Bayesian emulation and history matching of JUNE.

We analyze JUNE: a detailed model of COVID-19 transmission with high spatial and demographic resolution, developed as part of the RAMP initiative. JUNE requires substantial computational resources to evaluate, making model calibration and general uncertainty analysis extremely challenging. We describe and employ the uncertainty quantification approaches of Bayes linear emulation and history matching to mimic JUNE and to perform a global parameter search, hence identifying regions of parameter space that produce acceptable matches to observed data, and demonstrating the capability of such methods. This article is part of the theme issue 'Technical challenges of modelling real-life epidemics and examples of overcoming these'.

Genome Canada precision medicine strategy for structured national implementation of epitope matching in renal transplantation.

Advances in immunology support the understanding that precise structural epitopes on the antibody-accessible region of the HLA molecule determine antigenicity and challenge the need for identity across the full HLA molecule to minimize graft immunogenicity. Retrospective studies confirm that quantitative measurement of epitope-level mismatching between donor and recipient is an informative marker of graft rejection and survival and suggest that prospective allocation of donor organs based on this principle may improve graft survival. Here we describe the process for rigorous prospective evaluation of this hypothesis in a formal national proof-of-concept program for epitope-based matching. This encompasses broad societal consultation to engage the public, patients and providers; the development of clear allocation policies with strategies to support candidates who may be difficult to match; molecular and sequencing methods and web-based calculators enabling rapid epitope typing and recipient selection; precise immunological monitoring of the graft response; information systems permitting real-time monitoring of clinical outcomes; and assessment of health benefit and economic cost. The results of this objective evaluation can then be provided to payers and policy-makers for review, and adoption if of proven benefit.

Mental health of staff working in intensive care during Covid-19.

BACKGROUND: Staff working in intensive care units (ICUs) have faced significant challenges during the COVID-19 pandemic which have the potential to adversely affect their mental health. AIMS: To identify the rates of probable mental health disorder in staff working in ICUs in nine English hospitals during June and July 2020. METHODS: An anonymized brief web-based survey comprising standardized questionnaires examining depression, anxiety symptoms, symptoms of post-traumatic stress disorder (PTSD), well-being and alcohol use was administered to staff. RESULTS: Seven hundred and nine participants completed the surveys comprising 291 (41%) doctors, 344 (49%) nurses and 74 (10%) other healthcare staff. Over half (59%) reported good well-being; however, 45% met the threshold for probable clinical significance on at least one of the following measures: severe depression (6%), PTSD (40%), severe anxiety (11%) or problem drinking (7%). Thirteen per cent of respondents reported frequent thoughts of being better off dead, or of hurting themselves in the past 2 weeks. Within the sample used in this study, we found that doctors reported better mental health than nurses across a range of measures. CONCLUSIONS: We found substantial rates of probable mental health disorders, and thoughts of self-harm, amongst ICU staff; these difficulties were especially prevalent in nurses. Whilst further work is needed to better understand the real level of clinical need amongst ICU staff, these results indicate the need for a national strategy to protect the mental health, and decrease the risk of functional impairment, of ICU staff whilst they carry out their essential work during COVID-19.

Waldenstrom macroglobulinemia cells devoid of BTKC481S or CXCR4WHIM-like mutations acquire resistance to ibrutinib through upregulation of Bcl-2 and AKT resulting in vulnerability towards venetoclax or MK2206 treatment.

Although ibrutinib is highly effective in Waldenstrom macroglobulinemia (WM), no complete remissions in WM patients treated with ibrutinib have been reported to date. Moreover, ibrutinib-resistant disease is being steadily reported and is associated with dismal clinical outcome (overall survival of 2.9-3.1 months). To understand mechanisms of ibrutinib resistance in WM, we established ibrutinib-resistant in vitro models using validated WM cell lines. Characterization of these models revealed the absence of BTKC481S and CXCR4WHIM-like mutations. BTK-mediated signaling was found to be highly attenuated accompanied by a shift in PI3K/AKT and apoptosis regulation-associated genes/proteins. Cytotoxicity studies using the AKT inhibitor, MK2206±ibrutinib, and the Bcl-2-specific inhibitor, venetoclax±ibrutinib, demonstrated synergistic loss of cell viability when either MK22016 or venetoclax were used in combination with ibrutinib. Our findings demonstrate that induction of ibrutinib resistance in WM cells can arise independent of BTKC481S and CXCR4WHIM-like mutations and sustained pressure from ibrutinib appears to activate compensatory AKT signaling as well as reshuffling of Bcl-2 family proteins for maintenance of cell survival. Combination treatment demonstrated greater (and synergistic) antitumor effect and provides rationale for development of therapeutic strategies encompassing venetoclax+ibrutinib or PI3K/AKT inhibitors+ibrutinib in ibrutinib-resistant WM.

