Long-term risk prediction after major lower limb amputation: 1-year results of the PERCEIVE study.

BACKGROUND: Decision-making when considering major lower limb amputation is complex and requires individualized outcome estimation. It is unknown how accurate healthcare professionals or relevant outcome prediction tools are at predicting outcomes at 1-year after major lower limb amputation. METHODS: An international, multicentre prospective observational study evaluating healthcare professional accuracy in predicting outcomes 1 year after major lower limb amputation and evaluation of relevant outcome prediction tools identified in a systematic search of the literature was undertaken. Observed outcomes at 1 year were compared with: healthcare professionals' preoperative predictions of death (surgeons and anaesthetists), major lower limb amputation revision (surgeons) and ambulation (surgeons, specialist physiotherapists and vascular nurse practitioners); and probabilities calculated from relevant outcome prediction tools. RESULTS: A total of 537 patients and 2244 healthcare professional predictions of outcomes were included. Surgeons and anaesthetists had acceptable discrimination (C-statistic = 0.715), calibration and overall performance (Brier score = 0.200) when predicting 1-year death, but performed worse when predicting major lower limb amputation revision and ambulation (C-statistics = 0.627 and 0.662 respectively). Healthcare professionals overestimated the death and major lower limb amputation revision risks. Consultants outperformed trainees, especially when predicting ambulation. Allied healthcare professionals marginally outperformed surgeons in predicting ambulation. Two outcome prediction tools (C-statistics = 0.755 and 0.717, Brier scores = 0.158 and 0.178) outperformed healthcare professionals' discrimination, calibration and overall performance in predicting death. Two outcome prediction tools for ambulation (C-statistics = 0.688 and 0.667) marginally outperformed healthcare professionals. CONCLUSION: There is uncertainty in predicting 1-year outcomes following major lower limb amputation. Different professional groups performed comparably in this study. Two outcome prediction tools for death and two for ambulation outperformed healthcare professionals and may support shared decision-making.

Talking cervixes: How times materialise during the first stage of labour.

The clock occupies a prominent position in many feminist and midwifery critiques of the medicalisation of labour and birth. Concern has long focused on the production of standardised 'progress' during labour via the expectation that once in 'established' labour, birthing people's cervixes should dilate at a particular rate, measurable in centimetres and clock time. In this article we draw on 37 audio- or video-recordings of women labouring in two UK midwife-led units in NHS hospital settings to develop a more nuanced critique of the way in which times materialise during labour. Mobilising insights from literature that approaches time as relational we suggest that it is helpful to explore the making of times during labour as multiple, uncertain and open-ended. This moves analysis of time during labour and birth beyond concern with particular forms of time (such as the clock or the body) towards understanding how times are constituted through interactions (for example, between midwives, cervixes, clocks, people in labour and their birth partners), and what they do.

Understanding how to create healthier places: A qualitative study exploring the complex system of urban development decision-making.

Tackling complex system challenges like creating healthy environments requires understanding priorities and structures affecting multiple actors. This qualitative study, involving 132 multi-sectoral stakeholders spanning the urban development decision-making system, explores how to influence healthier place-making. Using thematic analysis we develop themes around competing stakeholder priorities; structural 'rules' and influential relationships; and justifying a focus on health, requiring greater clarity and consensus around definitions of 'healthy' urban development. Building on the socio-ecological model we highlight how a multi-faceted approach is required for change at multiple levels in the complex system to target individual actor motivations, organisational priorities and structural 'rules'.

The Relation Between Discipline Identity and Academic Achievement Within a Marketized Higher Education Context: A Serial Mediation Model of Approaches to Learning and Course Complaints.

Social-psychological dimensions of learning are under-researched, but they affect student achievement. Within a marketized higher education context in England, United Kingdom, this study examined whether the relation between students' social identities as members of their discipline and academic achievement could be further understood by considering the mediating roles of approaches to learning and frequency of making course complaints. Undergraduates (N = 679) completed a questionnaire to assess these constructs. As expected, approaches to learning and course complaining both acted as serial mediators of the link between discipline identification and academic achievement: stronger discipline identification was related to more deep approaches to learning, less complaining, and higher achievement, whereas weaker discipline identification was related to more surface approaches to learning, more complaining, and lower achievement. The findings suggest that addressing these social-psychological aspects of learning could improve students' academic achievement.

