Systematic single-variant and gene-based association testing of thousands of phenotypes in 394,841 UK Biobank exomes

Genome-wide association studies have successfully discovered thousands of common variants associated with human diseases and traits, but the landscape of rare variations in human disease has not been explored at scale. Exome-sequencing studies of population biobanks provide an opportunity to systematically evaluate the impact of rare coding variations across a wide range of phenotypes to discover genes and allelic series relevant to human health and disease. Here, we present results from systematic association analyses of 4,529 phenotypes using single-variant and gene tests of 394,841 individuals in the UK Biobank with exome-sequence data. We find that the discovery of genetic associations is tightly linked to frequency and is correlated with metrics of deleteriousness and natural selection. We highlight biological findings elucidated by these data and release the dataset as a public resource alongside the Genebass browser for rapidly exploring rare-variant association results.

Risk factors for TB in Australia and their association with delayed treatment completion

BACKGROUND: Australia has a low incidence of TB and has committed to eliminating the disease. Identification of risk factors associated with TB is critical to achieving this goal.METHODS: We undertook a prospective cohort study involving persons receiving TB treatment in four Australian jurisdictions. Risk factors and their association with delayed treatment completion (treatment delayed by at least 1 month) were analysed using univariate analyses and multivariate logistic regression.RESULTS: Baseline surveys were completed for 402 persons with TB. Most (86.1%) were born overseas. Exposure to a person with TB was reported by 19.4%. Diabetes mellitus (10.2%), homelessness (9.2%), cigarette smoking (8.7%), excess alcohol consumption (6.0%) and mental illness (6.2%) were other common risk factors. At follow-up, 24.8% of patients had delayed treatment completion, which was associated with adverse events (34.1%, aOR 6.67, 95% CI 3.36-13.27), excess alcohol consumption (6.0%, aOR 21.94, 95% CI 6.03-79.85) and HIV co-infection (2.7%, aOR 8.10, 95% CI 1.16-56.60).CONCLUSIONS: We identified risk factors for TB and their association with delayed treatment completion, not all of which are routinely collected for surveillance purposes. Recognition of these risk factors should facilitate patient-centred care and assist Australia in reaching TB elimination.

Understanding the implementation and medium-longer term sustainability of the primary care prescribing safety intervention, PINCER: preliminary results from a longitudinal process evaluation

Introduction

Medication errors are an important cause of morbidity and mortality across primary care in England. In the National Health Service, approximately 71% of 237 million medication errors made annually are attributable to primary care(1). The complex pharmacist-led IT-based intervention to reduce clinically important medication errors (PINCER) intervention has been shown to significantly reduce medication errors when tested in a cluster randomised controlled trial and when implemented on a larger scale across one geographical region of England. However, with a national rollout of PINCER now underway across England, there remains a limited understanding of whether and how wider implementation, impact and medium-longer term sustainability across diverse regions is achieved, and what factors may influence these processes.

Aim

This study aimed to explore the contextual factors that influenced the nature and extent of translation, implementation and sustained use of PINCER in diverse settings over time.

Methods

Intervention developers and personnel involved in the PINCER rollout and staff members from Academic Health Science Networks (AHSNs), Clinical Commissioning Groups (CCGs) and general practices from four regions of England, UK, were purposively recruited via research team connections and Clinical Research Networks. Interviews aimed to capture short-term (≤6 months), medium-term (6 – 18 months) and long-term (≥ 18 months) use of PINCER. Interview guides were informed by Normalisation Process Theory (NPT). Semi-structured, face-to-face or telephone interviews were conducted and digitally recorded. A preliminary thematic analysis was performed on the data collected.

