title: Next generation exome sequencing of paediatric inflammatory bowel disease patients identifies rare and novel variants in candidate genes.
abstract: BACKGROUND
  Multiple 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.
  
  
  OBJECTIVE
  To 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.
  
  
  METHODS
  DNA 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.
  
  
  RESULTS
  Across 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.
  
  
  CONCLUSIONS
  For 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.
authors.affiliation: Genetic Epidemiology and Genomic Informatics Group, Human Genetics & Genomic Medicine, University of Southampton, University Hospital Southampton NHS Foundation Trust, Southampton, UK.
authors.forename: Katja
authors.initials: K
authors.lastname: Christodoulou
authors.forename: Anthony E
authors.initials: AE
authors.lastname: Wiskin
authors.forename: Jane
authors.initials: J
authors.lastname: Gibson
authors.forename: William
authors.initials: W
authors.lastname: Tapper
authors.forename: Claire
authors.initials: C
authors.lastname: Willis
authors.forename: Nadeem A
authors.initials: NA
authors.lastname: Afzal
authors.forename: Rosanna
authors.initials: R
authors.lastname: Upstill-Goddard
authors.forename: John W
authors.initials: JW
authors.lastname: Holloway
authors.forename: Michael A
authors.initials: MA
authors.lastname: Simpson
authors.forename: R Mark
authors.initials: RM
authors.lastname: Beattie
authors.forename: Andrew
authors.initials: A
authors.lastname: Collins
authors.forename: Sarah
authors.initials: S
authors.lastname: Ennis
mesh_terms: D000293:Adolescent; D017668:Age of Onset; D002648:Child; D002675:Child, Preschool; D015331:Cohort Studies; D003093:Colitis, Ulcerative / Q000235:genetics; D003198:Computer Simulation; D003424:Crohn Disease / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods; D059472:Exome / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D056726:Genetic Association Studies / Q000379:methods; D020022:Genetic Predisposition to Disease; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000235:genetics*; D008297:Male; D008957:Models, Genetic; D009154:Mutation; D053473:Nod2 Signaling Adaptor Protein / Q000235:genetics; D010641:Phenotype
chemical_list: C429018:NOD2 protein, human; D053473:Nod2 Signaling Adaptor Protein