Implementation of an ISO15189 accredited next-generation sequencing service with the fully automated Ion Torrent Genexus: the experience of a clinical diagnostic laboratory

AIMS

Next-generation sequencing (NGS) is integral to the delivery of personalised medicine for targeted cancer therapy. Average turnaround times (TAT) from reference laboratories with advanced expertise in sequencing are typically 2-3 weeks. Prolonged TAT for biomarker analysis can adversely affect patient outcomes. The project aim was to establish an accredited NGS service integrated within a routine clinical diagnostic laboratory, in a designated tertiary cancer centre with no previous experience in NGS or bioinformatics.

METHODS

Platform selected was the novel Ion Torrent Genexus Sequencer with automated onboard library preparation, templating, sequencing and data analysis, with subsequent reporting using Oncomine Reporter software.Entire workflow validation was performed with a targeted panel, the Oncomine Precision Assay, on formalin-fixed paraffin embedded clinical tumour samples. Oncomine Reporter software was used to report on variants including mutations, copy number variations and fusions across 50 key genes.Samples included surgical resections, biopsies, cytology and commercial reference material. Assessment of criteria included analytical sensitivity, specificity, limit of detection, accuracy, repeatability and reproducibility, with the establishment of performance metrics and quality parameters.

RESULTS

High sensitivity, specificity and reproducibility were achieved. DNA/RNA input requirements optimised to >10 ng, and sequencing performance established with a limit of detection of 5% when depth of coverage of 2500X was reached. This NGS service attained ISO15189 accreditation with no non-conformances and >56% reduction in TAT.

CONCLUSION

Successful implementation, clinical validation and accreditation of a novel NGS technology was achieved in this institution, with a significantly improved TAT of results to oncologists.

Severe Aortic Valvular Incompetence From IgG4-Related Disease: An Unusual Entity

IgG4-related disease (IgG4-RD) is a new clinical entity characterized by lymphoplasmacytic lesions rich in IgG4-positive plasma cells. Myocardial involvement is extremely rare and not a typical cardiovascular manifestation of IgG4-RD. We report a rare case of IgG4-RD-associated myocardial mass causing severe aortic incompetence, successfully treated with surgery and corticosteroids. (Level of Difficulty: Intermediate.).

Real-world outcomes and toxicity of adjuvant chemotherapy in NSCLC: a single-center experience

Aim: Adjuvant chemotherapy in NSCLC is associated with modest benefits and significant toxicity. We sought to evaluate the toxicity of adjuvant chemotherapy and disease-specific outcomes in a real-world population. Methods: We performed a retrospective analysis of patients undergoing adjuvant chemotherapy for NSCLC in an Irish center over a 7-year period. We described treatment-associated toxicity, recurrence-free survival and overall survival. Results: 62 patients underwent adjuvant chemotherapy. Treatment-associated hospitalisation occurred in 29% of patients. Relapse was recorded in 56% of patients and median recurrence-free survival was 27 months. Conclusion: High rates of disease recurrence and treatment-associated morbidity were observed in patients receiving adjuvant chemotherapy for NSCLC. Novel therapeutic strategies are required to improve outcomes in this population.

Plasma and rectal mucosal oxylipin levels during aspirin and eicosapentaenoic acid treatment in the seAFOod polyp prevention trial

BACKGROUND

Aspirin and eicosapentaenoic acid (EPA) have colorectal polyp prevention activity, alone and in combination. This study measured levels of plasma and rectal mucosal oxylipins in participants of the seAFOod 2 × 2 factorial, randomised, placebo-controlled trial, who received aspirin 300 mg daily and EPA 2000 mg free fatty acid, alone and in combination, for 12 months.

METHODS

Resolvin (Rv) E1, 15-epi-lipoxin (LX) A₄ and respective precursors 18-HEPE and 15-HETE (with chiral separation) were measured by ultra-high performance liquid chromatography-tandem mass spectrometry in plasma taken at baseline, 6 months and 12 months, as well as rectal mucosa obtained at trial exit colonoscopy at 12 months, in 401 trial participants.

RESULTS

Despite detection of S- and R- enantiomers of 18-HEPE and 15-HETE in ng/ml concentrations, RvE1 or 15‑epi-LXA₄ were not detected above a limit of detection of 20 pg/ml in plasma or rectal mucosa, even in individuals randomised to both aspirin and EPA. We have confirmed in a large clinical trial cohort that prolonged (12 months) treatment with EPA is associated with increased plasma 18-HEPE concentrations (median [inter-quartile range] total 18-HEPE 0.51 [0.21-1.95] ng/ml at baseline versus 0.95 [0.46-4.06] ng/ml at 6 months [P<0.0001] in those randomised to EPA alone), which correlate strongly with respective rectal mucosal 18-HEPE levels (r = 0.82; P<0.001), but which do not predict polyp prevention efficacy by EPA or aspirin.

CONCLUSION

Analysis of seAFOod trial plasma and rectal mucosal samples has not provided evidence of synthesis of the EPA-derived specialised pro-resolving mediator RvE1 or aspirin-trigged lipoxin 15‑epi-LXA₄. We cannot rule out degradation of individual oxylipins during sample collection and storage but readily measurable precursor oxylipins argues against widespread degradation.

IL-36 expression is increased in NSCLC with IL-36 stimulation of lung cancer cells promoting a pro-tumorigenic phenotype

The IL-36 cytokines are a recently described subset of the IL-1 family of cytokines, and have been shown to play a role in the pathogenesis of respiratory diseases such as asthma and COPD. Given the common aetiological links between COPD and lung cancer development, as well as the involvement of other IL-1 family members in lung tumorigenesis, the aim of this work was to investigate the role of IL-36 cytokines in the pathogenesis of lung cancer. In this study we demonstrate that expression of IL-36 cytokines and receptor mRNA and protein are significantly increased in lung cancer tissue compared to adjacent non-tumour tissue. In vitro assays showed that stimulation of two lung cancer cell lines, SKMES-1 human squamous cell and LLC murine lung cancer, with IL-36R agonists resulted in increased cellular migration and proliferation. All IL-36 cytokines induced the expression of pro-inflammatory chemokines in both lung cancer cell lines with synergistic effects identified upon co-stimulation of cells with IL-17, IL-22 and TNFα. Furthermore, we report that IL-36 cytokines induce protein expression of the immune checkpoint inhibitor protein PD-L1 on lung cancer cells. Taken together, this data indicates that targeting IL-36R signalling may be a useful targeted therapy for lung cancer patients with IL-36R⁺ cancer cells.

