occur. The creature is assumed to have a life cycle with two stages, namely juvenile and adult, giving rise to a delay differential system. The creature could represent an insect crop pest whilst the patches could represent neighbouring farms. Given that it is common to control crop pests by adult impulsive culling, we impose an adult impulsive culling regime on each patch. We find conditions on the regimes such that the pest will be eradicated on both patches simultaneously. The regime on one patch is assumed to be independent of the regime on the other patch to reflect the possibility that the patches represent farms with different owners where each owner has autonomy in their pest control decisions. In the special case where the birth functions on both patches are of an Allee type, we calculate explicit finite upper bounds for the number of culls needed on each patch to guarantee eradication. Simulations corroborate our theoretical results.     

AUTHORIZING PSYCHIATRIC RESEARCH: PRINCIPLES,PRACTICES AND PROBLEMS

Psychiatric research is advancing rapidly, with studies revealing new investigative tools and technologies that are aimed at improving the treatment and care of patients with psychiatric disorders. However, the ethical framework in which such research is conducted is not as well developed as we might expect. In this paper we argue that more thought needs to be given to the principles that underpin research in psychiatry and to the problems associated with putting those principles into practice. In particular, we comment on some of the difficulties posed by the twin imperatives of ensuring that we respect the autonomy and interests of the research subject and, at the same time, enable potentially beneficial psychiatric research to flourish. We do not purport to offer a blueprint for the future; we do, however, seek to advance the debate by identifying some of the key questions to which better answers are required.     

New insights in the genetics of adrenocortical tumors, pheochromocytomas and paragangliomas.

Recent advances in the molecular genetic of adrenal tumors give new insights in the pathophysiology of these neoplasms in both hereditary and sporadic cases. The practice of genetic counselling in patients with adrenal tumors have been recently changed by the identification and the understanding of new specific hereditary cancer susceptibility syndromes. In the case of sporadic adrenocortical tumors these progress also offer new prognosis predictors.The genetic predisposition to adrenocortical cancer in children has been well established in the Li-Fraumeni and Beckewith-Wiedeman syndromes due to germline p53 mutation located at 17p13 and dysregulation of the imprinted IGF-2 locus at 11p15, respectively. Adrenocortical tumors are also observed in Multiple Endocrine Neoplasia type I syndrome. Cushing's syndrome due to primary pigmented nodular adrenocortical disease have been observed in patients with germline PRKAR1A inactivating mutations. Interestingly allelic loss at 17p13 and 11p15 have been observed in sporadic adrenocortical cancer and somatic PRKAR1A mutations in secreting adrenocortical adenomas. The potential interest of these finding for the diagnosis of these tumors will be discussed. In the case of pheochromocytoma and paraganglioma, the demonstration that three genes encoding three succinate dehydrogenase subunits (SDHD, SDHB, SDHC), belonging to the complex II of the respiratory chain in the mitochondria, are involved in the genetics of familial and especially in apparently sporadic phaeochromocytomas have dramatically modified our practice. Up to date, four diagnosis of familal disease (multiple endocrine neoplasia type II, von Hippel Lindau disease, neurofibromatosis type 1 and hereditary paraganglioma) should be discussed and causative mutations in six different phaechomocytoma susceptibility genes (RET, VHL, NF1, SDHB, SDHD, SDHC) could be identified. In this review, we will perform an update compiling these new clinical, genetic and functional data recently published. We will suggest guidelines for the practice of the phaeochomocytoma genetic testing in the patients and their families, and for an early detection of tumors in the patients or in individuals determined to be at-risk of disease by the presymptomatic genetic testing.     

Heat stress during development makes antlion larvae more responsive to vibrational cues

We investigated the effects of heat stress on the responsiveness to vibrational cues, our measure of perceptual ability, in Myrmeleon bore antlion larvae (Neuroptera: Myrmeleontidae). We reared these trap-building predatory larvae under 2 heat stress regimes (mild, 30°C, and harsh, 36°C), and after they progressed from one instar stage to another, we tested their perceptual ability in common unchallenging conditions. We hypothesized that exposure to the harsh heat stress regime would impose costs resulting in handicapped vibration responsiveness. We found that the harsh heat stress regime generated more stressful conditions for the larvae, as evidenced by increased mortality and postponed molting, and the loss of body mass among larger larvae. Furthermore, among the individuals who remained alive, those originating from the harsh heat stress regime were characterized by higher vibration responsiveness. Our results suggest 2 not mutually exclusive scenarios. Costly heat stress conditions can sieve out individuals characterized by poor perceptual ability or surviving individuals can attempt to hunt more efficiently to compensate for the physiological imbalance caused by heat stress. Both of these mechanisms fit into the ongoing debate over how adaptation and plasticity contribute to shaping insect communities exposed to heat stress.     

