Persistent IDH mutations are not associated with increased relapse or death in patients with IDH-mutated acute myeloid leukemia undergoing allogeneic hematopoietic cell transplant with post-transplant cyclophosphamide.

The presence of measurable residual disease (MRD) prior to an allogeneic hematopoietic transplant (alloHCT) in Acute Myeloid Leukemia (AML) has been shown to be associated with an increased risk of post-transplant relapse. Since the Isocitrate Dehydrogenase genes (IDH1/2) are mutated in a considerable proportion of patients with AML, we studied if these mutations would serve as useful targets for MRD. Fifty-five IDH-mutated AML patients undergoing non-myeloablative alloHCT with post-transplant cyclophosphamide at a single center were sequenced at baseline using a multi-gene panel followed by targeted testing for persistent IDH mutations at the pre- and post-alloHCT timepoints by digital droplet PCR or error-corrected next generation sequencing. The cohort included patients who had been treated with IDH inhibitors pre- and post-transplant (20% and 17% for IDH1 and 38% and 28% for IDH2). Overall, 55% of patients analyzed had detectable IDH mutations during complete remission prior to alloHCT. However, there were no statistically significant differences in overall survival (OS), relapse-free survival (RFS), and cumulative incidence of relapse (CIR) at 3 years between patients who tested positive or negative for a persistent IDH mutation during remission (OS: IDH1 p=1, IDH2 p=0.87; RFS: IDH1 p=0.71, IDH2 p= 0.78; CIR: IDH1 p=0.92, IDH2 p=0.97). There was also no difference in the prevalence of persistent IDH mutation between patients who did and did not receive an IDH inhibitor (p=0.59). Mutational profiling of available relapse samples showed that 8 out of 9 patients still exhibited the original IDH mutation, indicating that the IDH mutations remained stable through the course of the disease. This study demonstrates that persistent IDH mutations during remission is not associated with inferior clinical outcomes after alloHCT in patients with AML.

Measurable Residual IDH1 before Allogeneic Transplant for Acute Myeloid Leukemia.

Measurable residual disease (MRD) in adults with acute myeloid leukemia (AML) in complete remission is an important prognostic marker, but detection methodology requires optimization. The persistence of mutated NPM1 or FLT3-ITD in the blood of adult patients with AML in first complete remission (CR1) prior to allogeneic hematopoetic cell transplant (alloHCT) has been established as associated with increased relapse and death after transplant. The prognostic implications of persistence of other common AML-associated mutations, such as IDH1, at this treatment landmark however remains incompletely defined. We performed testing for residual IDH1 variants (IDH1m) in pre-transplant CR1 blood of 148 adult patients undergoing alloHCT for IDH1-mutated AML at a CIBMTR site between 2013-2019. No post-transplant differences were observed between those testing IDH1m positive (n=53, 36%) and negative pre-transplant (overall survival: p = 0.4; relapse: p = 0.5). For patients with IDH1 mutated AML co-mutated with NPM1 and/or FLT3-ITD, only detection of persistent mutated NPM1 and/or FLT3-ITD was associated with significantly higher rates of relapse (p = 0.01). These data, from the largest study to date, do not support the detection of IDH1 mutation in CR1 blood prior to alloHCT as evidence of AML MRD or increased post-transplant relapse risk.

Contrived Materials and a Data Set for the Evaluation of Liquid Biopsy Tests: A Blood Profiling Atlas in Cancer (BLOODPAC) Community Study.

The Blood Profiling Atlas in Cancer (BLOODPAC) Consortium is a collaborative effort involving stakeholders from the public, industry, academia, and regulatory agencies focused on developing shared best practices on liquid biopsy. This report describes the results from the JFDI (Just Freaking Do It) study, a BLOODPAC initiative to develop standards on the use of contrived materials mimicking cell-free circulating tumor DNA, to comparatively evaluate clinical laboratory testing procedures. Nine independent laboratories tested the concordance, sensitivity, and specificity of commercially available contrived materials with known variant-allele frequencies (VAFs) ranging from 0.1% to 5.0%. Each participating laboratory utilized its own proprietary evaluation procedures. The results demonstrated high levels of concordance and sensitivity at VAFs of >0.1%, but reduced concordance and sensitivity at a VAF of 0.1%; these findings were similar to those from previous studies, suggesting that commercially available contrived materials can support the evaluation of testing procedures across multiple technologies. Such materials may enable more objective comparisons of results on materials formulated in-house at each center in multicenter trials. A unique goal of the collaborative effort was to develop a data resource, the BLOODPAC Data Commons, now available to the liquid-biopsy community for further study. This resource can be used to support independent evaluations of results, data extension through data integration and new studies, and retrospective evaluation of data collection.

