A gene pathogenicity tool "GenePy" identifies missed biallelic diagnoses in the 100,000 Genomes Project

PURPOSE

The 100,000 Genomes Project diagnosed a quarter of affected participants, but 26% of diagnoses were not on the applied gene panel(s); with many being de novo variants. Assessing biallelic variants without a gene panel is more challenging.

METHODS

We sought to identify missed biallelic diagnoses using GenePy, which incorporates allele frequency, zygosity, and a user-defined deleterious metric, generating an aggregate GenePy score per gene, per participant. We calculated GenePy scores for 2862 recessive disease genes in 78,216 100,000 Genomes Project participants. For each gene, we ranked participant GenePy scores and scrutinized affected participants without a diagnosis, whose scores ranked among the top 5 for each gene. In cases which participant phenotypes overlapped with the disease gene of interest, we extracted rare variants and applied phase, ClinVar, and ACMG classification.

RESULTS

3184 affected individuals without a molecular diagnosis had a top-5-ranked GenePy score and 682 of 3184 (21%) had phenotypes overlapping with a top-ranking gene. In 122 of 669 (18%) phenotype-matched cases (excluding 13 withdrawn participants), we identified a putative missed diagnosis (2.2% of all undiagnosed participants). A further 334 of 669 (50%) cases have a possible missed diagnosis but require functional validation.

CONCLUSION

Applying GenePy at scale has identified 456 potential diagnoses, demonstrating the value of novel diagnostic strategies.

Sustained Increase in Pediatric Inflammatory Bowel Disease Incidence Across the South West United Kingdom Over the Last 10 Years

BACKGROUND

Pediatric inflammatory bowel disease (pIBD) incidence has increased over the last 25 years. We aim to report contemporaneous trends across the South West United Kingdom.

METHODS

Data were provided from centers covering the South West United Kingdom (Bristol, Oxford, Cardiff, Exeter, and Southampton), with a total area at-risk population (<18 years of age) of 2 947 534. Cases were retrieved from 2013 to 2022. Incident rates were reported per 100 000 at-risk population, with temporal trends analyzed through correlation. Subgroup analysis was undertaken for age groups (0-6, 6-11, and 12-17 years of age), sex, and disease subtype. Choropleth maps were created for local districts.

RESULTS

In total, 2497 pIBD cases were diagnosed between 2013 and 2022, with a mean age of 12.6 years (38.7% female). Diagnosis numbers increased from 187 to 376, with corresponding incidence rates of 6.0 per 100 000 population per year (2013) to 12.4 per 100 000 population per year (2022) (b = 0.918, P < .01). Female rates increased from 5.1 per 100 000 population per year in 2013 to 11.0 per 100 000 population per year in 2022 (b = 0.865, P = .01). Male rates increased from 5.7 per 100 000 population per year to 14.4 per 100 000 population per year (b = 0.832, P = .03). Crohn's disease incidence increased from 3.1 per 100 000 population per year to 6.3 per 100 000 population per year (b = 0.897, P < .01). Ulcerative colitis increased from 2.3 per 100 000 population per year to 4.3 per 100 000 population per year (b = 0.813, P = .04). Inflammatory bowel disease unclassified also increased, from 0.6 per 100 000 population per year to 1.8 per 100 000 population per year (b = 0.851, P = .02). Statistically significant increases were seen in those ≥12 to 17 years of age, from 11.2 per 100 000 population per year to 24.6 per 100 000 population per year (b = 0.912, P < .01), and the 7- to 11-year-old age group, with incidence rising from 4.4 per 100 000 population per year to 7.6 per 100 000 population per year (b = 0.878, P = .01). There was no statistically significant increase in very early onset inflammatory bowel disease (≤6 years of age) (b = 0.417, P = .231).

CONCLUSIONS

We demonstrate significant increases in pIBD incidence across a large geographical area including multiple referral centers. Increasing incidence has implications for service provision for services managing pIBD.

Improved clinical outcomes with early anti-tumour necrosis factor alpha therapy in children with newly diagnosed Crohn's disease: real world data from the international prospective PIBD-SETQuality inception cohort study

BACKGROUND & AIMS

Treatment guidelines for paediatric Crohn's disease (CD) suggest early use of anti-tumour necrosis factor alpha (anti-TNF) in high-risk individuals. The aim is to evaluate the effect of early anti-TNF in a real-world cohort.

METHODS

Children with newly-diagnosed CD were prospectively recruited at 28 participating sites of the international observational PIBD-SETQuality study. Outcomes were compared at 3 months, 1 and 2 years between patients receiving early anti-TNF (<90 days after diagnosis) and those not receiving early anti-TNF. Outcomes included sustained steroid-free remission (SSFR) without treatment intensification (specified as SSFR*) and sustained steroid-free mild/inactive disease without treatment intensification (specified as SSFMI*). Penalised logistic regression model-based standardisation was applied to estimate the relative risks (RR) of early therapy on outcomes. RRs were estimated for high-risk and low-risk patients based on presence of predictors of poor outcome (POPOs) and disease activity at diagnosis.

RESULTS

In total, 331 children (median age 13.9 years [IQR 12.2 - 15.3]) were enrolled, with 135 (41%) receiving early anti-TNF. At 1 year, patients on early anti-TNF had higher rates of SSFR* (30% vs. 14%, p<0.001) and SSFMI* (69% vs. 33%, p<0.001), with RRs of 2.95 (95%CI 1.63-5.36) and 4.67 (95%CI 2.46-8.87) respectively. At 1 year, the RRs for SSFMI* were higher, and statistically significant in high-risk patients, i.e. those with moderate/severe disease compared to mild/inactive disease at diagnosis (5.50 [95%CI 2.51-12.05]) vs. 2.91 [95%CI 0.92-9.11]), and those with any POPO compared to no POPO (5.05 [95%CI 2.45-10.43] vs. 3.41 [95%CI 0.54-21.7]).

CONCLUSION

In this cohort of children with newly-diagnosed CD, early anti-TNF demonstrated superior effectiveness in high-risk patients.

Supervised Machine Learning Classifies Inflammatory Bowel Disease Patients by Subtype Using Whole Exome Sequencing Data

BACKGROUND

Inflammatory bowel disease [IBD] is a chronic inflammatory disorder with two main subtypes: Crohn's disease [CD] and ulcerative colitis [UC]. Prompt subtype diagnosis enables the correct treatment to be administered. Using genomic data, we aimed to assess machine learning [ML] to classify patients according to IBD subtype.

METHODS

Whole exome sequencing [WES] from paediatric/adult IBD patients was processed using an in-house bioinformatics pipeline. These data were condensed into the per-gene, per-individual genomic burden score, GenePy. Data were split into training and testing datasets [80/20]. Feature selection with a linear support vector classifier, and hyperparameter tuning with Bayesian Optimisation, were performed [training data]. The supervised ML method random forest was utilised to classify patients as CD or UC, using three panels: 1] all available genes; 2] autoimmune genes; 3] 'IBD' genes. ML results were assessed using area under the receiver operating characteristics curve [AUROC], sensitivity, and specificity on the testing dataset.

