A catalog of associations between rare coding variants and COVID-19 outcomes

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease-19 (COVID-19), a respiratory illness that can result in hospitalization or death. We investigated associations between rare genetic variants and seven COVID-19 outcomes in 543,213 individuals, including 8,248 with COVID-19. After accounting for multiple testing, we did not identify any clear associations with rare variants either exome-wide or when specifically focusing on (i) 14 interferon pathway genes in which rare deleterious variants have been reported in severe COVID-19 patients; (ii) 167 genes located in COVID-19 GWAS risk loci; or (iii) 32 additional genes of immunologic relevance and/or therapeutic potential. Our analyses indicate there are no significant associations with rare protein-coding variants with detectable effect sizes at our current sample sizes. Analyses will be updated as additional data become available, with results publicly browsable at https://rgc-covid19.regeneron.com.

Optimized multimatrix calibration concept for liquid chromatography mass spectrometry-based bioanalysis methods

In this paper, a calibration procedure for LC/MS-based bioanalysis methods, termed "A/B fortification", is proposed. The concept relies on the post-extraction fortification (B-spike) of an aliquot of the injection-ready sample extract for the determination and compensation of specific signal suppression or enhancement effects compared to matrix-free extract prepared in buffer or mobile phase. Conventional analyte recovery, observed due to the incomplete extraction of analytes from the sample or losses during a cleanup, is determined by the conventional pre-extraction fortification (A-spike) of a blank sample that belongs to the same type of matrix as the sample with the unknown analyte concentration. This approach permits a higher throughput than conventional sample fortification strategies. The results obtained by utilizing the A/B fortification concept were extensively compared against conventional methods (representative bank matrix fortification, sample fortification and internal standard). The proposed concept (based on the pre-fortification of a reference matrix and post-fortification of the sample) was found to be significantly less biased than internal standard-based techniques. The A/B fortification indicated a better accuracy than the sample fortification or representative blank matrix fortification approach and, most importantly, produced significantly fewer outliers. This was linked to the fact that in the case of the A/B fortification, the uncertainty of the subtraction of two peak areas (fortified minus unfortified sample) is reduced, because fortifications are not made prior to the extraction step but are made into the final injection-ready sample extract. Fortification into an injection-ready aliquot eliminates all sample processing-related differences (procedural errors), which can affect conventional sample fortification-based quantifications.

Correlation between work impairment, scores of rhinitis severity and asthma using the MASK-air® App

BACKGROUND

In allergic rhinitis, a relevant outcome providing information on the effectiveness of interventions is needed. In MASK-air (Mobile Airways Sentinel Network), a visual analogue scale (VAS) for work is used as a relevant outcome. This study aimed to assess the performance of the work VAS work by comparing VAS work with other VAS measurements and symptom-medication scores obtained concurrently.

METHODS

All consecutive MASK-air users in 23 countries from 1 June 2016 to 31 October 2018 were included (14 189 users; 205 904 days). Geolocalized users self-assessed daily symptom control using the touchscreen functionality on their smart phone to click on VAS scores (ranging from 0 to 100) for overall symptoms (global), nose, eyes, asthma and work. Two symptom-medication scores were used: the modified EAACI CSMS score and the MASK control score for rhinitis. To assess data quality, the intra-individual response variability (IRV) index was calculated.

RESULTS

A strong correlation was observed between VAS work and other VAS. The highest levels for correlation with VAS work and variance explained in VAS work were found with VAS global, followed by VAS nose, eye and asthma. In comparison with VAS global, the mCSMS and MASK control score showed a lower correlation with VAS work. Results are unlikely to be explained by a low quality of data arising from repeated VAS measures.

CONCLUSIONS

VAS work correlates with other outcomes (VAS global, nose, eye and asthma) but less well with a symptom-medication score. VAS work should be considered as a potentially useful AR outcome in intervention studies.

Growing up with interfering neighbours: the influence of time of learning and vocabulary knowledge on written word learning in children

Evidence suggests that new vocabulary undergoes a period of strengthening and integration offline, particularly during sleep. Practical questions remain, however, including whether learning closer to bedtime can optimize consolidation, and whether such an effect varies with vocabulary ability. To examine this, children aged 8-12-years-old (n 59) were trained on written novel forms (e.g. BANARA) in either the morning (long delay) or the evening (short delay). Immediately after training and the next day, lexical competition (a marker of integration) was assessed via speeded semantic decisions to neighbouring existing words (e.g. BANANA); explicit memory was measured via recognition and recall tasks. There were no main effects indicating performance changes across sleep for any task, counter to studies of spoken word learning. However, a significant interaction was found, such that children with poorer vocabulary showed stronger lexical competition on the day after learning if there was a short delay between learning and sleep. Furthermore, while poorer vocabulary was associated with slower novel word recognition speed before and after sleep for the long delay group, this association was only present before sleep for the short delay group. Thus, weak vocabulary knowledge compromises novel word acquisition, and when there is a longer period of post-learning wake, this disadvantage remains after a consolidation opportunity. However, when sleep occurs soon after learning, consolidation processes can compensate for weaker encoding and permit lexical integration. These data provide preliminary suggestion that children with poorer vocabulary may benefit from learning new words closer to bedtime.