Results

Forty-eight participants from 30 establishments, including two intervention developers, three involved in the PINCER rollout and five AHSN, seven CCG and thirty-one general practice employees were interviewed between June 2018 – June 2020. Their engagement with PINCER had either been in the medium (n=13) or long-term (n=17), (range 8 months - 5 years plus). Emerging themes identified in the preliminary analysis were: development and spread which incorporated intervention and training improvements as well as uptake, perceptions of PINCER which included awareness of PINCER as well as opinions on it and factors influencing the use of PINCER and sustainability which were mainly contextual but also related to PINCER functionalities. Within the development and spread theme, and relating to perceptions of PINCER theme, clear communication and ensuring there was an understanding of what PINCER entailed was considered important in initiating interest and uptake. Overall, PINCER was perceived positively. Key challenges to the implementation of PINCER identified were initial IT issues and workload. Policies advocating the use of PINCER, evidencing impact in reductions in the number of patients identified as being ‘at risk’ of hazardous prescribing and being able to benchmark results against other CCGs and practices helped facilitate the implementation and sustainability. Some changes made to prescribing and monitoring processes as a result of the implementation and use of PINCER, appeared to have become embedded into routine practice giving an indication of sustainable use.

Conclusion

Further interviews will establish if and how PINCER has been more widely adopted and normalised within primary care, in order to generate important learning to support its optimal and sustainable impact.

References

1. Elliott R, Camacho E, Campbell F, Jankovic D, St James MM, Kaltenthaler E, et al. Prevalence and economic burden of medication errors in the NHS in England. Rapid evidence synthesis and economic analysis of the prevalence and burden of medication error in the UK. 2018.

Abstract 4461: Analysis of circulating tumor DNA (ctDNA) identifies on-treatment genomic alterations in a phase 2 study of veliparib plus FOLFIRI ± bevacizumab vs. placebo plus FOLFIRI ± bevacizumab in metastatic colorectal cancer (mCRC)

Changes in plasma ctDNA are used as a surrogate molecular marker of response to determine clinical efficacy and provide insights into potential resistance mechanisms to targeted therapeutics. Detection of genomic alterations in circulating tumor DNA (ctDNA) in colorectal cancer has been widely employed as an approach to measure real-time changes in the tumor genome. In order to understand mechanisms of resistance to the PARP inhibitor, Veliparib (ABT-888), pathogenic alterations in oncogenes and DNA Damage Response (DDR) genes were profiled longitudinally in plasma ctDNA and associated to clinical response to Veliparib concurrent to FOLFIRI +/- Bevacizumab.

Methods: 215 serial plasma samples collected at Baseline, Cycle 2 (28 days post-treatment) and at disease progression (Final Visit) from 78 patients (pts) with mCRC in the NCT02305758 clinical trial were selected for the current study, consisting of ~50% partial responders (PR), ~30% stable disease (SD) pts and 5% Non-responders (PD). Detection of ctDNA mutations was accomplished using a targeted, error-correctible NGS assay encompassing 63 cancer driver genes, tumor suppressors & DDR genes. Paired pre- and on-treatment plasma samples were evaluable from 81% pts selected.

Results: Veliparib (VPRB) pts with longest PFS experienced the largest fold change reductions in total cfDNA concentration by end of treatment (EOT). Interestingly, in both treatment arms, the ctDNA mutant fraction per pt decreased by EOT (median = -41%). In support of this correlation, the ctDNA mutational burden also decreased by 28% in VPRB pts and 39% in PLAC pts, largely driven by PR pts with longer PFS. Overall, tumor-specific mutations detected in ctDNA had 88% concordance with tissue, particularly in common mCRC driver mutations. Baseline KRAS mutations were detected in 46% pts (mostly PR & PD) and are eliminated or diminished in 28% pts (14% VPRB, 14% Placebo) by EOT. 30 DDR & MMR genes were found to be frequently altered in all pts, notably APC & MSH3, at both baseline and EOT. However, by EOT, RAD1, XRCC3, BRCA1 and CHEK1 mutations were acquired or increased, while TP53BP1, POLD1 and ERCC5 mutations were eliminated or reduced, prominently in VPRB PR pts.

Conclusions: Broadly, a reduction in ctDNA fraction and pathogenic mutation burden, notably in KRAS, is evidenced in both treatment arms and appears to trend with longer PFS at least in Veliparib-treated pts. Despite these prognostic ctDNA changes, VPRB-specific DDR mutation changes may provide insight into VPRB mechanism of action and resistance in mCRC and is under further exploration at earlier post-treatment timepoints and in SD pts. These data could add insights into alterations acquired earlier in the treatment regimen and the relationship of these alterations with resistance to PARPi in mCRC.

