CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

BACKGROUND

The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors.

RESULTS

Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic.

CONCLUSIONS

Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.

High Resolution Study of ^{40}Ca to Constrain Potassium Nucleosynthesis in NGC 2419

The globular cluster NGC 2419 was the first to exhibit a Mg-K anticorrelation, linked to hydrogen burning at temperatures between 80-260 MK. However, the key K-destroying reaction, ^{39}K(p,γ)^{40}Ca, has a large rate uncertainty in this range. We significantly constrain this rate with a high resolution ^{39}K(^{3}He,d)^{40}Ca study. We resolve the E_{r}^{c.m.}=154  keV resonance in ^{39}K+p for the first time, increasing the previous rate by up to a factor 13 and reducing its 1σ width by up to a factor of 42. Reaction network calculations for NGC 2419 suggest that this could lower temperatures needed to reproduce the Mg-K anticorrelation.

Effects of empagliflozin on progression of chronic kidney disease: a prespecified secondary analysis from the empa-kidney trial

BACKGROUND

Sodium-glucose co-transporter-2 (SGLT2) inhibitors reduce progression of chronic kidney disease and the risk of cardiovascular morbidity and mortality in a wide range of patients. However, their effects on kidney disease progression in some patients with chronic kidney disease are unclear because few clinical kidney outcomes occurred among such patients in the completed trials. In particular, some guidelines stratify their level of recommendation about who should be treated with SGLT2 inhibitors based on diabetes status and albuminuria. We aimed to assess the effects of empagliflozin on progression of chronic kidney disease both overall and among specific types of participants in the EMPA-KIDNEY trial.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA), and included individuals aged 18 years or older with an estimated glomerular filtration rate (eGFR) of 20 to less than 45 mL/min per 1·73 m2, or with an eGFR of 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher. We explored the effects of 10 mg oral empagliflozin once daily versus placebo on the annualised rate of change in estimated glomerular filtration rate (eGFR slope), a tertiary outcome. We studied the acute slope (from randomisation to 2 months) and chronic slope (from 2 months onwards) separately, using shared parameter models to estimate the latter. Analyses were done in all randomly assigned participants by intention to treat. EMPA-KIDNEY is registered at ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and then followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroups of eGFR included 2282 (34·5%) participants with an eGFR of less than 30 mL/min per 1·73 m2, 2928 (44·3%) with an eGFR of 30 to less than 45 mL/min per 1·73 m2, and 1399 (21·2%) with an eGFR 45 mL/min per 1·73 m2 or higher. Prespecified subgroups of uACR included 1328 (20·1%) with a uACR of less than 30 mg/g, 1864 (28·2%) with a uACR of 30 to 300 mg/g, and 3417 (51·7%) with a uACR of more than 300 mg/g. Overall, allocation to empagliflozin caused an acute 2·12 mL/min per 1·73 m2 (95% CI 1·83-2·41) reduction in eGFR, equivalent to a 6% (5-6) dip in the first 2 months. After this, it halved the chronic slope from -2·75 to -1·37 mL/min per 1·73 m2 per year (relative difference 50%, 95% CI 42-58). The absolute and relative benefits of empagliflozin on the magnitude of the chronic slope varied significantly depending on diabetes status and baseline levels of eGFR and uACR. In particular, the absolute difference in chronic slopes was lower in patients with lower baseline uACR, but because this group progressed more slowly than those with higher uACR, this translated to a larger relative difference in chronic slopes in this group (86% [36-136] reduction in the chronic slope among those with baseline uACR <30 mg/g compared with a 29% [19-38] reduction for those with baseline uACR ≥2000 mg/g; ptrend<0·0001).

INTERPRETATION

Empagliflozin slowed the rate of progression of chronic kidney disease among all types of participant in the EMPA-KIDNEY trial, including those with little albuminuria. Albuminuria alone should not be used to determine whether to treat with an SGLT2 inhibitor.

FUNDING

Boehringer Ingelheim and Eli Lilly.

Impact of primary kidney disease on the effects of empagliflozin in patients with chronic kidney disease: secondary analyses of the EMPA-KIDNEY trial

BACKGROUND

The EMPA-KIDNEY trial showed that empagliflozin reduced the risk of the primary composite outcome of kidney disease progression or cardiovascular death in patients with chronic kidney disease mainly through slowing progression. We aimed to assess how effects of empagliflozin might differ by primary kidney disease across its broad population.

METHODS

EMPA-KIDNEY, a randomised, controlled, phase 3 trial, was conducted at 241 centres in eight countries (Canada, China, Germany, Italy, Japan, Malaysia, the UK, and the USA). Patients were eligible if their estimated glomerular filtration rate (eGFR) was 20 to less than 45 mL/min per 1·73 m2, or 45 to less than 90 mL/min per 1·73 m2 with a urinary albumin-to-creatinine ratio (uACR) of 200 mg/g or higher at screening. They were randomly assigned (1:1) to 10 mg oral empagliflozin once daily or matching placebo. Effects on kidney disease progression (defined as a sustained ≥40% eGFR decline from randomisation, end-stage kidney disease, a sustained eGFR below 10 mL/min per 1·73 m2, or death from kidney failure) were assessed using prespecified Cox models, and eGFR slope analyses used shared parameter models. Subgroup comparisons were performed by including relevant interaction terms in models. EMPA-KIDNEY is registered with ClinicalTrials.gov, NCT03594110.

FINDINGS

Between May 15, 2019, and April 16, 2021, 6609 participants were randomly assigned and followed up for a median of 2·0 years (IQR 1·5-2·4). Prespecified subgroupings by primary kidney disease included 2057 (31·1%) participants with diabetic kidney disease, 1669 (25·3%) with glomerular disease, 1445 (21·9%) with hypertensive or renovascular disease, and 1438 (21·8%) with other or unknown causes. Kidney disease progression occurred in 384 (11·6%) of 3304 patients in the empagliflozin group and 504 (15·2%) of 3305 patients in the placebo group (hazard ratio 0·71 [95% CI 0·62-0·81]), with no evidence that the relative effect size varied significantly by primary kidney disease (pheterogeneity=0·62). The between-group difference in chronic eGFR slopes (ie, from 2 months to final follow-up) was 1·37 mL/min per 1·73 m2 per year (95% CI 1·16-1·59), representing a 50% (42-58) reduction in the rate of chronic eGFR decline. This relative effect of empagliflozin on chronic eGFR slope was similar in analyses by different primary kidney diseases, including in explorations by type of glomerular disease and diabetes (p values for heterogeneity all >0·1).

