title: Exome sequencing of 75 individuals from multiply affected coeliac families and large scale resequencing follow up.
abstract: Coeliac disease (CeD) is a highly heritable common autoimmune disease involving chronic small intestinal inflammation in response to dietary wheat. The human leukocyte antigen (HLA) region, and 40 newer regions identified by genome wide association studies (GWAS) and dense fine mapping, account for ∼40% of the disease heritability. We hypothesized that in pedigrees with multiple individuals with CeD rare [minor allele frequency (MAF) <0.5%] mutations of larger effect size (odds ratios of ∼2-5) might exist. We sequenced the exomes of 75 coeliac individuals of European ancestry from 55 multiply affected families. We selected interesting variants and genes for further follow up using a combination of: an assessment of shared variants between related subjects, a model-free linkage test, and gene burden tests for multiple, potentially causal, variants. We next performed highly multiplexed amplicon resequencing of all RefSeq exons from 24 candidate genes selected on the basis of the exome sequencing data in 2,248 unrelated coeliac cases and 2,230 controls. 1,335 variants with a 99.9% genotyping call rate were observed in 4,478 samples, of which 939 were present in coding regions of 24 genes (Ti/Tv 2.99). 91.7% of coding variants were rare (MAF <0.5%) and 60% were novel. Gene burden tests performed on rare functional variants identified no significant associations (p<1×10(-3)) in the resequenced candidate genes. Our strategy of sequencing multiply affected families with deep follow up of candidate genes has not identified any new CeD risk mutations.
authors: Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom.
authors: Vanisha
authors: V
authors: Mistry
authors: Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom.
authors: Nicholas A
authors: NA
authors: Bockett
authors: Division of Medicine, University College London, London, WC1E 6JF, United Kingdom.
authors: Adam P
authors: AP
authors: Levine
authors: UCL Advanced Diagnostics, Molecular Profiling Laboratory, Sarah Cannon-UCL Laboratories, Ground Floor, Shropshire House, 1 Capper Street, London, WC1E 6JA, United Kingdom.
authors: Muddassar M
authors: MM
authors: Mirza
authors: Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom.
authors: Karen A
authors: KA
authors: Hunt
authors: King's College London, Division of Diabetes and Nutritional Sciences, Gastroenterology, The Rayne Institute, St Thomas' Hospital, Westminster Bridge Road, London SE1 7EH, United Kingdom.
authors: Paul J
authors: PJ
authors: Ciclitira
authors: Medical Research Council Prion Unit, Department of Neurodegenerative Disease, University College London Institute of Neurology, London WC1N 3BG, United Kingdom.
authors: Holger
authors: H
authors: Hummerich
authors: Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, California 91010, United States of America.
authors: Susan L
authors: SL
authors: Neuhausen
authors: Division of Genetics and Molecular Medicine, Kings College London School of Medicine, 8th Floor Tower Wing, Guy's Hospital, London SE1 9RY, United Kingdom.
authors: Michael A
authors: MA
authors: Simpson
authors: University College London Genetics Institute, Gower Street, London WC1E 6BT, United Kingdom.
authors: Vincent
authors: V
authors: Plagnol
authors: Blizard Institute, Barts and The London School of Medicine and Dentistry, 4 Newark Street, London E1 2AT, United Kingdom.
authors: David A
authors: DA
authors: van Heel
mesh_terms: D016022:Case-Control Studies; D002446:Celiac Disease / Q000235:genetics*; D059472:Exome; D005260:Female; D005500:Follow-Up Studies; D005787:Gene Frequency; D008040:Genetic Linkage; D020022:Genetic Predisposition to Disease; D006801:Humans; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
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