Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20

Article metrics

Abstract

To identify multiple sclerosis (MS) susceptibility loci, we conducted a genome-wide association study (GWAS) in 1,618 cases and used shared data for 3,413 controls. We performed replication in an independent set of 2,256 cases and 2,310 controls, for a total of 3,874 cases and 5,723 controls. We identified risk-associated SNPs on chromosome 12q13–14 (rs703842, P = 5.4 × 10−11; rs10876994, P = 2.7 × 10−10; rs12368653, P = 1.0 × 10−7) and upstream of CD40 on chromosome 20q13 (rs6074022, P = 1.3 × 10−7; rs1569723, P = 2.9 × 10−7). Both loci are also associated with other autoimmune diseases1,2,3,4,5. We also replicated several known MS associations (HLA-DR15, P = 7.0 × 10−184; CD58, P = 9.6 × 10−8; EVI5-RPL5, P = 2.5 × 10−6; IL2RA, P = 7.4 × 10−6; CLEC16A, P = 1.1 × 10−4; IL7R, P = 1.3 × 10−3; TYK2, P = 3.5 × 10−3) and observed a statistical interaction between SNPs in EVI5-RPL5 and HLA-DR15 (P = 0.001).

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

Figure 1: Chromosome 12q13–14 region and association with MS.
Figure 2: Chromosome 20q13 region and association with MS.

Change history

  • 24 November 2009

    In the version of this article initially published, the 8th SNP in Table 3 was incorrectly listed as rs8118449. The correct identification number for this SNP is rs8112449. The error has been corrected in the HTML and PDF versions of the article.

References

  1. 1

    Jacobson, E.M. et al. A CD40 Kozak sequence polymorphism and susceptibility to antibody-mediated autoimmune conditions: the role of CD40 tissue-specific expression. Genes Immun. 8, 205–214 (2007).

  2. 2

    Raychaudhuri, S. et al. Common variants at CD40 and other loci confer risk of rheumatoid arthritis. Nat. Genet. 40, 1216–1223 (2008).

  3. 3

    Bailey, R. et al. Association of the vitamin D metabolism gene CYP27B1 with type 1 diabetes. Diabetes 56, 2616–2621 (2007).

  4. 4

    Fung, E. et al. Analysis of 17 autoimmune disease-associated variants in type 1 diabetes identifies 6q23/TNFAIP3 as a susceptibility locus. Genes Immun. 10, 188–191 (2008).

  5. 5

    Barton, A. et al. Rheumatoid arthritis susceptibility loci at chromosomes 10p15, 12q13 and 22q13. Nat. Genet. 40, 1156–1159 (2008).

  6. 6

    Hafler, D.A. et al. Risk alleles for multiple sclerosis identified by a genomewide study. N. Engl. J. Med. 357, 851–862 (2007).

  7. 7

    Rubio, J.P. et al. Replication of KIAA0350, IL2RA, RPL5 and CD58 as multiple sclerosis susceptibility genes in Australians. Genes Immun. 9, 624–630 (2008).

  8. 8

    International Multiple Sclerosis Genetics Consortium. The expanding genetic overlap between multiple sclerosis and type I diabetes. Genes Immun. 10, 11–14 (2009).

  9. 9

    Aulchenko, Y.S. et al. Genetic variation in the KIF1B locus influences susceptibility to multiple sclerosis. Nat. Genet. 40, 1402–1403 (2008).

  10. 10

    Ban, M. et al. Replication analysis identifies TYK2 as a multiple sclerosis susceptibility factor. Eur. J. Hum. Genet. advance online publication, doi: 10.1038/ejhg.2009.41 (18 March 2009).

  11. 11

    Adorini, L. & Penna, G. Control of autoimmune diseases by the vitamin D endocrine system. Nat. Clin. Pract. Rheumatol. 4, 404–412 (2008).

  12. 12

    Chen, S. et al. Modulatory effects of 1,25-dihydroxyvitamin D3 on human B cell differentiation. J. Immunol. 179, 1634–1647 (2007).