Peritonitis in Continuous Ambulatory Peritoneal Dialysis (CAPD) Patients: A Randomized Clinical Trial of Cotrimoxazole Prophylaxis

A double-blind randomized controlled trial compared the effectiveness of prophylactic oral trimethoprim/sulfamethoxazole (cotrimoxazole) to a placebo in preventing peritonitis in continuous ambulatory peritoneal dialysis (CAPD) patients. A daily trimethoprim/sulfamethoxazole dose of 160/800 mg gives a steady state dialysate concentration of 1.07/4.35 mg/L in the final dwell of each dosing interval. Identification of a 40% reduction in peritonitis probability with 80% statistical power and a type 1 error probability of 0.05 required 52 subjects per group. With stratification by previous peritonitis, 56 were allocated to cotrimoxazole and 49 to placebo. For cotrimoxazole there were five deaths and seven catheter losses. For placebo there were three deaths and nine catheter losses. There were 20 withdrawals from cotrimoxazole and 9 from the placebo group. With respect to time to peritonitis, there was no statistically significant difference between cotrimoxazole and placebo groups (p = 0.19). At 6 months, 64.1% of cotrimoxazole and 62.5% of placebo were peritonitis free; at 12 months 41.9% of cotrimoxazole and 35% of placebo were peritonitis free. There was no effect (p > 0.05) of age, sex, catheter care technique, spike or luer, or dialysate additives. Previous peritonitis increased the risk of peritonitis by 2.06 (95% CI, 3.61–1.18) while frequent (six weekly) extension tubing changes increased the risk of by 1.79, (95% CI, 3.04–1.02) when compared to six monthly changes. Cotrimoxazole appears ineffective in prevention of CAPD peritonitis.

Demonstration of 220/280 GHz Multichroic Feedhorn-Coupled TES Polarimeter

We describe the design and measurement of feedhorn-coupled, transition-edge sensor (TES) polarimeters with two passbands centered at 220 GHz and 280 GHz, intended for observations of the cosmic microwave background. Each pixel couples polarized light in two linear polarizations by use of a planar orthomode transducer and senses power via four TES bolometers, one for each band in each linear polarization. Previous designs of this detector architecture incorporated passbands from 27 to 220 GHz; we now demonstrate this technology at frequencies up to 315 GHz. Observational passbands are defined with an on-chip diplexer, and Fourier-transform-spectrometer measurements are in excellent agreement with simulations. We find coupling from feedhorn to TES bolometer using a cryogenic, temperature-controlled thermal source. We determine the optical efficiency of our device is η = 77% ± 6% (75% ± 5%) for 220 (280) GHz, relative to the designed passband shapes. Lastly, we compare two power-termination schemes commonly used in wide-bandwidth millimeter-wave polarimeters and find equal performance in terms of optical efficiency and passband shape.

Students with specific learning disabilities experiences of pre-registration physiotherapy education: a qualitative study

BACKGROUND

Attainment gaps for students with disabilities have been noted in pre-registration physiotherapy courses in the UK. Previous research suggests disclosure, lack of staff knowledge and poor communication between University and placement sites may be relevant, but these are limited to small case studies with students with visual or physical disabilities. The purpose of this study was to explore disabled physiotherapy students' experiences of their education in order to elucidate factors that may influence success.

METHODS

Qualitative study drawing on phenomenological traditions. Four focus groups including 15 students with disabilities were conducted. Transcripts were analysed thematically. Procedures for transparency and rigour such as member checking and peer debriefing were implemented.

RESULTS

Three major themes were derived from data. "It was quite a relief" explores the personal and social implications of diagnosis. "They're not natural" focuses on academic assessment and the specifics of adjustments made and not made within that context. "My dyslexia doesn't switch off" explores the inaccessibility of the learning environment and dissects the contrast between the 24-h nature of having a specific learning condition and the somewhat piecemeal nature of adjustments during their education.