Coinhibition of the deubiquitinating enzymes, USP14 and UCHL5, with VLX1570 is lethal to ibrutinib- or bortezomib-resistant Waldenstrom macroglobulinemia tumor cells.

The survival of Waldenstrom macroglobulinemia (WM) tumor cells hinges on aberrant B-cell receptor (BCR) and MYD88 signaling. WM cells upregulate the proteasome function to sustain the BCR-driven growth while maintaining homeostasis. Clinically, two treatment strategies are used to disrupt these complementary yet mutually exclusive WM survival pathways via ibrutinib (targets BTK/MYD88 node) and bortezomib (targets 20 S proteasome). Despite the success of both agents, WM patients eventually become refractory to treatment, highlighting the adaptive plasticity of WM cells and underscoring the need for development of new therapeutics. Here we provide a comprehensive preclinical report on the anti-WM activity of VLX1570, a novel small-molecule inhibitor of the deubiquitinating enzymes (DUBs), ubiquitin-specific protease 14 (USP14) and ubiquitin carboxyl-terminal hydrolase isozyme L5 (UCHL5). Both DUBs reside in the 19 S proteasome cap and their inhibition by VLX1570 results in rapid and tumor-specific apoptosis in bortezomib- or ibrutinib-resistant WM cells. Notably, treatment of WM cells with VLX1570 downregulated BCR-associated elements BTK, MYD88, NFATC, NF-κB and CXCR4, the latter whose dysregulated function is linked to ibrutinib resistance. VLX1570 administered to WM-xenografted mice resulted in decreased tumor burden and prolonged survival (P=0.0008) compared with vehicle-treated mice. Overall, our report demonstrates significant value in targeting USP14/UCHL5 with VLX1570 in drug-resistant WM and carries a high potential for clinical translation.

Nimbolide targets BCL2 and induces apoptosis in preclinical models of Waldenströms macroglobulinemia.

Neem leaf extract (NLE) has medicinal properties, which have been attributed to its limonoid content. We identified the NLE tetranorterpenoid, nimbolide, as being the key limonoid responsible for the cytotoxicity of NLE in various preclinical models of human B-lymphocyte cancer. Of the models tested, Waldenströms macroglobulinemia (WM) cells were most sensitive to nimbolide, undergoing significant mitochondrial mediated apoptosis. Notably, nimbolide toxicity was also observed in drug-resistant (bortezomib or ibrutinib) WM cells. To identify putative targets of nimbolide, relevant in WM, we used chemoinformatics-based approaches comprised of virtual in silico screening, molecular modeling and target-ligand reverse docking. In silico analysis revealed the antiapoptotic protein BCL2 was the preferential binding partner of nimbolide. The significance of this finding was further tested in vitro in RS4;11 (BCL2-dependent) tumor cells, in which nimbolide induced significantly more apoptosis compared with BCL2 mutated (Jurkat BCL2(Ser70-Ala)) cells. Lastly, intraperitoneal administration of nimbolide in WM tumor xenografted mice, significantly reduced tumor growth and IgM secretion in vivo, while modulating the expression of several proteins as seen on immunohistochemistry. Overall, our data demonstrate that nimbolide is highly active in WM cells, as well as other B-cell cancers, and engages BCL2 to exert its cytotoxic activity.

Economic consequences incurred by living kidney donors: a Canadian multi-center prospective study.

Some living kidney donors incur economic consequences as a result of donation; however, these costs are poorly quantified. We developed a framework to comprehensively assess economic consequences from the donor perspective including out-of-pocket cost, lost wages and home productivity loss. We prospectively enrolled 100 living kidney donors from seven Canadian centers between 2004 and 2008 and collected and valued economic consequences ($CAD 2008) at 3 months and 1 year after donation. Almost all (96%) donors experienced economic consequences, with 94% reporting travel costs and 47% reporting lost pay. The average and median costs of lost pay were $2144 (SD 4167) and $0 (25th-75th percentile 0, 2794), respectively. For other expenses (travel, accommodation, medication and medical), mean and median costs were $1780 (SD 2504) and $821 (25th-75th percentile 242, 2271), respectively. From the donor perspective, mean cost was $3268 (SD 4704); one-third of donors incurred cost >$3000, and 15% >$8000. The majority of donors (83%) reported inability to perform usual household activities for an average duration of 33 days; 8% reported out-of-pocket costs for assistance with these activities. The economic impact of living kidney donation for some individuals is large. We advocate for programs to reimburse living donors for their legitimate costs.