Short-term risk prediction after major lower limb amputation: PERCEIVE study.

BACKGROUND: The accuracy with which healthcare professionals (HCPs) and risk prediction tools predict outcomes after major lower limb amputation (MLLA) is uncertain. The aim of this study was to evaluate the accuracy of predicting short-term (30 days after MLLA) mortality, morbidity, and revisional surgery. METHODS: The PERCEIVE (PrEdiction of Risk and Communication of outcomE following major lower limb amputation: a collaboratIVE) study was launched on 1 October 2020. It was an international multicentre study, including adults undergoing MLLA for complications of peripheral arterial disease and/or diabetes. Preoperative predictions of 30-day mortality, morbidity, and MLLA revision by surgeons and anaesthetists were recorded. Probabilities from relevant risk prediction tools were calculated. Evaluation of accuracy included measures of discrimination, calibration, and overall performance. RESULTS: Some 537 patients were included. HCPs had acceptable discrimination in predicting mortality (931 predictions; C-statistic 0.758) and MLLA revision (565 predictions; C-statistic 0.756), but were poor at predicting morbidity (980 predictions; C-statistic 0.616). They overpredicted the risk of all outcomes. All except three risk prediction tools had worse discrimination than HCPs for predicting mortality (C-statistics 0.789, 0.774, and 0.773); two of these significantly overestimated the risk compared with HCPs. SORT version 2 (the only tool incorporating HCP predictions) demonstrated better calibration and overall performance (Brier score 0.082) than HCPs. Tools predicting morbidity and MLLA revision had poor discrimination (C-statistics 0.520 and 0.679). CONCLUSION: Clinicians predicted mortality and MLLA revision well, but predicted morbidity poorly. They overestimated the risk of mortality, morbidity, and MLLA revision. Most short-term risk prediction tools had poorer discrimination or calibration than HCPs. The best method of predicting mortality was a statistical tool that incorporated HCP estimation.

Hughes abdominal closure versus standard mass closure to reduce incisional hernias following surgery for colorectal cancer: the HART RCT.

BACKGROUND: Incisional hernias can cause chronic pain and complications and affect quality of life. Surgical repair requires health-care resources and has a significant associated failure rate. A prospective, multicentre, single-blinded randomised controlled trial was conducted to investigate the clinical effectiveness and cost-effectiveness of the Hughes abdominal closure method compared with standard mass closure following surgery for colorectal cancer. The study randomised, in a 1 : 1 ratio, 802 adult patients (aged ≥ 18 years) undergoing surgical resection for colorectal cancer from 28 surgical departments in UK centres. INTERVENTION: Hughes abdominal closure or standard mass closure. MAIN OUTCOME MEASURES: The primary outcome was the incidence of incisional hernias at 1 year, as assessed by clinical examination. Within-trial cost-effectiveness and cost-utility analyses over 1 year were conducted from an NHS and a social care perspective. A key secondary outcome was quality of life, and other outcomes included the incidence of incisional hernias as detected by computed tomography scanning. RESULTS: The incidence of incisional hernia at 1-year clinical examination was 50 (14.8%) in the Hughes abdominal closure arm compared with 57 (17.1%) in the standard mass closure arm (odds ratio 0.84, 95% confidence interval 0.55 to 1.27; p = 0.4). In year 2, the incidence of incisional hernia was 78 (28.7%) in the Hughes abdominal closure arm compared with 84 (31.8%) in the standard mass closure arm (odds ratio 0.86, 95% confidence interval 0.59 to 1.25; p = 0.43). Computed tomography scanning identified a total of 301 incisional hernias across both arms, compared with 100 identified by clinical examination at the 1-year follow-up. Computed tomography scanning missed 16 incisional hernias that were picked up by clinical examination. Hughes abdominal closure was found to be less cost-effective than standard mass closure. The mean incremental cost for patients undergoing Hughes abdominal closure was £616.45 (95% confidence interval -£699.56 to £1932.47; p = 0.3580). Quality of life did not differ significantly between the study arms at any time point. LIMITATIONS: As this was a pragmatic trial, the control arm allowed surgeon discretion in the approach to standard mass closure, introducing variability in the techniques and equipment used. Intraoperative randomisation may result in a loss of equipoise for some surgeons. Follow-up was limited to 2 years, which may not have been enough time to see a difference in the primary outcome. CONCLUSIONS: Hughes abdominal closure did not significantly reduce the incidence of incisional hernias detected by clinical examination and was less cost-effective at 1 year than standard mass closure in colorectal cancer patients. Computed tomography scanning may be more effective at identifying incisional hernias than clinical examination, but the clinical benefit of this needs further research. FUTURE WORK: An extended follow-up using routinely collected NHS data sets aims to report on incisional hernia rates at 2-5 years post surgery to investigate any potential mortality benefit of the closure methods. Furthermore, the proportion of incisional hernias identified by a computed tomography scan (at 1 and 2 years post surgery), but not during clinical examination (occult hernias), proceeding to surgical repair within 3-5 years after the initial operation will be explored. TRIAL REGISTRATION: This trial is registered as ISRCTN25616490. FUNDING: This project was funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme and will be published in full in Health Technology Assessment; Vol. 26, No. 34. See the NIHR Journals Library website for further project information.