INTERPRETATION

In a broad range of patients with chronic kidney disease at risk of progression, including a wide range of non-diabetic causes of chronic kidney disease, empagliflozin reduced risk of kidney disease progression. Relative effect sizes were broadly similar irrespective of the cause of primary kidney disease, suggesting that SGLT2 inhibitors should be part of a standard of care to minimise risk of kidney failure in chronic kidney disease.

FUNDING

Boehringer Ingelheim, Eli Lilly, and UK Medical Research Council.

Improved Measurement of the Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

Reactor neutrino experiments play a crucial role in advancing our knowledge of neutrinos. In this Letter, the evolution of the flux and spectrum as a function of the reactor isotopic content is reported in terms of the inverse-beta-decay yield at Daya Bay with 1958 days of data and improved systematic uncertainties. These measurements are compared with two signature model predictions: the Huber-Mueller model based on the conversion method and the SM2018 model based on the summation method. The measured average flux and spectrum, as well as the flux evolution with the ^{239}Pu isotopic fraction, are inconsistent with the predictions of the Huber-Mueller model. In contrast, the SM2018 model is shown to agree with the average flux and its evolution but fails to describe the energy spectrum. Altering the predicted inverse-beta-decay spectrum from ^{239}Pu fission does not improve the agreement with the measurement for either model. The models can be brought into better agreement with the measurements if either the predicted spectrum due to ^{235}U fission is changed or the predicted ^{235}U, ^{238}U, ^{239}Pu, and ^{241}Pu spectra are changed in equal measure.

Precision Measurement of Reactor Antineutrino Oscillation at Kilometer-Scale Baselines by Daya Bay

We present a new determination of the smallest neutrino mixing angle θ_{13} and the mass-squared difference Δm_{32}^{2} using a final sample of 5.55×10^{6} inverse beta-decay (IBD) candidates with the final-state neutron captured on gadolinium. This sample is selected from the complete dataset obtained by the Daya Bay reactor neutrino experiment in 3158 days of operation. Compared to the previous Daya Bay results, selection of IBD candidates has been optimized, energy calibration refined, and treatment of backgrounds further improved. The resulting oscillation parameters are sin^{2}2θ_{13}=0.0851±0.0024, Δm_{32}^{2}=(2.466±0.060)×10^{-3}  eV^{2} for the normal mass ordering or Δm_{32}^{2}=-(2.571±0.060)×10^{-3}  eV^{2} for the inverted mass ordering.

Utility of SARS-CoV-2 Genomic Sequencing for Understanding Transmission and School Outbreaks

OBJECTIVE

An understanding of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) transmission in schools is important. It is often difficult, using epidemiological information alone, to determine whether cases associated with schools represent multiple introductions from the community or transmission within the school. We describe the use of whole genome sequencing (WGS) in multiple schools to investigate outbreaks of SARS-CoV-2 in the pre-Omicron period.

STUDY DESIGN

School outbreaks were identified for sequencing by local public health units based on multiple cases without known epidemiological links. Cases of SARS-CoV-2 from students and staff from 4 school outbreaks in Ontario underwent WGS and phylogenetic analysis. The epidemiological clinical cohort data and genomic cluster data are described to help further characterize these outbreaks.

RESULTS

A total of 132 positive SARS-CoV-2 cases among students and staff from 4 school outbreaks were identified with 65 (49%) of cases able to be sequenced with high-quality genomic data. The 4 school outbreaks consisted of 53, 37, 21 and 21 positive cases; within each outbreak there were between 8 and 28 different clinical cohorts identified. Among the sequenced cases, between 3 and 7 genetic clusters, defined as different strains, were identified in each outbreak. We found genetically different viruses within several clinical cohorts.

CONCLUSIONS

WGS, together with public health investigation, is a useful tool to investigate SARS-CoV-2 transmission within schools. Its early use has the potential to better understand when transmission may have occurred, can aid in evaluating how well mitigation interventions are working and has the potential to reduce unnecessary school closures when multiple genetic clusters are identified.

Extramedullary Hematopoiesis Identified in Pleural Fluid of a Patient with Bilateral Pleural Effusions and Associated Myelofibrosis

Introduction/Objective

Extramedullary hematopoiesis (EMH) is the formation of blood cells outside of the bone marrow medullary spaces. EMH is typically seen in the spleen or liver and in association with bone marrow replacement disorders, hemoglobinopathies, and other hematological disorders. Rarely EMH can occur in the pleural cavity of patients resulting in subsequent pleural effusions. These cases can accurately be diagnosed with identification of megakaryocytes and other hematopoietic elements in the pleural fluid.

Methods/Case Report

We present a 67 year old male with a past medical history of pericardial effusion, Jak 2 positive Myelofibrosis (Post PV/ET), and type II diabetes mellitus, who presented with complaint of shortness of breath for 10 days. The patient did not require oxygen at home and denied any cough or hemoptysis. In the emergency department a Chest X ray was ordered which showed bilateral pulmonary effusions. These effusions were attributed to worsening congestive heart failure, and diuretic therapy was started. With no resolution of the pleural effusions, the decision was made to conduct a thoracentesis and remove the fluid. Interventional radiology then performed a thoracentesis removing 1000 mL from each the left and right pleural spaces. Cytological preparation of the fluid demonstrated myeloid and erythroid precursors as well as occasional megakaryocytes. The diagnosis of extramedullary hematopoiesis was made and the effusion did not recur.

Results (if a Case Study enter NA)

NA.

Conclusion

Extramedullary hematopoiesis of the pleural space is rare. However it must be considered in the differential diagnosis of a patient with persistent effusions and concomitant bone marrow replacement disease such as myelofibrosis. Prompt removal and cytological evaluation of the pleura fluid for hematopoietic elements should be performed in order to diagnose and manage the patient most effectively.