RESULTS

A total of 906 patients were included in analysis [600 CD, 306 UC]. Training data included 488 patients, balanced according to the minority class of UC. The autoimmune gene panel generated the best performing ML model [AUROC = 0.68], outperforming an IBD gene panel [AUROC = 0.61]. NOD2 was the top gene for discriminating CD and UC, regardless of the gene panel used. Lack of variation in genes with high GenePy scores in CD patients was the best classifier of a diagnosis of UC.

DISCUSSION

We demonstrate promising classification of patients by subtype using random forest and WES data. Focusing on specific subgroups of patients, with larger datasets, may result in better classification.

Recent developments in the assessment and management of inflammatory bowel disease in childhood: a narrative review

Background and Objective

The landscape of paediatric inflammatory bowel disease (pIBD) continues to evolve in an era of increasing incidence. There have been rapid developments in understanding, as we begin to perceive IBD as a spectrum of conditions, alongside advancements in monitoring and treatment. The objective of this article was to provide an overview of recent advances and challenges in the management of pIBD, with a focus on sustainable healthcare, personalised therapy, genomics, new drugs and avenues for future optimisation.

Methods

We present a narrative review that synthesises and summarises recent research (2017-2022) related to pIBD. We undertook a structured search of the literature (PubMed and Medline) and additional articles were identified through manual searches of reference lists. Evidence tables were compiled for disease outcomes.

Key Content and Findings

In this review we outline current practice, integrating clinical guidelines and contemporary research. We discuss initial investigations (including suggested threshold for paediatric faecal calprotectin), specialist investigations for disease monitoring [with reference to video capsule endoscopy (VCE) and therapeutic drug levels] and outline new and established treatment options. Biomarkers and genomic testing are examined as important tools for individualising care and identifying potential therapeutic targets, including for top-down therapy. Despite these advances, significant challenges remain, including the need for further research to understand the mechanisms of disease and the translation of these advances into real-world improvements in practice.

Conclusions

Recent advances in understanding of the pathogenesis of pIBD, alongside genomic and pharmacological developments have added more tools to the armamentarium for the treatment of these conditions and highlighted ongoing areas of research need.

A scoping review: urinary markers of metabolic maturation in infants with CHD and the relationship to growth

BACKGROUND

Growth failure in infants born with CHD is a persistent problem, even in those provided with adequate nutrition.

OBJECTIVE

To summarise the published data describing the change in urinary metabolites during metabolic maturation in infants with CHD and identify pathways amenable to therapeutic intervention.

DESIGN

Scoping review.

ELIGIBILITY CRITERIA

Studies using qualitative or quantitative methods to describe urinary metabolites pre- and post-cardiac surgery and the relationship with growth in infants with CHD.

SOURCES OF EVIDENCE

NICE Healthcare Databases website was used as a tool for multiple searches.

RESULTS

347 records were identified, of which 37 were duplicates. Following the removal of duplicate records, 310 record abstracts and titles were screened for inclusion. The full texts of eight articles were reviewed for eligibility, of which only two related to infants with CHD. The studies included in the scoping review described urinary metabolites in 42 infants. A content analysis identified two overarching themes of metabolic variation predictive of neurodevelopmental abnormalities associated with anaerobic metabolism and metabolic signature associated with the impact on gut microbiota, inflammation, energy, and lipid digestion.

CONCLUSION

The results of this scoping review suggest that there are considerable gaps in our knowledge relating to metabolic maturation of infants with CHD, especially with respect to growth. Surgery is a key early life feature for CHD infants and has an impact on the developing biochemical phenotype with implications for metabolic pathways involved in immunomodulation, energy, gut microbial, and lipid metabolism. These early life fingerprints may predict those individuals at risk for neurodevelopmental abnormalities.

Pedi-R-MAPP | the development, testing, validation, and refinement of a digital nutrition awareness tool

BACKGROUND & AIMS

The Remote Malnutrition Application (R-MAPP) was developed during the COVID-19 pandemic to provide support for health care professionals (HCPs) working in the community to complete remote nutritional assessments and provide practical guidance for nutritional care. R-MAPP was adapted into Pediatric Remote Malnutrition Application (Pedi-R-MAPP) using a modified Delphi consensus, with the goal of providing a structured approach to completing a nutrition focused assessment as part of a technology enabled care service (TECS) consultation. The aim of this study was to develop and validate a digital version of Pedi-R-MAPP using the IDEAS framework (Integrate, Design, Assess and Share).

METHODS

A ten-step process was completed using the IDEAS framework. This involved the four concept processes; Stage-1, Integrate (Step 1-3) identify the problem, specify the goal, and use an evidence-based approach. Stage-2, (Step 4-7) design iteratively and rapidly with user feedback. Stage 3, (Step 8-9) Assess rigorously, and Stage 4 (Step 9-10) publish and launch of the tool.

RESULTS

Stage 1:Evidence-based development, Pedi-R-MAPP was developed using Delphi consensus methodology. Stage 2:Iteration & design, HCPs (n = 22) from UK, Europe, South Africa, and North America were involved four workshops to further develop a paper prototype of the tool and complete small-scale testing of a beta version of the tool which resulted in eight iterations. Stage 3:Assess rigorously, Small scale retrospective testing of the tool on children with congenital heart disease (n = 80) was completed by a single researcher, with iterative changes made to improve agreement with summary advice. Large scale testing amongst (n = 745) children in different settings was completed by specialist paediatric dietitians (n = 15) advice who recorded agreement with the summary advice compared with their own clinical assessment. Paediatric dietitians were in overall agreement with the summary advice in the tool 86% (n = 640), compared to their own clinical practice. The main reasons for disagreement were i) frequency of planned review 57.1% (n = 60/105), ii) need for ongoing dietetic review due to chronic condition 20.0% (n = 21/105), iii) disagreement with recommendation for discharge 16.2% (n = 17/105) and iv) concerns with faltering growth and/or need for condition specific growth charts 6.7% (7/105). Iterative changes were made to the algorithm, leading to an improvement in agreement of the summary advice on re-evaluation to 98% (p=<0.0001).

CONCLUSION

A digital version of the Pedi-R-MAPP nutrition awareness tool was developed using the IDEAS framework. The summary advice provided by the tool achieved a high level of agreement when compared to paediatric dietetic assessment, by providing a structured approach to completing a remote nutrition focused assessment, along with identifying the frequency of follow-up or an in-person assessment.

The Pediatric Crohn Disease Morbidity Index (PCD-MI): Development of a Tool to Assess Long-Term Disease Burden Using a Data-Driven Approach

BACKGROUND/OBJECTIVE

Heterogeneity and chronicity of Crohn disease (CD) make prediction of outcomes difficult. To date, no longitudinal measure can quantify burden over a patient's disease course, preventing assessment and integration into predictive modeling. Here, we aimed to demonstrate the feasibility of constructing a data driven, longitudinal disease burden score.

METHODS

Literature was reviewed for tools used in assessment of CD activity. Themes were identified to construct a pediatric CD morbidity index (PCD-MI). Scores were assigned to variables. Data were extracted automatically from the electronic patient records at Southampton Children's Hospital, diagnosed from 2012 to 2019 (inclusive). PCD-MI scores were calculated, adjusted for duration of follow up and assessed for variation (ANOVA) and distribution (Kolmogorov-Smirnov).

