Sequencing-Based Genotyping and Association Analysis of the MICA and MICB Genes in Type 1 Diabetes

Sequencing-Based Genotyping and Association Analysis of the MICA and MICB Genes in Type 1 Diabetes Sarah F. Field , Sergey Nejentsev , Neil M. Walker , Joanna M.M. Howson , Lisa M. Godfrey , Jennifer D. Jolley , Matthew P.A. Hardy and John A. Todd From the Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Addenbrooke's Hospital, Cambridge, U.K Corresponding author: John A. Todd, JDRF/WT Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Addenbrooke's Hospital, Hills Road, Cambridge, CB2 0XY, U.K. E-mail: john.todd{at}cimr.cam.ac.uk Abstract OBJECTIVE— The nonclassical major histocompatibility complex (MHC) class I chain-related molecules (MICs), encoded within the MHC, function in immunity. The transmembrane polymorphism in MICA ( MICA-STR ) has been reported to be associated with type 1 diabetes. In this study, we directly sequenced both of the highly polymorphic MIC genes ( MICA and MICB ) in order to establish whether they are associated with type 1 diabetes independently of the known type 1 diabetes MHC class II genes HLA-DRB1 and HLA-DQB1 . RESEARCH DESIGN AND METHODS— We developed a sequencing-based typing method and genotyped MICA and MICB in 818 families (2,944 individuals) with type 1 diabetes from the U.K. and U.S. (constructing the genotype from single nucleotide polymorphisms in exons 2–4 of MICA and 2–5 of MICB ) and additionally genotyped the MICA-STR in 2,023 type 1 diabetic case subjects and 1,748 control subjects from the U.K. We analyzed the association of the MICA and MICB alleles and genotypes with type 1 diabetes using regression methods. RESULTS— We identified known MICA and MICB alleles and discovered four new MICB alleles. Based on this large-scale and detailed genotype data, we found no evidence for association of MICA and MICB with type 1 diabetes independently of the MHC class II genes ( MICA P = 0.08, MICA-STR P = 0.76, MICB P = 0.03, after conditioning on HLA-DRB1 and HLA-DQB1 ). CONCLUSIONS— Common MICA and MICB genetic variations including the MICA-STR are not associated, in a primary way, with susceptibility to type 1 diabetes. LD, linkage disequilibrium MHC, major histocompatibility complex MIC, MHC class I chain-related molecule, nsSNP, nonsynonymous single nucleotide polymorphism rpart, recursive partitioning SBT, sequencing-ba