Direct Measurement of Resonances in ^{7}Be(α,γ)^{11}C Relevant to νp-Process Nucleosynthesis

We have performed the first direct measurement of two resonances of the ^{7}Be(α,γ)^{11}C reaction with unknown strengths using an intense radioactive ^{7}Be beam and the DRAGON recoil separator. We report on the first measurement of the 1155 and 1110 keV resonance strengths of 1.73±0.25(stat)±0.40(syst)  eV and 125_{-25}^{+27}(stat)±15(syst)  meV, respectively. The present results have reduced the uncertainty in the ^{7}Be(α,γ)^{11}C reaction rate to ∼9.4%-10.7% over T=1.5-3  GK, which is relevant for nucleosynthesis in the neutrino-driven outflows of core-collapse supernovae (νp process). We find no effect of the new, constrained reaction rate on νp-process nucleosynthesis.

First Measurement of High-Energy Reactor Antineutrinos at Daya Bay

This Letter reports the first measurement of high-energy reactor antineutrinos at Daya Bay, with nearly 9000 inverse beta decay candidates in the prompt energy region of 8-12 MeV observed over 1958 days of data collection. A multivariate analysis is used to separate 2500 signal events from background statistically. The hypothesis of no reactor antineutrinos with neutrino energy above 10 MeV is rejected with a significance of 6.2 standard deviations. A 29% antineutrino flux deficit in the prompt energy region of 8-11 MeV is observed compared to a recent model prediction. We provide the unfolded antineutrino spectrum above 7 MeV as a data-based reference for other experiments. This result provides the first direct observation of the production of antineutrinos from several high-Q_{β} isotopes in commercial reactors.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

Joint Determination of Reactor Antineutrino Spectra from ^{235}U and ^{239}Pu Fission by Daya Bay and PROSPECT

A joint determination of the reactor antineutrino spectra resulting from the fission of ^{235}U and ^{239}Pu has been carried out by the Daya Bay and PROSPECT Collaborations. This Letter reports the level of consistency of ^{235}U spectrum measurements from the two experiments and presents new results from a joint analysis of both data sets. The measurements are found to be consistent. The combined analysis reduces the degeneracy between the dominant ^{235}U and ^{239}Pu isotopes and improves the uncertainty of the ^{235}U spectral shape to about 3%. The ^{235}U and ^{239}Pu antineutrino energy spectra are unfolded from the jointly deconvolved reactor spectra using the Wiener-SVD unfolding method, providing a data-based reference for other reactor antineutrino experiments and other applications. This is the first measurement of the ^{235}U and ^{239}Pu spectra based on the combination of experiments at low- and highly enriched uranium reactors.

Diagnostic yield of genome sequencing for fetal structural anomalies

OBJECTIVE

Genome sequencing (GS >30x) is beginning to be adopted as a comprehensive genome-wide test for the diagnosis of rare disease in the post-natal setting. Recent studies demonstrated the utility of exome sequencing (ES) in prenatal diagnosis, we investigate the potential benefits for GS to act as a comprehensive prenatal test for diagnosis of fetal abnormalities.

METHODS

We performed GS on a prospective cohort of 37 singleton fetuses with ultrasound-identified structural abnormalities undergoing invasive prenatal testing. GS was performed in parallel with standard diagnostic testing, and the prioritized variants were classified according to ACMG guidelines and reviewed by a panel of board-certified laboratory and clinical geneticists.

RESULTS

Diagnostic sequence variants were identified in 5 fetuses (14%), with pathogenic variants found in NIPBL, FOXF1, RERE, AMMECR1, and FLT4. A further 7 fetuses (19%) had variants of uncertain significance (VUS) that may explain the phenotypes. Importantly, GS also identified all pathogenic variants reported by clinical microarray (2 CNVs, 5%).

CONCLUSION

Prenatal GS offered diagnoses (sequence variants and CNVs) in 19% of fetuses with structural anomalies. GS has the potential of replacing multiple consecutive tests, including microarray, gene panels, and WES, to provide the most comprehensive analysis in a timely manner necessary for prenatal diagnosis. This article is protected by copyright. All rights reserved. What's already known about this topic? Current prenatal diagnostic protocol in Canada includes rapid aneuploidy detection (RAD) followed by microarray analysis. The diagnostic yield of Exome sequencing in fetuses with ultrasound abnormalities and negative results by RAD and CMA is 8.5 to 10%. However, the clinical utility of genome sequencing in prenatal settings is not established. What does this study add? This study demonstrates that RAD followed by genome sequencing has a diagnostic yield of ∼19% in fetuses with ultrasound abnormalities. Parental follow up testing to determine the inheritance of potentially pathogenic variants can further increase the diagnostic yield.

Frontal Fibrosing Alopecia survey of severity assessment methods in routine clinical practice and validation of the IFFACG measurement guidance

BACKGROUND

Lack of validated and responsive outcome measures in the management of Frontal Fibrosing Alopecia (FFA) significantly limits our ability to assess disease progression and treatment response over time.

OBJECTIVES

The aim of this study was to understand how FFA extent and progression is currently assessed in UK specialist centres, validate components of the International FFA Cooperative Group (IFFACG) statement on FFA assessment, and identify pragmatic advice to improve FFA management in clinic.

METHODS

Consultant Dermatologists with a specialist interest in hair loss (n=17) were invited to take part. Preferred FFA assessment methods were explored using questionnaires and clinical scenarios. Participants were asked to identify and mark the current hairline in 10 frontal and 10 temporal hairline images, with assessment repeated 3 months later (to assess intra-individual variability) and 12 months later (to test whether inter-individual accuracy could be improved with simple instruction).