RESULTS

Nineteen clinical/biological features across five themes were included in the PCD-MI including blood/fecal/radiological/endoscopic results, medication usage, surgery, growth parameters, and extraintestinal manifestations. Maximal score was 100 after accounting for follow-up duration. PCD-MI was assessed in 66 patients, mean age 12.5 years. Following quality filtering, 9528 blood/fecal test results and 1309 growth measures were included. Mean PCD-MI score was 14.95 (range 2.2-32.5); data were normally distributed ( P = 0.2) with 25% of patients having a PCD-MI < 10. There was no difference in the mean PCD-MI when split by year of diagnosis, F -statistic 1.625, P = 0.147.

CONCLUSIONS

PCD-MI is a calculatable measure for a cohort of patients diagnosed over an 8-year period, integrating a wide-range of data with potential to determine high or low disease burden. Future iterations of the PCD-MI require refinement of included features, optimized scores, and validation on external cohorts.

A gene pathogenicity tool 'GenePy' identifies missed biallelic diagnoses in the 100,000 Genomes Project

The 100,000 Genomes Project (100KGP) diagnosed a quarter of recruited affected participants, but 26% of diagnoses were in genes not on the chosen gene panel(s); with many being de novo variants of high impact. However, assessing biallelic variants without a gene panel is challenging, due to the number of variants requiring scrutiny. We sought to identify potential missed biallelic diagnoses independent of the gene panel applied using GenePy - a whole gene pathogenicity metric. GenePy scores all variants called in a given individual, incorporating allele frequency, zygosity, and a user-defined deleterious metric (CADD v1.6 applied herein). GenePy then combines all variant scores for individual genes, generating an aggregate score per gene, per participant. We calculated GenePy scores for 2862 recessive disease genes in 78,216 individuals in 100KGP. For each gene, we ranked participant GenePy scores for that gene, and scrutinised affected individuals without a diagnosis whose scores ranked amongst the top-5 for each gene. We assessed these participants' phenotypes for overlap with the disease gene associated phenotype for which they were highly ranked. Where phenotypes overlapped, we extracted rare variants in the gene of interest and applied phase, ClinVar and ACMG classification looking for putative causal biallelic variants. 3184 affected individuals without a molecular diagnosis had a top-5 ranked GenePy gene score and 682/3184 (21%) had phenotypes overlapping with one of the top-ranking genes. After removing 13 withdrawn participants, in 122/669 (18%) of the phenotype-matched cases, we identified a putative missed diagnosis in a top-ranked gene supported by phasing, ClinVar and ACMG classification. A further 334/669 (50%) of cases have a possible missed diagnosis but require functional validation. Applying GenePy at scale has identified potential diagnoses for 456/3183 (14%) of undiagnosed participants who had a top-5 ranked GenePy score in a recessive disease gene, whilst adding only 1.2 additional variants (per individual) for assessment.

Prediction of Crohn's Disease Stricturing Phenotype Using a NOD2-derived Genomic Biomarker

BACKGROUND

Crohn's disease (CD) is highly heterogenous and may be complicated by stricturing behavior. Personalized prediction of stricturing will inform management. We aimed to create a stricturing risk stratification model using genomic/clinical data.

METHODS

Exome sequencing was performed on CD patients, and phenotype data retrieved. Biallelic variants in NOD2 were identified. NOD2 was converted into a per-patient deleteriousness metric ("GenePy"). Using training data, patients were stratified into risk groups for fibrotic stricturing using NOD2. Findings were validated in a testing data set. Models were modified to include disease location at diagnosis. Cox proportional hazards assessed performance.

RESULTS

Six hundred forty-five patients were included (373 children and 272 adults); 48 patients fulfilled criteria for monogenic NOD2-related disease (7.4%), 24 of whom had strictures. NOD2 GenePy scores stratified patients in training data into 2 risk groups. Within testing data, 30 of 161 patients (18.6%) were classified as high-risk based on the NOD2 biomarker, with stricturing in 17 of 30 (56.7%). In the low-risk group, 28 of 131 (21.4%) had stricturing behavior. Cox proportional hazards using the NOD2 risk groups demonstrated a hazard ratio (HR) of 2.092 (P = 2.4 × 10-5), between risk groups. Limiting analysis to patients diagnosed aged < 18-years improved performance (HR-3.164, P = 1 × 10-6). Models were modified to include disease location, such as terminal ileal (TI) disease or not. Inclusion of NOD2 risk groups added significant additional utility to prediction models. High-risk group pediatric patients presenting with TI disease had a HR of 4.89 (P = 2.3 × 10-5) compared with the low-risk group patients without TI disease.

CONCLUSIONS

A NOD2 genomic biomarker predicts stricturing risk, with prognostic power improved in pediatric-onset CD. Implementation into a clinical setting can help personalize management.

A Scoping Review: Urinary Markers of Metabolic Maturation in Preterm Infants and Future Interventions to Improve Growth

Background: Growth failure in infants born preterm is a significant issue, increasing the risk of poorer neurodevelopmental outcomes and metabolic syndrome later in life. During the first 1000 days of life biological systems mature rapidly involving developmental programming, cellular senescence, and metabolic maturation, regulating normal growth and development. However, little is known about metabolic maturation in infants born preterm and the relationship with growth. Objective: To examine the available evidence on urinary markers of metabolic maturation and their relationship with growth in infants born preterm. Eligibility criteria: Studies including in this scoping review using qualitative or quantitative methods to describe urinary markers of metabolic maturation and the relationship with growth in infants born preterm. Results: After a screening process 15 titles were included in this review, from 1998–2021 drawing from China (n = 1), Italy (n = 3), Germany (n = 3), Greece (n = 1), Japan (n = 2), Norway (n = 1), Portugal (n = 1), Spain (n = 2) and USA (n = 1). The included studies examined urinary metabolites in 1131 infants. A content analysis identified 4 overarching themes relating to; (i) metabolic maturation relative to gestational age, (ii) metabolic signature and changes in urinary metabolites over time, (iii) nutrition and (iv) growth. Conclusion: The results of this scoping review suggest there are considerable gaps in our knowledge relating to factors associated with metabolic instability, what constitutes normal maturation of preterm infants, and how the development of reference phenome age z scores for metabolites of interest could improve nutritional and growth outcomes.

NOD2 in Crohn's disease- unfinished business

Studies of Crohn's disease consistently implicate NOD2 as the most important gene in disease pathogenesis since first being identified in 2001. Since this point, genome-wide association, next-generation sequencing, and functional analyses have all confirmed a key role for NOD2, but despite this, NOD2 also has significant unresolved complexity. More recent studies have reinvigorated an early hypothesis that NOD2 may be a single-gene cause of disease, and the distinct ileal stricturing phenotype seen with NOD2-related disease presents an opportunity for personalised diagnosis, disease prediction and targeted therapy. The genomics of NOD2 has much that remains unknown, including the role of rare variation, phasing of variants across the haplotype block and the role of variation in the NOD2-regulatory regions. Here, we discuss the evidence and the unmet needs of NOD2-research, based on recently published evidence, and suggest methods that may meet these requirements.