Impact of the COVID-19 pandemic on cancer care in Ireland - Perspectives from a COVID-19 and Cancer Working Group

Upon the COVID-19 pandemic onset in Ireland, cancer service disruptions occurred due to prioritisation of COVID-19 related care, redeployment of staff, initial pausing of screening, diagnostic, medical and surgical oncology procedures, staff shortages due to COVID-19 infection and impacts on the physical and mental health of cancer healthcare workers. This was coupled with reluctance among people with symptoms suspicious for cancer to attend for clinical evaluation, due to concerns of contracting the virus. This was further compounded by a cyber-attack on national health service IT systems on May 14th 2021. The Irish Cancer Society, a national cancer charity with a role in advocacy, research and patient supports, convened a multi-disciplinary stakeholder group (COVID-19 and Cancer Working Group) to reflect on and understand the impact of the pandemic on cancer patients and services in Ireland, and discuss potential mitigation strategies. Perspectives on experiences were gathered across domains including timeliness of data acquisition and its conversion into intelligence, and the resourcing of cancer care to address cancer service impacts. The group highlighted aspects for future research to understand the long-term pandemic impact on cancer outcomes, while also highlighting potential strategies to support cancer services, build resilience and address delayed diagnosis. Additional measures include the need for cancer workforce recruitment and retention, increased mental health supports for both patients and oncology professionals, improvements to public health messaging, a near real-time multimodal national cancer database, and robust digital and physical infrastructure to mitigate impacts of the current pandemic and future challenges to cancer care systems.

The psychedelic renaissance: the next trip for psychiatry?

The psychedelic research renaissance is gaining traction. Preliminary clinical studies of the hallucinogenic fungi, psilocybin, with psychological support, have indicated improvements in mood, anxiety and quality of life. A seminal, open-label study demonstrated marked reductions in depression symptoms in participants with treatment-resistant depression (TRD). The associated neurobiological processes involve alterations in brain connectivity, together with altered amygdala and default mode network activity. At the cellular level, psychedelics promote synaptogenesis and neural plasticity. Prompted by the promising preliminary studies, a randomized, double-blind trial has recently been launched across Europe and North America to investigate the efficacy of psilocybin in TRD. One of these centres is based in Ireland - CHO Area 7 and Tallaght University Hospital. The outcome of this trial will determine whether psilocybin with psychological support will successfully translate into the psychiatric clinic for the benefit of patients.

Improved diagnostic accuracy for apical hypertrophic cardiomyopathy

Introduction

The diagnosis of apical hypertrophic cardiomyopathy (ApHCM) is contingent on demonstrating apical maximum wall thickness (MWT) of ≥15mm; the same threshold as other HCM subtypes. However, the myocardium naturally tapers towards the apex in healthy individuals, so ≥15mm MWT is proportionately higher in the apex than in naturally thicker basal segments. Using cardiac magnetic resonance (CMR), relative ApHCM has been described (typical ECG features, loss of apical tapering, cavity obliteration but hypertrophy &lt;15mm). Wall thickness measurement using machine learning now exceeds human performance.

Purpose

We aimed to redefine the optimal diagnostic threshold for ApHCM using segment-specific criteria based on a large cohort of healthy control subjects.

Methods

Segmental wall thickness was measured using healthy subjects from the UK Biobank using a clinically validated machine learning algorithm1,2. A normative reference range was established for all 16 segments, conditioned to body surface area (BSA), sex and age. Derived segment-specific wall thickness thresholds were used to define optimal disease thresholds for patients clinically managed with overt (MWT ≥15mm) and relative ApHCM (MWT &lt;15mm, but typical ECG and imaging findings).

Results

4118 UK biobank subjects were used to define normal segmental thicknesses and reference ranges. These were applied to ApHCM (73 overt, 31 relative). There were no apical wall thickness age related differences. The upper limit of the 95% confidence interval corresponded to a combined maximum apical MWT for both males and females of 10.4mm using non-indexed measurement, or 5.6mm/m2 when indexed to BSA. Non-indexed segmental threshold identified 100% of ApHCM patients (true positives), 81% (25 of 31) relative ApHCM and 3% (115 of 4118) of healthy UK biobank subjects (false positives). Indexed segmental thresholds improved the diagnostic potential in relative ApHCM without an increase in false positives (100% of ApHCM patients, 84% (26 of 31) of relative ApHCM patients, and 3% healthy UK biobank (127 of 4118).

Conclusion

We propose new diagnostic criteria for ApHCM using segmental indexed apical wall thickness of &gt;5.6 mm/m2 to better identify inappropriate apical hypertrophy in those whose wall thickness does not meet current criteria for diagnosis.

Funding Acknowledgement

Type of funding sources: Foundation. Main funding source(s): British Heart Foundation

Asymmetric septal thickening is observed in hypertrophic cardiomyopathy mutation carriers without left ventricular hypertrophy: insights from AI analysis

Funding Acknowledgements

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Dr Hughes is supported by the British Heart Foundation (grant number FS/17/82/33222).

Background

Hypertrophic cardiomyopathy (HCM) is a common inherited cardiac disease characterised by left ventricular hypertrophy (LVH), often, with asymmetric septal thickening. Despite the prevalence of inherited mutations present in &gt;50% of cases, there is variable phenotypic expression in those with abnormal sarcomere protein genes. In individuals with abnormal genes but without LVH, we hypothesised that there is subtle asymmetric septal hypertrophy, detectable by the increased precision offered by an artificial intelligence (AI) tool for measuring wall thickness.

Purpose

We explored the septal-lateral ratio measured by AI in individuals with an identified genotype but no left ventricular hypertrophy as a component of sub-clinical HCM.

Methods

43 individuals with identified genotype, but no left ventricular hypertrophy (G+LVH-) and 97 age-, sex- and disease-matched controls underwent CMR. Patients were excluded if they had a maximum wall thickness (MWT) of ≥13mm. A clinically validated AI tool was used to measure the MWT, for each segment in the 16-segment AHA model. The septal-lateral ratio was calculated using the septal segment with the largest MWT and the lateral segment with the largest MWT.

