Prevalence and Clinical Features of Inflammatory Bowel Diseases Associated With Monogenic Variants, Identified by Whole-Exome Sequencing in 1000 Children at a Single Center

Abstract

Background & aims: A proportion of infants and young children with inflammatory bowel diseases (IBDs) have subtypes associated with a single gene variant (monogenic IBD). We aimed to determine the prevalence of monogenic disease in a cohort of pediatric patients with IBD.

Methods: We performed whole-exome sequencing analyses of blood samples from an unselected cohort of 1005 children with IBD, aged 0-18 years (median age at diagnosis, 11.96 years) at a single center in Canada and their family members (2305 samples total). Variants believed to cause IBD were validated using Sanger sequencing. Biopsies from patients were analyzed by immunofluorescence and histochemical analyses.

Results: We identified 40 rare variants associated with 21 monogenic genes among 31 of the 1005 children with IBD (including 5 variants in XIAP, 3 in DOCK8, and 2 each in FOXP3, GUCY2C, and LRBA). These variants occurred in 7.8% of children younger than 6 years and 2.3% of children aged 6-18 years. Of the 17 patients with monogenic Crohn's disease, 35% had abdominal pain, 24% had nonbloody loose stool, 18% had vomiting, 18% had weight loss, and 5% had intermittent bloody loose stool. The 14 patients with monogenic ulcerative colitis or IBD-unclassified received their diagnosis at a younger age, and their most predominant feature was bloody loose stool (78%). Features associated with monogenic IBD, compared to cases of IBD not associated with a single variant, were age of onset younger than 2 years (odds ratio [OR], 6.30; P = .020), family history of autoimmune disease (OR, 5.12; P = .002), extra-intestinal manifestations (OR, 15.36; P < .0001), and surgery (OR, 3.42; P = .042). Seventeen patients had variants in genes that could be corrected with allogeneic hematopoietic stem cell transplantation.

Conclusions: In whole-exome sequencing analyses of more than 1000 children with IBD at a single center, we found that 3% had rare variants in genes previously associated with pediatric IBD. These were associated with different IBD phenotypes, and 1% of the patients had variants that could be potentially corrected with allogeneic hematopoietic stem cell transplantation. Monogenic IBD is rare, but should be considered in analysis of all patients with pediatric onset of IBD.

Keywords: Genetics; HSCT; Prevalence; Risk Factor.

Figure 1:. Flowchart of WES pediatric IBD study.

A) Flowchart of WES in pediatric IBD study. 1,644,648 variants were called. Following variant prioritization 1,124,679 were ExAC MAF < 0.01 and 379,588 high/med impact severity. Variants then underwent GEMINI Pedigree Analysis and inheritance modelling. In the known monogenic IBD genes 5 were autosomal dominant (AD); 6 autosomal recessive (AR); 9 compound heterozygotes (CH) (note CH in Table 2 is denoted by AR a/b); and 11 X-linked recessive (XL) inheritance. B) Familial inheritance-based analysis by age group of the sequenced cohort. Bar graph displays the sequencing of the cohort – based on singletons (probands alone); incomplete trios; complete trios; complete quads by age group. A ‘trio’ is defined as a sequenced proband and both parents. An ‘incomplete trio’ is a proband and any relative. A ‘complete quad’ is a proband, both parents and a relative. C) Principal Component Analysis. Ethnic diversity demonstrated amongst the cohort.

Figure 2:. Characteristics of identified monogenic IBD population.

A) Variant Type. Variant types identified using WES in the pediatric IBD cohort. B) Gene Variants identified on WES analysis. Graph demonstrates gene variants with the most common highlighted in bold. C) Age at Diagnosis as per Variant Class. Epithelial barrier response defects; T- and B- cell differentiation defect; Hyper- and Auto-inflammatory disorders; Regulatory T-cells and immune regulation; and other. Colors represent the color used in Table 2. D) Age at diagnosis of IBD and disease phenotype. Crohn’s disease (CD), Ulcerative Colitis (UC), IBD-unclassified (IBD-U). Graph displays monogenic pediatric IBD variant diagnosed in VEOIBD age group (35%) indicated by blue line and over 10 years of age (55%) (Paris 1b) indicated by red line. E) Odds ratio analysis of phenotypic features of identified monogenic IBD. Odds ratios and their confidence intervals were computed using logistic regression models (see Supplemental Materials). Age (in years); EIM = extra-intestinal manifestation; FHx – family history; AI = autoimmune. Each horizontal line represents the 95% confidence interval for odds ratio (red dot). Dashed line indicates expected value of 1.0. *represents statistical significance (p<0.05 after Bonferroni correction). F) Age at Hematopoietic stem cell transplant. Age of patient at time of HSCT (in years) with identified monogenic IBD variant in ARPC1B (P8), IL10RB (P29), LRBA (P15), SH2D1A (P19), XIAP (P24). Green line refers to age of diagnosis of IBD. Red line refers to age of monogenic diagnosis. Blue line refers to age of HSCT.