Bowel cancer treatment involves surgery for the majority of patients. A complication of this surgery is the formation of a hernia at the site of the incision in the abdominal wall, known as an incisional hernia. The lining of the abdomen, fat or the intestine can squeeze through the gap and form a lump under the skin. An incisional hernia can form any time after surgery and can cause serious complications and pain, and can also affect the patient's quality of life. Surgery to correct incisional hernias is not always successful, so finding a way of preventing them is important. This research compares the traditional way of sewing up the abdomen, where the two sides are brought together in one layer with a continuous thread, with an alternative method called the Hughes abdominal closure method/Hughes repair. In the Hughes repair, a series of horizontal and vertical stitches are arranged to spread the load and ease the tension across the wound. A total of 802 patients from 28 sites in the UK were recruited to the trial. Half of the patients were randomly allocated to have traditional abdominal closure and half were randomised to have Hughes abdominal closure. All were followed up for 1 year after surgery to assess whether or not an incisional hernia had occurred. We also assessed quality of life during follow-up, and we compared the costs and benefits of each procedure to see which option was the better value for money. By comparing the results from the two methods, it was hoped that the best method of abdominal closure to reduce the risk of an incisional hernia occurring would be found. The analysis of the data suggested that the risk of an incisional hernia was no different with either closure method. Furthermore, Hughes abdominal closure was more expensive and provided less value for money than standard abdominal closure.

Clinical and cost-effectiveness of paramedic administered fascia iliaca compartment block for emergency hip fracture (RAPID 2)-protocol for an individually randomised parallel-group trial.

BACKGROUND: Approximately 75,000 people fracture a hip each year in the UK. This painful injury can be devastating-with a high associated mortality rate-and survivors likely to be more dependent and less mobile. Pain relief at the scene of injury is known to be inadequate. Intravenous morphine is usually given by paramedics, but opioids are less effective for dynamic pain and can cause serious side effects, including nausea, constipation, delirium and respiratory depression. These may delay surgery, require further treatment and worsen patient outcomes. We completed a feasibility study of paramedic-provided fascia iliaca compartment block (FICB), testing the intervention, trial methods and data collection. The study (RAPID) demonstrated that a full trial was feasible. In this subsequent study, we aim to test safety, clinical and cost-effectiveness of paramedic-provided FICB as pain relief to patients with suspected hip fracture in the prehospital environment. METHODS: We will conduct a pragmatic multi-centre individually randomised parallel-group trial, with a 1:1 allocation between usual care (control) and FICB (intervention). Hospital clinicians in five sites (paired ambulance services and receiving hospitals) in England and Wales will train 220 paramedics to administer FICB. The primary outcome is change in pain score from pre-randomisation to arrival at the emergency department. One thousand four hundred patients are required to find a clinically important difference between trial arms in the primary outcome (standardised statistical effect ~ 0.2; 90% power, 5% significance). We will use NHS Digital (England) and the SAIL (Secure Anonymised Information Linkage) databank (Wales) to follow up patient outcomes using routine anonymised linked data in an efficient study design, and questionnaires to capture patient-reported outcomes at 1 and 4 months. Secondary outcomes include mortality, length of hospital stay, job cycle time, prehospital medications including morphine, presence of hip fracture, satisfaction, mobility, and NHS costs. We will assess safety by monitoring serious adverse events (SAEs). DISCUSSION: The trial will help to determine whether paramedic administered FICB is a safe, clinically and cost-effective treatment for suspected hip fracture in the pre-hospital setting. Impact will be shown if and when clinical guidelines either recommend or reject the use of FICB in routine practice in this context. TRIAL REGISTRATION: ISRCTN15831813 . Registered on 22 September 2021.