Results

The mean septal-lateral ratio of the G+LVH- patients was 1.22 (SD 0.22) and the mean septal-lateral ratio of the matched controls was 1.14 (SD 0.15) with a statistically significant mean difference of 0.08 (p=0.01). There was no significant difference between the MWT of the G+LVH- patients at 10.3mm (SD 2.2) and healthy volunteers at 10.1mm (SD 1.8) (p = 0.61).

Conclusion

G+LVH- patients have a 7% increase in their septal-lateral ratio compared with age-matched controls despite the lack of difference in the MWT. Using increased precision offered by AI, early features of HCM can be observed in patients without overt LVH.

Improving the diagnostic accuracy of apical hypertrophic cardiomyopathy using machine learning

Funding Acknowledgements

Type of funding sources: Private grant(s) and/or Sponsorship. Main funding source(s): Dr Hughes is supported by the British Heart Foundation (grant number FS/17/82/33222).

Introduction

The imaging criteria for diagnosis of apical hypertrophic cardiomyopathy (ApHCM) is a maximum wall thickness (MWT) ≥15mm. CMR enables detection of subtle phenotypic features (e.g. loss of apical tapering, cavity obliteration) and coupled with characteristic electrocardiogram changes, ApHCM can be diagnosed without overt hypertrophy. However, these patients are not captured by current diagnostic criteria.

Purpose

We sought to use a machine learning tool to quantify wall thickness and identify patients with ‘relative’ ApHCM that do not reach current diagnostic thresholds.

Methods

CMR images from 4118 healthy participants from the UK Biobank were segmented automatically with a clinically validated machine learning algorithm and wall thickness measured at all point in the myocardium by solving a solution to Laplace’s equation. MWT were pooled into 16 AHA segments and indexed to body surface area (BSA). The non-indexed and indexed segmental upper limit of normal was calculated as the mean + 3 standard deviations (the equivalent of 95% confidence interval after correcting for multiple [16] comparisons using the Bonferroni method).

Results

73 overt ApHCM subjects (MWT&gt;15mm) and 31 relative ApHCM subjects underwent CMR scanning. In healthy controls, the non-indexed (and indexed) upper limits were calculated for the apical-anterior 10.2mm (5.2 mm/m2), apical-septal 11.1mm (5.6 mm/m2), apical-inferior 10.5mm (5.3 mm/m2) and apical-lateral 10.1mm (5.2 mm/m2) segments. With a non-indexed cut-off, all (73 of 73) overt ApHCM and 84% (26 of 31) relative ApHCM were classified as having an abnormally thick apex. 3% (127 of 4118) of the healthy UK Biobank cohort were classified as abnormal, as expected. Using an indexed cut-off, all overt ApHCM and 87% (27/31) relative ApHCM were classified as abnormal, and 3% (123 of 4118) of the healthy UK Biobank cohort were misclassified.

Conclusion

We can successfully classify 87% of relative ApHCM patients from a normative reference range derived from a large cohort of healthy patients – a significant improvement on existing methods. We show that the specificity and sensitivity is increased when MWT is indexed to BSA. For practical clinical application, we recommend a cut-off of 10mm or an indexed cut-off of 5mm/m2 in any apical segment to diagnose apical LVH. Overt and relative apical HCM examplesHealthy controls AHA maps (non-indexed)

13C-glucose-fructose labeling reveals comparable exogenous CHO oxidation during exercise when consuming 120 g/h in fluid, gel, jelly chew, or coingestion

We examined the effects of carbohydrate (CHO) delivery form on exogenous CHO oxidation, gastrointestinal discomfort, and exercise capacity. In a randomized repeated-measures design [after 24 h of high CHO intake (8 g·kg^-1) and preexercise meal (2 g·kg^-1)], nine trained males ingested 120 g CHO·h^-1 from fluid (DRINK), semisolid gel (GEL), solid jelly chew (CHEW), or a coingestion approach (MIX). Participants cycled for 180 min at 95% lactate threshold, followed by an exercise capacity test (150% lactate threshold). Peak rates of exogenous CHO oxidation (DRINK 1.56 ± 0.16, GEL 1.58 ± 0.13, CHEW 1.59 ± 0.08, MIX 1.66 ± 0.02 g·min^-1) and oxidation efficiency (DRINK 72 ± 8%, GEL 72 ± 5%, CHEW 75 ± 5%, MIX, 75 ± 6%) were not different between trials (all P > 0.05). Despite ingesting 120 g·h^-1, participants reported minimal symptoms of gastrointestinal distress across all trials. Exercise capacity was also not significantly different (all P > 0.05) between conditions (DRINK 446 ± 350, GEL 529 ± 396, CHEW 596 ± 416, MIX 469 ± 395 s). Data represent the first time that rates of exogenous CHO oxidation (via stable isotope methodology) have been simultaneously assessed with feeding strategies (i.e., preexercise CHO feeding and the different forms and combinations of CHO during exercise) commonly adopted by elite endurance athletes. We conclude that 120 g·h^-1 CHO (in a 1:0.8 ratio of maltodextrin or glucose to fructose) is a practically tolerable strategy to promote high CHO availability and oxidation during exercise.NEW & NOTEWORTHY We demonstrate comparable rates of exogenous CHO oxidation from fluid, semisolid, solid, or a combination of sources. Considering the sustained high rates of total and exogenous CHO oxidation and relative lack of gastrointestinal symptoms, consuming 120 g CHO·h^-1 appears to be a well-tolerated strategy to promote high CHO availability during exercise. Additionally, this is the first time that rates of exogenous CHO oxidation have been assessed with feeding strategies (e.g., coingestion of multiple CHO forms) typically reported by endurance athletes.

Dietary Inorganic Nitrate as an Ergogenic Aid: An Expert Consensus Derived via the Modified Delphi Technique

Introduction

Dietary inorganic nitrate is a popular nutritional supplement, which increases nitric oxide bioavailability and may improve exercise performance. Despite over a decade of research into the effects of dietary nitrate supplementation during exercise there is currently no expert consensus on how, when and for whom this compound could be recommended as an ergogenic aid. Moreover, there is no consensus on the safe administration of dietary nitrate as an ergogenic aid. This study aimed to address these research gaps.