Droplet digital PCR for the detection of second-generation tyrosine kinase inhibitor-resistant BCR::ABL1 kinase domain mutations in chronic myeloid leukemia.

One of the indications for BCR::ABL1 mutation testing in chronic myeloid leukemia (CML) is when tyrosine kinase inhibitor therapy (TKI) needs to be changed for unsatisfactory response. In this study, we evaluated a droplet digital PCR (ddPCR)-based multiplex strategy for the detection and quantitation of transcripts harbouring mutations conferring resistance to second-generation TKIs (2GTKIs). Parallel quantitation of e13a2, e14a2 and e1a2 BCR::ABL1 fusion transcripts enables to express results as percentage of mutation positive- over total BCR::ABL1 transcripts. We determined the limit of blank in 60 mutation-negative samples. Accuracy was demonstrated by further analysis of 48 samples already studied by next generation sequencing (NGS). Mutations could be called down to 0.5% and across 3-logs of BCR::ABL1 levels. Retrospective review of BCR::ABL1 NGS results in 513 consecutive CML patients with non-optimal response to first- or second-line TKI therapy suggested that a ddPCR-based approach targeted against 2GTKI-resistant mutations would score samples as mutation-negative in 22% of patients with warning response to imatinib but only in 6% of patients with warning response to 2GTKIs. We conclude ddPCR represents an attractive method for easy, accurate and rapid screening for 2GTKI-resistant mutations impacting on TKI selection, although ddPCR cannot identify compound mutations.

Between Laboratory Reproducibility of DNA Extraction from Human Blood and Fresh Frozen Tissue.

Standardization of molecular diagnostics is fundamental for effective application of genetic analyses in personalized medicine. The amount of DNA extracted from a specimen can have a significant impact on diagnostic accuracy, especially in cases where the diagnostic variant has a low concentration such as cancer. Blood and tissue samples were supplied to genetic laboratories to assess the reproducibility of extraction methodologies; DNA was extracted using participants' routine procedures and returned to the external quality assessment provider. The amount of DNA was measured by two independent analytical techniques, fluorescence intensity of intercalating dye and digital PCR; DNA quality was evaluated by DNA integrity number scores. The amount of DNA extracted varied widely between and within participants and for different blood volumes, indicating that consistent diagnostic quality is challenging even within a single test center. The median digital PCR-measured amount of DNA was on average six times higher than the intercalating dye measurements obtained in this study, indicating the possibility that the latter quantitative method may significantly underestimate the amount of DNA, thus making it not fit for purpose. Standardization of genetic diagnostic tests will require a significant improvement in the reproducibility of DNA extraction; this could be achieved if suppliers and users of DNA extraction kits validate their extraction methodology using reliable quantitative measurements or reference materials.

Building a Social Mandate for Climate Action: Lessons from COVID-19.

The COVID-19 imposed lockdown has led to a number of temporary environmental side effects (reduced global emissions, cleaner air, less noise), that the climate community has aspired to achieve over a number of decades. However, these benefits have been achieved at a massive cost to welfare and the economy. This commentary draws lessons from the COVID-19 crisis for climate change. It discusses whether there are more sustainable ways of achieving these benefits, as part of a more desirable, low carbon resilient future, in a more planned, inclusive and less disruptive way. In order to achieve this, we argue for a clearer social contract between citizens and the state. We discuss how COVID-19 has demonstrated that behaviours can change abruptly, that these changes come at a cost, that we need a 'social mandate' to ensure these changes remain in the long-term, and that science plays an important role in informing this process. We suggest that deliberative engagement mechanisms, such as citizens' assemblies and juries, could be a powerful way to build a social mandate for climate action post-COVID-19. This would enable behaviour changes to become more accepted, embedded and bearable in the long-term and provide the basis for future climate action.

A comparative study of digital PCR and real-time qPCR for the detection and quantification of HPV mRNA in sentinel lymph nodes of cervical cancer patients.