Automated next-generation profiling of genomic alterations in human cancers.

The lack of validated, distributed comprehensive genomic profiling assays for patients with cancer inhibits access to precision oncology treatment. To address this, we describe elio tissue complete, which has been FDA-cleared for examination of 505 cancer-related genes. Independent analyses of clinically and biologically relevant sequence changes across 170 clinical tumor samples using MSK-IMPACT, FoundationOne, and PCR-based methods reveals a positive percent agreement of >97%. We observe high concordance with whole-exome sequencing for evaluation of tumor mutational burden for 307 solid tumors (Pearson r = 0.95) and comparison of the elio tissue complete microsatellite instability detection approach with an independent PCR assay for 223 samples displays a positive percent agreement of 99%. Finally, evaluation of amplifications and translocations against DNA- and RNA-based approaches exhibits >98% negative percent agreement and positive percent agreement of 86% and 82%, respectively. These methods provide an approach for pan-solid tumor comprehensive genomic profiling with high analytical performance.

PrEdiction of Risk and Communication of outcomE followIng major lower limb amputation: a collaboratiVE study (PERCEIVE)-protocol for the PERCEIVE qualitative study.

INTRODUCTION: Deciding whether to proceed with a major lower limb amputation is life-changing and complex, and it is crucial that the right decision is made at the right time. However, medical specialists are known to poorly predict risk when assessing patients for major surgery, and there is little guidance and research regarding decisions about amputation. The process of shared decision-making between doctors and patients during surgical consultations is also little understood. Therefore, the aim of this study is to analyse in depth the communication, consent, risk prediction and decision-making process in relation to major lower limb amputation. METHODS AND ANALYSIS: Consultations between patients and surgeons at which major lower limb amputation is discussed will be audio-recorded for 10-15 patients. Semi-structured follow-up interviews with patients (and relatives/carers) will then be conducted at two time points: as soon as possible/appropriate after a decision has been reached regarding surgery, and approximately 6 months later. Semi-structured interviews will also be conducted with 10-15 healthcare professionals working in the UK National Health Service (NHS) involved in amputation decision-making. This will include surgeons, anaesthetists and specialist physiotherapists at 2-4 NHS Health Boards/Trusts in Wales and England. Discourse analysis will be used to analyse the recorded consultations; interviews will be analysed thematically. Finally, workshops will be held with patients and healthcare professionals to help synthesise and interpret findings. ETHICS AND DISSEMINATION: The study has been approved by Wales REC 7 (20/WA/0351). Study findings will be published in international peer-reviewed journal(s) and presented at national and international scientific meetings. Findings will also be disseminated to a wide NHS and lay audience via presentations at meetings and written summaries for key stakeholder groups.

Isolation and Identification of Inter-Species Enterovirus Recombinant Genomes.