Methods

The modified Delphi technique was used to establish the views of 12 expert panel members on the use of dietary nitrate as an ergogenic aid. Over three iterative rounds (two via questionnaire and one via videoconferencing), the expert panel members voted on 222 statements relating to dietary nitrate as an ergogenic aid. Consensus was reached when > 80% of the panel provided the same answer (i.e. yes or no). Statements for which > 80% of the panel cast a vote of insufficient evidence were categorised as such and removed from further voting. These statements were subsequently used to identify directions for future research.

Results

The 12 panel members contributed to voting in all three rounds. A total of 39 statements (17.6%) reached consensus across the three rounds (20 yes, 19 no). In round one, 21 statements reached consensus (11 yes, 10 no). In round two, seven further statements reached consensus (4 yes, 3 no). In round three, an additional 11 statements reached consensus (5 yes, 6 no). The panel agreed that there was insufficient evidence for 134 (60.4%) of the statements, and were unable to agree on the outcome of the remaining statements.

Conclusions

This study provides information on the current expert consensus on dietary nitrate, which may be of value to athletes, coaches, practitioners and researchers. The effects of dietary nitrate appear to be diminished in individuals with a higher aerobic fitness (peak oxygen consumption [V̇O_2peak] > 60 ml/kg/min), and therefore, aerobic fitness should be taken into account when considering use of dietary nitrate as an ergogenic aid. It is recommended that athletes looking to benefit from dietary nitrate supplementation should consume 8–16 mmol nitrate acutely or 4–16 mmol/day nitrate chronically (with the final dose ingested 2–4 h pre-exercise) to maximise ergogenic effects, taking into consideration that, from a safety perspective, athletes may be best advised to increase their intake of nitrate via vegetables and vegetable juices. Acute nitrate supplementation up to ~ 16 mmol is believed to be safe, although the safety of chronic nitrate supplementation requires further investigation. The expert panel agreed that there was insufficient evidence for most of the appraised statements, highlighting the need for future research in this area.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s40279-022-01701-3.

Machine learning of language use on Twitter reveals weak and non-specific predictions

Depressed individuals use language differently than healthy controls and it has been proposed that social media posts can be used to identify depression. Much of the evidence behind this claim relies on indirect measures of mental health and few studies have tested if these language features are specific to depression versus other aspects of mental health. We analysed the Tweets of 1006 participants who completed questionnaires assessing symptoms of depression and 8 other mental health conditions. Daily Tweets were subjected to textual analysis and the resulting linguistic features were used to train an Elastic Net model on depression severity, using nested cross-validation. We then tested performance in a held-out test set (30%), comparing predictions of depression versus 8 other aspects of mental health. The depression trained model had modest out-of-sample predictive performance, explaining 2.5% of variance in depression symptoms (R² = 0.025, r = 0.16). The performance of this model was as-good or superior when used to identify other aspects of mental health: schizotypy, social anxiety, eating disorders, generalised anxiety, above chance for obsessive-compulsive disorder, apathy, but not significant for alcohol abuse or impulsivity. Machine learning analysis of social media data, when trained on well-validated clinical instruments, could not make meaningful individualised predictions regarding users’ mental health. Furthermore, language use associated with depression was non-specific, having similar performance in predicting other mental health problems.

Smartphone App–Based Noncontact Ecological Momentary Assessment With Experienced and Naïve Older Participants: Feasibility Study

Background

Smartphone app–based ecological momentary assessment (EMA) without face-to-face contact between researcher and participant (app-based noncontact EMA) potentially provides a valuable data collection tool when geographic, time, and situational factors (eg, COVID-19 restrictions) place constraints on in-person research. Nevertheless, little is known about the feasibility of this method, particularly in older and naïve EMA participants.

Objective

This study aims to assess the feasibility of app-based noncontact EMA as a function of previous EMA experience, by recruiting and comparing a group of participants who had never participated in EMA before against a group of participants who had been part of an earlier in-person EMA study, and age, by recruiting middle-aged to older adults.

Methods

Overall, 151 potential participants were invited via email; 46.4% (70/151) enrolled in the study by completing the baseline questionnaire set and were emailed instructions for the EMA phase. Of these participants, 67% (47/70) downloaded an EMA app and ran the survey sequence for 1 week. In total, 5 daytime surveys and 1 evening survey, each day, assessed participants’ listening environment, social activity, and conversational engagement. A semistructured exit telephone interview probed the acceptability of the method. As markers of feasibility, we assessed the enrollment rate, study completion rate, reason for noncompletion, EMA survey response rate, and likelihood of reporting an issue with survey alerts and requested assistance from researchers, family, or friends.

Results

Enrollment rates among invitees (63.3% vs 38.2%; P=.004) and completion rates among enrollees (83.9% vs 53.8%; P<.001) were higher in the experienced than in the naïve EMA group. On average, experienced participants responded to 64.1% (SD 30.2%) of the daytime EMA surveys, and naïve participants responded to 54.3% (SD 29.5%) of the daytime EMA surveys (P=.27). Among participants who retrospectively reported issues with survey alerts, only 19% (3/16) requested researcher assistance during data collection. Older participants were more likely to report not being alerted to EMA surveys (P=.008), but age was unrelated to all other markers of feasibility. Post hoc analyses of the effect of the phone operating system on markers of feasibility revealed that response rates were higher among iOS users (mean 74.8%, SD 20.25%) than among Android users (mean 48.5%, SD 31.35%; P=.002).

Conclusions

Smartphone app–based noncontact EMA appears to be feasible, although participants with previous EMA experience, younger participants, and iOS users performed better on certain markers of feasibility. Measures to increase feasibility may include extensive testing of the app with different phone types, encouraging participants to seek timely assistance for any issues experienced, and recruiting participants who have some previous EMA experience where possible. The limitations of this study include participants’ varying levels of existing relationship with the researcher and the implications of collecting data during the COVID-19 social restrictions.

Mitral valve replacement due to Libman-Sacks endocarditis: lower limb cellulitis as a red herring

A 56-year-old woman was admitted due to new ulceration and acute digital ischaemia on a background of chronic leg ulcers bilaterally. Vasculitis screening returned strongly positive lupus anticoagulant levels and elevated anticardiolipin antibodies; these remained elevated at repeat testing. A diagnosis of antiphospholipid syndrome was made. Transthoracic echocardiogram identified a mitral valve lesion suggestive of vegetation and mild mitral valve regurgitation. Blood cultures taken throughout her inpatient admission were negative. Mechanical mitral valve replacement was performed 3 months later, and subsequent culture of the excised tissue returned as sterile. Histological examination showed no morphological signs of infective endocarditis.