Science and the sources of hype.

It has been suggested that genomic research is frequently inappropriately hyped, in both the popular press and the scientific literature, and that this hype has the potential to create a range of social concerns. This paper maps the complex array of social forces that contribute to the phenomenon of hype, including the pressure to publish, the increasingly intense commercialization agenda, the messaging emanating from research institutions, the news media and, even, the public itself. These numerous and interrelated factors create a 'hype pipeline' that will be difficult to counter without the utilization of a wide range of policy strategies.

DTC genetic testing: pendulum swings and policy paradoxes.

After decades of optimistic portrayals, there has been a shift in the way that the popular press represents genomic research. A skeptical view has become more common. The central reason for this pendulum swing away from popular support is the harsh truth that most genetic risk information just isn't that predictive. This reality has created a fascinating policy paradox. If, as many in the scientific community are now saying, genetic information is not the oracle of our future health as we were once led to believe, and if access does not, for most, cause harm, why regulate the area? Why worry about shoddy direct-to-consumer (DTC) genetic testing companies? One primary justification, and one endorsed by the recent Canadian College of Medical Geneticists (CCMG) Policy Statement on DTC Genetics Testing, is that information that is conveyed to the public about genetics via marketing and to those who access DTC tests should, at a minimum, be accurate.

Science spin: iPS cell research in the news.

Big scientific developments have always been spun to meet particular social agendas. We have seen it in the context of global warming, nuclear power, and genetically modified organisms. But few stories illustrate the phenomenon of spin as well as the reaction, and concomitant media coverage, that surrounded the November 2007 announcement regarding the reprogramming of skin cells to produce cells with qualities comparable to those of human embryonic stem cells (hESCs) known as induced pluripotent stem (iPS) cells.

Direct-to-consumer genetic testing: good, bad or benign?

A wide variety of genetic tests are now being marketed and sold in direct-to-consumer (DTC) commercial transactions. However, risk information revealed through many DTC testing services, especially those based on emerging genome wide-association studies, has limited predictive value for consumers. Some commentators contend that tests are being marketed prematurely, while others support rapid translation of genetic research findings to the marketplace. The potential harms and benefits of DTC access to genetic testing are not yet well understood, but some large-scale studies have recently been launched to examine how consumers understand and use genetic risk information. Greater consumer access to genetic tests creates a need for continuing education for health care professionals so they can respond to patients' inquiries about the benefits, risks and limitations of DTC services. Governmental bodies in many jurisdictions are considering options for regulating practices of DTC genetic testing companies, particularly to govern quality of commercial genetic tests and ensure fair and truthful advertising. Intersectoral initiatives involving government regulators, professional bodies and industry are important to facilitate development of standards to govern this rapidly developing area of personalized genomic commerce.

Willingness to pay for genetic testing: a study of attitudes in a Canadian population.

BACKGROUND: This article reports results of a 2008 telephone survey of approximately 1,200 residents of the Province of Alberta, Canada. The majority of respondents reside in urban centers, have some post-secondary education, and report annual family income near or above the Canadian average. The goal was to explore attitudes and interest regarding different types of genetic tests. METHODS: Respondents were asked about their willingness to pay for tests to gain information about genetic factors related to manageable conditions, serious, unpreventable disease, healthy food choices, psychiatric conditions, going bald (asked of men only), and gaining weight. The price categories were CAD 0, CAD 1-499, CAD 500-1,999 and CAD 2,000+. Respondents were also asked about factors that would motivate interest in genetic testing, such as availability of treatment, curiosity, and reproductive decision-making. They were also asked if the public health insurance system should pay for certain types of tests. RESULTS: Across all test categories, few respondents expressed willingness to pay more than CAD 500 out of their own pocket. 62% stated that the public health insurance system should pay for genetic tests for manageable conditions and opinion was divided about whether the government should fund tests for serious, unpreventable conditions and tests to inform healthy eating choices. CONCLUSION: The principal motivator for interest in genetic testing was to learn clinically relevant details to inform health-related decisions. Curiosity about genetic risk had only a modest impact on consumer interest. In general, younger respondents (18-35 years) expressed somewhat greater willingness to pay than older respondents, especially those 65 and older.

