Patient and Health Care Provider Needs and Preferences in Understanding Pharmacogenomic and Genomic Testing: A Meta-Data Analysis

Tests that feature genomic indicators can now be used to guide the pharmacological treatment of patients. To better identify the needs and preferences of patients and health care providers in facilitating their understanding of information related to such pharmacogenomic tests (PGx), a review of literature on knowledge translation and health literacy in the context of testing was conducted. Using a grounded theory-based approach, a comparative analysis of data from 36 studies meeting the criteria for the meta-data analysis has revealed the recurrence of three principal themes: (a) knowledge and understanding of genetics and pharmacogenomics; (b) experiences with genetic, genomic, or PGx testing (decision about the test, information delivery, and understanding of test results); and (c) educational/informational resources. This synthesis sheds light on each theme from the standpoint of both patients and health care providers and suggests avenues in which to direct efforts to support the introduction of pharmacogenomic tests in current practice.

Knowledge and understanding of pharmacogenomic testing among patients and health care professionals: A scoping review

OBJECTIVE

To support the introduction of pharmacogenomic tests in current practice, this study identifies the factors associated with a better understanding of the information related to genetic, genomic and/or pharmacogenomic tests by patients and health care professionals.

METHODS

Following a scoping review methodology, a search for literature was conducted with keywords related to health literacy and knowledge translation in the context of pharmacogenomic tests. Since only 6 articles were identified, the context of genetic or genomic testing were added to the inclusion criteria, leading to 24 articles.

RESULTS

Fourteen of the studies analyzed focused on genetic predictive, diagnostic or carrier tests, or concerned genetics in general, while ten addressed or included the use of pharmacogenomic tests. Demographic, individual, experiential and contextual factors were associated with a better understanding of the information related to genetic, genomic and/or pharmacogenomic tests among the targeted populations.

RESEARCH IMPLICATIONS

Our review shows that there is currently little empirical research available to identify the factors to consider in order to develop educational tools and resources specific to pharmacogenomics.

CONCLUSION

Expanding our review to include genetic and genomic testing factors can serve as a starting point for the evidence to be validated in future empirical research.

Inflammatory bowel disease patient perceptions of diagnostic and monitoring tests and procedures

Background

Inflammatory Bowel Disease (IBD) with its high incidence and prevalence rates in Canada generates a heavy burden of tests and procedures. The purpose of this study is to gain a better understanding of the transfer of information from physician to patient, as well as the patient understanding and perceptions about the tests and procedures that are ordered to them in the context of IBD diagnosis and monitoring.

Methods

An online questionnaire was completed by 210 IBD patients in Canada. Information on the five most-often used tests or procedures in IBD diagnosis/monitoring was collected. These include: general blood test, colonoscopy, colon biopsy, medical imaging and stool testing.

Results

The general blood test is both the most ordered and most refused tool. It is also the one with which patients are the least comfortable, the one that generates the least concern and the one about which physicians provide the least information. The stool test is the test/procedure with which patients are the most comfortable. Procedures raise more concerns among patients and physicians provide more information about why they are needed, their impact and the risks they present. Very little information is provided to patients about the risks of having false positives or negative tests.

Conclusions

This study provides an initial understanding of patient perceptions, the transfer of information from a physician to a patient and a patient’s understanding of the tests and procedures that will be required to treat IBD throughout what is a lifelong disease. The present study takes a first step in better understanding the acceptance of the test or procedure by IBD patients, which is essential for them to adhere to the monitoring process.

Electronic supplementary material

The online version of this article (10.1186/s12876-019-0946-8) contains supplementary material, which is available to authorized users.

A luminous blue kilonova and an off-axis jet from a compact binary merger at z = 0.1341

The recent discovery of a gamma-ray burst (GRB) coincident with the gravitational-wave (GW) event GW170817 revealed the existence of a population of low-luminosity short duration gamma-ray transients produced by neutron star mergers in the nearby Universe. These events could be routinely detected by existing gamma-ray monitors, yet previous observations failed to identify them without the aid of GW triggers. Here we show that GRB150101B is an analogue of GRB170817A located at a cosmological distance. GRB150101B is a faint short burst characterized by a bright optical counterpart and a long-lived X-ray afterglow. These properties are unusual for standard short GRBs and are instead consistent with an explosion viewed off-axis: the optical light is produced by a luminous kilonova, while the observed X-rays trace the GRB afterglow viewed at an angle of ~13°. Our findings suggest that these properties could be common among future electromagnetic counterparts of GW sources.