CONCLUSIONS

This study indicates that having a specific learning disability or anxiety creates a number of hurdles to success in physiotherapy education. Most were within the University setting and were perceived to result from staff ignorance or piecemeal approaches to inclusion. A lack of consistency alongside facilitated dialogue and acknowledgement of enhancements results in frustration, ambiguity towards disclosure and reinforcement of a deficit model. Such an approach belies the intention of the profession and the NHS and does not maximise the potential of widening participation.

Predictive impact of rare genomic copy number variations in siblings of individuals with autism spectrum disorders

Identification of genetic biomarkers associated with autism spectrum disorders (ASDs) could improve recurrence prediction for families with a child with ASD. Here, we describe clinical microarray findings for 253 longitudinally phenotyped ASD families from the Baby Siblings Research Consortium (BSRC), encompassing 288 infant siblings. By age 3, 103 siblings (35.8%) were diagnosed with ASD and 54 (18.8%) were developing atypically. Thirteen siblings have copy number variants (CNVs) involving ASD-relevant genes: 6 with ASD, 5 atypically developing, and 2 typically developing. Within these families, an ASD-related CNV in a sibling has a positive predictive value (PPV) for ASD or atypical development of 0.83; the Simons Simplex Collection of ASD families shows similar PPVs. Polygenic risk analyses suggest that common genetic variants may also contribute to ASD. CNV findings would have been pre-symptomatically predictive of ASD or atypical development in 11 (7%) of the 157 BSRC siblings who were eventually diagnosed clinically.

Inadequate specialist care referrals for high-risk asthma patients in the UK: an adult population-based cohort 2006-2017

OBJECTIVE

To improve asthma morbidity and mortality in the UK, national asthma guidelines recommend referral to \ specialist care for the following high-risk groups, after a hospital admission for asthma, ≥3 courses of oral corticosteroids (OCS) in 12 months, an incident high-dose inhaled corticosteroid (ICS) prescription or addition of a fourth asthma drug to a patient's maintenance regimen. We sought to assess the prevalence and temporal change of referrals to identify unmet needs.

METHODS

We used UK electronic healthcare records, 2006-2017, to identify high-risk asthma patients managed within primary care. Referrals to respiratory clinics in secondary care were measured, within 3 months before or 6 months after, an incident ICS, third OCS in a year, or fourth asthma drug; or 12 months after a hospital admission for asthma. A nested case-control and conditional logistic regression was used to evaluate factors associated with receiving a referral.

RESULTS

A total of 246,116 asthma patients were eligible. There was a slight increase in secondary care referrals from 2014 onwards but the percentage remained low with <20% in each high-risk group referred for specialist care. The factors in the past year that were most strongly associated with receiving a referral were a hospital admission or A&E visit for asthma, ≥3 OCS courses, ≥2 add-on drugs, or high-dose ICS prescription.

CONCLUSIONS

The majority of high-risk asthma patients were not referred for specialist care, as recommended by national guidelines. Compared to other risk factors, those admitted to hospital were most likely to receive a referral.

P3509Leukocyte derived tumour necrosis factor modulates cardiac function in health and disease

Purpose

Tumour necrosis factor alpha (TNFα) regulates both normal and pathophysiological cardiac function. The regulatory role of TNFα derived from different sources (leukocyte versus cardiac cells) in cardiac physiology is unclear. Deficiency of iRhom2 protein prevents circulating immune cells from shedding TNFα (and CD62L, an adhesion molecule essential for effective immune function). Here we investigated the role of leukocyte derived TNFα in constitutive cardiac function and after cardiac injury.

Methods

Adult iRhom2-deficient mice (KO) and wildtype (Wt) littermates, of both genders, underwent echocardiography to assess cardiac physiologic function at least 1 week before receiving a single dose of isoproterenol (300mg/kg IP) to induce cellular death in 10% of the cardiomyoctes [1]. Cardiac echocardiography was repeated 36 hours after isoproterenol. Peripheral and cardiac-resident leukocytes were phenotyped by flow cytometry and molecular markers of cardiac stress (atrial and brain natriuretic protein, ANP, BNP) and inflammation (NFkB) were quantified using RT-PCR.

