Next Generation Exome Sequencing of Paediatric Inflammatory Bowel Disease Patients Identifies Rare and Novel Variants in Candida
Total Page：16
File Type：pdf, Size：1020Kb
Gut Online First, published on April 28, 2012 as 10.1136/gutjnl-2011-301833 Inflammatory bowel disease ORIGINAL ARTICLE Gut: first published as 10.1136/gutjnl-2011-301833 on 28 April 2012. Downloaded from Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes Katja Christodoulou,1 Anthony E Wiskin,2 Jane Gibson,1 William Tapper,1 Claire Willis,2 Nadeem A Afzal,3 Rosanna Upstill-Goddard,1 John W Holloway,4 Michael A Simpson,5 R Mark Beattie,3 Andrew Collins,1 Sarah Ennis1 < Additional materials are ABSTRACT published online only. To view Background Multiple genes have been implicated by Significance of this study these files please visit the association studies in altering inflammatory bowel journal online (http://gut.bmj. com/content/early/recent). disease (IBD) predisposition. Paediatric patients often What is already known on this subject? manifest more extensive disease and a particularly < For numbered affiliations see Genome-wide association studies have impli- end of article. severe disease course. It is likely that genetic cated numerous candidate genes for inflamma- predisposition plays a more substantial role in this group. tory bowel disease (IBD), but evidence of Correspondence to Objective To identify the spectrum of rare and novel causality for specific variants is largely absent. Dr Sarah Ennis, Genetic variation in known IBD susceptibility genes using exome Furthermore, by design, genome-wide associa- Epidemiology and Genomic sequencing analysis in eight individual cases of childhood Informatics Group, Human tion studies are limited to the study of Genetics, Faculty of Medicine, onset severe disease. common variants and overlook the functionally University of Southampton, Design DNA samples from the eight patients underwent detrimental variation imposed by rare/novel Duthie Building (Mailpoint 808), targeted exome capture and sequencing. Data were mutation. Southampton General Hospital, processed through an analytical pipeline to align < Southampton SO16 6YD, UK; Exome analysis is fully informative for the [email protected] sequence reads, conduct quality checks, and identify and spectrum of variation within the protein coding annotate variants where patient sequence differed from sequence of genes. It has been used to KC and AEW contributed equally the reference sequence. For each patient, the entire successfully identify disease causing variants to this study. complement of rare variation within strongly associated in Mendelian disorders, but its potential to candidate genes was catalogued. Revised 27 March 2012 identify the missing heritability in complex http://gut.bmj.com/ Accepted 1 April 2012 Results Across the panel of 169 known IBD diseases such as paediatric IBD has not yet susceptibility genes, approximately 300 variants in 104 been realised. genes were found. Excluding splicing and HLA-class variants, 58 variants across 39 of these genes were What are the new findings? classified as rare, with an alternative allele frequency of < This study examines genetic variants from the <5%, of which 17 were novel. Only two patients with perspective of the patient rather than the d early onset Crohn’s disease exhibited rare deleterious gene for each paediatric case a profile of on September 25, 2021 by guest. Protected copyright. variations within NOD2: the previously described R702W deleterious variation is determined across variant was the sole NOD2 variant in one patient, while a comprehensive panel of known IBD genes. the second patient also carried the L1007 frameshift < Paediatric IBD patients carry a wide spectrum of insertion. Both patients harboured other potentially low frequency variants within candidate IBD damaging mutations in the GSDMB, ERAP2 and SEC16A genes. genes. The two patients severely affected with ulcerative < In silico analyses indicate a substantial propor- colitis exhibited a distinct profile: both carried potentially tion of these mutations are potentially detrimental variation in the BACH2 and IL10 genes not deleterious. seen in other patients. < Consistent with complex inheritance, this small Conclusion For each of the eight individuals studied, all subset of patients with severe IBD exhibit non-synonymous, truncating and frameshift mutations a varied profile of mutation with limited across all known IBD genes were identified. A unique sharing of specific variants across the set of profile of rare and potentially damaging variants was eight exomes. evident for each patient with this complex disease. figures of 3.1 for CD, 1.4 for UC and 0.6 for IBD INTRODUCTION unclassified (IBDU).1 While the precise aetiology Ulcerative colitis (UC) and Crohn’s disease (CD) and