Neurogenetics: advancing the "next-generation" of brain research

There can be little doubt that genetics has transformed our understanding of mechanisms mediating brain disorders. The last two decades have brought tremendous progress in terms of accurate molecular diagnoses and knowledge of the genes and pathways that are involved in a large number of neurological and psychiatric disorders. Likewise, new methods and analytical approaches, including genome array studies and "next-generation" sequencing technologies, are bringing us deeper insights into the subtle complexities of the genetic architecture that determines our risks for these disorders. As we now seek to translate these discoveries back to clinical applications, a major challenge for the field will be in bridging the gap between genes and biology. In this Overview of Neuron's special review issue on neurogenetics, we reflect on progress made over the last two decades and highlight the challenges as well as the exciting opportunities for the future.     

Reconsidering counselling and consent

In the current era patient autonomy is enormously important. However, recently there has also been some movement back to ensure that trust in the doctor's skill, knowledge and virtue is not excluded in the process. These new nuances of informed consent have been referred to by terms such as beneficent paternalism, experience‐based paternalism and we would add virtuous paternalism. The purpose of this paper is to consider the history and current problematic nature of counselling and consent. Starting with the tradition founded by Hippocrates we trace and seek to understand how relevant aspects of the patient‐doctor relationship have evolved under the influences of subsequent moral theories. Finally we tentatively endorse certain modes of counselling in the current era in order to promote morally sound, good clinical practice.     

TOWARD A GENDER-SENSITIVE ASSISTED REPRODUCTION POLICY

The recent case of the UK woman who lost her legal struggle to be impregnated with her own frozen embryos, raises critical issues about the meaning of reproductive autonomy and the scope of regulatory practices. I revisit this case within the context of contemporary debate about the moral and legal dimensions of assisted reproduction. I argue that the gender neutral context that frames discussion of regulatory practices is unjust unless it gives appropriate consideration to the different positions women and men occupy in relation to reproductive processes and their options for autonomous choice. First, I consider relevant legal rulings, media debate, and scholarly commentary. Then I discuss the concept of reproductive autonomy imbedded in this debate. I argue that this concept conflates informed consent and reproductive autonomy, thereby providing an excessively narrow reading of autonomy that fails to give due regard to relations among individuals or the social, political and economic environment that shapes their options. I contrast this notion of autonomy with feminist formulations that seek to preserve respect for the agency of individuals without severing them from the conditions of their embodiment, their surrounding social relationships, or the political contexts that shape their options. Taking these considerations into account I weigh the advantages of regulation over the commercial market arrangement that prevails in some countries and suggest general guidelines for a regulatory policy that would more equitably resolve conflicting claims to reproductive autonomy.     

Autobiologies on YouTube: narratives of direct-to-consumer genetic testing

Despite a growing personal genomics market, little is known about how people engage with the possibilities offered by direct-to-consumer (DTC) genetic testing. In order to help address this gap, this study deploys narrative analysis of YouTube videos posted by individuals who have purchased DTC genetic testing for disease. Genetic testing is said to be contributing to new states of illness, where individuals may become “patients-in-waiting.” In the videos analyzed, we found a new form of storytelling about this ambiguous state of illness, which we refer to as autobiology. Autobiology – the study of, and story about, one's own biology – concerns narratives of sense-making through forms of biological practice, as well as wayfaring narratives which interweave genetic markers and family histories of disease. These autobiologies – part of a broader shift toward public stories about genetics and other healthcare technologies – exhibit playfulness, as well as being bound with consumerist practices.     

A care perspective on coercion and autonomy

In the Netherlands there is a growing debate over the possibility of introducting 'compassionate interference' as a form of good psychiatric care. Instead of respecting the autonomy of the patient by adopting an attitude of non-interference, professional carers should take a more active and commited role. There was a great deal of hostile reaction to this suggestion, the most commonly voiced criticism being that it smacked of 'modern paternalism'. Still, the current conception of care leaves us with a paradox. On the one hand patients are regarded as individuals who have a strong interest in ( and a right to) freedom and non-interference; on the other hand many of them have a desperate need for flourishing, viable relationships. In fact, part of their problem is that they cannot relate very well with other people. This creates a dichotomy, because respecting patients' autonomy often means that they cannot be given the help they so desperately need. In this respect current care practices do not answer the caring needs of these patients.The criticism on care practices is to be considerd as important. It invites us to reexamine and reevaluate the current conception of caring relationships and its main values. In line with this reexamination an alternative perspective on care is introduced in this paper, a perspective in which `compassionate interference' is not so much a threat to autonomy, but a means of attaining autonomy. For this we need a different definition of autonomy than that commonly used in current care practice.     