Results

Peripheral leukocytes from iRhom2 KO mice failed to shed CD62L in response to isoproterenol induced cardiac injury (e.g. neutrophils CD62L Mean Fluorescence Intensity KO: 9149±4616, Wt: 972±558, p<0.0001, n=9). iRhom2-deficient mice had higher cardiac output at baseline (KO 23±2 mL/min, n=11) compared to their wildtype littermates (Wt 18±3 mL/min, n=9). Wild type mice increased contractility after isoproterenol (Wt ejection fraction: baseline 60±6%, isoproterenol 68±6%, n=8) whilst iRhom2-deficient mice were unable to (KO ejection fraction: baseline 66±9%, isoproterenol 61±5%, n=8). ANP and BNP mRNA were elevated in ventricular tissue of iRhom2-knockout mice after isoproterenol, when compared to naïve tissue (ANP 2ΔCT: 3x increase, BNP 2ΔCT: 1.6x increase) whereas only ANP was elevated in wildtypes (ANP 2ΔCT: 2.7x increase, BNP 2ΔCT: 0.9x increase). No difference in immune cell infiltration of ventricular cardiac tissue was observed (number of CD45+ cells KO: 3014±3482, Wt: 2555±1411, p=0.7, n=9) NFkB mRNA was upregulated at baseline (2ΔCT KO: 0.2±0.08, Wt: 0.1±0.09) suggesting constitutive cardiac inflammation in iRhom2-deficient mice.

Conclusions

Inability to shed CD62L and TNFα is associated with constitutive and acquired cardiac dysfunction in iRhom2-deficient mice. These data support the hypothesis that leukocyte-derived TNFα is required for maintaining cardiac function in health and disease.

Acknowledgement/Funding

National Institute of Academic Anaesthesia/Royal College of Anaesthetists/British Journal of Anaesthesia; National Institute for Health Research

Priorities for future research into asthma diagnostic tools: A PAN-EU consensus exercise from the European asthma research innovation partnership (EARIP)

The diagnosis of asthma is currently based on clinical history, physical examination and lung function, and to date, there are no accurate objective tests either to confirm the diagnosis or to discriminate between different types of asthma. This consensus exercise reviews the state of the art in asthma diagnosis to identify opportunities for future investment based on the likelihood of their successful development, potential for widespread adoption and their perceived impact on asthma patients. Using a two-stage e-Delphi process and a summarizing workshop, a group of European asthma experts including health professionals, researchers, people with asthma and industry representatives ranked the potential impact of research investment in each technique or tool for asthma diagnosis and monitoring. After a systematic review of the literature, 21 statements were extracted and were subject of the two-stage Delphi process. Eleven statements were scored 3 or more and were further discussed and ranked in a face-to-face workshop. The three most important diagnostic/predictive tools ranked were as follows: "New biological markers of asthma (eg genomics, proteomics and metabolomics) as a tool for diagnosis and/or monitoring," "Prediction of future asthma in preschool children with reasonable accuracy" and "Tools to measure volatile organic compounds (VOCs) in exhaled breath."

Functional DNA methylation signatures for autism spectrum disorder genomic risk loci: 16p11.2 deletions and CHD8 variants

Background

Autism spectrum disorder (ASD) is a common and etiologically heterogeneous neurodevelopmental disorder. Although many genetic causes have been identified (> 200 ASD-risk genes), no single gene variant accounts for > 1% of all ASD cases. A role for epigenetic mechanisms in ASD etiology is supported by the fact that many ASD-risk genes function as epigenetic regulators and evidence that epigenetic dysregulation can interrupt normal brain development. Gene-specific DNAm profiles have been shown to assist in the interpretation of variants of unknown significance. Therefore, we investigated the epigenome in patients with ASD or two of the most common genomic variants conferring increased risk for ASD. Genome-wide DNA methylation (DNAm) was assessed using the Illumina Infinium HumanMethylation450 and MethylationEPIC arrays in blood from individuals with ASD of heterogeneous, undefined etiology (n = 52), and individuals with 16p11.2 deletions (16p11.2del, n = 9) or pathogenic variants in the chromatin modifier CHD8 (CHD8^+/−, n = 7).

Results

DNAm patterns did not clearly distinguish heterogeneous ASD cases from controls. However, the homogeneous genetically-defined 16p11.2del and CHD8^+/− subgroups each exhibited unique DNAm signatures that distinguished 16p11.2del or CHD8^+/− individuals from each other and from heterogeneous ASD and control groups with high sensitivity and specificity. These signatures also classified additional 16p11.2del (n = 9) and CHD8 (n = 13) variants as pathogenic or benign. Our findings that DNAm alterations in each signature target unique genes in relevant biological pathways including neural development support their functional relevance. Furthermore, genes identified in our CHD8^+/− DNAm signature in blood overlapped differentially expressed genes in CHD8^+/− human-induced pluripotent cell-derived neurons and cerebral organoids from independent studies.

Conclusions

DNAm signatures can provide clinical utility complementary to next-generation sequencing in the interpretation of variants of unknown significance. Our study constitutes a novel approach for ASD risk-associated molecular classification that elucidates the vital cross-talk between genetics and epigenetics in the etiology of ASD.

Electronic supplementary material

The online version of this article (10.1186/s13148-019-0684-3) contains supplementary material, which is available to authorized users.