Citation Format: Cyril Y. Ramathal, Erin Murphy, Elizabeth Asque, Arne Jason Grundstad, Peter Ansell, Lei He, Yan Luo, Jordan Berlin, Jeff Waring. Analysis of circulating tumor DNA (ctDNA) identifies on-treatment genomic alterations in a phase 2 study of veliparib plus FOLFIRI ± bevacizumab vs. placebo plus FOLFIRI ± bevacizumab in metastatic colorectal cancer (mCRC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4461.

Multidrug-resistant tuberculosis in Australia, 1998-2012

OBJECTIVE

To describe the epidemiology and outcomes of multidrug-resistant tuberculosis (MDR-TB) diagnosed in Australia between 1998 and 2012.

DESIGN

A retrospective review was undertaken involving all patients with laboratory-confirmed MDR-TB notified in Australia between 1998 and 2012 inclusive. Demographic, clinical and laboratory features are described. Clinical outcomes were defined according to World Health Organization definitions of treatment success (cure and treatment completion), treatment failure, death, loss to follow-up (including transfer out), or not evaluated at treatment completion.

RESULTS

A total of 244 cases of MDR-TB were diagnosed in Australia during the study period, representing 1.4% of all TB cases notified. The majority were born outside Australia, including one third in Papua New Guinea. Of those with treatment outcome data available, treatment success was demonstrated in 81%. Treatment success was positively associated with use of a second-line injectable agent. Those born in Papua New Guinea were less likely to achieve treatment success.

CONCLUSION

MDR-TB is uncommon in Australia. The large number of cases born in Papua New Guinea, and the poorer outcomes in this cohort, represent challenges with cross-border management of MDR-TB in the Torres Strait. Australia has an ongoing role in the prevention and management of MDR-TB locally and in the region.

Impact of 5-HTTLPR on hippocampal subregional activation in older adults

Studies have shown that a functional polymorphism of the serotonin transporter gene (5-HTTLPR) impacts performance on memory-related tasks and the hippocampal structures that subserve these tasks. The short (s) allele of 5-HTTLPR has been linked to greater susceptibility for impaired memory and smaller hippocampal volume compared to the long allele (l). However, previous studies have not examined the associations between 5-HTTLPR allele and activation in subregions of the hippocampus. In this study, we used functional magnetic resonance imaging (fMRI) to measure activation in hippocampal and temporal lobe subregions in 36 elderly non-clinical participants performing a face-name encoding and recognition task. Although there were no significant differences in task performance between s allele carriers and l homozygotes, right CA1 and right parahippocampal activation during recognition errors was significantly greater in individuals bearing the s allele. In an exploratory analysis, we determined that these effects were more pronounced in s allele carriers with the apolipoprotein ɛ4 allele. Our results suggest that older individuals with the s allele inefficiently allocate neural resources while making errors in recognizing face-name associations, which could negatively impact memory performance during more challenging tasks.

The structure of the small animal consultation

OBJECTIVES

To analyse the structure of small animal consultations in order to increase understanding of the consultation processes, locate decision-making in the wider practice context and stimulate further research.

METHODS

Analysis of 48 video-recorded consultations from first opinion small animal practices. These consultations were time and thematically coded in order to enable analysis.

RESULTS

The mean length of the recorded consultations was 11 minutes and 45 seconds with a range of 4-28 minutes. Analysis indicates that both the clinical tasks and communication taking place in the consultation are often performed in an iterative and interactive fashion in contrast to the sequential methods frequently being taught.

CLINICAL SIGNIFICANCE

This study shows that the consultation is a complex process that is often performed in an iterative and interactive fashion and that may be difficult to complete within the 10 minutes frequently allocated. This warrants further research.