Incidence and Prevalence of Paediatric Inflammatory Bowel Disease Continues to Increase in the South of England

OBJECTIVE

The incidence of paediatric inflammatory bowel disease (IBD) has been increasing over 25 years; however, contemporary trends are not established and the impact of COVID-19 on case rates is unclear.

METHODS

Data from Southampton Children's hospital prospective IBD database were retrieved for 2002-2021. Incidence rates were calculated based on referral area populations and temporal trends analysed. Disease prevalence for those aged <18 years was calculated for 2017-2021. Monoclonal prescriptions were reported.

RESULTS

In total, 1150 patients were included (mean age at diagnosis 12.63 years, 40.5% female). An estimated 704 patients had Crohn's disease (61.2%), 385 had ulcerative colitis (33.5%), and 61 had IBD unclassified (5.3%). Overall IBD incidence increased, β = 0.843, P = 3 × 10 -6 , driven by Crohn's disease, β = 0.732, P = 0.00024 and ulcerative colitis, β = 0.816, P = 0.000011. There was no change in IBDU incidence, β = 0.230, P = 0.33. From 2002-2021, 51 patients were diagnosed <6 years of age, 160 patients aged 6 to <10 years and 939 patients aged 10 to <18 years of age. Increased incidence was observed in patients aged 10 to <18 years of age (β = 0.888, P = 1.8 × 10 -7 ). There was no significant change in incidence of IBD in <6 years (β = 0.124, P = 0.57), or 6 to <10 years (β = 0.146, P = 0.54). IBD prevalence increased by an average of 1.71%/year from 2017 to 2021, β = 0.979, P = 0.004. The number of new monoclonal prescriptions increased from 6 in 2007 to 111 in 2021.

CONCLUSIONS

IBD incidence continues to increase in Southern England. Compounding prevalence and increased monoclonal usage has implications for service provision.

Deleterious Genetic Variation Across the NOD Signaling Pathway Is Associated With Reduced NFKB Signaling Transcription and Upregulation of Alternative Inflammatory Transcripts in Pediatric Inflammatory Bowel Disease

BACKGROUND

Inflammatory bowel disease may arise with inadequate immune response to intestinal bacteria. NOD2 is an established gene in Crohn's disease pathogenesis, with deleterious variation associated with reduced NFKB signaling. We hypothesized that deleterious variation across the NOD2 signaling pathway impacts on transcription.

METHODS

Treatment-naïve pediatric inflammatory bowel disease patients had ileal biopsies for targeted autoimmune RNA-sequencing and blood for whole exome sequencing collected at diagnostic endoscopy. Utilizing GenePy, a per-individual, per-gene score, genes within the NOD signaling pathway were assigned a quantitative score representing total variant burden. Where multiple genes formed complexes, GenePy scores were summed to create a "complex" score. Normalized transcript expression of 95 genes within this pathway was retrieved. Regression analysis was performed to determine the impact of genomic variation on gene transcription.

RESULTS

Thirty-nine patients were included. Limited clustering of patients based on NOD signaling transcripts was related to underlying genomic variation. Patients harboring deleterious variation in NOD2 had reduced NOD2 (β = -0.702, P = 4.3 × 10-5) and increased NFKBIA (β = 0.486, P = .001), reflecting reduced NFKB signal activation. Deleterious variation in the NOD2-RIPK2 complex was associated with increased NLRP3 (β = 0.8, P = 3.1475 × 10-8) and TXN (β = -0.417, P = 8.4 × 10-5) transcription, components of the NLRP3 inflammasome. Deleterious variation in the TAK1-TAB complex resulted in reduced MAPK14 transcription (β = -0.677, P = 1.7 × 10-5), a key signal transduction protein in the NOD2 signaling cascade and increased IFNA1 (β = 0.479, P = .001), indicating reduced transcription of NFKB activators and alternative interferon transcription in these patients.

CONCLUSIONS

Data integration identified perturbation of NOD2 signaling transcription correlated with genomic variation. A hypoimmune NFKB signaling transcription response was observed. Alternative inflammatory pathways were activated and may represent therapeutic targets in specific patients.

Transition Services for Paediatric Inflammatory Bowel Disease: A Multicentre Study of Practice in the United Kingdom

OBJECTIVES

Patients with paediatric inflammatory bowel disease (IBD) constitute one of the largest cohorts requiring transition from paediatric to adult services. Standardised transition care improves short and long-term patient outcomes. This study aimed to detail the current state of transition services for IBD in the United Kingdom (UK).

METHODS

We performed a nationwide study to ascertain current practice, facilities and resources for children and young people with IBD. Specialist paediatric IBD centres were invited to contribute data on: timing of transition/transfer of care; transition resources available including clinics, staff and patient information; planning for future improvement.

RESULTS

Twenty of 21 (95%) of invited centres responded. Over 90% of centres began the transition process below 16 years of age and all had completed transfer to adult care at 18 years of age. The proportion of patients in the transition process at individual centres varied from 10% to 50%.Joint clinics were held in every centre, with a mean of 12.9 clinics per year. Adult and paediatric gastroenterologists attended at all sites. Availability of additional team members was patchy across the UK, with dietetic, psychological and surgical attendance available in <50% centres. A structured transition tool was used in 75% of centres. Sexual health, contraception and pregnancy were discussed by <60% of teams.

CONCLUSIONS

This study provides real-world clinical data on UK-wide transition services. These data can be used to develop a national strategy to complement current transition guidelines, focused on standardising services whilst allowing for local implementation.

Routine abdominal magnetic resonance imaging can determine psoas muscle area in paediatric Crohn's disease and correlates with bioelectrical impedance spectroscopy measures of lean mass

BACKGROUND

Paediatric Crohn's disease (CD) has been associated with undernutrition. Accurate and accessible measures of body composition would provide data to personalise nutritional therapy. We assessed feasibility of MRI-derived measures of psoas cross-sectional area (PCSA) in paediatric CD and correlated with anthropometric and bioelectrical impedance spectroscopy (BIS) measures.

METHODS

MRI small bowel/pelvis images of patients with CD, aged <18 years, were retrieved. Patients with concurrent anthropometric and BIS measurements were eligible for inclusion. The PCSA at L3 was calculated by two assessors and combined. To assess reproducibility of measures we calculated the coefficient of variation (CoV). Age, height-Z-scores, weight-Z-scores and BIS measures were correlated with PCSA. Using normal paediatric data from CT-scans we derived psoas area Z-scores for our cohort.

RESULTS

10 patients were included. Mean age at MRI scan was 14.6 years (11.7-16.3). PCSA was calculated for all MRI scans. There was high reproducibility between measurers, mean CoV 0.099. There was a significant positive correlation between PCSA and BIA-derived fat free mass, Pearson correlation coefficient (PCC) 0.831, p = 0.003. Correlation coefficients for PCSA and Height-for-age Z-score, weight-for-age -Z-score and age were PCC 0.343- p = 0.33, PCC = 0.222- p = 0.54, and PCC 0.6034- p = 0.065, respectively. The mean PCSA Z-score was -1.81, with 70% of the patients having a Z-score < -2.0.