Positive-strand RNA virus evolution is partly attributed to the process of recombination. Although common between closely genetically related viruses, such as within species of the Enterovirus genus of the Picornaviridae family, inter-species recombination is rarely observed in nature. Recent studies have shown recombination is a ubiquitous process, resulting in a wide range of recombinant genomes and progeny viruses. While not all recombinant genomes yield infectious progeny virus, their existence and continued evolution during replication have critical implications for the evolution of the virus population. In this study, we utilised an in vitro recombination assay to demonstrate inter-species recombination events between viruses from four enterovirus species, A-D. We show that inter-species recombinant genomes are generated in vitro with polymerase template-switching events occurring within the virus polyprotein coding region. However, these genomes did not yield infectious progeny virus. Analysis and attempted recovery of a constructed recombinant cDNA revealed a restriction in positive-strand but not negative-strand RNA synthesis, indicating a significant block in replication. This study demonstrates the propensity for inter-species recombination at the genome level but suggests that significant sequence plasticity would be required in order to overcome blocks in the virus life cycle and allow for the production of infectious viruses.

The PERCEIVE quantitative study: PrEdiction of Risk and Communication of outcome following major lower-limb amputation: protocol for a collaboratiVE study.

BACKGROUND: Accurate prediction of outcomes following surgery with high morbidity and mortality rates is essential for informed shared decision-making between patients and clinicians. It is unknown how accurately healthcare professionals predict outcomes following major lower-limb amputation (MLLA). Several MLLA outcome-prediction tools have been developed. These could be valuable in clinical practice, but most require validation in independent cohorts before routine clinical use can be recommended. The primary aim of this study is to evaluate the accuracy of healthcare professionals' predictions of outcomes in adult patients undergoing MLLA for complications of chronic limb-threatening ischaemia (CLTI) or diabetes. Secondary aims include the validation of existing outcome-prediction tools. METHOD: This study is an international, multicentre prospective observational study including adult patients undergoing a primary MLLA for CLTI or diabetes. Healthcare professionals' accuracy in predicting outcomes at 30-days (death, morbidity and MLLA revision) and 1-year (death, MLLA revision and ambulation) will be evaluated. Sixteen existing outcome-prediction tools specific to MLLA will be examined for validity. Data collection began on 1 October 2020; the end of follow-up will be 1 May 2022. The C-statistic, Hosmer-Lemeshow test, reclassification tables and Brier score will be used to evaluate the predictive performance of healthcare professionals and prediction tools, respectively. STUDY REGISTRATION AND DISSEMINATION: This study will be registered locally at each centre in accordance with local policies before commencing data collection, overseen by local clinician leads. Results will be disseminated to all centres, and any subsequent presentation(s) and/or publication(s) will follow a collaborative co-authorship model.

A Multicenter External Validation of a Score Model to Predict Risk of Events in Patients With Brugada Syndrome.

A multivariate risk score model was proposed by Sieira et al in 2017 for sudden death in Brugada syndrome; their validation in 150 patients was highly encouraging, with a C-index of 0.81; however, this score is yet to be validated by an independent group. A total of 192 records of patients with Brugada syndrome were collected from 2 centers in the United Kingdom and retrospectively scored according to a score model by Sieira et al. Data were compiled summatively over follow-up to mimic regular risk re-evaluation as per current guidelines. Sudden cardiac death survivor data were considered perievent to ascertain the utility of the score before cardiac arrest. Scores were compared with actual outcomes. Sensitivity in our cohort was 22.7%, specificity was 57.6%, and C-index was 0.58. In conclusion, up to 75% of cardiac arrest survivors in this cohort would not have been offered a defibrillator if evaluated before their event. This casts doubt on the utility of the score model for primary prevention of sudden death. Inherent issues with modern risk scoring strategies decrease the likelihood of success even in robustly designed tools such as the Sieira score model.

Imprecise recombinant viruses evolve via a fitness-driven, iterative process of polymerase template-switching events.

Recombination is a common feature of many positive-strand RNA viruses, playing an important role in virus evolution. However, to date, there is limited understanding of the mechanisms behind the process. Utilising in vitro assays, we have previously shown that the template-switching event of recombination is a random and ubiquitous process that often leads to recombinant viruses with imprecise genomes containing sequence duplications. Subsequently, a process termed resolution, that has yet to be mechanistically studied, removes these duplicated sequences resulting in a virus population of wild type length genomes. Using defined imprecise recombinant viruses together with Oxford Nanopore and Illumina high throughput next generation sequencing technologies we have investigated the process of resolution. We show that genome resolution involves subsequent rounds of template-switching recombination with viral fitness resulting in the survival of a small subset of recombinant genomes. This alters our previously held understanding that recombination and resolution are independent steps of the process, and instead demonstrates that viruses undergo frequent and continuous recombination events over a prolonged period until the fittest viruses, predominantly those with wild type length genomes, dominate the population.