A faint gamma-ray burst (GRB 170817A) has been recently detected in coincidence with the gravitational wave (GW) event GW 170817. Here, the authors report that another faint short GRB at a cosmological distance (GRB150101B) and its late time emission are analogous to the neutron star merger event GRB 170817A.

Patients' perception of their involvement in shared treatment decision making: Key factors in the treatment of inflammatory bowel disease

OBJECTIVES

This study aims to characterize the relationships between the quality of the information given by the physician, the involvement of the patient in shared decision making (SDM), and outcomes in terms of satisfaction and anxiety pertaining to the treatment of inflammatory bowel disease (IBD).

METHODS

A Web survey was conducted among 200 Canadian patients affected with IBD. The theoretical model of SDM was adjusted using path analysis. SAS software was used for all statistical analyses.

RESULTS

The quality of the knowledge transfer between the physician and the patient is significantly associated with the components of SDM: information comprehension, patient involvement and decision certainty about the chosen treatment. In return, patient involvement in SDM is significantly associated with higher satisfaction and, as a result, lower anxiety as regards treatment selection.

CONCLUSIONS

This study demonstrates the importance of involving patients in shared treatment decision making in the context of IBD.

PRACTICE IMPLICATIONS

Understanding shared decision making may motivate patients to be more active in understanding the relevant information for treatment selection, as it is related to their level of satisfaction, anxiety and adherence to treatment. This relationship should encourage physicians to promote shared decision making.

Exploring the Use of a Participative Design in the Early Development of a Predictive Test: The Importance of Physician Involvement

In this study, we contribute to the personalized medicine and health care management literature by developing and testing a new participative design approach. We propose that involving gastroenterologists in the development of a predictive test to assist them in their clinical decision-making process for the treatment of inflammatory bowel diseases will increase the likelihood of their acceptance of the innovation. Based on data obtained from 6 focus groups across Canada from a total of 28 physicians, analyses reveal that current tools do not enable discriminating between treatment options to find the best fit for each patient. Physicians expect a new predictive tool to have the capability of showing clear reliability and significant benefits for the patient, while being accessible in a timely manner that facilitates clinical decisions. Physicians also insist on their key role in the implementation process, hence confirming the relevance and importance of participative designs in personalized medicine.

Escherichia coli EAST1 toxin toxicity of variants 17-2 and O 42

EAST1 (EnteroAggregative heat-Stable Toxin 1) is a 4.1kDa toxin that was first detected in the enteroaggregative Escherichia coli (EAEC) strain 17-2 (O3:H2) isolated from the stools of a Chilean child with diarrhoea. Accordingly, EAST1 is thought to play a role in the pathogenicity of EAEC. The goal of this study was to obtain purified biologically active forms of two EAST1 variants (17-2 and O 42). Purified toxin samples were treated with protein disulfide isomerase (PDI) to ascertain the integrity of the disulfide bridges. Since EAST1 is often compared to STa (heat-Stable Toxin a), both purified EAST1 variants were tested for biological activity using the suckling mouse assay, the reference test for STa. A positive gut to body (G/B) weight ratio was not observed for any of the EAST1 preparations tested, although STa was active. Exposure of the purified toxins to T84 cell monolayers, an epithelial cell line derived from a human colon carcinoma, in modified Ussing flux chambers resulted in a rapidly attained and prolonged increase in short circuit current, a sensitive measure of net ion transport. Responses to 17-2 and O 42 variants were comparable in magnitude and inhibitable by bumetanide and DASU-02, indicating net anion secretion. The results demonstrate that EAST1 toxin stimulates anion secretion by T84 cell monolayers and it is sustained for the duration of toxin exposure.

Presence of Escherichia coli carrying the EAST1 toxin gene in farm animals

Enteroaggregative Escherichia coli (EAEC) heat-stable toxin 1 (EAST1) is a small toxin of proteic nature. The reference strain producing this toxin was originally detected in the stools of a diarrheic Chilean child. Today, we know that EAST1 is not solely associated with EAEC but also with many other diarrheic E. coli families. Some studies have established the role of EAST1 in human outbreaks of diarrhea. In addition, isolates from farm animals were shown, more recently, to carry the astA gene coding for EAST1. However, the relation between the presence of EAST1 and disease is not conclusive. In this article, the current state of the knowledge on the presence and probable role of EAST1 in farm animal diseases is reviewed and discussed.