Systems genetics in “-omics” era: current and future development

The systems genetics is an emerging discipline that integrates high-throughput expression profiling technology and systems biology approaches for revealing the molecular mechanism of complex traits, and will improve our understanding of gene functions in the biochemical pathway and genetic interactions between biological molecules. With the rapid advances of microarray analysis technologies, bioinformatics is extensively used in the studies of gene functions, SNP–SNP genetic interactions, LD block–block interactions, miRNA–mRNA interactions, DNA–protein interactions, protein–protein interactions, and functional mapping for LD blocks. Based on bioinformatics panel, which can integrate “-omics” datasets to extract systems knowledge and useful information for explaining the molecular mechanism of complex traits, systems genetics is all about to enhance our understanding of biological processes. Systems biology has provided systems level recognition of various biological phenomena, and constructed the scientific background for the development of systems genetics. In addition, the next-generation sequencing technology and post-genome wide association studies empower the discovery of new gene and rare variants. The integration of different strategies will help to propose novel hypothesis and perfect the theoretical framework of systems genetics, which will make contribution to the future development of systems genetics, and open up a whole new area of genetics.     

Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations

Sensitivity and flexibility are typical properties of biological systems. These properties are here investigated in a model for simple and complex intracellular calcium oscillations. In particular, the influence of external periodic forcing is studied. The main point of the study is to compare responses of the system in a chaotic regime with those obtained in a regular periodic regime. We show that the response to external signals in terms of the range of synchronization is not significantly different in regular and chaotic Ca2+ oscillations. However, both types of oscillation are highly flexible in regimes with weak dissipation. Therefore, we conclude that dissipation of free energy is a suitable index characterizing flexibility. For biological systems this appears to be of special importance since for thermodynamic reasons, notably in view of low free energy consumption, dissipation should be minimized.     

Efficient immunization strategies on complex networks

In this paper, we proposed an efficient immunization—“high-risk immunization”. The standard SIRS model was modified, respectively, on WS small-world network and BA scale-free network. Based on our new SIRS model, the density of infected individuals was analyzed from a theoretical point of view, and computer simulation was implemented on different networks. The results indicate that the high-risk immunization is effective, and it is economic and feasible in practice.     

Periprocedural routines of coronary angioplasty--extreme diversity with unrevealed consequences

Our objective was to evaluate the current trends of coronary angioplasty periprocedural care in the state of Israel. PTCA technology has undergone through some major developments and refinements, which have yielded new algorithms and routines. With this shift of paradigms, some of the periprocedural routines (these include medications and dosing before, during and after the procedure, as well as the handling of anti-coagulation, femoral sheath removal and the extent of patient monitoring post-PTCA) have been partially re-established. In order to assess trends in periprocedural care, we elected to analyze the current state of practice in the state of Israel. A questionnaire was sent to every cardiac catheterization laboratory in Israel that performs PTCA. An authorized senior cardiologist representing the laboratory submitted the information required for our survey. A nurse-to-nurse telephone questionnaire was conducted simultaneously to cross-examine the validity of the data. All centers submitted results. The average heparin dose for PTCA varied between 5000 and 15 000 units, ACT was monitored routinely by some and not at all by others, post-PTCA heparin administration was routinely administered by some institutions and not by others, and the mean femoral sheath dwell time ranged from 4 to 18 h. Post-PTCA cardiac monitoring varied from 6 to more than 24 h. Some institutions prescribed to all patients nitrates, calcium channel blockers and low-molecular-weight heparin, while others did not. We conclude that there is profound variability in the periprocedural routines that may translate into a significant cost increase, patient discomfort, a prolonged monitoring and hospital stay, and potential patient morbidity. We suggest that these routines should be critically evaluated, and that if they do not contribute to the procedural success and patient well-being they should be abandoned.     

Research on dead human bodies: African perspectives on moral status

A useful concept that can be invoked to resolve complex bioethical issues is that of moral status (or, human dignity). In this article, we apply this concept to dead human bodies in order to support our view that research on such bodies is permissible. Instead of drawing from salient Western theories of human dignity that account for it by appeals to autonomy or rationality, we will base our investigation on emerging conceptions in African theories of moral status as articulated by Thaddeus Metz and Munamato Chemhuru. Our conclusion is that neither of these theories of moral status, one secular, and the other religious, can accommodate the intuition that we have direct duties of respect towards such bodies because, in relation to Metz's conception, they lack the capacity to enter into social relationships while on Chemhuru's conception, dead bodies appear not to have any meaningful purpose within the hierarchy that captures the ontological systems that determine such status. Consequently, we argue that our analysis provides support for the use of unclaimed cadavers in training and research in medical institutions.     