Fetal deaths in Ireland due to SARS-CoV-2 placentitis caused by SARS-CoV-2 Alpha

CONTEXT

- A severe third wave of COVID-19 disease affected Ireland in the first 3 months of 2021. In this wave, 1 second trimester miscarriage and 6 stillbirths were observed in the Irish population due to placental insufficiency as a result of SARS-CoV-2 placentitis. This observation was at odds with the country's previous experience with COVID-19 disease in pregnant mothers.

OBJECTIVE

- To describe the clinical and pathological features of these pregnancy losses.

DESIGN

- Retrospective review of clinical and pathological data of cases of second trimester miscarriage, stillbirth or neonatal death identified by perinatal pathologists as being due to SARS-CoV-2 placentitis during the third wave of COVID-19 in Ireland.

RESULTS

- Clinical and pathological data was available for review in 6 pregnancies. Sequencing or genotyping of the virus identified SARS-CoV-2 Alpha (B.1.1.7) in all cases. Three of the 6 cases had maternal thrombocytopenia, while fetal growth restriction was not prominent suggesting a rapidly progressive placental disease.

CONCLUSIONS

- The identification of SARS-CoV-2 Alpha in all these cases suggests that the emergence of the variant was associated with an increased risk of fetal death due to SARSCoV-2 placentitis when compared to the original virus. Maternal thrombocytopenia, may have potential as a clinical marker of placentitis but other inflammatory markers need investigation. Three of the 6 women had been assessed for reduced fetal movements in hospital some days before the fetal deaths actually occurred; this could suggest that there may be a window for intervention in some cases.

Core curriculum in pathology for future Irish medical students

Pathology is important in training to become a medical doctor but as curricula become more integrated, there is a risk that key aspects of pathology may be excluded. Following a survey of the current delivery of teaching in Ireland under the auspices of the Faculty of Pathology at the Royal College of Physicians of Ireland, suggested components of a core curriculum in pathology have been developed to be delivered at some stage during the medical course. These have been based on key principles and themes required by the Medical Council in Ireland. Professionalism is one of the core principles emphasised by the Medical Council. It includes the role of the pathologist in patient care and other professional values such as patient-centred care, clinical competencies and skills, e.g. explaining results, and knowledge under the various sub-disciplines, i.e. histopathology (including neuropathology), clinical microbiology, haematology, chemical pathology and immunology. In each of these, we suggest key aspects and activities that the medical graduate should be comfortable in carrying out. The methods of delivery of teaching and assessment across pathology disciplines have evolved and adapted to recent circumstances. Lessons have been learned and insights gained during the COVID-19 pandemic as educators have risen to the challenge of continuing to educate medical students. Integrated and multi-disciplinary teaching is recommended to reflect best the professional environment of the medical graduate who works as an integral part of a multi-disciplinary team, with the minimum dependence on the traditional lecture, where at all possible. Finally, options on assessment are discussed, e.g. multiple-choice questions, including their respective advantages and disadvantages.

Solitary fibrous tumour of mediastinum: an often asymptomatic neoplasm

Solitary fibrous tumours (SFTs) are rare neoplasms derived from mesenchymal cell lines. They are often asymptomatic, follow an indolent growth pattern and are more often benign than malignant. Here, we present a case of a very large, asymptomatic mediastinal SFT in an otherwise healthy man. A 67-year-old Irish man was referred for workup of an asymptomatic murmur. Auscultation of the lung fields revealed diminished breath sounds on the right side. Chest X-ray identified a 20 cm mass localised within the thorax. CT of the thorax confirmed a pleural based, solid lesion with no local invasion. CT-guided core biopsies were reported as consistent with SFT. Primary excision of the lesion was undertaken via median sternotomy. Histological examination confirmed a diagnosis of SFT. The patient remains well at this time. Primary excisive surgery is a safe and effective treatment modality for SFTs.

Antiglomerular basement membrane (anti-GBM) disease with clinical and histological features that bridge the typical to atypical spectrum

We describe antiglomerular basement membrane (anti-GBM) disease with rapidly progressive glomerulonephritis and concurrent parainfluenza pneumonia. Circulating anti-GBM antibodies were barely detectable and disappeared rapidly following corticosteroids, cyclophosphamide and plasma exchange. Kidney biopsy demonstrated strong linear GBM staining for IgG and IgG4 and unusually prominent endocapillary hypercellularity, suggesting 'atypical anti-GBM disease', although glomerular necrosis and crescents were also seen. When kidney function deteriorated further, despite persistently absent circulating anti-GBM antibodies, a repeat kidney biopsy was performed, showing crescents in 100% of glomeruli with ongoing endocapillary hypercellularity and strong IgG and IgG4 GBM staining. This case highlights complexities in the diagnosis of anti-GBM disease, with clinical and histological features bridging the atypical to typical anti-GBM disease spectrum. We hypothesise that these findings might be explained by the presence of IgG4 (rather than traditional IgG1 or IgG3) autoantibodies. To our knowledge, this is also the first report of parainfluenza associated with anti-GBM disease.

Transbronchial lung cryobiopsy (TBLC) in the diagnosis of interstitial lung disease: experience of first 100 cases performed under conscious sedation with flexible bronchoscope

BACKGROUND

Diagnosing the aetiology of interstitial lung disease (ILD) may require histology via a surgical lung biopsy (SLB). SLB is associated with significant complications. Transbronchial lung cryobiopsy (TBLC) can provide large, adequate biopsies with fewer complications offering a potential alternative to SLB.

AIMS

This study evaluated the safety, diagnostic yield and impact of TBLC on diagnostic certainty in the multidisciplinary diagnosis (MDD) of ILD within routine clinical practice.

METHODS

A retrospective study of all TBLC performed in a tertiary institute from March 2014 to December 2016 was performed. Procedures were performed using a flexible bronchoscope and cryoprobe without fluoroscopic guidance.