Stimulation of DNA repair by the spermatidal TP1 protein

The chromatin remodeling process that takes place during spermiogenesis in mammals is characterized by a transient increase in DNA single-strand breaks (SSB). The mammalian transition proteins (TPs) are expressed at a high level at mid-spermiogenesis steps coincident with chromatin remodeling and could be involved in the repair of these lesions since SSB are no longer detected in terminally differentiated spermatids. We report that TP1 can stimulate the repair of SSB in vitro and demonstrate that in vivo repair of UV-induced DNA lesions is enhanced in mammalian cells stably expressing TP1. These results suggest that, aside from its role in DNA compaction, this major transition protein may contribute to the yet unidentified enzymatic activity responsible for the repair of SSB at mid-spermiogenesis steps. These results also suggest that the TP1 proteins have the potential to participate in the repair process following genotoxic insults and therefore may play an active role in the maintenance of the integrity of the male haploid genome during spermiogenesis.

Comparative study of the coupling between topoisomerase I activity and high-mobility group proteins in E. coli and mammalian cells

It is now well established that the HMG box DNA-binding motif can alter the topology of double-stranded DNA in several ways. Using the spermatid-specific tsHMG as a model protein of the HMG-1/-2 family, we have demonstrated that its expression in E. coli produces an increase in plasmid supercoiling density that is likely a consequence of its ability to constrain free supercoils in vivo. As demonstrated in vitro, stabilization of free DNA supercoils by tsHMG prevents topoisomerase I from gaining access to the template and could represent a mechanism for the apparent inhibition of topoisomerase I in bacteria. A similar modulation of eukaryotic topoisomerase I activity was not detected after expression of the tsHMG in mammalian cells. This differential response is discussed in terms of the marked difference in DNA packaging and accessibility of free supercoils in prokaryotic vs. eukaryotic cells.

Architectural DNA-binding properties of the spermatidal transition proteins 1 and 2

Mammalian spermiogenesis is characterized by replacement of somatic histones by a set of basic nuclear transition proteins thought to be actively involved in the chromatin remodeling process. The two major transition proteins of the elongating spermatids, namely TP1 and TP2, were expressed and purified using a bacterial expression system. Both topoisomerase and ligase-mediated supercoiling assays demonstrated that TP1, as well as TP2, did not produce detectable changes in the twist and/or writhe of DNA molecules upon binding. Ligase-mediated circularization assay further demonstrated that neither of the transition proteins under study produced bends in linear DNA but that they both have the capacity to stimulate oligomerization of linear DNA fragments. We further established that the transition proteins are in vitro substrates for the Ca+2-phospholipid-dependent protein kinase (PKC) as well as the cAMP-dependent protein kinase (PKA). PKC phosphorylation was found to strongly weaken the DNA-condensing ability of TP2. These results suggest that the major transition proteins represent architectural factors able to stabilize DNA in a nonsupercoiled state, thereby promoting DNA condensation.

The testis-specific high-mobility-group protein, a phosphorylation-dependent DNA-packaging factor of elongating and condensing spermatids

Mammalian spermiogenesis is characterized by a striking restructuring of the spermatid chromatin caused by the replacement of nucleohistones with transition proteins and their subsequent replacement with nucleoprotamines. The onset of nuclear elongation and chromatin condensation in spermatids is accompanied by a general decrease in the transcriptional activity of the DNA. A recently identified testis-specific high-mobility-group (tsHMG) protein, similar to the human mitochondrial transcription factor I and to the linker-associated protein delta of Tetrahymena thermophila micronuclei, is thought to play a structural role in this process. We confirm by immunoblot analysis of fractionated germ cells that the presence of tsHMG is restricted to transcriptionally quiescent elongating and condensing spermatids. Purified recombinant tsHMG protein displays preferential binding to supercoiled plasmid DNA, which reversibly protects the DNA against the DNA-relaxing activity of eukaryotic topoisomerase I and also impairs the transcriptional activity of this template when assayed in vitro. The tsHMG protein can also introduce negative supercoils into a relaxed plasmid substrate in a topoisomerase I-dependent manner. We also show that the tsHMG protein is the substrate of a Ca2+-phospholipid-dependent protein kinase (protein kinase C) present in testis extracts of adult mice and demonstrate that phosphorylation by protein kinase C is required for both the DNA-binding and the topoisomerase I-dependent supercoiling activities of tsHMG. Our results support the hypothesis that the spermatid tsHMG protein is a topological factor (transition protein) that can modulate the activity of topoisomerase I. This activity could contribute to the important transition in chromatin structure which leads to the decrease in DNA metabolism observed at the early stages of spermatid elongation.

Intramolecular recombination in polyomavirus DNA is controlled by promoter elements

We show here that intramolecular homologous recombination in polyomavirus (Py) DNA depends upon discrete sequence elements of the viral regulatory region which are believed to regulate transcription initiation and exert little or no cis-control over replication. Either deleting the viral early promoter (EP) or inverting the viral late promoter (LP) strongly impairs viral DNA recombination under conditions allowing viral DNA replication to proceed undisturbed. These findings suggest that bi-directional transcription proceeding from the intergenic region favors intramolecular recombination.