RESULTS

All 17 clinicians (100%) completed the questionnaire at each time interval. We identified a wide variation in assessment techniques between our experts. Measurements were perceived as the most accurate method of assessing frontal recession whereas photography was preferred for temporal recession. Inter-rater reliability between clinicians measuring the frontal hairline scenarios indicated a moderate strength of agreement (ICC 0.613; 95% CI: 0.398 to 0.848), yet intra-rater reliability was found to be poor with wide limits of agreement (-8.71mm to 9.92mm) on follow-up. Importantly, when clear guidance was provided on how the hairline should be identified (questionnaire 3), inter-rater reliability improved significantly, with an ICC 0.702 suggesting moderate agreement (95% CI: 0.508 to 0.890; p<0.001). A similar pattern was seen with temporal hairline measurements, which again improved in accuracy with instruction.

CONCLUSION

We show that accuracy of measurements in FFA can be improved with simple instruction and validate components of the IFFACG measurement recommendations.

519 Outcomes of Management with Ilizarov Frames in Bone Infection: An Observational Study

Aim

The successful treatment and eradication of bone infection requires a multifaceted approach and may recur even after excision if resultant bone void is not managed effectively. This paper aims to review the clinical effectiveness of antibiotic-impregnated bone void filler and current empirical antibiotic guidelines.

Method

We report a retrospective study of 18 patients with chronic osteomyelitis following injury or surgery managed via Ilizarov Ring Fixator (IRF). All patients were managed by IRF stabilisation procedures with debridement, microbiological sampling, and bone void filling with antibiotic-impregnated biocomposite material, in addition to culture-specific systemic antimicrobial therapy.

Results

Patients were followed up for a mean of 15.9 months. Infection was eradicated in 94.1% of patients in a grossly comorbid demographic. Comorbidities associated with increased risk of osteomyelitis were noted in 72.2% of patients. Anaerobic bacteria were identified in culture for four (22.2%) of the 18 patients.

Conclusions

We detected a higher than suspected growth of anaerobes in our samples, suggesting the need for metronidazole in empirical antibiotic treatment. This study would suggest that the use of STIMULAN® may be preferable in this National Health Service from a cost-effect perspective, as our results are comparable to those using other bone void fillers.

1323 Assessment of The Appropriate Use of Imaging and Reporting in Acute Pancreatitis in A Secondary Care Setting

Aim

Acute pancreatitis is the world's most common gastrointestinal disease requiring hospital admission. Our audit aim was to assess the timeframe within which Abdominal Ultrasound Scans (USS) and Computerised Tomography (CT) were performed, reported indications for CT and the prognostic factors noted in imaging reports.

Method

A retrospective search included admissions with acute pancreatitis between 01/09/19 to 30/11/19, collecting demographics, admission time & date, time and date of both radiological investigations and imaging reports. Patients under the age of 18 were excluded.

Results

This search identified 75 patients (M:F, 40:35) with a median age of 53 (18-95) years. USS were performed within 24 hours of admission in 40.0% (n = 30) of cases. Out of the patients (n = 44) who received a CT scan, 15.9% (n = 7) were scanned after more than 72 hours of onset of symptoms and 84.1% (n = 37) were scanned within less than 72 hours. Furthermore, 88.6%(n = 39) of CT request indications were in keeping with our standards. The average length of hospital stay was 6.1 days when scanned within 72 hours and 11.8 days when scanned after more than 72 hours.

Conclusions

Only 17.3% (n = 13) of the patients audited met all our standards and were managed according to the guidelines. The average length of hospital stay was half in those who had a CT scan after more than 72 hours of admission and this was also used to monitor disease progression/regression.

Genetic contributors to risk of schizophrenia in the presence of a 22q11.2 deletion

Schizophrenia occurs in about one in four individuals with 22q11.2 deletion syndrome (22q11.2DS). The aim of this International Brain and Behavior 22q11.2DS Consortium (IBBC) study was to identify genetic factors that contribute to schizophrenia, in addition to the ~20-fold increased risk conveyed by the 22q11.2 deletion. Using whole-genome sequencing data from 519 unrelated individuals with 22q11.2DS, we conducted genome-wide comparisons of common and rare variants between those with schizophrenia and those with no psychotic disorder at age ≥25 years. Available microarray data enabled direct comparison of polygenic risk for schizophrenia between 22q11.2DS and independent population samples with no 22q11.2 deletion, with and without schizophrenia (total n = 35,182). Polygenic risk for schizophrenia within 22q11.2DS was significantly greater for those with schizophrenia (padj = 6.73 × 10-6). Novel reciprocal case-control comparisons between the 22q11.2DS and population-based cohorts showed that polygenic risk score was significantly greater in individuals with psychotic illness, regardless of the presence of the 22q11.2 deletion. Within the 22q11.2DS cohort, results of gene-set analyses showed some support for rare variants affecting synaptic genes. No common or rare variants within the 22q11.2 deletion region were significantly associated with schizophrenia. These findings suggest that in addition to the deletion conferring a greatly increased risk to schizophrenia, the risk is higher when the 22q11.2 deletion and common polygenic risk factors that contribute to schizophrenia in the general population are both present.

Impacts on staff after implementation of a respiratory protection program in a Victorian public hospital

BACKGROUND

In October 2020, the Royal Melbourne Hospital implemented a Respiratory Protection Program (RPP), which was initiated by the Victorian Government. This study was to evaluate the effectiveness of the program.

METHODS

A cohort of 158 employees, who were identified as high risk to respiratory biohazard exposure, were invited to participate in the RPP. We provided a bundle of interventions, which included an online training package, and mandatory quantitative fit testing. The main outcomes included the participants' knowledge and attitude toward respiratory protection equipment (RPE), which were assessed via an online survey. Their donning and doffing skills, and user seal check techniques on four different types of N95 respirators were also assessed by an observer using a pre-determined marking sheet. We compared these outcomes before and after participation in the program.

RESULTS

There was a total of 125 participants, all of whom completed the knowledge and attitude assessment, and 69 completed the skill assessment before and after the program. There was a statistically significant improvement in their knowledge scores, donning and doffing skills, and user seal check techniques after participation in the RPP. Participants also reported significant increased level of confidence in their RPE knowledge, training and skills; and workplace safety.