Examining the municipal-level representativeness of the Canadian Longitudinal Study on Aging (CLSA) cohort: an analysis using Calgary participant baseline data. / Examen de la représentativité à l'échelle municipale de la cohorte de l'Étude longitudinale canadienne sur le vieillissement (ELCV) : une analyse des données de référence des participants de Calgary.

INTRODUCTION: The Canadian Longitudinal Study on Aging (CLSA) is a rich, nationally representative population-based resource that can be used for multiple purposes. Although municipalities may wish to use CLSA data to address local policy needs, how well localized CLSA cohorts reflect municipal populations is unknown. Because Calgary, Alberta, is home to one of 11 CLSA data collection sites, our objective was to explore how well the Calgary CLSA sample represented the general Calgary population on select sociodemographic variables. METHODS: Baseline characteristics (i.e. sex, marital status, ethnicity, education, retirement status, income, immigration, internal migration) of CLSA participants who visited the Calgary data collection site between 2011 and 2015 were compared to analogous profiles derived from the 2011 National Household Survey (NHS) and 2016 Census datasets, which spanned the years when data were collected on the CLSA participants. RESULTS: Calgary CLSA participants were representative of the Calgary population for age, sex and Indigenous identity. Discrepancies of over 5% with the NHS and/or 2016 Census were found for marital status, measures of ethnic diversity (i.e. immigrant status, place of birth, non-official language spoken at home), internal migration, income, retirement status and education. CONCLUSION: Voluntary studies face challenges in recruiting fully representative cohorts. Communities opting to use CLSA data at a municipal level, including the 10 other CLSA data collection sites, should exercise caution when interpreting the results of these analyses, as CLSA participants may not be fully representative of the local population on select characteristics of interest.

Development of a Chewing Robot With Built-in Humanoid Jaws to Simulate Mastication to Quantify Robotic Agents Release From Chewing Gums Compared to Human Participants.

Medicated chewing gum has been recognised as a new advanced drug delivery method, with a promising future. Its potential has not yet been fully exploited because currently there is no gold standard for testing the release of agents from chewing gum in vitro. This study presents a novel humanoid chewing robot capable of closely replicating the human chewing motion in a closed environment, incorporating artificial saliva and allowing measurement of xylitol release from the gum. The release of xylitol from commercially available chewing gum was quantified following both in vitro and in vivo mastication. The chewing robot demonstrated a similar release rate of xylitol as human participants. The greatest release of xylitol occurred during the first 5 minutes of chewing and after 20 minutes of chewing only a low amount of xylitol remained in the gum bolus, irrespective of the chewing method used. Saliva and artificial saliva solutions respectively were collected after 5, 10, 15 and 20 minutes of continuous chewing and the amount of xylitol released from the chewing gum determined. Bioengineering has been implemented as the key engineering strategy to create an artificial oral environment that closely mimics that found in vivo. These results demonstrate the chewing robot with built-in humanoid jaws could provide opportunities for pharmaceutical companies to investigate and refine drug release from gum, with reduced patient exposure and reduced costs using this novel methodology.

Managing contacts of chlamydia: should clinics implement a test and wait process?

British guidelines recommend epidemiological treatment for all chlamydia contacts during the look back period. Some UK sexual health clinics follow a test and wait process for chlamydia contacts presenting after 14 days of exposure. The aim of this retrospective service evaluation was to determine the potential impact of implementing such a process for chlamydia contacts at our clinic. We reviewed the patient records of 548 chlamydia contacts over a 1-year period, and 588 patients with chlamydia over a 5-month period. Demographic and clinical characteristics data were collected.Chlamydia prevalence was 46% (254/548) in contacts, with prevalence varying by age (p=.008) and sexual risk (p=.04), but not by time since exposure (p=.29). For patients with chlamydia, there was a mean of 1.9 days between results notification and attending for treatment; a mean of 2.2 attempts were required to contact patients to return for treatment. Chlamydia prevalence in contacts is high. Not giving empirical treatment to contacts presenting after 14 days of exposure would result in 13.1% of the cohort needing to return for treatment. Patients found to have chlamydia returned promptly once informed of positive results.