RESULTS

One hundred procedures were performed on 85 patients. A total of 272 cryobiopsies were obtained with a mean biopsy diameter of 5.9 ± 3.2 mm. Ninety-seven percent contained alveolated lung tissue. Diagnosis based against MDD gold standard was confirmed using TBLC in 67.1% of patients and in 72/100 procedures. Three patients proceeded to SLB. The addition of histological information changed the clinic-radiological diagnosis in twelve patients. The most common diagnosis based on clinical-radiologic-pathologic correlation at MDD was idiopathic pulmonary fibrosis (IPF) (51.2%) and hypersensitivity pneumonitis (15.9%). Moderate bleeding occurred in 18% of cases and five patients (5%) developed pneumothorax requiring intervention. Eleven patients required admission, with a mean length of stay of 1.3 ± 0.9 days.

CONCLUSION

TBLC aids the diagnosis of ILD in the appropriate patient and may be an acceptable alternative to SLB with fewer complications. Further work on standardizing the procedure is required.

A rare case of a pulmonary valve papillary fibroelastoma

CASE

A 67-year-old female presented with an exceedingly rare cardiac neoplasm - papillary fibroelastoma. This is made rarer still as it occurred on the pulmonary valve. The patient complained of a prolonged history of chest discomfort. Magnetic resonance imaging and echocardiography revealed a pulmonary valve papillary fibroelastoma. Surgical excision proved curative and the patient remains asymptomatic to date.

DISCUSSION

The literature surrounding papillary fibroelastomas is discussed. Primary cardiac tumours are uncommon. Papillary fibroelastomas occurring the right side of the heart comprise less than 0.05% of these. They have a characteristic macroscopic appearance which allow them to be easily identified with echocardiography and at surgical excision. They can present in a variety of ways including classical cardiac symptoms, embolic complications or as an incidental finding. Surgical excision is the definitive treatment.

Cryptosporidium spp. in groundwater supplies intended for human consumption - A descriptive review of global prevalence, risk factors and knowledge gaps

Cryptosporidiosis is one of the leading causes of diarrhoeal illness and mortality induced by protozoan pathogens worldwide. As a largely waterborne disease, emphasis has been given to the study of Cryptosporidium spp. in surface waters, readily susceptible to pathogenic contamination. Conversely, the status of Cryptosporidium in potable groundwater sources, generally regarded as a pristine and "safe" drinking-water supply owing to (sub)-soil protection, remains largely unknown. As such, this investigation presents the first literature review aimed to ascertain the global prevalence of Cryptosporidium in groundwater supply sources intended for human consumption. Thirty-seven peer-reviewed studies were identified and included in the review. Groundwater sample and supply detection rates (estimated 10-20%) indicate Cryptosporidium is frequently present in domestic groundwater sources, representing a latent health concern for groundwater consumers. Specifically, sample (10.4%) and source (19.1%) detection rates deriving from comprehensive "temporal" investigations are put forward as representative of a contamination 'baseline' for Cryptosporidium in 'domestic' groundwater supplies. Proposed 'baseline' prevalence figures are largely applicable in preventive risk-based catchment and groundwater quality management including the formulation of Quantitative Microbial Risk Assessment (QMRA). Notwithstanding, a large geographical disparity in available investigations and lack of standardized reporting restrict the transferability of research findings. Overall, the mechanisms responsible for Cryptosporidium transport and ingress into groundwater supplies remain ambiguous, representing a critical knowledge gap, and denoting a distinctive lack of integration between groundwater and public-health sub-disciplines among investigations. Key recommendations and guidelines are provided for prospective studies directed at more integrative and multi-disciplinary research.

0686 Diabetes Sleep Treatment Trial: The Effect Of Treatment Of OSA With CPAP On Glycemic Control In Type 2 Diabetes

Introduction

Evidence remains unclear whether treatment of OSA with CPAP results in improved glycemic control. This study evaluated if CPAP improved glucose control compared to sham-CPAP and the effect of adherence to active CPAP on glucose control after 6 and 12 weeks of treatment.

Methods

This was a multi-center, double-blind clinical trial. Participants were adults with type 2 diabetes (T2D), A1C≥6.5%, apnea + hypopnea index (AHI)≥10, and naïve to CPAP. All participants received diabetes education. Glucose control was evaluated with frucostamine and A1C levels; CPAP adherence with a wireless modem system. Statistical analysis followed an “intent-to-treat” approach with linear mixed modeling. The dose of active CPAP was calculated as the percentage of days with active CPAP use≥4 hours and the average adherence of active CPAP with sham coded as “0”dose”.

Results

Randomized participants (N=98, CPAP=50; sham-CPAP=48) were primarily middle-aged (age=58.7±9.8 years), White (75%), males (57%) obese (BMI=36.2±6.6), suboptimal glucose control (A1C=7.9%±0.9) and OSA (AHI=23.9±14.4). There were no significant baseline differences except in A1C (Active CPAP=7.7%±0.8; sham-CPAP=8.1%±1.0). There was no significant difference in use of their devices at 6 or 12 weeks. Based on linear mixed modeling, participants on active CPAP had improved A1C (b (SE): -.76 (.24), P&lt;.01) and frucostamine (-21.8 (10.5), P=.04) at 6 weeks with A1C trending to significance at 12 weeks (p=0.10). Both the % of cumulative days of active CPAP usage (≥4 hours/day) (.002 (.003), P=.09) and cumulative hours of active CPAP use (.03 (.03), P=.08) showed a trend being associated with greater change in A1C but not in frucostamine (P=.61, P=.51). The rate of change in A1C varied by time, increasing the % of cumulative days of CPAP use (≥4 hours/day) at week 6 predicted greater change in A1C (.006 (.002), P=.01) than week 12 (.002 (.003), P=.38). Higher average hours of CPAP usage were associated with greater change in A1C (.08 (.03), P=.01) at week 6 compared to week 12 (.03 (.03), P=.47).

Conclusion

In our study, individuals with T2D and OSA, adherence to active CPAP use improved glycemic control over 6 weeks.

Support

NIDDK grant R01DK096028; CTRI grant UL1TR001857 and UL1TR000005.