CONCLUSION

This initial report of the implementation of a novel RPP in a Victorian major tertiary hospital provides guidance on the benefits to respiratory protection, staff knowledge, skills, confidence and morale that can be acquired from a scalable online training package combined with mandatory quantitative fit testing.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Tokophobia and fear of birth: a workshop consensus statement on current issues and recommendations for future research

Objective: To discuss and develop a statement on the current state of the evidence and opinion in Fear of Childbirth (FoC) and Tokophobia (Tocophobia), and to provide recommendations. Background: A group met in 2019 to discuss the state of clinical and academic knowledge relating to FoC/Tokophobia. Five key areas were agreed as the focus of the meeting. Methods: 12 internationally acknowledged experts, in this or a closely related area (e.g. PTSD) met to discuss their understanding of the evidence for FoC/ Tokophobia and current practice. The consensus described in this paper constitutes the expression of the general opinion of the participants and does not necessarily imply unanimity. Keys points: Work focussed on tokophobia is recent and there remains a wide range of issues, which were addressed in the workshop including complexity in defining prevalence, a theoretical lack of understanding, which creates challenge for robust assessment and the identification of risk factors. An improved aetiological and developmental understanding of the tokophobia is required to underpin appropriate, effective and evidence-based interventions. Evaluation of pathways of care and relevant interventions, should be a focus of future research. Conclusion: Significant gaps remain within the FoC/tokophobia knowledge base. Further research is necessary.

Myeloid Sarcoma Involving the Central Nervous System Without Evidence of Preexisting Hematologic Disease: A Case Report

Introduction/Objective

Myeloid sarcoma within the central nervous system is a rare presentation of an infiltrative mass of immature myeloid cells. It is typically found in association with myeloid dysplastic syndrome, myeloproliferative disorder, or acute myeloid leukemia. Rarely, it can occur in the absence of these diseases.

Methods

We present the case of 68-year-old female with worsening nausea and headaches. Brain MRI showed diffuse pachymeningeal enhancement with numerous nodular enhancing extra-axial masses overlying both cerebral hemispheres.

Results

Open biopsy of these masses showed gelatinous, hemorrhagic, brown tissue measuring 3.0 x 2.0 x 0.7 cm. Histologically, the specimen shows a diffuse polymorphous atypical myeloid proliferation consisting of all three cell lineages. There are nodules composed predominantly of large blastoid cells with 1 to 2 prominent oblong nucleoli, consistent with erythroblasts and early erythroid precursors. In between the nodules there are myeloid cells in different stages of maturation, including numerous eosinophilic precursors. Scattered megakaryocytes are also identified.

Immunohistochemistry shows positivity for E-cadherin, CD235a and spectrin which highlight the immature erythroid cells. MPO, muramidase, and CD33 are positive in myeloid elements. Eosinophilic peroxidase highlights numerous eosinophilic precursors. CD34 is positive in the endothelial cells and very rare hematopoietic cells. CD20 and PAX 5 highlights B-cells, CD3 highlights T-cells, and CD4 highlights monocytic precursors, monocytes, histiocytes and a subset of T-cells.

Conclusion

Additional work up at the time of biopsy including FLOW cytometry and bone marrow biopsies showed no evidence of hematologic pathology. In summary the histologic and immunohistochemical findings demonstrate a tumor composed of proliferating immature myeloid cells most consistent with myeloid sarcoma without any evidence of hematological disease.

Improved Constraints on Sterile Neutrino Mixing from Disappearance Searches in the MINOS, MINOS+, Daya Bay, and Bugey-3 Experiments

Searches for electron antineutrino, muon neutrino, and muon antineutrino disappearance driven by sterile neutrino mixing have been carried out by the Daya Bay and MINOS+ collaborations. This Letter presents the combined results of these searches, along with exclusion results from the Bugey-3 reactor experiment, framed in a minimally extended four-neutrino scenario. Significantly improved constraints on the θ_{μe} mixing angle are derived that constitute the most constraining limits to date over five orders of magnitude in the mass-squared splitting Δm_{41}^{2}, excluding the 90% C.L. sterile-neutrino parameter space allowed by the LSND and MiniBooNE observations at 90% CL_{s} for Δm_{41}^{2}<13  eV^{2}. Furthermore, the LSND and MiniBooNE 99% C.L. allowed regions are excluded at 99% CL_{s} for Δm_{41}^{2}<1.6 eV^{2}.

BNST transient activity associates with approach behavior in a stressful environment and is modulated by the parabrachial nucleus

Studies demonstrate a role for the bed nucleus of the stria terminalis (BNST) in modulating affective behavior and stress-reward integration. To explore the dynamic nature of in vivo BNST activity associated with anxiety-like behavior in a stress-inducing context, we utilized fiber photometry and detected BNST calcium transients in mice during the novelty-suppressed feeding task (NSFT). Phasic BNST activity emerged time-locked to novel object or food pellet approach during NSFT. The parabrachial nucleus (PBN) has a large input to the BNST and is thought to function as a danger signal, in arousal responses and in feeding behavior. To explore a potential role for the PBN as a contributor to BNST activity in NSFT, we investigated whether chemogenetic regulation of PBN activity altered the dynamic BNST response synchronized to NSFT approach behavior. We found that activation of the hM3D(G_q) DREADD in the PBN enhanced the observed transient signal in the BNST synchronized to the consummatory food approach, and was associated at the behavioral level with increased latency to consume food. Because the PBN has multiple efferent pathways, we next used a transsynaptic anterograde AAV-based strategy to express hM3D(G_q) specifically in PBN-innervated BNST (BNST^PBN) neurons in male and female mice. Activation of hM3D(G_q) in these BNST^PBN neurons increased latency to consume food in female, but not male mice. To further explore the population of BNST neurons contributing to phasic BNST activity associated with NSFT, we turned to PKCδ neurons in BNST. BNST(PKCδ) neurons are implicated in stress and food-related behavior, and we previously found that the expression of this kinase is regulated in the BNST by stress in a sex-dependent manner. Here, we demonstrate close apposition of CGRP, a marker of PBN terminals, adjacent to BNST(PKCδ) cells. Finally, we find that PKCδ-expressing BNST cells exhibit a large transient signal synchronized to the consummatory food approach similar to that seen with bulk BNST activity measures. Taken together these data demonstrate phasic BNST activity at a global and cell-specific level that is driven in part by PBN activity at the time of NSFT consummatory approach behavior.

