title: Sequencing PDX1 (insulin promoter factor 1) in 1788 UK individuals found 5% had a low frequency coding variant, but these variants are not associated with Type 2 diabetes.
abstract: OBJECTIVE
  Genome-wide association studies have identified >30 common variants associated with Type 2 diabetes (>5% minor allele frequency). These variants have small effects on individual risk and do not account for a large proportion of the heritable component of the disease. Monogenic forms of diabetes are caused by mutations that occur in <1:2000 individuals and follow strict patterns of inheritance. In contrast, the role of low frequency genetic variants (minor allele frequency 0.1-5%) in Type 2 diabetes is not known. The aim of this study was to assess the role of low frequency PDX1 (also called IPF1) variants in Type 2 diabetes.
  
  
  METHODS
  We sequenced the coding and flanking intronic regions of PDX1 in 910 patients with Type 2 diabetes and 878 control subjects.
  
  
  RESULTS
  We identified a total of 26 variants that occurred in 5.3% of individuals, 14 of which occurred once. Only D76N occurred in >1%. We found no difference in carrier frequency between patients (5.7%) and control subjects (5.0%) (P=0.46). There were also no differences between patients and control subjects when analyses were limited to subsets of variants. The strongest subset were those variants in the DNA binding domain where all five variants identified were only found in patients (P=0.06).
  
  
  CONCLUSIONS
  Approximately 5% of UK individuals carry a PDX1 variant, but there is no evidence that these variants, either individually or cumulatively, predispose to Type 2 diabetes. Further studies will need to consider strategies to assess the role of multiple variants that occur in <1 in 1000 individuals.
authors.affiliation: Institute of Biomedical and Clinical Science Genetics of Complex Traits, Peninsula College of Medicine and Dentistry, University of Exeter, Barrack Road, Exeter, UK. emma.edghill@pms.ac.uk
authors.forename: E L
authors.initials: EL
authors.lastname: Edghill
authors.forename: A
authors.initials: A
authors.lastname: Khamis
authors.forename: M N
authors.initials: MN
authors.lastname: Weedon
authors.forename: M
authors.initials: M
authors.lastname: Walker
authors.forename: G A
authors.initials: GA
authors.lastname: Hitman
authors.forename: M I
authors.initials: MI
authors.lastname: McCarthy
authors.forename: K R
authors.initials: KR
authors.lastname: Owen
authors.forename: S
authors.initials: S
authors.lastname: Ellard
authors.forename: A
authors.initials: A
authors.lastname: T Hattersley
authors.forename: T M
authors.initials: TM
authors.lastname: Frayling
mesh_terms: D000293:Adolescent; D000328:Adult; D016022:Case-Control Studies; D003924:Diabetes Mellitus, Type 2 / Q000453:epidemiology / Q000235:genetics*; D005260:Female; D055106:Genome-Wide Association Study; D018398:Homeodomain Proteins / Q000235:genetics*; D006801:Humans; D008297:Male; D008875:Middle Aged; D009154:Mutation / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017422:Sequence Analysis, DNA; D015534:Trans-Activators / Q000235:genetics*; D006113:United Kingdom / Q000453:epidemiology; D044465:White People / Q000235:genetics*; D055815:Young Adult
chemical_list: D018398:Homeodomain Proteins; D015534:Trans-Activators; C084010:pancreatic and duodenal homeobox 1 protein