Inflammation and Oral Contraceptive Use in Female Athletes Before the Rio Olympic Games

This study investigated the association between synthetic ovarian hormone use [i.e., the oral contraceptive (OC) pill] and basal C-reactive protein (CRP), peripheral blood immune cell subsets, and circulating pro- and anti-inflammatory cytokine concentrations in elite female athletes. Elite female athletes (n = 53) selected in Rio Summer Olympic squads participated in this study; 25 were taking an OC (AthletesOC) and 28 were naturally hormonally cycling (AthletesNC). Venous blood samples were collected at rest for the determination of sex hormones, cortisol, CRP, peripheral blood mononuclear memory and naïve CD4+ T-cells, CD8+ T-cells and natural killer cells, as well as pro- and anti-inflammatory cytokine concentrations. C-reactive protein concentrations were elevated (p < 0.001) in AthletesOC (median = 2.02, IQR = 3.15) compared to AthletesNC (median = 0.57, IQR = 1.07). No differences were reported for cortisol, cytokines, or PBMC immune cell subsets, although there was a trend (p = 0.062) for higher IL-6 concentrations in AthletesNC. Female Olympians had substantially higher CRP concentrations, a marker of inflammation and tissue damage, before the Rio Olympic Games if they used an OC. Future research should examine the potential consequences for athlete performance/recovery so that, if necessary, practitioners can implement prevention programs.

The Maudsley Early Onset Schizophrenia Study: The effect of age of onset and illness duration on fronto-parietal gray matter

Objective

In Early Onset Schizophrenia (EOS; onset before the 18th birthday) late brain maturational changes may interact with disease mechanisms leading to a wave of back to front structural changes during adolescence. To further explore this effect we examined the relationship between age of onset and duration of illness on brain morphology in adolescents with EOS.

Subjects and methods

Structural brain magnetic resonance imaging scans were obtained from 40 adolescents with EOS. We used Voxel Based Morphometry and multiple regressions analyses, implemented in SPM, to examine the relationship between gray matter volume with age of onset and illness duration.

Results

Age of onset showed a positive correlation with regional gray matter volume in the right superior parietal lobule (Brodmann Area 7). Duration of illness was inversely related to regional gray matter volume in the left inferior frontal gyrus (BA 11/47).

Conclusions

Parietal gray matter loss may contribute to the onset of schizophrenia while orbitofrontal gray matter loss is associated with illness duration.

Coeliac disease presenting with chorea

Chorea can be genetic or acquired, and often leads to a challenging diagnostic conundrum. In a significant proportion, there is no specific identifiable cause. Chorea is a rare but potentially reversible neurological manifestation of coeliac disease, usually presenting insidiously and often presumed to be associated with typical gastrointestinal symptoms. We report a patient with rapidly progressive generalised chorea, but without preceding gastrointestinal symptoms, who was subsequently diagnosed with coeliac disease. A gluten-free diet resulted in complete resolution of the chorea.

Differential Diagnosis of Epithelioid Malignant Mesothelioma With Lung and Breast Pleural Metastasis: A Systematic Review Compared With a Standardized Panel of Antibodies-A New Proposal That May Influence Pathologic Practice

CONTEXT.—

Pleural mesothelioma is a rare cancer with an often-challenging diagnosis because of its potential to be a great mimicker of many other tumors. Among them, primary lung and breast cancers are the 2 main causes of pleural metastasis. The development and application of targeted therapeutic agents have made it even more important to achieve an accurate diagnosis. In this setting, international guidelines have recommended the use of 2 positive and 2 negative immunohistochemical biomarkers.

OBJECTIVES.—

To define the most highly specific and sensitive minimum set of antibodies for routine practice to use for the separation of epithelioid malignant mesothelioma from lung and breast metastasis and to determine the most relevant expression cutoff.

DESIGN.—

To provide information at different levels of expression of 16 mesothelial and epithelial biomarkers, we performed a systematic review of articles published between 1979 and 2017, and we compared those data to results from the Mesothelioma Telepathology Network (MESOPATH) of the standardized panel used in routine practice database since 1998.

RESULTS.—

Our results indicate that the following panel of markers-calretinin (poly)/thyroid transcription factor 1 (TTF-1; clone 8G7G3/1) and calretinin (poly)/estrogen receptor-α (ER-α; clone EP1)-should be recommended; ultimately, based on the MESOPATH database, we highlight their relevance which are the most sensitive and specific panel useful to the differential diagnosis at 10% cutoff.

CONCLUSIONS.—

Highlighted by their relevance in the large cohort reported, we recommend 2 useful panels to the differential diagnosis at 10% cutoff.

Lung cancer in young patients: tumour characteristics and treatment in an Irish population

Background

Lung cancer is the leading cause of cancer death in both sexes in Ireland. Studies suggest that lung cancer in younger patients has distinct characteristics. The aim of this study is to define the characteristics of lung cancer in patients 55-year-old or younger in an Irish population.

Methods

Data was collected retrospectively from local medical records and the hospital electronic database regarding all patients diagnosed with lung cancer aged 55-year-old and younger, from 2010–2016. Information regarding patient demographics, smoking status, tumour histology, molecular analysis, stage and location, diagnostic modality and initial treatment choice was collected. In all cases the diagnosis of lung cancer was confirmed at the regional lung cancer multidisciplinary team (MDT) meeting.

Results

In total, 8% (n=130) of all cases of lung cancer diagnosed from 2010 to 2016 in our center occurred in patients aged 55 years old or younger; 83% (n=108) were 45 to 55-year-old, 15% (n=19) were 35 to 44-year-old and 2% (n=3) were younger than 35-year-old; 88% (n=115) of patients reported a smoking history. There was a female preponderance (58%, n=76), higher rates of NSCLC non-squamous subtype (53%, n=69) and an upper lobe predominance (42%, n=54); 53% (n=68) of patients had IV or extensive disease at presentation. Epidermal growth factor receptor (EGFR), anaplastic lymphoma kinase (ALK) and Kirsten rat sarcoma oncogene (KRAS) mutation rates were 9% (n=4) and 3% (n=1) and 80% (n=4) respectively.

Conclusions

Lung cancer in younger patients has distinct characteristics. This study suggests a female preponderance, high smoking rates and a predilection for the upper lobes. Further large-scale multicenter studies are required to verify these results and to clarify the responsible mechanisms.

Practical Hydration Solutions for Sports

Personalized hydration strategies play a key role in optimizing the performance and safety of athletes during sporting activities. Clinicians should be aware of the many physiological, behavioral, logistical and psychological issues that determine both the athlete’s fluid needs during sport and his/her opportunity to address them; these are often specific to the environment, the event and the individual athlete. In this paper we address the major considerations for assessing hydration status in athletes and practical solutions to overcome obstacles of a given sport. Based on these solutions, practitioners can better advise athletes to develop practices that optimize hydration for their sports.