Viscous placebo and carbohydrate breakfasts similarly decrease appetite and increase resistance exercise performance compared with a control breakfast in trained males

Given the common view that pre-exercise nutrition/breakfast is important for performance, the present study investigated whether breakfast influences resistance exercise performance via a physiological or psychological effect. Twenty-two resistance-trained, breakfast-consuming men completed three experimental trials, consuming water-only (WAT), or semi-solid breakfasts containing 0 g/kg (PLA) or 1·5 g/kg (CHO) maltodextrin. PLA and CHO meals contained xanthan gum and low-energy flavouring (approximately 122 kJ), and subjects were told both 'contained energy'. At 2 h post-meal, subjects completed four sets of back squat and bench press to failure at 90 % ten repetition maximum. Blood samples were taken pre-meal, 45 min and 105 min post-meal to measure serum/plasma glucose, insulin, ghrelin, glucagon-like peptide-1 and peptide tyrosine-tyrosine concentrations. Subjective hunger/fullness was also measured. Total back squat repetitions were greater in CHO (44 (sd 10) repetitions) and PLA (43 (sd 10) repetitions) than WAT (38 (sd 10) repetitions; P < 0·001). Total bench press repetitions were similar between trials (WAT 37 (sd 7) repetitions; CHO 39 (sd 7) repetitions; PLA 38 (sd 7) repetitions; P = 0·130). Performance was similar between CHO and PLA trials. Hunger was suppressed and fullness increased similarly in PLA and CHO, relative to WAT (P < 0·001). During CHO, plasma glucose was elevated at 45 min (P < 0·05), whilst serum insulin was elevated (P < 0·05) and plasma ghrelin suppressed at 45 and 105 min (P < 0·05). These results suggest that breakfast/pre-exercise nutrition enhances resistance exercise performance via a psychological effect, although a potential mediating role of hunger cannot be discounted.

Minimal Compared With Standard Monitoring During Sofosbuvir-Based Hepatitis C Treatment: A Randomized Controlled Trial

Background

Oral direct-acting antiviral agents (DAAs) for hepatitis C virus (HCV) became government subsidized in Australia in March 2016, bringing the interferon era to a close. The ideal monitoring schedule for patients receiving DAAs is unclear.

Methods

This study is a randomized controlled trial comparing standard with minimal monitoring in adults receiving sofosbuvir-based therapy for HCV genotypes 1 or 3. Exclusion criteria were cirrhosis or predicted poor adherence. Standard monitoring included blood tests and face-to-face clinic visits at treatment weeks 4 and 12 and 12 weeks after treatment completion. Minimal monitoring included a phone call at weeks 4 and 12 and one set of blood tests plus a clinic visit 12 weeks after treatment completion. The coprimary outcomes were as follows: (1) proportion of participants with sustained virological response; (2) staff time spent on patient support; and (3) patient satisfaction on a 10-point Likert scale.

Results

Thirty-six patients were randomized to standard monitoring and 38 to minimal monitoring. Sustained virological response at 12 weeks after the end of treatment was documented in 32 of 36 (89%) in the standard versus 37 of 38 (97%) in the minimal monitoring group. Staff time was nonsignificantly longer in the standard group (median 69 [interquartile range {IQR}, 54–80] versus 52 [IQR, 40–75] minutes). Patient satisfaction scores were not different (mean 9.8 of 10 standard versus 9.6 of 10 minimal group). There was no difference in adverse events or unplanned hospital visits; mean per-patient blood test costs were higher in the standard monitoring group ($432 versus $123, P < .001).

Conclusions

On-treatment monitoring with blood tests and clinic visits may not be necessary during sofosbuvir-based HCV treatment in selected patients.

AutoMicrobic System for Biochemical Identification of Listeria Species Isolated From Foods: Collaborative Study

A collaborative study was conducted to evaluate the performance of the AutoMicrobic System Gram- Positive Identification (GPI) and Gram-Negative Identification (GNI) test kits to biochemically characterize Listeria spp. Thirteen laboratories each tested 97 food and environmental isolates, representing the 7 species of Listeria, as well as 11 additional genera of Gram-positive rods. Each collaborator inoculated both a GPI and a GNI card with a pure culture of each organism. The AutoMicrobic System identified the isolates and printed out the biochemical results. The GPI card is used to obtain a species identification and a mannitol reaction result, and the GNI card is used to obtain rhamnose and xylose reaction results. Organisms are classified into species groups and can be further distinguished on the basis of hemolysis or nitrate reduction tests. The AutoMicrobic System method correctly classified 90.8% of the Listeria spp. isolates and 100% of the non-Listeria isolates. The AutoMicrobic System method was adopted first action by AOAC International for the biochemical characterization of Listeria spp. isolated from food and environmental sources.

Extraction of the ^{235}U and ^{239}Pu Antineutrino Spectra at Daya Bay

This Letter reports the first extraction of individual antineutrino spectra from ^{235}U and ^{239}Pu fission and an improved measurement of the prompt energy spectrum of reactor antineutrinos at Daya Bay. The analysis uses 3.5×10^{6} inverse beta-decay candidates in four near antineutrino detectors in 1958 days. The individual antineutrino spectra of the two dominant isotopes, ^{235}U and ^{239}Pu, are extracted using the evolution of the prompt spectrum as a function of the isotope fission fractions. In the energy window of 4-6 MeV, a 7% (9%) excess of events is observed for the ^{235}U (^{239}Pu) spectrum compared with the normalized Huber-Mueller model prediction. The significance of discrepancy is 4.0σ for ^{235}U spectral shape compared with the Huber-Mueller model prediction. The shape of the measured inverse beta-decay prompt energy spectrum disagrees with the prediction of the Huber-Mueller model at 5.3σ. In the energy range of 4-6 MeV, a maximal local discrepancy of 6.3σ is observed.