BACKGROUND: Qualitative analyses showed that the presence of HPV mRNA in sentinel lymph nodes of cervical cancer patients with pN0 status is associated with significantly decreased recurrence free survival. To further address the clinical potential of the strategy and to define prognostic threshold levels it is necessary to use a quantitative assay. Here, we compare two methods of quantification: digital PCR and standard quantitative PCR. METHODS: Serial dilutions of 5 ng-5 pg RNA (≙ 500-0.5 cells) of the cervical cancer cell line SiHa were prepared in 5 µg RNA of the HPV-negative human keratinocyte cell line HaCaT. Clinical samples consisted of 10 sentinel lymph nodes with varying HPV transcript levels. Reverse transcription of total RNA (5 µg RNA each) was performed in 100 µl and cDNA aliquots were analyzed by qPCR and dPCR. Digital PCR was run in the RainDrop® Digital PCR system (RainDance Technologies) using a probe-based detection of HPV E6/E7 cDNA PCR products with 11 µl template. qPCR was done using a Rotor Gene Q 5plex HRM (Qiagen) amplifying HPV E6/E7 cDNA in a SYBR Green format with 1 µl template. RESULTS: For the analysis of both, clinical samples and serial dilution samples, dPCR and qPCR showed comparable sensitivity. With regard to reproducibility, both methods differed considerably, especially for low template samples. Here, we found with qPCR a mean variation coefficient of 126% whereas dPCR enabled a significantly lower mean variation coefficient of 40% (p = 0.01). Generally, we saw with dPCR a substantial reduction of subsampling errors, which most likely reflects the large cDNA amounts available for analysis. CONCLUSIONS: Compared to real-time PCR, dPCR shows higher reliability. Thus, our HPV mRNA dPCR assay holds promise for the clinical evaluation of occult tumor cells in histologically tumor-free lymph nodes in future studies.

'Green' on the ground but not in the air: Pro-environmental attitudes are related to household behaviours but not discretionary air travel.

The rise in greenhouse gas emissions from air travel could be reduced by individuals voluntarily abstaining from, or reducing, flights for leisure and recreational purposes. In theory, we might expect that people with pro-environmental value orientations and concerns about the risks of climate change, and those who engage in more pro-environmental household behaviours, would also be more likely to abstain from such voluntary air travel, or at least to fly less far. Analysis of two large datasets from the United Kingdom, weighted to be representative of the whole population, tested these associations. Using zero-inflated Poisson regression models, we found that, after accounting for potential confounders, there was no association between individuals' environmental attitudes, concern over climate change, or their routine pro-environmental household behaviours, and either their propensity to take non-work related flights, or the distances flown by those who do so. These findings contrasted with those for pro-environmental household behaviours, where associations with environmental attitudes and concern were observed. Our results offer little encouragement for policies aiming to reduce discretionary air travel through pro-environmental advocacy, or through 'spill-over' from interventions to improve environmental impacts of household routines.

Public Reception of Climate Science: Coherence, Reliability, and Independence.

Possible measures to mitigate climate change require global collective actions whose impacts will be felt by many, if not all. Implementing such actions requires successful communication of the reasons for them, and hence the underlying climate science, to a degree that far exceeds typical scientific issues which do not require large-scale societal response. Empirical studies have identified factors, such as the perceived level of consensus in scientific opinion and the perceived reliability of scientists, that can limit people's trust in science communicators and their subsequent acceptance of climate change claims. Little consideration has been given, however, to recent formal results within philosophy concerning the relationship between truth, the reliability of evidence sources, the coherence of multiple pieces of evidence/testimonies, and the impact of (non-)independence between sources of evidence. This study draws on these results to evaluate exactly what has (and, more important, has not yet) been established in the empirical literature about the factors that bias the public's reception of scientific communications about climate change.

Geoengineering, climate change scepticism and the 'moral hazard' argument: an experimental study of UK public perceptions.

Many commentators have expressed concerns that researching and/or developing geoengineering technologies may undermine support for existing climate policies-the so-called moral hazard argument. This argument plays a central role in policy debates about geoengineering. However, there has not yet been a systematic investigation of how members of the public view the moral hazard argument, or whether it impacts on people's beliefs about geoengineering and climate change. In this paper, we describe an online experiment with a representative sample of the UK public, in which participants read one of two arguments (either endorsing or rejecting the idea that geoengineering poses a moral hazard). The argument endorsing the idea of geoengineering as a moral hazard was perceived as more convincing overall. However, people with more sceptical views and those who endorsed 'self-enhancing' values were more likely to agree that the prospect of geoengineering would reduce their motivation to make changes in their own behaviour in response to climate change. The findings suggest that geoengineering is likely to pose a moral hazard for some people more than others, and the implications for engaging the public are discussed.

Exploring early public responses to geoengineering.

Proposals for geoengineering the Earth's climate are prime examples of emerging or 'upstream' technologies, because many aspects of their effectiveness, cost and risks are yet to be researched, and in many cases are highly uncertain. This paper contributes to the emerging debate about the social acceptability of geoengineering technologies by presenting preliminary evidence on public responses to geoengineering from two of the very first UK studies of public perceptions and responses. The discussion draws upon two datasets: qualitative data (from an interview study conducted in 42 households in 2009), and quantitative data (from a subsequent nationwide survey (n=1822) of British public opinion). Unsurprisingly, baseline awareness of geoengineering was extremely low in both cases. The data from the survey indicate that, when briefly explained to people, carbon dioxide removal approaches were preferred to solar radiation management, while significant positive correlations were also found between concern about climate change and support for different geoengineering approaches. We discuss some of the wider considerations that are likely to shape public perceptions of geoengineering as it enters the media and public sphere, and conclude that, aside from technical considerations, public perceptions are likely to prove a key element influencing the debate over questions of the acceptability of geoengineering proposals.