CONCLUSIONS

These data demonstrate the feasibility of deriving measures of body composition from routine MRI imagine. There was significant positive correlation between PCSA and BIS-derived lean mass. Further studies are required to confirm applicability of normal ranges prior to routine clinical implementation.

The impact of national lockdown on nutritional status of children with inflammatory bowel disease

BACKGROUND

The COVID-19 pandemic has had wide-reaching primary and secondary health implications. The UK government implemented a national lockdown to slow the rate of infection at the end of March 2020, lasting until early summer 2020. The results from a UK nationwide survey suggest the majority of inflammatory bowel disease patients were followed up using technology-enabled care services (TECS) during this time. We therefore aimed to explore the impact of the pandemic on nutritional status of children with inflammatory bowel disease, focusing on the effect of national lockdown from March to early summer 2020.

METHODS

A retrospective study was conducted. All patients with a diagnosis of inflammatory bowel disease, aged <18 years, and under the care of Southampton Children's Hospital were eligible for inclusion. Those patients who attended an outpatient appointment during time period 1 (November 2019 to February 2020), and following the period of national lockdown, time period 2 (July to November 2020), were included in the analysis.

RESULTS

In total, 116 patients had paired measures. Using the World Health Organization criteria of nutritional status, 19% (n = 22/116) were mildly malnourished with a body mass index Z score (BMIZ) < -1. In this group, the mean BMIZ was -1.3 ± 0.9 at time point 1 versus -1.9 ± 0.9 at time point 2 (p = 0.03). The mean BMIZ score of those children who were overweight at time point 1 was 1.2 ± 1.2 versus 1.6 ± 1.4 at time point 2 (p = 0.2) During the period of lockdown, 27% of malnourished children (n = 6/22), 2% of normally nourished children (BMIZ > -1 to < 1) (n = 1/51) (p ≤ 0.0001) and none of the overweight children (BMIZ > 1) (n = 0/43) children (p ≤ 0.0001) had a TECS nutrition review.

CONCLUSIONS

Dietetic reviews were severely restricted during the first national lockdown. Patients with low BMIZ prior to lockdown became more malnourished. During the ongoing pandemic, it is important to identify those children with nutrition risk, focusing support on this group of children.

Growth failure is rare in a contemporary cohort of paediatric inflammatory bowel disease patients

AIM

We assessed growth in a paediatric inflammatory bowel disease (PIBD) cohort.

METHODS

Paediatric inflammatory bowel disease patients were eligible if they were diagnosed at Southampton Children's Hospital from 2011 to 2018. Weight and height standard deviation scores (SDS) were retrieved. Mean SDS values, SDS change and anti-TNF status were analysed at diagnosis and during follow-up.

RESULTS

Four hundred and ninety patients were included, 313 with Crohn's disease (CD). CD patients presented with mean height SDS -0.13, -0.1 at 1-year, -0.11 at 2-years and -0.03 at 5 years, reflecting preserved linear growth. There was no significant height-SDS change from diagnosis to 5-year follow-up, +0.12, 95%-CI: 0.48 to -0.24. Mean weight-SDS at diagnosis was -0.39, driven by CD patients (-0.65). Mean weight-SDS approached 0 after 1 year and remained at the 50th centile throughout follow-up. Growth in ulcerative colitis was maintained. In multivariable regression males had worse height growth from diagnosis to transition (P = .036). Anti-TNF treatment (P = .013) and surgical resection (P = .005) were also associated with poorer linear growth. Patients treated with anti-TNF therapy had lower height-SDS compared to those never treated with anti-TNF at 1 year (-0.2 vs -0.01, P = .22), 2-years (-0.27 vs -0.01, P = .07) and 5 years (-0.21 vs 0.25, P = .051).

CONCLUSION

Height was generally maintained in Crohn's disease, and impaired linear growth was rare in this cohort.

Ileal Transcriptomic Analysis in Paediatric Crohn's Disease Reveals IL17- and NOD-signalling Expression Signatures in Treatment-naïve Patients and Identifies Epithelial Cells Driving Differentially Expressed Genes

BACKGROUND AND AIMS

Crohn's disease [CD] arises through host-environment interaction. Abnormal gene expression results from disturbed pathway activation or response to bacteria. We aimed to determine activated pathways and driving cell types in paediatric CD.

METHODS

We employed contemporary targeted autoimmune RNA sequencing, in parallel to single-cell sequencing, to ileal tissue derived from paediatric CD and controls. Weighted gene co-expression network analysis [WGCNA] was performed and differentially expressed genes [DEGs] were determined. We integrated clinical data to determine co-expression modules associated with outcomes.

RESULTS

In all, 27 treatment-naive CD [TN-CD], 26 established CD patients and 17 controls were included. WGCNA revealed a 31-gene signature characterising TN-CD patients, but not established CD, nor controls. The CSF3R gene is a hub within this module and is key in neutrophil expansion and differentiation. Antimicrobial genes, including S100A12 and the calprotectin subunit S100A9, were significantly upregulated in TN CD compared with controls [p = 2.61 x 10-15 and p = 9.13 x 10-14, respectively] and established CD [both p = 0.0055]. Gene-enrichment analysis confirmed upregulation of the IL17-, NOD- and Oncostatin-M-signalling pathways in TN-CD patients, identified in both WGCNA and DEG analyses. An upregulated gene signature was enriched for transcripts promoting Th17-cell differentiation and correlated with prolonged time to relapse [correlation-coefficient-0.36, p = 0.07]. Single-cell sequencing of TN-CD patients identified specialised epithelial cells driving differential expression of S100A9. Cell groups, determined by single-cell gene expression, demonstrated enrichment of IL17-signalling in monocytes and epithelial cells.

CONCLUSIONS

Ileal tissue from treatment-naïve paediatric patients is significantly upregulated for genes driving IL17-, NOD- and Oncostatin-M-signalling. This signal is driven by a distinct subset of epithelial cells expressing antimicrobial gene transcripts.

Analysis and Hierarchical Clustering of Blood Results Before Diagnosis in Pediatric Inflammatory Bowel Disease

BACKGROUND

Pediatric inflammatory bowel disease (PIBD) is associated with a diagnostic delay. Blood tests are a routine part of the work-up in children with chronic abdominal symptoms (pain, diarrhea). Normal blood tests cannot exclude PIBD. We analyzed blood results at diagnosis over a 5-year period.

METHODS

Patients diagnosed from 2013 to 2017 were identified from the Southampton-PIBD database. Results were obtained up to 100 days before diagnostic endoscopy. Erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), albumin, hemoglobin, platelets, packed cell volume (PCV), white cell count (WCC), and alanine transferase (ALT) were analyzed. Hierarchical clustering was applied to normalized results.

