title: Exome sequencing analysis reveals variants in primary immunodeficiency genes in patients with very early onset inflammatory bowel disease.
abstract: OBJECTIVE
  Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed at 5 years of age or younger, frequently presents with a different and more severe phenotype than older-onset IBD. We investigated whether patients with VEO-IBD carry rare or novel variants in genes associated with immunodeficiencies that might contribute to disease development.
  
  
  METHODS
  Patients with VEO-IBD and parents (when available) were recruited from the Children's Hospital of Philadelphia from March 2013 through July 2014. We analyzed DNA from 125 patients with VEO-IBD (age, 3 wk to 4 y) and 19 parents, 4 of whom also had IBD. Exome capture was performed by Agilent SureSelect V4, and sequencing was performed using the Illumina HiSeq platform. Alignment to human genome GRCh37 was achieved followed by postprocessing and variant calling. After functional annotation, candidate variants were analyzed for change in protein function, minor allele frequency less than 0.1%, and scaled combined annotation-dependent depletion scores of 10 or less. We focused on genes associated with primary immunodeficiencies and related pathways. An additional 210 exome samples from patients with pediatric IBD (n = 45) or adult-onset Crohn's disease (n = 20) and healthy individuals (controls, n = 145) were obtained from the University of Kiel, Germany, and used as control groups.
  
  
  RESULTS
  Four hundred genes and regions associated with primary immunodeficiency, covering approximately 6500 coding exons totaling more than 1 Mbp of coding sequence, were selected from the whole-exome data. Our analysis showed novel and rare variants within these genes that could contribute to the development of VEO-IBD, including rare heterozygous missense variants in IL10RA and previously unidentified variants in MSH5 and CD19.
  
  
  CONCLUSIONS
  In an exome sequence analysis of patients with VEO-IBD and their parents, we identified variants in genes that regulate B- and T-cell functions and could contribute to pathogenesis. Our analysis could lead to the identification of previously unidentified IBD-associated variants.
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia. Electronic address: Kelsen@email.chop.edu.
authors.forename: Judith R
authors.initials: JR
authors.lastname: Kelsen
authors.affiliation: Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia.
authors.forename: Noor
authors.initials: N
authors.lastname: Dawany
authors.affiliation: Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Massachusetts General Hospital for Children.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Moran
authors.affiliation: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Germany.
authors.forename: Britt-Sabina
authors.initials: BS
authors.lastname: Petersen
authors.affiliation: Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Sarmady
authors.affiliation: Department of Biomedical Health Informatics, The Children's Hospital of Philadelphia.
authors.forename: Ariella
authors.initials: A
authors.lastname: Sasson
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia.
authors.forename: Helen
authors.initials: H
authors.lastname: Pauly-Hubbard
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia.
authors.forename: Alejandro
authors.initials: A
authors.lastname: Martinez
authors.affiliation: Division of Immunology and Allergy, The Children's Hospital of Philadelphia.
authors.forename: Kelly
authors.initials: K
authors.lastname: Maurer
authors.affiliation: Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology and Hepatology, Department of Microbiology and Immunology, and The Jill Robert's Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, New York.
authors.forename: Joanne
authors.initials: J
authors.lastname: Soong
authors.affiliation: Nucleic Acid/Polymerase Chain Reaction Core, The Children's Hospital of Philadelphia.
authors.forename: Eric
authors.initials: E
authors.lastname: Rappaport
authors.affiliation: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Germany.
authors.forename: Andre
authors.initials: A
authors.lastname: Franke
authors.affiliation: Department of Clinical Bioinformatics, Saarland University, Germany.
authors.forename: Andreas
authors.initials: A
authors.lastname: Keller
authors.affiliation: Division of Pediatric Gastroenterology, Hepatology, and Nutrition, Massachusetts General Hospital for Children.
authors.forename: Harland S
authors.initials: HS
authors.lastname: Winter
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia.
authors.forename: Petar
authors.initials: P
authors.lastname: Mamula
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia.
authors.forename: David
authors.initials: D
authors.lastname: Piccoli
authors.affiliation: Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology and Hepatology, Department of Microbiology and Immunology, and The Jill Robert's Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, New York.
authors.forename: David
authors.initials: D
authors.lastname: Artis
authors.affiliation: Joan and Sanford I. Weill Department of Medicine, Division of Gastroenterology and Hepatology, Department of Microbiology and Immunology, and The Jill Robert's Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medical College, New York, New York.
authors.forename: Gregory F
authors.initials: GF
authors.lastname: Sonnenberg
authors.affiliation: Analytic and Translational Unit Center for Human Genetic Research Department of Medicine, Massachusetts General Hospital; The Broad Institute of MIT and Harvard.
authors.forename: Mark
authors.initials: M
authors.lastname: Daly
authors.affiliation: Division of Immunology and Allergy, The Children's Hospital of Philadelphia.
authors.forename: Kathleen E
authors.initials: KE
authors.lastname: Sullivan
authors.affiliation: Division of Gastroenterology, Hepatology, and Nutrition, The Children's Hospital of Philadelphia.
authors.forename: Robert N
authors.initials: RN
authors.lastname: Baldassano
authors.affiliation: Division of Human Genetics, The Children's Hospital of Philadelphia; Department of Pediatrics, Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania; Department of Molecular Medicine, University Sapienza, Rome, Italy.
authors.forename: Marcella
authors.initials: M
authors.lastname: Devoto
mesh_terms: D000293:Adolescent; D000328:Adult; D000375:Aging / Q000235:genetics*; D018941:Antigens, CD19 / Q000235:genetics; D018797:Cell Cycle Proteins / Q000235:genetics; D002648:Child; D002675:Child, Preschool; D059472:Exome; D005260:Female; D005787:Gene Frequency; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D005858:Germany; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007153:Immunologic Deficiency Syndromes / Q000235:genetics*; D007223:Infant; D007231:Infant, Newborn; D015212:Inflammatory Bowel Diseases / Q000235:genetics* / Q000276:immunology*; D053709:Interleukin-10 Receptor alpha Subunit / Q000235:genetics; D008297:Male; D008875:Middle Aged; D009154:Mutation; D017422:Sequence Analysis, DNA
chemical_list: D018941:Antigens, CD19; D018797:Cell Cycle Proteins; D053709:Interleukin-10 Receptor alpha Subunit; C118481:MSH5 protein, human
keywords: CVID; Common Variable Immune Deficiency; IBD; Inherited Defects; Innate and Adaptive Immunity