Mepilex Border Sacrum and Heel Dressings for the Prevention of Pressure Ulcers: A NICE Medical Technology Guidance

Mepilex Border Sacrum and Heel dressings are self-adherent, multilayer foam dressings designed for use on the heel and sacrum aiming to prevent pressure ulcers. The dressings are used in addition to standard care protocols for pressure ulcer prevention. The National Institute for Health and Care Excellence (NICE) selected Mepilex Border Sacrum and Heel dressings for evaluation. The External Assessment Centre (EAC) critiqued the company's submission. Thirteen studies (four randomised controlled trials and nine nonrandomised comparative studies) were included. The majority of studies compared Mepilex Border Sacrum dressings (plus standard care) with standard care alone. Comparative evidence for Mepilex Border Heel dressings was limited. A meta-analysis indicated a non-statistically significant difference in favour of Mepilex Border Sacrum dressings for pressure ulcer incidence [RR 0.51 (95% CI 0.22-1.18)]. The company produced a de novo cost model, which was critiqued by the EAC. After the EAC updated input parameters, cost savings of £19 per patient compared with standard care alone for pressure ulcer prevention were estimated with Mepilex Border dressings predicted to be cost saving in 57% of iterations. The Medical Technologies Advisory Committee reviewed the evidence and judged that, although Mepilex Border Heel and Sacrum dressings have potential to prevent pressure ulcers in people who are considered to be at risk in acute care settings, further evidence is required to address uncertainties around the claimed benefits of the dressings and the incidence of pressure ulcers in an NHS acute-care setting. After a public consultation, NICE published this as Medical Technology Guidance 40.

Thiemann disease and familial digital arthropathy - brachydactyly: two sides of the same coin?

Background

Familial digital arthropathy-brachydactyly (FDAB) and Thiemann disease are non-inflammatory digital arthropathies with many phenotypic similarities. Thirty-three cases of Thiemann disease have been described so far (Mangat et al, Ann Rheum Dis 64:11-2, 2005; Ha et al, Thiemann's disease: a case Report, 2017) but no gene variants have been identified as causative to date. FDAB is reported in only a few patients and has been associated with three heterozygous missense variants in the Transient receptor potential vanilloid 4 (TRPV4) gene. We report a TRPV4 variant in a father and son referred with a diagnosis of Thiemann disease and compare the clinical and radiological features of Thiemann disease with Familial digital arthropathy-brachydactyly (FDAB). We hypothesize that these two entities may be one and the same.

Methods

We describe a father and son referred with a diagnosis of Thiemann disease who were subsequently identified with a heterozygous variant (c.809G > T) in TRPV4. The identical genetic variant was previously reported to cause FDAB. A PUBMED® database search was conducted to retrieve articles related to Thiemann disease and FDAB. We were able to review the clinical and radiological findings of nineteen individuals affected by Thiemann disease and compare them with three families affected by FDAB.

Results

Thiemann disease initially affects the proximal interphalangeal joints and primarily the middle phalangeal bases. In FDAB, the distal phalangeal joints are first affected with the middle phalangeal heads being the primary site of changes. Radial deviation has only been described in FDAB. Our analysis determined that 5 of 20 individuals affected by Thiemann disease have clinical and radiological findings that also fit well with FDAB.

Conclusion

FDAB and Thiemann disease are non-inflammatory digital arthropathies with phenotypic overlap. Although more extensive joint involvement, a distal hand joint preponderance and brachydactyly are expected in FDAB, there are striking clinical and radiological similarities between the two entities. Our analysis suggests that these two phenotypes may represent phenotypic variability of the same entity. Despite many attempts to identify other reported patients affected by Thiemann disease, we were not able to procure DNA from any of the cases to verify our findings. Genetic testing of an affected individual will be crucial in order to provide accurate reproductive genetic counselling about the autosomal dominant nature of this condition.

Electronic supplementary material

The online version of this article (10.1186/s13023-019-1138-x) contains supplementary material, which is available to authorized users.

Measurement of the Electron Antineutrino Oscillation with 1958 Days of Operation at Daya Bay

We report a measurement of electron antineutrino oscillation from the Daya Bay Reactor Neutrino Experiment with nearly 4 million reactor ν[over ¯]_{e} inverse β decay candidates observed over 1958 days of data collection. The installation of a flash analog-to-digital converter readout system and a special calibration campaign using different source enclosures reduce uncertainties in the absolute energy calibration to less than 0.5% for visible energies larger than 2 MeV. The uncertainty in the cosmogenic ^{9}Li and ^{8}He background is reduced from 45% to 30% in the near detectors. A detailed investigation of the spent nuclear fuel history improves its uncertainty from 100% to 30%. Analysis of the relative ν[over ¯]_{e} rates and energy spectra among detectors yields sin^{2}2θ_{13}=0.0856±0.0029 and Δm_{32}^{2}=(2.471_{-0.070}^{+0.068})×10^{-3}  eV^{2} assuming the normal hierarchy, and Δm_{32}^{2}=-(2.575_{-0.070}^{+0.068})×10^{-3}  eV^{2} assuming the inverted hierarchy.

A Type 1 Diabetes Genetic Risk Score Predicts Progression of Islet Autoimmunity and Development of Type 1 Diabetes in Individuals at Risk

OBJECTIVE

We tested the ability of a type 1 diabetes (T1D) genetic risk score (GRS) to predict progression of islet autoimmunity and T1D in at-risk individuals.

RESEARCH DESIGN AND METHODS

We studied the 1,244 TrialNet Pathway to Prevention study participants (T1D patients' relatives without diabetes and with one or more positive autoantibodies) who were genotyped with Illumina ImmunoChip (median [range] age at initial autoantibody determination 11.1 years [1.2-51.8], 48% male, 80.5% non-Hispanic white, median follow-up 5.4 years). Of 291 participants with a single positive autoantibody at screening, 157 converted to multiple autoantibody positivity and 55 developed diabetes. Of 953 participants with multiple positive autoantibodies at screening, 419 developed diabetes. We calculated the T1D GRS from 30 T1D-associated single nucleotide polymorphisms. We used multivariable Cox regression models, time-dependent receiver operating characteristic curves, and area under the curve (AUC) measures to evaluate prognostic utility of T1D GRS, age, sex, Diabetes Prevention Trial-Type 1 (DPT-1) Risk Score, positive autoantibody number or type, HLA DR3/DR4-DQ8 status, and race/ethnicity. We used recursive partitioning analyses to identify cut points in continuous variables.