RESULTS

Two hundred fifty-six patients were included (Crohn's disease [CD], 151; ulcerative colitis [UC], 95; IBD-unclassified, 10; median age, 13.48 years; 36.7% female). Hierarchical clustering of patients revealed novel groupings enriched for CD and UC, characterized by specific patterns of results. In PIBD, 9% presented with all normal blood tests, 21.9% with normal CRP and ESR. Abnormal results were seen in all tests (ESR, 56.4% of patients; CRP, 53.4%; albumin, 28%; hemoglobin, 61.9%; platelets, 55.6%; PCV, 64.6%; WCC, 22.7%; and ALT, 7.2%). Normal inflammatory markers were more common in UC compared with CD (UC, 34%; CD, 15.8%; P = 0.0035). UC (14.4% normal) presented with all normal results more frequently than CD (CD, 5.3%; P = 0.02). CRP, ESR, and platelets were significantly higher in CD compared with UC. Albumin and hemoglobin were significantly lower.

CONCLUSIONS

Most cases of PIBD present with >1 abnormal blood result, although 1/11 patients presents with normal blood tests and 1/5 present with normal inflammatory markers. Hierarchical clustering offers the potential to produce novel groupings to inform disease categorization and best management.

Genetic Sequencing of Pediatric Patients Identifies Mutations in Monogenic Inflammatory Bowel Disease Genes that Translate to Distinct Clinical Phenotypes

OBJECTIVES

Monogenic inflammatory bowel disease (IBD) comprises rare Mendelian causes of gut inflammation, often presenting in infants with severe and atypical disease. This study aimed to identify clinically relevant variants within 68 monogenic IBD genes in an unselected pediatric IBD cohort.

METHODS

Whole exome sequencing was performed on patients with pediatric-onset disease. Variants fulfilling the American College of Medical Genetics criteria as "pathogenic" or "likely pathogenic" were assessed against phenotype at diagnosis and follow-up. Individual patient variants were assessed and processed to generate a per-gene, per-individual, deleteriousness score.

RESULTS

Four hundred one patients were included, and the median age of disease-onset was 11.92 years. In total, 11.5% of patients harbored a monogenic variant. TRIM22-related disease was implicated in 5 patients. A pathogenic mutation in the Wiskott-Aldrich syndrome (WAS) gene was confirmed in 2 male children with severe pancolonic inflammation and primary sclerosing cholangitis. In total, 7.3% of patients with Crohn's disease had apparent autosomal recessive, monogenic NOD2-related disease. Compared with non-NOD2 Crohn's disease, these patients had a marked stricturing phenotype (odds ratio 11.52, significant after correction for disease location) and had undergone significantly more intestinal resections (odds ratio 10.75). Variants in ADA, FERMT1, and LRBA did not meet the criteria for monogenic disease in any patients; however, case-control analysis of mutation burden significantly implicated these genes in disease etiology.

DISCUSSION

Routine whole exome sequencing in pediatric patients with IBD results in a precise molecular diagnosis for a subset of patients with IBD, providing the opportunity to personalize therapy. NOD2 status informs risk of stricturing disease requiring surgery, allowing clinicians to direct prognosis and intervention.

Impact of COVID-19 on the diagnosis, assessment and management of children with inflammatory bowel disease in the UK: implications for practice

The assessment and management of patients with known, or suspected, paediatric inflammatory bowel disease (PIBD) has been hugely impacted by the COVID-19 pandemic. Although current evidence of the impact of COVID-19 infection in children with PIBD has provided a degree of reassurance, there continues to be the potential for significant secondary harm caused by the changes to normal working practices and reorganisation of services. Disruption to the normal running of diagnostic and assessment procedures, such as endoscopy, has resulted in the potential for secondary harm to patients including delayed diagnosis and delay in treatment. Difficult management decisions have been made in order to minimise COVID-19 risk for this patient group while avoiding harm. Initiating and continuing immunosuppressive and biological therapies in the absence of normal surveillance and diagnostic procedures have posed many challenges. Despite this, changes to working practices, including virtual clinic appointments, home faecal calprotectin testing kits and continued intensive support from clinical nurse specialists and other members of the multidisciplinary team, have resulted in patients still receiving a high standard of care, with those who require face-to-face intervention being highlighted. These changes have the potential to revolutionise the way in which patients receive routine care in the future, with the inclusion of telemedicine increasingly attractive for stable patients. There is also the need to use lessons learnt from this pandemic to plan for a possible second wave, or future pandemics as well as implementing some permanent changes to normal working practices. In this review, we describe the diagnosis, management and direct impact of COVID-19 in paediatric patients with IBD. We summarise the guidance and describe the implemented changes, evolving evidence and the implications of this virus on paediatric patients with IBD and working practices.

Inflammatory bowel disease: long-term therapeutic challenges

Introduction: Long-term, sustained, remission is the ultimate goal of contemporary inflammatory bowel disease (IBD) therapy. Avoiding complications, surgery and malignancy, alongside minimizing the side effects of medications are vital. However, the reality of treatment involves patients losing response to therapy, or developing complications requiring cessation of medication. The reasons underlying this are numerous and include medication and host-related influences. Underpinning the response to medication, long-term outcomes and loss of response are individual etiological factors including the molecular cause of disease and individual pharmacogenomic influences.Areas covered: In this review, we discuss the long-term outcome of IBD, with a focus on pediatric-onset illness and discuss the factors leading to loss of treatment response whilst briefly considering the future of personalized therapy as a strategy to improve long-term outcomes.Expert opinion: Research findings are now moving toward clinical translation, including application of novel medications targeting new pathways. The integration of biological and multiomic data to predict disease outcome will provide personalized therapeutic management.

Review article: the genetics of the human leucocyte antigen region in inflammatory bowel disease

BACKGROUND

The human leucocyte antigen (HLA) complex, located at chromosome 6p21.3 is a highly polymorphic region containing the classical class I and II HLA genes. The region is highly associated with inflammatory bowel disease (IBD), largely through genome-wide association studies (GWAS).

AIMS

To review the role of HLA in immune function, summarise data on risk/protective HLA genotypes for IBD, discuss the role of HLA in IBD pathogenesis, treatment and examine limitations that might be addressed by future research.

METHODS

An organised search strategy was used to collate articles describing HLA genes in IBD, including Crohn's disease and ulcerative colitis.

RESULTS

All classical HLA genes with variation (including HLA-A, B, C, DRB1, DQA1, DQB1, DPA1 and DPB1) harbour IBD-associated genotypes. The most implicated gene is HLA-DRB1, with HLA-DRB1*03:01 the most associated risk allele in both Crohn's disease and ulcerative colitis. Elucidating precise disease associations is challenging due to high linkage disequilibrium between HLA genotypes. The mechanisms by which risk alleles cause disease are multifactorial, with the best evidence indicating structural and electrostatic alteration impacting antigen binding and downstream signalling. Adverse medication events have been associated with HLA genotypes including with thiopurines (pancreatitis) and anti-TNF agents (antibody formation).

CONCLUSIONS

The HLA complex is associated with multiple risk/protective alleles for IBD. Future research utilising long-read technology, ascertainment of zygosity and integration in disease modelling will improve the functional understanding and clinical translation of genetic findings.