pathogenesis is complex and incompletely are the two main clinical phenotypes of inflam- understood, it is widely accepted that IBD occurs as This paper is freely available matory bowel disease (IBD), both resulting in the result of a dysregulated mucosal immune online under the BMJ Journals chronic and relapsing inflammation. The incidence response to commensal gut flora in the genetically unlocked scheme, see http:// 2 gut.bmj.com/site/about/ of IBD in the paediatric population of the UK is 5.2 susceptible host. Familial aggregation of disease unlocked.xhtml per 100 000 children per year, with breakdown implies a strong genetic component,3 although CopyrightChristodoulou Article K, Wiskin author AE, Gibson (or J, et their al. Gut (2012).employer) doi:10.1136/gutjnl-2011-301833 2012. Produced by BMJ Publishing Group Ltd (& BSG) under licence. 1 of 8 Inflammatory bowel disease mutation in the XIAP gene (X-linked inhibition of apoptosis Significance of this study gene) for which the child was hemizygous. After haematopoietic Gut: first published as 10.1136/gutjnl-2011-301833 on 28 April 2012. Downloaded from progenitor cell transplant treatment, as recommended for XIAP deficiency, the IBD resolved, suggesting that the Crohn’s-like How might it impact on clinical practice in the foreseeable 10 future? illness seen in this patient was driven by this single mutation. < Functional studies are required to confirm in silico assessment As next generation sequencing technology advances, it of variation impact on biology. becomes increasingly affordable. Nevertheless, while costs < Even mutations confirmed to confer susceptibility must be remain in the region of several hundred pounds per sample, considered among the full profile of disease predisposing targeted analyses of those patient groups most likely to yield variation present in any individual. positive results is prudent. Prioritisation of cases with strong < As the cost of next generation sequencing falls and the family history and/or patients representing the phenotypic ‘extreme’ of common traits is a useful strategy.11 One such number of mutation profiles increases, there is clear potential ‘ ’ for genetic characterisation of IBD phenotypic sub-types example of an extreme phenotype is paediatric disease in which facilitating targeted therapeutic intervention/personalised onset is particularly early. Genetic susceptibility is thought to medicine. play a more important role in the aetiology of early-onset IBD than in late-onset IBD.12 This is supported by a higher rate of positive family history of IBD in patients with a younger age at diagnosis compared to the older age group, suggesting that an earlier presentation may be due to a higher burden of disease- environmental factors may play a greater role in ulcerative causing mutations in the genomes of these affected children colitis.4 compared to those in whom disease manifests later in life.13 In Over recent years, genome-wide association studies (GWAS) addition, environmental confounding factors such as smoking have been applied with huge success to identify common genes are less likely to be exerting an influence on disease in paediatric involved in both CD and UC. Genes with replicated evidence for cohorts. It has also been suggested that early-onset disease may strong association suggest that pathways involving disruption in itself be a more aggressive phenotype; in CD, earlier age at of the innate and adaptive immune system, compromised diagnosis is associated with a greater need for surgery and e epithelial barrier function and impaired autophagy play increased small bowel disease.12 14 a significant role in disease.2 However, despite the identification Two of the most comprehensive association studies investi- of over one hundred unique genes in IBD susceptibility, these gating IBD have used adult cohorts, but a recent GWAS of 3246 common variants in combination account for less than a quarter early-onset IBD cases successfully identified five new loci asso- e of the genetic risk.5 7 The source of this missing heritability is ciated with childhood susceptibility as well as replicating loci the subject of much debate with various explanations: over- previously implicated in adult-onset disease.15 Early-onset estimates of original heritability statistics; underpowered GWAS disease genes have also been located using linkage analysis and studies (in terms of sample size and single nucleotide poly- candidate gene sequencing approaches undertaken in two http://gut.bmj.com/ morphism (SNP) coverage) to detect common variants associ- unrelated consanguineous families.16 Despite distinct clinical ated with decreasing effect sizes; poorly investigated epistatic and histopathological features of the CD and UC phenotypes, and geneeenvironment interactions; and rare variation.8