Communicating environmental risks: Clarifying the severity effect in interpretations of verbal probability expressions.

Verbal probability expressions are frequently used to communicate risk and uncertainty. The Intergovernmental Panel on Climate Change (IPCC), for example, uses them to convey risks associated with climate change. Given the potential for human action to mitigate future environmental risks, it is important to understand how people respond to these expressions. In 3 studies employing a novel manipulation of event severity (so as to avoid any confound with event base rate), we demonstrated a systematic effect of event severity on the interpretation of verbal probability expressions. Challenging a previous finding in the literature, expressions referring to a severe event were interpreted as indicating a higher probability than those referring to a more neutral event. The finding was demonstrated in scenarios communicating risks relating to climate change (Studies 1 and 2) and replicated in scenarios involving nanotechnology and nuclear materials (Study 3). This is the first direct demonstration of an effect of outcome severity on the interpretation of verbal probability expressions, correcting a previous (potentially problematic) conclusion attributable to a flawed experimental design.

Integration of metabolomics and transcriptomics data to aid biomarker discovery in type 2 diabetes.

Type 2 diabetes (T2D), one of the most common diseases in the western world, is characterized by insulin resistance and impaired beta-cell function but currently it is difficult to determine the precise pathophysiology in individual T2D patients. Non-targeted metabolomics technologies have the potential for providing novel biomarkers of disease and drug efficacy, and are increasingly being incorporated into biomarker exploration studies. Contextualization of metabolomics results is enhanced by integration of study data from other platforms, such as transcriptomics, thus linking known metabolites and genes to relevant biochemical pathways. In the current study, urinary NMR-based metabolomic and liver, adipose, and muscle transcriptomic results from the db/db diabetic mouse model are described. To assist with cross-platform integration, integrative pathway analysis was used. Sixty-six metabolites were identified in urine that discriminate between the diabetic db/db and control db/+ mice. The combined analysis of metabolite and gene expression changes revealed 24 distinct pathways that were altered in the diabetic model. Several of these pathways are related to expected diabetes-related changes including changes in lipid metabolism, gluconeogenesis, mitochondrial dysfunction and oxidative stress, as well as protein and amino acid metabolism. Novel findings were also observed, particularly related to the metabolism of branched chain amino acids (BCAAs), nicotinamide metabolites, and pantothenic acid. In particular, the observed decrease in urinary BCAA catabolites provides direct corroboration of previous reports that have inferred that elevated BCAAs in diabetic patients are caused, in part, by reduced catabolism. In summary, the integration of metabolomics and transcriptomics data via integrative pathway mapping has facilitated the identification and contextualization of biomarkers that, presuming further analytical and biological validation, may be useful in future T2D clinical studies by identifying patient populations that share common disease pathophysiology and therefore may identify those patients that may respond better to a particular class of anti-diabetic drugs.

Evaluating science arguments: evidence, uncertainty, and argument strength.

Public debates about socioscientific issues are increasingly prevalent, but the public response to messages about, for example, climate change, does not always seem to match the seriousness of the problem identified by scientists. Is there anything unique about appeals based on scientific evidence-do people evaluate science and nonscience arguments differently? In an attempt to apply a systematic framework to people's evaluation of science arguments, the authors draw on the Bayesian approach to informal argumentation. The Bayesian approach permits questions about how people evaluate science arguments to be posed and comparisons to be made between the evaluation of science and nonscience arguments. In an experiment involving three separate argument evaluation tasks, the authors investigated whether people's evaluations of science and nonscience arguments differed in any meaningful way. Although some differences were observed in the relative strength of science and nonscience arguments, the evaluation of science arguments was determined by the same factors as nonscience arguments. Our results suggest that science communicators wishing to construct a successful appeal can make use of the Bayesian framework to distinguish strong and weak arguments.

Estimating the probability of negative events.

How well we are attuned to the statistics of our environment is a fundamental question in understanding human behaviour. It seems particularly important to be able to provide accurate assessments of the probability with which negative events occur so as to guide rational choice of preventative actions. One question that arises here is whether or not our probability estimates for negative events are systematically biased by their severity. In a minimal experimental context involving an unambiguous, objective representation of probability, we found that participants judged a controllable event as more likely to occur when its utility was extremely negative than when it was more neutral. A decision-theoretic explanation based on loss function asymmetries is advanced which supports the claim that probability estimates are not intrinsically biased by utilities.