Canada: public health genomics.

Canada has a diverse population of 32 million people and a universal, publicly funded health care system provided through provincial and territorial health insurance plans. Public health activities are resourced at provincial/territorial level with strategic coordination from national bodies. Canada has one of the longest-standing genetics professional specialty organizations and is one of the few countries offering master's level training designed specifically for genetic counselors. Prenatal screening is offered as part of routine clinical prenatal services with variable uptake. Surveillance of the effect of prenatal screening and diagnosis on the birth prevalence of congenital anomalies is limited by gaps and variations in surveillance systems. Newborn screening programs vary between provinces and territories in terms of organization and conditions screened for. The last decade has witnessed a four-fold increase in requests for genetic testing, especially for late onset diseases. Tests are performed in provincial laboratories or outside Canada. There is wide variation in participation in laboratory quality assurance schemes, and there are few regulatory frameworks in Canada that are directly relevant to genetics testing services or population genetics. Health technology assessment in Canada is conducted by a diverse range of organizations, several of which have produced reports related to genetics. Several large-scale population cohort studies are underway or planned, with initiatives to harmonize their conduct and the management of ethical issues, both within Canada and with similar projects in other countries.

Media portrayal of herbal remedies versus pharmaceutical clinical trials: impacts on decision.

The use of Complementary and Alternative Medicines (CAM) in Europe and North America is increasing significantly with a concomitant growth in business interest. Users are educated and self-empowered and rely on information sources beyond mainstream medical practitioners. Not surprisingly, media coverage, much of dubious quality, has increased to meet demand for information. Here we present data from a study that explores how knowledge is translated in the socioeconomic-political context of CAM as compared to conventional pharmaceuticals. Specifically, we are interested in the nature of the information provided by clinical trials and the media and how this might impact decision-making regarding the use of CAM versus conventional pharmaceuticals and the reporting of conflicts of interest and industry funding of research. Our results suggest that, in the media, there were significant errors of omission in describing clinical trial quality and a serious under-reporting of risks of herbal remedies. Consumers, who often self-administer CAM are not being provided with information sufficient to make informed choices about treatment alternatives. The next step in the research is to determine whether these reporting dynamics in describing CAM clinical trials differ from those of reporting on pharmaceutical clinical trials.

Law and policy in the era of reproductive genetics.

The extent to which society utilises the law to enforce its moral judgments remains a dominant issue in this era of embryonic stem cell research, preimplantation genetic diagnosis, and human reproductive cloning. Balancing the potential health benefits and diverse moral values of society can be a tremendous challenge. In this context, governments often adopt legislative bans and prohibitions and rely on the inflexible and often inappropriate tool of criminal law. Legal prohibitions in the field of reproductive genetics are not likely to reflect adequately the depth and diversity of competing stakeholder positions. Rather, a comprehensive and readily responsive regulatory policy is required. Such a policy must attend to the evolving scientific developments and ethical considerations. We outline a proposal for effective, responsive, and coherent oversight of new reproductive genetic technologies.

Tissue banking, patient rights, and confidentiality: tensions in law and policy.

The collection, storage and analysis of tissue samples, including genetic data, has become an increasingly common part of biomedical research. Though there are many scientific justifications for the creation of tissue and DNA databanks, the storage and use of human tissue continues to create legal dilemmas. In this paper, the impact and relevance of existing common law principles are reviewed. It is noted that the Canadian common law rules covering consent and confidentiality may create challenges for the research community. Emerging health information legislation does, however, create a somewhat more lenient research environment, largely because these laws allow, in some circumstances, research on identifiable health information without consent. Nevertheless, conflicts between existing common law, research ethics policy and new health information legislation illustrate profound policy dilemmas created by research involving storage and use of tissue and genetic material.

Genetic technologies, health care policy and the patent bargain.

The idea of granting patents on human genetic material continues to cause controversy. The debate is largely focussed on the moral acceptability of human gene patents, the impact of gene patents on the research environment and the value of patents to stimulate innovation and the commercialization and dissemination of genetic discoveries. As highlighted by a recent controversy in Canada, patents can also have a profound effect on health policy and access to genetic services. Creative and bold patent reform initiatives are necessary to ensure that society will, to the highest degree possible, reap the health care benefits of the genetic revolution.