Typing Chlamydia trachomatis by detection of restriction fragment length polymorphism in the gene encoding the major outer membrane protein

A method that avoids culture was devised to determine serovars of Chlamydia trachomatis. Polymerase chain reaction was used first to amplify a part of the chlamydial genome that included the leader sequence and all four variable domains of the major outer membrane protein (MOMP) of the 15 serovars of C. trachomatis. The amplified DNA was then digested simultaneously with restriction endonucleases AluI and MspI and the resulting fragments separated on 10% polyacrylamide gels. After silver staining, a total of 13 characteristic patterns were observed for the 15 serovars, leaving two ambiguities that were resolved using alternate enzymes. Analysis of 40 clinical isolates revealed patterns indistinguishable from those of the prototype serovars including, unexpectedly, 5 Ba serovars. The same PCR procedure also allowed amplification of the MOMP gene of two avian Chlamydia psittaci and one Chlamydia pneumoniae isolates.

Antidepressant and other centrally acting drugs regulate glucocorticoid receptor messenger RNA levels in rat brain

The effect of imipramine, desipramine, ketanserin and lithium on Type II glucocorticoid receptor (GR) mRNA levels was studied in rat brain regions involved in the control of the hypothalamo-pituitary-adrenal (HPA) axis, the dysregulation of which has been implicated in the pathophysiology of major depression. Northern blot analysis of Type II GR mRNA showed that treatment of male rats with either desipramine or imipramine increased hypothalamic and hippocampal GR mRNA levels. Upregulation of GR mRNA following administration of imipramine was found in brain regions of female rats, while desipramine had no effect. Ketanserin increased levels of GR mRNA in hippocampus of male, but not female, rats. Lithium also was able to induce important increases rat brain GR mRNA; this effect was particularly marked in females. We conclude that desipramine, imipramine, ketanserin and lithium can modulate GR mRNA in regions of rat brain involved in the control of the HPA axis and may have a common mechanism of action at the level of the GR gene. Sexual dimorphism for drug regulation of brain GR mRNA content was shown and may be related to sex differences in the prevalence of certain affective disorders.

Informed consent in emergency settings

It is often difficult for emergency physicians to comply with the doctrine of informed consent. Patients suffering true emergencies require immediate treatment, and patients who are unable to give consent, because they are either incompetent or underage, are seen frequently in emergency departments. We examine the legal requirements of informed consent in emergency settings, with specific examples illustrated by Connecticut statutes General guidelines for developing departmental policies are suggested.

Prophylactic lidocaine: uncertain benefits in emergency settings

The need to determine whether prophylactic lidocaine has any therapeutic value is generally recognized, and further investigations have been urged: A carefully designed clinical trial of routine lidocaine administration should be carried out to provide definitive information for the physician treating patients who have had myocardial infarction. Such trials should begin immediately, in view of the magnitude of the problem and the fact that routine prophylaxis of arrhythmias after myocardial infarction is not common policy. Such a study, if well designed, can answer the question... Carefully designed trials must be conducted with patients included in the study as soon as possible after the onset of symptoms, preferably during the prehospital phase, and the medication must be administered in a random-controlled fashion. Although these requirements pose no extraordinary problems of research design and method, they lead to prohibiting ethical conflicts. Without resolving these conflicts, through the elaboration of acceptable standards which bypass traditional informed consent, the value of lidocaine prophylaxis will remain uncertain, as will the many other emergency therapeutic maneuvers of unproven effectiveness.

Errors of intuitive logic among physicians

The effectiveness of specific training in statistics and decision-making principles upon physicians' judgmental skills was assessed by means of problems of intuitive logical reasoning. The responses of 43 statistically sophisticated physicians (SP) were compared to those of 42 practicing physicians (PP), 43 clinical nurses (CN) and 41 hospital laborers (HL). On problems evaluating use of faulty heuristics in judgments of conditional probabilities, the SP group's responses were the most biased. The proportion of subjects displaying consistent use of a particular heuristic in solving the three problems were 0.36 (SP), 0.45 (PP), 0.35 (CN) and 0.41 (HL). On problems assessing use of prevalence rate data in estimating probabilities, SP performed substantially better than the other three groups: 34% of their responses were accurate. However, 37% of their responses reflected ignorance of prevalence information concepts. We conclude that intensive statistical and decision-making training of physicians is likely to be of only limited value for improving clinicians' judgmental skills.