Uptake and cell-killing activities of a series of Victoria blue derivatives in a mouse mammary tumour cell line

The triarylmethane dye Victoria blue BO (VBBO) is a known photosensitizer which has been shown to induce a cytotoxic response in vitro. Several novel Victoria blue derivatives, with varying physicochemical properties, have been compared to VBBO, with respect both to dark toxicity and phototoxicity, on a mouse mammary tumour cell line, EMT6. Photosensitizer uptake was observed using confocal fluorescence microscopy. The chemical differences, particularly in the naphthyl substitution of the derivatives were shown to alter the light:dark toxicity differential and the uptake of the photosensitizers.

Safety and complexity

PURPOSE

Current thinking about "patient safety" emphasises the causal relationship between the work environment and the delivery of clinical care. This research draws on the theory of normal accidents to extend this analysis and better understand the "organisational factors" that threaten safety.

DESIGN/METHODOLOGY/APPROACH

Ethnographic research methods were used, with observations of the operating department setting for 18 month and interviews with 80 members of hospital staff. The setting for the study was the Operating Department of a large teaching hospital in the North-West of England.

FINDINGS

The work of the operating department is determined by inter-dependant, "tightly coupled" organisational relationships between hospital departments based upon the timely exchange of information, services and resources required for the delivery of care. Failures within these processes, manifest as "breakdowns" within inter-departmental relationships lead to situations of constraint, rapid change and uncertainty in the work of the operating department that require staff to break with established routines and work with increased time and emotional pressures. This means that staff focus on working quickly, as opposed to working safely. ORIGINALITY VALUE: Analysis of safety needs to move beyond a focus on the immediate work environment and individual practice, to consider the more complex and deeply structured organisational systems of hospital activity. For departmental managers the scope for service planning to control for safety may be limited as the structured "real world" situation of service delivery is shaped by inter-department and organisational factors that are perhaps beyond the scope of departmental management.

Rules and guidelines in clinical practice: a qualitative study in operating theatres of doctors' and nurses' views

BACKGROUND

The current orthodoxy within patient safety research and policy is characterised by a faith in rules based systems which limit the capacity for individual discretion, and hence fallibility. However, guidelines have been seen as stifling innovation and eroding trust. Our objectives were to explore the attitudes towards guidelines of doctors and nurses working together in surgical teams and to examine the extent to which trusting relationships are maintained in a context governed by explicit rules.

METHODS

Fourteen consultant grade surgeons of mixed specialty, 12 consultant anaesthetists, and 15 nurses were selected to reflect a range of roles. Participant observation was combined with semi-structured interviews.

RESULTS

Doctors' views about the contribution of guidelines to safety and to clinical practice differed from those of nurses. Doctors rejected written rules, instead adhering to the unwritten rules of what constitutes acceptable behaviour for members of the medical profession. In contrast, nurses viewed guideline adherence as synonymous with professionalism and criticised doctors for failing to comply with guidelines.

CONCLUSIONS

While the creation of a "safety culture" requires a shared set of beliefs, attitudes and norms in relation to what is seen as safe clinical practice, differences of opinion on these issues exist which cannot be easily reconciled since they reflect deeply ingrained beliefs about what constitutes professional conduct. While advocates of standardisation (such as nurses) view doctors as rule breakers, doctors may not necessarily regard guidelines as legitimate or identify with the rules written for them by members of other social groups. Future safety research and policy should attempt to understand the unwritten rules which govern clinical behaviour and examine the ways in which such rules are produced, maintained, and accepted as legitimate.

Cold legs: a potential indicator of negative outcome in the rehabilitation of patients with patellofemoral pain syndrome

PURPOSE

The purpose of this paper is to explore the link between a poor outcome in response to an exercise based approach to physiotherapy, in patients with patellofemoral dysfunction and a self-report of legs feeling cold even in warm surroundings.

SCOPE

The study was carried out in the physiotherapy outpatients department of Burnley General Hospital, Lancashire, UK with 87 consecutively referred patients with a diagnosis of patellofemoral pain syndrome being assessed for suitability for entry into the study. Of these 77 entered the study with 14 (18%), of these responding 'Yes' to the question 'Do your legs feel cold even in warm surroundings?' All patients were assessed using four outcome measures prior to the commencement of a standardised rehabilitation programme consisting of lower limb biarticular muscle stretching, vastus medialis training and patella taping or biofeedback. The patients were reassessed using the same outcome measures 3 months after completing their course of treatment.