鸡快慢羽性状遗传学基础分析综合实验探索与实践

随着全国“卓越农林人才教育培养计划”的开展,我校动物科学专业设置了“卓越班”,以突出培养学生的系统思维和创新创业能力为目标开展了系列教育教学管理和课程改革。为此,我们以“鸡快、慢羽性状”为实验对象,设计了“鸡快慢羽性状遗传学基础分析”综合实验,突出培养学生用理论知识解决生产实践问题的思维和能力。本文重点介绍了该实验作为动物遗传学实验教学案例的实施过程及效果,首先从鸡的表型观察逐步深入到遗传学基础分析,利用遗传学理论指导鸡快、慢羽品系培育的育种实践。实验内容涉及伴性遗传规律和性别决定机制等遗传学理论知识,同时还涉及基因组DNA提取、基因扩增、酶切及电泳分析等一系列分子遗传学的技术方法。不仅有利于学生综合分析能力和专业技能的掌握,还有助于培养学生对动物科学专业的科研兴趣和创新意识。此综合性实验还展现了用遗传学理论指导动物品种培育实践过程,符合动物科学专业复合应用型人才培养目标的要求,其中的教学理念和方法可推广应用于其他生物学实验教学。     

The influence of predator regime on the behaviour and mortality of a freshwater amphipod, <Emphasis Type="Italic">Gammarus pulex</Emphasis>

In species with restricted dispersal, traits may become genetically fixed leading to local adaptations. Therefore, predator avoidance in a prey species may differ between populations experiencing different predator regimes, but also between sexes within a population due to different vulnerability to predators. In this study we used male and female Gammarus pulex from two different predator regimes: fishless ponds, where invertebrates are the dominant predators and ponds with predatory fish. In the laboratory we examined refuge use, mortality, leaf decomposition rate and pair-formation in G. pulex when exposed to predator cues from either invertebrate predators or fish. Individuals from fish ponds spent more time in refuge and had a higher mortality than those from fishless ponds independent of predator cues. There was no effect of pond predator regime or predator cues on leaf decomposition rates. Further, fewer individuals formed pairs in G. pulex from fish ponds than from fishless ponds. Male G. pulex had a higher mortality and a higher decomposition rate than females independent of predator cues. However, there was no difference in refuge use between sexes. Our study shows that there are general differences in behaviour traits, both between predator regimes and sexes in G. pulex.     

Straightforward inference of ancestry and admixture proportions through ancestry-informative insertion deletion multiplexing

Ancestry-informative markers (AIMs) show high allele frequency divergence between different ancestral or geographically distant populations. These genetic markers are especially useful in inferring the likely ancestral origin of an individual or estimating the apportionment of ancestry components in admixed individuals or populations. The study of AIMs is of great interest in clinical genetics research, particularly to detect and correct for population substructure effects in case-control association studies, but also in population and forensic genetics studies. This work presents a set of 46 ancestry-informative insertion deletion polymorphisms selected to efficiently measure population admixture proportions of four different origins (African, European, East Asian and Native American). All markers are analyzed in short fragments (under 230 basepairs) through a single PCR followed by capillary electrophoresis (CE) allowing a very simple one tube PCR-to-CE approach. HGDP-CEPH diversity panel samples from the four groups, together with Oceanians, were genotyped to evaluate the efficiency of the assay in clustering populations from different continental origins and to establish reference databases. In addition, other populations from diverse geographic origins were tested using the HGDP-CEPH samples as reference data. The results revealed that the AIM-INDEL set developed is highly efficient at inferring the ancestry of individuals and provides good estimates of ancestry proportions at the population level. In conclusion, we have optimized the multiplexed genotyping of 46 AIM-INDELs in a simple and informative assay, enabling a more straightforward alternative to the commonly available AIM-SNP typing methods dependent on complex, multi-step protocols or implementation of large-scale genotyping technologies.     

Individual good and common good: a communitarian approach to bioethics

The field of bioethics emerged in the late 1960s and early 1970s. Among its early issues were the protection of human research subjects, the rights of patients, abortion, and reproductive issues. Partly as a reflection of the times, and of those issues, the field became focused on autonomy and individual rights, and liberal individualism came to be the dominant ideology in the 1980s and 1990s. Communitarianism, as an alternative ideology focused more on the common good and the public interest than on autonomy, was a neglected approach. But many bioethical issues can not reasonably be reduced to questions of individualism and choice only. Issues of genetics and reproduction will of necessity touch on the society as a whole, its values, and its social institutions. Serious ethical analysis must take the social implications seriously and not simply assume that they should be left to autonomous choices of individuals. Human beings are social animals and our nature is distorted if we think of ourselves only as co-existing social atoms. Various approaches to communitarianism are outlined, and the question of the relationship between individual good and common good is confronted.