Exome Sequencing Analysis Reveals Variants in Primary Immunodeficiency Genes in Patients With Very Early Onset Inflammatory Bowel Disease.

Judith R Kelsen, Noor Dawany, Christopher J Moran, Britt-Sabina Petersen, Mahdi Sarmady, Ariella Sasson, Helen Pauly-Hubbard, Alejandro Martinez, Kelly Maurer, Joanne Soong, Eric Rappaport, Andre Franke, Andreas Keller, Harland S Winter, Petar Mamula, David Piccoli, David Artis, Gregory F Sonnenberg, Mark Daly, Kathleen E Sullivan, Robert N Baldassano, Marcella Devoto
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Gastroenterology (New York, N.Y. 1943)
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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.Very early onset inflammatory bowel disease (VEO-IBD), IBD diagnosed ≤5 y of age, 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.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 (ages 3 weeks 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 post-processing and variant calling. Following functional annotation, candidate variants were analyzed for change in protein function, minor allele frequency <0.1%, and scaled combined annotation dependent depletion scores ≤10. 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.Four-hundred genes and regions associated with primary immunodeficiency, covering approximately 6500 coding exons totaling > 1 Mbp of coding sequence, were selected from the whole exome data. Our analysis revealed 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.