CONCLUSIONS

Patients who responded 'Yes' to the question 'Do your legs feel cold even in warm surroundings?' reported higher pain levels and tolerated less physical activity than non-cold sufferers at initial assessment, these differences were statistically significant. The cold sufferers showed less improvement on all of the outcome measures although the differences between the two groups only reached statistical significance for one of the outcome measures. The implications of this in relation to clinical practice are discussed.

Tuberculosis notifications in Australia, 1999

Australia has one of the lowest incidence of tuberculosis in the world. The crude annual notification rate for tuberculosis (TB) has remained stable at between 5 and 6 per 100,000 population since 1991. In 1999, there were a total of 1,159 TB notifications in Australia of which 1,117 were new TB cases, and 42 were relapsed cases. The corresponding annual notification rate for new and relapsed TB was 5.9 and 0.2 per 100,000 population respectively. People born overseas accounted for 83 per cent of the notified cases. TB notification rates remain highest among overseas-born residents from high prevalence countries, and indigenous Australians. The lowest rates of disease are in the non-indigenous, Australian born population and data from the last 7 years indicate that the rate of tuberculosis in this population is continuing to fall.

Cytotoxicity and adjuvant activity of cationic photosensitizers in a multidrug resistant cell line

The toxicities and phototoxicities of methylene blue (MB), toluidine blue O (TBO) and Victoria blue BO (VBBO) in a murine mammary tumour cell line (EMT6-S) and a multidrug resistant (MDR) sub-line (EMT6-R) were measured and their efficacy against the resistant sub-line was compared to that of doxorubicin and cis-platinum. The MDR cell line was considerably more susceptible to VBBO than to the conventional agent doxorubicin. VBBO was also phototoxic whereas illumination did not alter the activity of doxorubicin or of cisplatin. Both TBO and MB showed limited light activation (2-fold) in both the sensitive and resistant cell lines. Pre-treatment with VBBO prior to exposure to doxorubicin caused a two-fold increase in doxorubicin toxicity in both cell lines. MB and TBO, however, increased doxorubicin toxicity in EMT6-R cells x2 and x3 respectively, but had less effect on the sensitive cell line (increase x1.4 and x2 respectively). Thus MB and TBO may act on the MDR cell line via a different mechanism to that of VBBO.

Increased cytotoxicity and phototoxicity in the methylene blue series via chromophore methylation

The cytotoxic and photodynamic activities of the commercially-available biological stains methylene blue (MB), 1,9-dimethyl MB (Taylor's Blue) and a newly synthesised compound, 1-methyl MB, were measured against the murine mammary tumour cell line, EMT-6. Both 1-methyl MB and 1,9-dimethyl MB exhibited increased dark toxicity with concomitant higher phototoxicity compared to MB at a light dose of 7.2 J cm-2. While increasing the light dose as a function of the fluence rate increased the photocytotoxicity of MB, this had little effect on the methylated derivatives. In vitro chemical testing proved that successive methylation rendered the phenothiazinium chromophore both more resistant to reduction to its inactive leuco form, and also led to increased levels of singlet-oxygen production, thus providing a possible explanation for the increased toxicities of the methylated derivatives. Comparisons are made with the benzo[a]phenothiazinium photosensitizer, EtNBS.

Effects of extracellular magnesium and beta adrenergic stimulation on contractile force and magnesium mobilization in the isolated rat heart