Handheld 3D scanning as a minimally invasive measuring technique for neonatal anthropometry

BACKGROUND

Measurement of length and head circumference (HC) in addition to weight is vital in assessing the nutritional status of preterm infants. Current anthropometry represents an interruption to preterm infants, and may not be possible in unstable infants. Handheld 3D scanning has the potential to perform bedside anthropometry (length and HC) in a less invasive manner. We aimed to evaluate the feasibility and performance of 3D scanning as a 'non-touch' measuring technique for routine anthropometry.

METHODS

Preterm infants born before 30 weeks gestation were recruited from a single neonatal unit. HC and length were measured both manually and by a handheld 3D scanner at recruitment and weekly until discharge. The two methods were compared using the Bland-Altman method and linear regression.

RESULTS

Seventeen infants had manual and 3D-scan measurements (67 HC, 87 length). The mean difference (95%CI) between manual and 3D-scan measures, as a percentage of the manual value, was 2.87% (2.27-3.47%) for HC and 3.10% (2.65-3.54%) for length. Correlation between manual and 3D measures was high; HC r = 0.957 and length 0.963. Bland-Altman plots showed reasonable agreement between the two methods, and there was a high correlation between scanner and manual measurements.

CONCLUSIONS

These data show a high correlation between measurements gathered from 3D scan images and standard anthropometry. However, 3D measures are not yet precise enough for routine clinical use. Refinement of technique/technology may translate into practical monitoring the growth of preterm infants with minimal handling and without interruption to developmental care.

Increased prevalence of anti-TNF therapy in paediatric inflammatory bowel disease is associated with a decline in surgical resections during childhood

BACKGROUND

Anti-tumour necrosis factor-α (anti-TNF) therapy use has risen in paediatric-onset inflammatory bowel disease (PIBD). Whether this has translated into preventing/delaying childhood surgery is uncertain. The Wessex PIBD cohort was analysed for trends in anti-TNF-therapy and surgery.

AIM

To assess patients diagnosed with PIBD within Wessex from 1997 to 2017. The prevalence of anti-TNF-therapy and yearly surgery rates (resection and perianal) during childhood (<18 years) were analysed (Pearson's correlation, multivariate regression, Fisher's exact).

RESULTS

Eight-hundred-and-twenty-five children were included (498 Crohn's disease, 272 ulcerative colitis, 55 IBD-unclassified), mean age at diagnosis 13.6 years (1.6-17.6), 39.6% female. The prevalence of anti-TNF-treated patients increased from 5.1% to 27.1% (2007-2017), P = 0.0001. Surgical resection-rate fell (7.1%-1.5%, P = 0.001), driven by a decrease in Crohn's disease resections (8.9%-2.3%, P = 0.001). Perianal surgery and ulcerative colitis resection-rates were unchanged. Time from diagnosis to resection increased (1.6-2.8 years, P = 0.028) but mean age at resection was unchanged. Patients undergoing resections during childhood were diagnosed at a younger age in the most recent 5 years (2007-2011 = 13.1 years, 2013-2017 = 11.9 years, P = 0.014). Resection-rate in anti-TNF-therapy treated (16.1%) or untreated (12.2%) was no different (P = 0.25). Patients started on anti-TNF-therapy <3 years post-diagnosis (11.6%) vs later (28.6%) had a reduction in resections, P = 0.047. Anti-TNF-therapy prevalence was the only significant predictor of resection-rate using multivariate regression (P = 0.011).

CONCLUSIONS

The prevalence of anti-TNF-therapy increased significantly, alongside a decrease in surgical resection-rate. Patients diagnosed at younger ages still underwent surgery during childhood. Anti-TNF-therapy may reduce the need for surgical intervention in childhood, thereby influencing the natural history of PIBD.

Personalising medicine in inflammatory bowel disease-current and future perspectives

Up to 25% of inflammatory bowel disease (IBD) presents during childhood, often with severe and extensive disease, leading to significant morbidity including delayed growth and nutritional impairment. The classical approach to management has centred on differentiation into Crohn's disease (CD) or ulcerative colitis (UC), with subsequent treatment based on symptoms, results and complications. However, IBD is a heterogeneous condition with substantial variation in phenotype, disease course and outcome, so whilst effective treatment exists one size does not fit all. The ability to predict disease course at diagnosis, alongside tailoring medications based on response gives the potential for a more 'personalised approach'. The move to a pre-emptive strategy to prevent IBD-related complications, whilst simultaneously minimising side effects and long-term toxicity from therapy, particularly in those with relatively indolent disease, has the potential to revolutionise care. In very early-onset IBD, personalised approaches to diagnosis and management have become the standard of treatment enabling clinicians to significantly alter the outcomes of the few children with monogenic disease. However, the promise of discoveries in genomics, microbiome and transcriptomics in paediatric IBD has not yet translated to clinical application for the vast majority of patients. Despite this, the opportunity presents itself to apply data gathered at diagnosis and follow-up to predict which patients are likely to progress to complicated disease, which will respond well and which will require additional therapy. Using complex mathematics and innovative, cutting-edge machine learning (ML) techniques gives the potential to use this data to develop personalised clinical care algorithms to treat patients more effectively, reduce toxicity and improve outcome. In this review, we will consider current management of paediatric IBD, discuss how precision medicine is making inroads into clinical practice already, examine the contemporary studies applying data to stratify patients and explore how future management may be revolutionised by personalisation with clinical, genomic and other multi-omic data.

Patient, parent and professional perception of the use of maintenance enteral nutrition in Paediatric Crohn's Disease

AIM

Maintenance enteral nutrition (MEN) is routinely used in Paediatric Crohn's Disease (CD) to prolong remission although there is limited evidence for efficacy and a lack of formal guidelines. This study surveyed patients', parents' and professional experience with MEN.

METHODS

Two questionnaires were developed to survey the experience of MEN; (i) Patients/Parents (children >10 years of age aimed to complete independently) and (ii) Dietitians. Questionnaires were sent to families prescribed MEN after exclusive enteral nutrition (EEN) between 2015-17 (n = 77) and dietitians working in paediatric regional centres in UK (n = 23).

RESULTS

Response rate to the questionnaires was 53% patients, 62% parents and 83% dietitians. Patients/parents reported medical/dietetic advice to be the primary factor affecting compliance, 30% patients reported side effects. Fifty-six per cent of patients/58% parents stated a preference for dietary advice rather than MEN. Dietetic responses indicated 79% used MEN after EEN as standard procedure and 79% did not have exit criteria for MEN. Sixty-eight per cent perceived the taste was the primary factor affecting patient compliance.

CONCLUSION

Patients' perception of the usefulness of MEN differs to professionals. This study highlights the extensive practice of MEN after EEN in clinical remission, which may not be nutritionally indicated. Patient preference is for dietary advice rather than MEN.