Coexistent sarcoidosis and lymphangioleiomyomatosis in a patient with cystic lung disease

A 45-year-old lady presented acutely with pleuritic chest pain, haemoptysis, and dyspnoea. Her background was significant for a 1.4 cm renal angiomyolipoma, and she was an ex-smoker without any relevant family history. A computed tomography (CT) pulmonary angiogram was negative for a pulmonary embolism but demonstrated diffuse cystic change throughout both lungs. A bronchoscopy confirmed a normal endobronchial tree, and pulmonary function tests demonstrated moderate airways obstruction, with reversibility and a normal diffusion capacity for carbon monoxide (DLCO). A video-assisted thoracoscopic surgery (VATS) lung biopsy showed non-caseating granulomas, and serum angiotensin converting enzyme (ACE) was elevated consistent with a diagnosis of pulmonary sarcoidosis. Further sectioning indicated focal areas that stained positive for Human Melanoma Black 45 (HMB-45), confirming lymphangioleiomyomatosis (LAM). A diagnosis of cystic lung disease secondary to coexistent sarcoidosis and LAM was made.

Response to tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) patients with de novo epidermal growth factor receptor (EGFR) T790M and S768I resistance mutations

e20557

Background: Patients with synchronous de novo EGFR sensitising and resistance mutations are rare. Little is known about the response of these patients to EGFR TKIs, especially in a Caucasian population. Methods: We identified NSCLC patients found to have EGFR mutations using PCR-based fragment length analysis, mass spectrometry-based genotyping (Sequenom), and Sanger sequencing using a large multi-institutional database. Baseline clinical characteristics, response rate, progression free survival (PFS) and overall survival (OS) were calculated. Results: From 2008-2015, we observed de novo synchronous EGFR sensitising and resistance mutations in 12 patients representing an overall incidence of 3.6% of EGFR mutants and 0.4% of all NSCLC patients tested. Seven patients were treated using EGFR TKI therapy with erlotinib. In all cases, T790M (n = 4,50%) or S768I (n = 4, 50%) occurred concurrently with another sensitising EGFR mutation, either L858R (n = 4, 34%) or exon 19 deletion (n = 8, 66%). Objective responses were seen in two patients (29%). Three further patients had stable disease lasting 6, 23 and 54 months respectively. The median progression-free survival was 24 months and the median overall survival was 34 months. All patients with baseline EGFR S768I mutations (n = 3) had an objective response or stable disease on erlotinib while two of four patients with T790M demonstrated de novo resistance. Conclusions: This is the largest Irish review of synchronous de novo EGFR mutations. The incidence of co-occurring EGFR mutations was 0.4% and erlotinib demonstrated activity in this cohort of patients. Ongoing trials will determine whether next-generation EGFR TKIs such as osimertinib are preferable as first-line therapy in these patients.

A multifactorial evaluation of illness risk factors in athletes preparing for the Summer Olympic Games

OBJECTIVES

Illness can disrupt training and competition performance of athletes. Few studies have quantified the relative contribution of the known medical, behavioural and lifestyle risk factors.

DESIGN

Cross-sectional.

METHODS

Olympic athletes from 11 sports (n=221) were invited to complete questionnaires administered nine months before the Rio 2016 Olympic Games. These included the Depression, Anxiety and Stress Questionnaire (DASS-21), Perceived Stress Scale (PSS), Dispositional Resilience Scale (DRS), Recovery-Stress Questionnaire (REST-Q-52 item), Low Energy in Females Questionnaire (LEAF-Q), a modified Personal and Household Hygiene questionnaire, Epworth Sleepiness Scale, Pittsburgh Sleep Quality Index, and custom-made questionnaires on probiotic usage and travel. An illness (case) was defined as an event which limited training or competition for greater hours in the prior month. Odds ratios and attributable fractions in the population (AFP) were utilised for categorical variables with independent t-tests or Wilcoxon rank-sum for continuous variables.

RESULTS

Eighty-one athletes responded (male, n=26; female, n=55). There were 16 illness cases and 65 controls. Female athletes were at higher odds of illness (OR=9.4, 95%CI 1.3-410, p=0.01, AFP=0.84). Low energy availability (LEAF-Q score ≥8: OR=7.4, 95%CI 0.78-352, p=0.04, AFP=0.76), depression symptoms (DASS-21: depression score >4, OR=8.4, 95%CI 1.1-59, p<0.01; AFP=0.39) and higher perceived stress (PSS: 10-item, p=0.04) were significantly associated with illness.

CONCLUSIONS

Female sex, low energy availability, and mental health are associated with sports incapacity (time loss) due to illness. Low energy availability had high attributable fractions in the population and stands out as a primary association with illness.

A regional analysis of epidermal growth factor receptor (EGFR) mutated lung cancer for HSE South

BACKGROUND

EGFR mutated lung cancer represents a subgroup with distinct clinical presentations, prognosis, and management requirements. We investigated the survival, prognostic factors, and real-world treatment of NSCLC patients with EGFR mutation in clinical practice.

METHODS

A retrospective review of all specimens sent for EGFR analysis from December 2009 to September 2015 was performed. Patient demographics, specimen type, EGFR mutation status/type, stage at diagnosis, treatment, response rate, and survival data were recorded.

RESULTS

27/334 (8%) patient specimens sent for EGFR testing tested positive for a sensitising EGFR mutation. The median age was 65 years (40-85 years). Exon 19 deletion represented the most commonly detected alteration, accounting for 39% (n = 11). First-line treatment for those with Exon 18, 19, or 21 alterations (n = 24) was with an EGFR tyrosine kinase inhibitor (TKI) in 79% (n = 19). Objective response rate among these patients was 74% and median duration of response was 13 months (range 7-35 months).

CONCLUSION

The incidence of EGFR mutation in our cohort of NSCLC is 9% which is consistent with mutation incidence reported in other countries. The rate of EGFR mutation in our population is slightly below that reported internationally, but treatment outcomes are consistent with published data. Real-world patient data have important contributions to make with regard to quality measurement, incorporating patient experience into guidelines and identifying safety signals.