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Letters to JMG
Association of RASGRP1 with type 1 diabetes is revealed by combined follow-up of two genome-wide studies
  1. H Q Qu1,
  2. S F A Grant2,3,
  3. J P Bradfield2,
  4. C Kim2,
  5. E Frackelton2,
  6. H Hakonarson2,3,
  7. C Polychronakos1
  1. 1
    Departments of Pediatrics and Human Genetics, McGill University, Montreal, Québec, Canada
  2. 2
    Center for Applied Genomics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  3. 3
    Department of Pediatrics and Division of Human Genetics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
  1. Professor C Polychronakos, McGill University Health Center (Children’s Hospital), 2300 Tupper, Montréal, Qc, H3H 1P3, Canada; constantin.polychronakos{at}mcgill.ca

Abstract

Background: The two genome-wide association studies published by us and by the Wellcome Trust Case–Control Consortium (WTCCC) revealed a number of novel loci, but neither had the statistical power to elucidate all of the genetic components of type 1 diabetes risk, a task for which larger effective sample sizes are needed.

Methods: We analysed data from two sources: (1) The previously published second stage of our study, with a total sample size of the two stages consisting of 1046 Canadian case–parent trios and 538 multiplex families with 929 affected offspring from the Type 1 Diabetes Genetics Consortium (T1DGC); (2) the Rapid Response 2 (RR2) project of the T1DGC, which genotyped 4417 individuals from 1062 non-overlapping families, including 2059 affected individuals (mostly sibling pairs) for the 1536 markers with the highest statistical significance for type 1 diabetes in the WTCCC results.

Results: One locus, mapping to a linkage disequilibrium (LD) block at chr15q14, reached statistical significance by combining results from two markers (rs17574546 and rs7171171) in perfect LD with each other (r2 = 1). We obtained a joint p value of 1.3×10−6, which exceeds by an order of magnitude the conservative threshold of 3.26×10−5 obtained by correcting for the 1536 single nucleotide polymorphisms (SNPs) tested in our study. Meta-analysis with the original WTCCC genome-wide data produced a p value of 5.83×10−9.

Conclusions: A novel type 1 diabetes locus was discovered. It involves RASGRP1, a gene known to play a crucial role in thymocyte differentiation and T cell receptor (TCR) signalling by activating the Ras signalling pathway.

https://doi.org/10.1136/jmg.2009.067140

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    Footnotes

    • ▸ An additional figure is published online only at http://jmg.bmj.com/content/vol46/issue8

    • Funding: This work was funded by the Children’s Hospital of Philadelphia, the Juvenile Diabetes Research Foundation International and Genome Canada. HQQ is supported by a fellowship from the Canadian Institutes of Health Research.

    • Competing interests: None.

    • Patient consent: Obtained.