Exclusive enteral nutrition in Crohn's disease: Evidence and practicalities

Exclusive enteral nutrition (EEN) is the first line therapy for paediatric Crohn's disease, providing a complete nutritional feed whilst simultaneously inducing remission in up to 80% of cases. The effect of EEN on systemic/local intestinal immune function and subsequent inflammation (including barrier permeability, direct anti-inflammatory effects and cytokine signalling pathways), alongside changes in the microbiome (specific species and broad taxonomic shifts, functional changes) are becoming clearer, however the exact mechanism for induction of remission in Crohn's disease remains uncertain. The evidence of efficacy in paediatric Crohn's disease is strong, with selected adult populations also benefiting from EEN. However despite recommendations from all major societies (ECCO, ESPGHAN, NASPGHAN and ESPEN) first-line use of EEN is varied and Europe/Australasia/Canada show significantly more routine use than other parts of North America. Growth and nutritional status are significantly improved with EEN compared to corticosteroids but long-term outcomes are sparse. This review discusses the evidence underlying the use of EEN, highlighting the mechanisms thought to underlie how EEN induces remission in Crohn's disease, when and how to use EEN, including practical issues in both paediatric and adult practice (formulation, compliance, volumes and administration), and summarises the ongoing research priorities.

Nutritional support in paediatric Crohn's disease: outcome at 12 months

AIM

Paediatric Crohn's disease (CD) is associated with growth delay and poor nutritional status. Maintenance enteral nutrition (MEN) supplementation is a potential adjunct to improve growth/prolong remission.

METHODS

Newly diagnosed CD patients were identified. Anthropometry, treatments and outcomes were collected for 12 months following diagnosis. Data are presented as medians.

RESULTS

A total of 102 patients were identified (age = 13 years, 76% male), 58 (57%) completed exclusive enteral nutrition (EEN) as induction therapy, and 77 (75%) entered clinical remission. Following induction, 58 (57%) of all patients continued MEN and 44 (43%) consumed normal diet (ND). BMI Z-score increased (diagnosis-12 months) for EEN (-1.41 to -0.21 (p = <0.0001)) and steroid groups (-0.97 to -0.11 (p = 0.001)). BMI Z-score increased (post induction - 12 months) for MEN (-0.62 to -0.44 (p = 0.04)) but not ND (-0.33 to -0.4 (p = 0.79)). Height Z-score did not increase for any treatment group over 12 months. MEN and ND group relapse rates were similar at six months, MEN = 21/58 (36%); ND = 21/44 (48%) (p = 0.24) and 12 months, MEN = 24/58 (41%); ND = 13/44 (30%) (p = 0.22). Fewer patients treated with EEN then MEN relapsed less than six months, 14 of 43 (33%), compared to patients treated with steroids then ND 16/29 (55%) (p = 0.09).

CONCLUSION

BMI Z-score increased but height Z-score remained unchanged over 12 months for the MEN group. Use of MEN was not associated with prolonged time to relapse. Prospective studies are required to examine the utility of MEN.

Assessing the growth of preterm infants using detailed anthropometry

AIM

Preterm infants display altered body composition compared to term infants, and weight gain is a crude indicator body composition. Childhood mid-upper arm circumference (MUAC) is a measure of nutritional status. This study investigates MUAC and mid-thigh circumference (MTC) to monitor growth in preterm infants.

METHODS

Preterm infants (<30-week gestation) were recruited. MUAC, MTC, weight, length and head circumference (HC) were measured at recruitment and weekly intervals until discharge. Descriptive, correlation and regression analyses were used.

RESULTS

Ninety-three infants were recruited. Median measurement duration was eight weeks (1-19). Median gestational age was 27 weeks (23-29). Analysis by curve estimation displayed a mean increase of 2.58 mm/week (left MUAC) (p ≤ 0.0001), 2.56 mm/week (right MUAC) (p ≤ 0.0001), 4.16 mm/week (left MTC) (p ≤ 0.0001), 4.20 mm/week (right MTC) (p ≤ 0.0001). Coefficients of determination (R² ) were calculated using a growth regression model for MUAC and MTC (0.866-0.917); measures were comparable to growth modelling of weight (0.913), length (0.945) and HC (0.928). High concordance between left and right MUAC and MTC generated a Pearson's correlation coefficient of 0.999 (MUAC) (p ≤ 0.001) and 0.994 (MTC) (p ≤ 0.001).

CONCLUSION

Data demonstrate the potential utility of MUAC and MTC as additional measures of growth in preterm infants that are reproducible over time. There is potential to gain insights to improve lean-mass accretion in preterm infants.

16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease

The human microbiome is of considerable interest to pediatric inflammatory bowel disease (PIBD) researchers with 1 potential mechanism for disease development being aberrant immune handling of the intestinal bacteria. This study analyses the fecal microbiome through treatment in newly diagnosed PIBD patients and compares to cohabiting siblings where possible. Patients were recruited on clinical suspicion of PIBD before diagnosis. Treatment-naïve fecal samples were collected, with further samples at 2 and 6 weeks into treatment. Samples underwent 16S ribosomal ribonucleic acid (RNA) gene sequencing and short-chain fatty acids (SCFAs) analysis, results were analyzed using quantitative-insights-into-microbial-ecology. Six PIBD patients were included in the cohort: 4 Crohn disease (CD), 1 ulcerative colitis (UC), 1 inflammatory bowel disease (IBD) unclassified, and median age 12.6 (range 10-15.1 years); 3 patients had an unaffected healthy sibling recruited. Microbial diversity (observed species/Chao1/Shannon diversity) was reduced in treatment-naïve patients compared to siblings and patients in remission. Principal coordinate analysis using Bray-Curtis dissimilarity and UniFrac revealed microbial shifts in CD over the treatment course. In treatment-naïve PIBD, there was reduction in functional ability for amino acid metabolism and carbohydrate handling compared to controls (P = .038) and patients in remission (P = .027). Metabolic function returned to normal after remission was achieved. SCFA revealed consistent detection of lactate in treatment-naïve samples. This study adds in-depth 16S rRNA sequencing analysis on a small longitudinal cohort to the literature and includes sibling controls and patients with UC/IBD unclassified. It highlights the initial dysbiosis, reduced diversity, altered functional potential, and subsequent shifts in bacteria from diagnosis over time to remission.

Classification of Paediatric Inflammatory Bowel Disease using Machine Learning

Paediatric inflammatory bowel disease (PIBD), comprising Crohn's disease (CD), ulcerative colitis (UC) and inflammatory bowel disease unclassified (IBDU) is a complex and multifactorial condition with increasing incidence. An accurate diagnosis of PIBD is necessary for a prompt and effective treatment. This study utilises machine learning (ML) to classify disease using endoscopic and histological data for 287 children diagnosed with PIBD. Data were used to develop, train, test and validate a ML model to classify disease subtype. Unsupervised models revealed overlap of CD/UC with broad clustering but no clear subtype delineation, whereas hierarchical clustering identified four novel subgroups characterised by differing colonic involvement. Three supervised ML models were developed utilising endoscopic data only, histological only and combined endoscopic/histological data yielding classification accuracy of 71.0%, 76.9% and 82.7% respectively. The optimal combined model was tested on a statistically independent cohort of 48 PIBD patients from the same clinic, accurately classifying 83.3% of patients. This study employs mathematical modelling of endoscopic and histological data to aid diagnostic accuracy. While unsupervised modelling categorises patients into four subgroups, supervised approaches confirm the need of both endoscopic and histological evidence for an accurate diagnosis. Overall, this paper provides a blueprint for ML use with clinical data.