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Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.

Nature genetics | Oct 9, 2011

More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 × 10(-16), odds ratio ≈ 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models.

Pubmed ID: 21983784 RIS Download

Mesh terms: Case-Control Studies | Cell Line | Genetic Predisposition to Disease | Genome-Wide Association Study | Humans | Inflammatory Bowel Diseases | Nod2 Signaling Adaptor Protein | RNA Splicing | Receptors, Interleukin | Sequence Analysis, DNA

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Associated grants

  • Agency: NCRR NIH HHS, Id: M01-RR00425
  • Agency: NIDDK NIH HHS, Id: P01 DK046763-08
  • Agency: NIAID NIH HHS, Id: AI062773
  • Agency: NHGRI NIH HHS, Id: U54 HG003067-01
  • Agency: NIDDK NIH HHS, Id: DK043351
  • Agency: NIDDK NIH HHS, Id: RC1 DK086502
  • Agency: NHGRI NIH HHS, Id: U01 HG005923-01
  • Agency: NIDDK NIH HHS, Id: U01 DK062432-07
  • Agency: NHGRI NIH HHS, Id: HG005923
  • Agency: NIDDK NIH HHS, Id: U01 DK062413-08
  • Agency: NIDDK NIH HHS, Id: R01 DK060049
  • Agency: NHGRI NIH HHS, Id: U54 HG003067
  • Agency: NIDDK NIH HHS, Id: DK062422
  • Agency: NIDDK NIH HHS, Id: U01 DK062413
  • Agency: NHGRI NIH HHS, Id: U01 HG005923
  • Agency: NIDDK NIH HHS, Id: P30 DK043351
  • Agency: NIDDK NIH HHS, Id: R21 DK084554-01
  • Agency: NIDDK NIH HHS, Id: R21 DK084554
  • Agency: NIDDK NIH HHS, Id: RC1 DK086502-01
  • Agency: NIDDK NIH HHS, Id: DK064869
  • Agency: NIDDK NIH HHS, Id: P30 DK063491-06
  • Agency: NIDDK NIH HHS, Id: DK062423
  • Agency: Canadian Institutes of Health Research, Id: 01038
  • Agency: NIAID NIH HHS, Id: AI067152
  • Agency: NIDDK NIH HHS, Id: R01 DK064869-01
  • Agency: NIDDK NIH HHS, Id: U01 DK062432
  • Agency: NIDDK NIH HHS, Id: R01 DK064869
  • Agency: NIDDK NIH HHS, Id: U01 DK062423-01
  • Agency: NIDDK NIH HHS, Id: R01 DK060049-08
  • Agency: NIDDK NIH HHS, Id: U01 DK062429
  • Agency: NIDDK NIH HHS, Id: P30 DK063491
  • Agency: NIDDK NIH HHS, Id: U01 DK062429-01
  • Agency: NIDDK NIH HHS, Id: U01 DK062422
  • Agency: NIAID NIH HHS, Id: AI065687
  • Agency: NIDDK NIH HHS, Id: DK83756
  • Agency: NIDDK NIH HHS, Id: P30 DK043351-18
  • Agency: Chief Scientist Office, Id: ETM/75
  • Agency: NIDDK NIH HHS, Id: U01 DK062422-01
  • Agency: Chief Scientist Office, Id: CZB/4/540
  • Agency: NIDDK NIH HHS, Id: DK062431
  • Agency: NIAID NIH HHS, Id: P01 AI065687
  • Agency: NIAID NIH HHS, Id: R01 AI062773-01A1
  • Agency: NIDDK NIH HHS, Id: DK060049
  • Agency: NIDDK NIH HHS, Id: U01 DK062420-06
  • Agency: NCRR NIH HHS, Id: M01 RR000425
  • Agency: NIAID NIH HHS, Id: R01 AI062773
  • Agency: NIDDK NIH HHS, Id: DK062420
  • Agency: NIDDK NIH HHS, Id: R21-DK84554-01
  • Agency: NIDDK NIH HHS, Id: U01-DK062413
  • Agency: NIDDK NIH HHS, Id: P30 DK043351-21
  • Agency: NIDDK NIH HHS, Id: R01 DK083756-01
  • Agency: NIDDK NIH HHS, Id: DK063491
  • Agency: NIDDK NIH HHS, Id: U01 DK062431-01
  • Agency: NIDDK NIH HHS, Id: U01 DK062423
  • Agency: NIDDK NIH HHS, Id: DK062429
  • Agency: NIDDK NIH HHS, Id: P01-DK046763
  • Agency: NIDDK NIH HHS, Id: DK086502
  • Agency: NIDDK NIH HHS, Id: P01 DK046763
  • Agency: NIDDK NIH HHS, Id: R01 DK083756
  • Agency: Medical Research Council, Id: G0800675
  • Agency: NIDDK NIH HHS, Id: DK062432
  • Agency: NIDDK NIH HHS, Id: DK062413
  • Agency: NIDDK NIH HHS, Id: U01 DK062420
  • Agency: NIDDK NIH HHS, Id: U01 DK062432-01
  • Agency: NIDDK NIH HHS, Id: U01 DK062431
  • Agency: NCRR NIH HHS, Id: M01 RR000425-30S1
  • Agency: Medical Research Council, Id: G0600329
  • Agency: NIAID NIH HHS, Id: U19 AI067152

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National Genome Research Network

The program of medical genome research is a large-scale biomedical research project which extends the national genome research net (NGFN) and will be funded by the federal ministry of education and research (BMBF) from 2008-2013. Currently the program includes two fields: * Research ** NGFN-Plus: With the aim on combating diseases that are central to health policy, several hundred researchers are systematically investigating the complex molecular interactions of the human body. They are organized in 26 Integrated Genome Research Networks. * Application ** NGFN-Transfer: The rapid transfer of results from medical genome research into medical and industrial application is the aim of the scientists from research institutes and biomedical enterprises that cooperate in eight Innovation Alliances. AREAS OF DISEASE * Cardiovascular disease * Cancer * Neuronal diseases * Infections and Inflammations * Environmental factors

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Primer3

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