An evaluation of the implementation of Safewards on an assessment and treatment unit for people with an intellectual disability.

This study evaluates the implementation of Safewards on an assessment and treatment unit (ATU) for people with an intellectual disability. There are no previous studies evaluating this model in this context and previous research has focused largely on acute mental health services. The 'Patient-Staff Conflict Shift Report' was used at baseline for 1 month and 1 year later, after all the interventions had been implemented, to evaluate the impact of Safewards. Significant reductions were found in conflict and containment measures used within the service after the implementation of Safewards. Staff who led on the interventions were also asked to give feedback on their experiences, the challenges they faced and how they would like to move forward. Safewards was generally seen as a positive approach by the team. Limitations of this study are highlighted and suggestions for future research are made.

Linkage mapping evidence for a syntenic QTL associated with flowering time in perennial C4 rhizomatous grasses Miscanthus and switchgrass.

Flowering in perennial species is directed via complex signalling pathways that adjust to developmental regulations and environmental cues. Synchronized flowering in certain environments is a prerequisite to commercial seed production, and so the elucidation of the genetic architecture of flowering time in Miscanthus and switchgrass could aid breeding in these underdeveloped species. In this context, we assessed a mapping population in Miscanthus and two ecologically diverse switchgrass mapping populations over 3 years from planting. Multiple flowering time quantitative trait loci (QTL) were identified in both species. Remarkably, the most significant Miscanthus and switchgrass QTL proved to be syntenic, located on linkage groups 4 and 2, with logarithm of odds scores of 17.05 and 21.8 respectively. These QTL regions contained three flowering time transcription factors: Squamosa Promoter-binding protein-Like, MADS-box SEPELLATA2 and gibberellin-responsive bHLH137. The former is emerging as a key component of the age-related flowering time pathway.

Inherited Rare, Deleterious Variants in ATM Increase Lung Adenocarcinoma Risk.

INTRODUCTION: Lung cancer is the leading cause of cancer deaths in the world, and lung adenocarcinoma (LUAD) is its most prevalent subtype. Symptoms are often found in advanced disease in which treatment options are limited. Identifying genetic risk factors will enable better identification of high-risk individuals. METHODS: To identify LUAD risk genes, we performed a case-control association study for gene-level burden of rare, deleterious variants (RDVs) in germline whole-exome sequencing data of 1083 patients with LUAD and 7650 controls, split into discovery and validation cohorts. Of these, we performed whole-exome sequencing on 97 patients and acquired the rest from multiple public databases. We annotated all rare variants for pathogenicity conservatively, using the guidelines of the American College of Medical Genetics and Genomics and ClinVar curation, and investigated gene-level RDV burden using penalized logistic regression. All statistical tests were two-sided. RESULTS: We discovered and replicated the finding that the burden of germline ATM RDVs was significantly higher in patients with LUAD versus controls (combined cohort OR = 4.6; p = 1.7e-04; 95% confidence interval = 2.2-9.5; 1.21% of cases; 0.24% of controls). Germline ATM RDVs were also enriched in an independent clinical cohort of 1594 patients from the MSK-IMPACT study (0.63%). In addition, we observed that an Ashkenazi Jewish (AJ) founder ATM variant, rs56009889, was statistically significantly more frequent in AJ cases versus AJ controls in our cohort (combined AJ cohort OR = 2.7, p = 6.9e-03, 95% confidence interval = 1.3-5.3). CONCLUSIONS: Our results indicate that ATM is a moderate-penetrance LUAD risk gene and that LUAD may be a part of the ATM-related cancer syndrome spectrum. Individuals with ATM RDVs are at an elevated LUAD risk and can benefit from increased surveillance (particularly computed tomography scanning), early detection, and chemoprevention programs, improving prognosis.