Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes

Abstract

BackgroundMultiple genes have been implicated by association studies in altering inflammatory bowel disease (IBD) predisposition. Paediatric patients often manifest more extensive disease and a particularly severe disease course. It is likely that genetic predisposition plays a more substantial role in this group.ObjectiveTo identify the spectrum of rare and novel variation in known IBD susceptibility genes using exome sequencing analysis in eight individual cases of childhood onset severe disease.DesignDNA samples from the eight patients underwent targeted exome capture and sequencing. Data were processed through an analytical pipeline to align sequence reads, conduct quality checks, and identify and annotate variants where patient sequence differed from the reference sequence. For each patient, the entire complement of rare variation within strongly associated candidate genes was catalogued.ResultsAcross the panel of 169 known IBD susceptibility genes, approximately 300 variants in 104 genes were found. Excluding splicing and HLA-class variants, 58 variants across 39 of these genes were classified as rare, with an alternative allele frequency of <5%, of which 17 were novel. Only two patients with early onset Crohn's disease exhibited rare deleterious variations within NOD2: the previously described R702W variant was the sole NOD2 variant in one patient, while the second patient also carried the L1007 frameshift insertion. Both patients harboured other potentially damaging mutations in the GSDMB, ERAP2 and SEC16A genes. The two patients severely affected with ulcerative colitis exhibited a distinct profile: both carried potentially detrimental variation in the BACH2 and IL10 genes not seen in other patients.ConclusionFor each of the eight individuals studied, all non-synonymous, truncating and frameshift mutations across all known IBD genes were identified. A unique profile of rare and potentially damaging variants was evident for each patient with this complex disease.

Systems biology in inflammatory bowel diseases

“…Exome sequencing analysis is informative for the whole spectrum of variation within the protein coding sequence of genes and carries the potential of identifying the missing heritability in complex diseases such as IBD. Recently, whole exome sequencing (the sequencing of the complete coding regions of the genome) applied in CD and pediatric IBD patients revealed novel low-frequency variants in known IBD genes 24,25 . Although all these approaches have contributed significantly to our knowledge of genetic alterations in IBD patients, up to date there is no study of sequencing the whole genome of IBD patients.…”

Wearing Red for Signaling: The Heme-Bach Axis in Heme Metabolism, Oxidative Stress Response and Iron Immunology

“…Consistent with the critical functions of Bach2 in the immune cells, genome-wide association studies (GWAS) suggest the involvement of Bach2 in the development of diverse immune system-related diseases, such as generalized vitiligo (Jin et al 2012), asthma (Ferreira et al 2011b), type 1 diabetes (Cooper et al 2008;Plagnol et al 2011), type 2 diabetes (Lee et al 2011), Crohn's disease Christodoulou et al 2013) and celiac disease (Dubois et al 2010). The utilization of Bach2-deficient mice in disease models related to these human diseases is expected to provide insight into the causal links and mechanistic basis of these conditions.…”

Role of Janus Kinase 3 in Mucosal Differentiation and Predisposition to Colitis

“…Ulcerative colitis is associated with defects in differentiation with reduced numbers of differentiated cells and reduced thickness of the mucous layer overlaying the colonic mucosa (3,4). Although different genes have been implicated in IBD (5), the role of epithelial Jak3 in ulcerative colitis is not known.…”