RESULTS

Higher T1D GRS significantly increased the rate of progression to T1D adjusting for DPT-1 Risk Score, age, number of positive autoantibodies, sex, and ethnicity (hazard ratio [HR] 1.29 for a 0.05 increase, 95% CI 1.06-1.6; P = 0.011). Progression to T1D was best predicted by a combined model with GRS, number of positive autoantibodies, DPT-1 Risk Score, and age (7-year time-integrated AUC = 0.79, 5-year AUC = 0.73). Higher GRS was significantly associated with increased progression rate from single to multiple positive autoantibodies after adjusting for age, autoantibody type, ethnicity, and sex (HR 2.27 for GRS >0.295, 95% CI 1.47-3.51; P = 0.0002).

CONCLUSIONS

The T1D GRS independently predicts progression to T1D and improves prediction along T1D stages in autoantibody-positive relatives.

Severe phenotype of X-linked dominant chondrodysplasia punctata

A prenatally ascertained case representing the more severe end of the X‐linked dominant chondrodysplasia punctata (CDPX2).

What are the similarities and differences in antimicrobial prescribing between Australian public and private hospitals?

BACKGROUND

Identifying themes associated with inappropriate prescribing in Australian public and private hospitals will help target future antimicrobial stewardship initiatives.

AIMS

To describe current antimicrobial prescribing practices, identify similarities and differences between hospital sectors and provide target areas for improvement specific to each hospital sector.

METHODS

All hospitals included in the study were part of the 2014 national antimicrobial prescribing survey and conducted one of the following: a whole hospital point prevalence survey, serial point prevalence surveys or a sample of randomly selected patients. Data on the types of antibiotics used, their indications for use and the quality of prescription based on compliance with national and local prescribing guidelines were collected.

RESULTS

Two hundred and two hospitals (166 public and 36 private) comprising 10 882 patients and 15 967 antimicrobial prescriptions were included. Public hospitals had higher proportions of prescriptions for treatment (81.5% vs 48.4%) and medical prophylaxis (8.8% and 4.6%), whilst private hospitals had significantly higher surgical prophylaxis use (9.6% vs 46.9%) (P < 0.001). In public hospitals, the main reasons for non-compliance of treatment prescriptions were spectrum being too broad (30.5%) while in private it was incorrect dosing. Prolonged duration was the main reason for non-compliance among surgical prophylaxis prescriptions in both types of hospitals.

CONCLUSIONS

Australian hospitals need to target specific areas to improve antimicrobial use. Specifically, unnecessary broad-spectrum therapy should be a priority area in public hospitals, whilst emphasis on curtailing antimicrobial overuse in surgical prophylaxis needs to be urgently addressed across in the private hospital sector.

A double-blind randomized controlled trial of ibuprofen compared to placebo for uncomplicated cellulitis of the upper or lower limb

OBJECTIVES

Cellulitis is a common skin infection resulting in inflammation that may take weeks to resolve despite appropriate antibiotics. It is unclear whether the adjunctive use of nonsteroidal anti-inflammatory drugs hastens the resolution of inflammation in patients with cellulitis.

METHODS

We conducted a double-blind, randomized controlled trial comparing ibuprofen 400 mg three times daily for 5 days with identical placebo in adults with uncomplicated cellulitis of the upper or lower limb who were treated with intravenous cefazolin via an outpatient parenteral antibiotic treatment service at one of two Australian hospitals. Participants were assessed twice daily by a study nurse. The primary outcome measure was the proportion of patients with regression of inflammation 48 hours after the first effective dose of parenteral antibiotics (trial registration ANZCTR 12611000515998).

RESULTS

Fifty-one patients were enrolled; 48 had sufficient data available to be included in the modified intention-to-treat analysis. Inflammation had begun to regress at 48 hours in 20 participants (80%) in the ibuprofen group compared to 15 (65%) in the placebo group (absolute risk difference +15%; 95% confidence interval -10 to +40; p >0.05). There was no significant difference in any secondary outcome. Ibuprofen appeared safe, with no patients developing renal impairment or necrotizing fasciitis.

CONCLUSIONS

This trial demonstrated no significant benefit of adjunctive ibuprofen in adults with uncomplicated cellulitis. The trial was powered to detect a large effect, and hence it is unclear whether the 15% absolute increase in the primary end point in the ibuprofen group was attributable to chance.

Head and neck target delineation using a novel PET automatic segmentation algorithm

PURPOSE

To evaluate the feasibility and impact of using a novel advanced PET auto-segmentation method in Head and Neck (H&N) radiotherapy treatment (RT) planning.

METHODS

ATLAAS, Automatic decision Tree-based Learning Algorithm for Advanced Segmentation, previously developed and validated on pre-clinical data, was applied to ¹⁸F-FDG-PET/CT scans of 20 H&N patients undergoing Intensity Modulated Radiation Therapy. Primary Gross Tumour Volumes (GTVs) manually delineated on CT/MRI scans (GTVp_CT/MRI), together with ATLAAS-generated contours (GTVp_ATLAAS) were used to derive the RT planning GTV (GTVp_final). ATLAAS outlines were compared to CT/MRI and final GTVs qualitatively and quantitatively using a conformity metric.

RESULTS

The ATLAAS contours were found to be reliable and useful. The volume of GTVp_ATLAAS was smaller than GTVp_CT/MRI in 70% of the cases, with an average conformity index of 0.70. The information provided by ATLAAS was used to grow the GTVp_CT/MRI in 10 cases (up to 10.6mL) and to shrink the GTVp_CT/MRI in 7 cases (up to 12.3mL). ATLAAS provided complementary information to CT/MRI and GTVp_ATLAAS contributed to up to 33% of the final GTV volume across the patient cohort.

CONCLUSIONS

ATLAAS can deliver operator independent PET segmentation to augment clinical outlining using CT and MRI and could have utility in future clinical studies.