NIDDK IBDGC Crohn's Disease Genome-Wide Association Study

This dataset contains data from a genome-wide association study performed with 968 Inflammatory Bowel Disease (IBD) affected cases and 995 unrelated controls using the Illumina HumanHap300 Genotyping BeadChip. Cases were selected to have Crohn's disease with ileal involvement, and controls were matched to cases based on sex and year of birth. Subjects were drawn from two cohorts: (1) persons with non-Jewish, European ancestry (561 cases and 563 controls), and (2) persons with Jewish ancestry (407 cases and 432 controls). Genotyping was performed at the Feinstein Institute for Medical Research. Seven-hundred fifty-four of the samples (468 cases and 286 controls) were taken from the NIDDK IBD Genetics Consortium cell line repository. These samples are identified in the IBD_Sample file. The subject IDs for these individuals may be used to request corresponding samples for follow-up research through the repository. In addition, complete phenotype data for these individuals are available, together with the Consortium's phenotyping manual and the forms used to collect the data. The remaining 1,209 samples were obtained from pre-existing collections ascertained through Cedars-Sinai Medical Center, Johns Hopkins University, University of Chicago, University of Montreal, University of Pittsburgh, University of Toronto, and the New York Health project (controls only). For these samples, only sex, cohort (Jewish vs. non-Jewish), and age at diagnosis (cases only) are available. Two-hundred three individuals from among the pre-existing samples did not provide consent to release their genotype data (designated as consent group 2 in the file IBD_Subject). Thus, individual genotype data are only provided for 1,760 samples. To compensate for this, we have provided summary results for each SNP. These are based on a stratified analysis testing case/control association. Fifty-one samples had a call rate less than 93% and were therefore excluded from this analysis, leaving an overall sample size of 1,963 - 51 = 1,912. X Chromosome Heterozygosity Nine samples have X chromosome heterozygosity that is neither consistent nor inconsistent with their phenotypic sex. One of these samples was found to have Turner Syndrome. The remaining 8 samples have heterozygosity ranging from 35-76%. ]]>
IBD Genetics Consortium: Phenotype FormNIDDK IBD Genetics Consortium: Phenotype Operating ManualThis dataset contains data from a genome-wide association study performed with 968 IBD-affected cases and 995 unrelated controls using the Illumina HumanHap300 Genotyping BeadChip. Cases were selected to have Crohn's disease with ileal involvement, and controls were matched to cases based on sex and year of birth. Subjects were drawn from two cohorts: (1) persons with non-Jewish, European ancestry (561 cases and 563 controls), and (2) persons with Jewish ancestry (407 cases and 432 controls). Genotyping was performed at the Feinstein Institute for Medical Research.Cases were selected to have Crohn's disease with ileal involvement. After genotyping was completed and updated phenotype information was obtained, two (non-repository) cases were identified as having Indeterminate Colitis instead of Crohn's disease, and one Crohn's case was found not to have ileal involvement (these three samples are nonetheless included in the dataset). Diagnosis of IBD required (i) one or more of the following symptoms: diarrhea, rectal bleeding, abdominal pain, fever or complicated perianal disease; (ii) occurrence of symptoms on two or more occasions separated by at least 8 weeks or ongoing symptoms of at least 6 weeks duration and (iii) objective evidence of inflammation from radiologic, endoscopic and histologic evaluation. Ileal Crohn's disease involvement was defined as mucosal ulceration, cobblestoning, stricturing or bowel wall thickening from endoscopy reports, barium X-rays, operative reports and/or pathology resection specimen reports. Individuals with either 'ileal only' or 'ileocolonic' were included. Within each of the non-Jewish and Jewish cohorts, controls were matched to cases based on sex and year of birth. In addition, controls were required to meet the following inclusion criteria: (1) no history of IBD among 1st and 2nd degree relatives, (2) never been diagnosed with IBD, and (3) never experienced chronic diarrhea, unexplained rectal bleeding, or unexplained weight loss.]]>
Case-control, trios, prospectively attained. 6 GRC sites and DCC Linkage (Yao-Shugart Y, Duerr RH, Brant SR, Rioux JD, Silverberg MS, Taylor KD, Schumm LP, Cho JH, Brant SR. SNP-based linkage screen identifies a significant locus on chromosome 13p.) and association studies. ]]>