This study investigates the metabolism of the divalent cation, magnesium (Mg2+) in the isolated perfused Langendorff's rat heart and ventricular slices in the absence and presence of catecholamines including isoprenaline, noradrenaline and adrenaline. Perfusion of the isolated rat heart with a physiological salt solution containing elevated extracellular Mg2+ [Mg2+]o (2.4 mM-6.0 mM) resulted in a marked and progressive decrease in the amplitude of contraction compared to control [Mg2+]o (1.2 mM). In contrast, perfusion of hearts with low (0-0.6 mM) [Mg2+]o caused a small transient increase in the amplitude of contraction which was often accompanied by arrhythmic activity. Perfusion of the heart with a nominally Mg2+ free medium resulted in a time-dependent net efflux of Mg2+ reaching a steady state after approximately 40-50 min of perfusion. This release of Mg2+ was associated with a concurrent decrease in total heart Mg2+. Stimulation of the heart with the beta adrenergic agonist, isoprenaline (10(-7) M) caused large increases in net Mg2+ efflux which was associated with marked increased in both rate and the amplitude of contraction. Similar effects on Mg2+ efflux were also observed during perfusion of the heart with the adenylate cyclase activator, forskolin (10(-5) M). Superfusion of paced ventricular segments with either isoprenaline, adrenaline or noradrenaline (all 10(-6) M) also resulted in a marked transient net efflux of Mg2+. Pre-treatment of segments with the beta adrenergic antagonist, propranolol (10(-5) M) competitively blocked the Mg2+ efflux evoked by the catecholamines. Similarly, pre-treatment of segments with the calcium (Ca2+) channel blocker, verapamil (10(-5) M) caused a significant (P < 0.05) decrease in net Mg2+ efflux evoked by isoprenaline. The results of this study indicate that (1) the perturbation of [Mg2+]o has an important influence on myocardial contractility and (2) the mobilization of Mg2+ in the heart is associated with beta adrenergic stimulation possibly via an elevation in intracellular adenosine 3.5 cyclic monophosphate (cyclic AMP).

A comparison of two methods of assessing cancer therapy-related symptoms

Patients undergoing outpatient cancer treatment experience a multitude of therapy-related symptoms. Complete assessment of these symptoms is essential for proper interventions to be provided and to enhance the quality of life of the patient. The primary purposes of the study were to compare the number of symptoms identified by a self-report instrument with those documented in the patient's medical record, and to examine the relationship between the number of self-reported symptoms and quality of life. Ninety-one oncology patients from three outpatient clinics participated in the study. The Oncology Treatment Toxicity Assessment Tool (OTTAT) and the Quality of Life Index (QLI) are self-report instruments, each with 37 items and 18 items, respectively. The mean number of symptoms reported on the OTTAT (mean = 11; range 0-37; SD 8) was significantly higher than that documented in the medical record (mean = 1.5 range 0-9; SD 1.6), (t = 8.7, p = 0.001). Higher scores on the OTTAT were significantly related to lower scores on the QLI (r = -0.67, p = 0.0001).

The RAD50 gene, a member of the double strand break repair epistasis group, is not required for spontaneous mitotic recombination in yeast

Mutations in the RAD50 gene of Saccharomyces cerevisiae have been shown to reduce double strand break repair, meiotic recombination, and radiation-inducible mitotic recombination. Several different point mutations (including ochre and amber alleles) have been previously examined for effects on spontaneous mitotic recombination and did not reduce the frequency of recombination. Instead, the rad50 mutations conferred a moderate hyper-rec phenotype. This paper examines a deletion/interruption allele of RAD50 that removes 998 of 1312 amino acids and adds 1.1 kb of foreign DNA. The results clearly indicate that spontaneous mitotic recombination can occur in the absence of RAD50; in fact, the frequency of recombination is elevated over the wild-type cell. One possible interpretation of these observations is that the initiating lesion in spontaneous recombination events in mitosis might not be a double strand break.

The role of magnetic resonance imaging in the investigation of undescended testes

The location of undescended impalpable testes is important because of the greatly increased risk of malignancy. Various imaging methods have been used in the past with only partial success. In many cases an exploratory laparotomy has been performed although even this has not proved completely successful. We describe the use of magnetic resonance imaging (MRI) in six adults with eight undescended testes. We were able to detect the position of six of the eight testes by this method. MRI does not use ionising radiation and is a useful method of locating these radiosensitive organs.

The detection of metastatic disease of the spine in oncology patients using MRI

The value of MRI in the diagnosis and management of patients with primary bone tumours has already been established.

The use of MRI in the detection of metastatic spinal disease is discussed in this paper.