title: Sequencing and association analysis of the type 1 diabetes-linked region on chromosome 10p12-q11.
abstract: BACKGROUND
  In an effort to locate susceptibility genes for type 1 diabetes (T1D) several genome-wide linkage scans have been undertaken. A chromosomal region designated IDDM10 retained genome-wide significance in a combined analysis of the main linkage scans. Here, we studied sequence polymorphisms in 23 Mb on chromosome 10p12-q11, including the putative IDDM10 region, to identify genes associated with T1D.
  
  
  RESULTS
  Initially, we resequenced the functional candidate genes, CREM and SDF1, located in this region, genotyped 13 tag single nucleotide polymorphisms (SNPs) and found no association with T1D. We then undertook analysis of the whole 23 Mb region. We constructed and sequenced a contig tile path from two bacterial artificial clone libraries. By comparison with a clone library from an unrelated person used in the Human Genome Project, we identified 12,058 SNPs. We genotyped 303 SNPs and 25 polymorphic microsatellite markers in 765 multiplex T1D families and followed up 22 associated polymorphisms in up to 2,857 families. We found nominal evidence of association in six loci (P = 0.05 - 0.0026), located near the PAPD1 gene. Therefore, we resequenced 38.8 kb in this region, found 147 SNPs and genotyped 84 of them in the T1D families. We also tested 13 polymorphisms in the PAPD1 gene and in five other loci in 1,612 T1D patients and 1,828 controls from the UK. Overall, only the D10S193 microsatellite marker located 28 kb downstream of PAPD1 showed nominal evidence of association in both T1D families and in the case-control sample (P = 0.037 and 0.03, respectively).
  
  
  CONCLUSIONS
  We conclude that polymorphisms in the CREM and SDF1 genes have no major effect on T1D. The weak T1D association that we detected in the association scan near the PAPD1 gene may be either false or due to a small genuine effect, and cannot explain linkage at the IDDM10 region.
authors.affiliation: Juvenile Diabetes Research Foundation/Wellcome Trust Diabetes and Inflammation Laboratory, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK. sergey.nejentsev@cimr.cam.ac.uk
authors.forename: Sergey
authors.initials: S
authors.lastname: Nejentsev
authors.forename: Luc J
authors.initials: LJ
authors.lastname: Smink
authors.forename: Deborah
authors.initials: D
authors.lastname: Smyth
authors.forename: Rebecca
authors.initials: R
authors.lastname: Bailey
authors.forename: Christopher E
authors.initials: CE
authors.lastname: Lowe
authors.forename: Felicity
authors.initials: F
authors.lastname: Payne
authors.forename: Jennifer
authors.initials: J
authors.lastname: Masters
authors.forename: Lisa
authors.initials: L
authors.lastname: Godfrey
authors.forename: Alex
authors.initials: A
authors.lastname: Lam
authors.forename: Oliver
authors.initials: O
authors.lastname: Burren
authors.forename: Helen
authors.initials: H
authors.lastname: Stevens
authors.forename: Sarah
authors.initials: S
authors.lastname: Nutland
authors.forename: Neil M
authors.initials: NM
authors.lastname: Walker
authors.forename: Anne
authors.initials: A
authors.lastname: Smith
authors.forename: Rebecca
authors.initials: R
authors.lastname: Twells
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Barratt
authors.forename: Charmain
authors.initials: C
authors.lastname: Wright
authors.forename: Lisa
authors.initials: L
authors.lastname: French
authors.forename: Yuan
authors.initials: Y
authors.lastname: Chen
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Deloukas
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Ian
authors.initials: I
authors.lastname: Dunham
authors.forename: John A
authors.initials: JA
authors.lastname: Todd
mesh_terms: D016022:Case-Control Studies; D002879:Chromosomes, Human, Pair 10; D017931:DNA Primers; D003922:Diabetes Mellitus, Type 1 / Q000235:genetics*; D005260:Female; D005787:Gene Frequency; D005819:Genetic Markers; D005838:Genotype; D006801:Humans; D008297:Male; D020161:Physical Chromosome Mapping; D020641:Polymorphism, Single Nucleotide
chemical_list: D017931:DNA Primers; D005819:Genetic Markers