  13. 13

    Boonstra, A. et al. 1alpha,25-Dihydroxyvitamin d3 has a direct effect on naive CD4(+) T cells to enhance the development of Th2 cells. J. Immunol. 167, 4974–4980 (2001).

  14. 14

    Penna, G. & Adorini, L. 1 Alpha,25-dihydroxyvitamin D3 inhibits differentiation, maturation, activation, and survival of dendritic cells leading to impaired alloreactive T cell activation. J. Immunol. 164, 2405–2411 (2000).

  15. 15

    Lemire, J.M. & Archer, D.C. 1,25-dihydroxyvitamin D3 prevents the in vivo induction of murine experimental autoimmune encephalomyelitis. J. Clin. Invest. 87, 1103–1107 (1991).

  16. 16

    Cantorna, M.T., Hayes, C.E. & DeLuca, H.F. 1,25-Dihydroxycholecalciferol inhibits the progression of arthritis in murine models of human arthritis. J. Nutr. 128, 68–72 (1998).

  17. 17

    Munger, K.L., Levin, L.I., Hollis, B.W., Howard, N.S. & Ascherio, A. Serum 25-hydroxyvitamin D levels and risk of multiple sclerosis. J. Am. Med. Assoc. 296, 2832–2838 (2006).

  18. 18

    Holick, M.F. Vitamin D deficiency. N. Engl. J. Med. 357, 266–281 (2007).

  19. 19

    van der Mei, I.A. et al. Vitamin D levels in people with multiple sclerosis and community controls in Tasmania, Australia. J. Neurol. 254, 581–590 (2007).

  20. 20

    Ishida, T. et al. CD40 signaling-mediated induction of Bcl-XL, Cdk4, and Cdk6. Implication of their cooperation in selective B cell growth. J. Immunol. 155, 5527–5535 (1995).

  21. 21

    Marzo, N. et al. Cyclin-dependent kinase 4 hyperactivity promotes autoreactivity in the immune system but protects pancreatic cell mass from autoimmune destruction in the nonobese diabetic mouse model. J. Immunol. 180, 1189–1198 (2008).

  22. 22

    Sekine, C. et al. Successful treatment of animal models of rheumatoid arthritis with small-molecule cyclin-dependent kinase inhibitors. J. Immunol. 180, 1954–1961 (2008).

  23. 23

    Satoh, J. et al. T cell gene expression profiling identifies distinct subgroups of Japanese multiple sclerosis patients. J. Neuroimmunol. 174, 108–118 (2006).

  24. 24

    Durie, F.H., Foy, T.M., Masters, S.R., Laman, J.D. & Noelle, R.J. The role of CD40 in the regulation of humoral and cell-mediated immunity. Immunol. Today 15, 406–411 (1994).

  25. 25

    Gerritse, K. et al. CD40–CD40 ligand interactions in experimental allergic encephalomyelitis and multiple sclerosis. Proc. Natl. Acad. Sci. USA 93, 2499–2504 (1996).

  26. 26

    Durie, F.H. et al. Prevention of collagen-induced arthritis with an antibody to gp39, the ligand for CD40. Science 261, 1328–1330 (1993).

  27. 27

    Jacobson, E.M., Concepcion, E., Oashi, T. & Tomer, Y.A. Graves' disease-associated Kozak sequence single-nucleotide polymorphism enhances the efficiency of CD40 gene translation: a case for translational pathophysiology. Endocrinology 146, 2684–2691 (2005).

  28. 28

    Barrett, J.C., Fry, B., Maller, J. & Daly, M.J. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21, 263–265 (2005).

  29. 29

    Poser, C.M. et al. New diagnostic criteria for multiple sclerosis: guidelines for research protocols. Ann. Neurol. 13, 227–231 (1983).

  30. 30

    McDonald, W.I. et al. Recommended diagnostic criteria for multiple sclerosis: guidelines from the International Panel on the diagnosis of multiple sclerosis. Ann. Neurol. 50, 121–127 (2001).

  31. 31

    Paty, D.W. et al. MRI in the diagnosis of MS: a prospective study with comparison of clinical evaluation, evoked potentials, oligoclonal banding, and CT. Neurology 38, 180–185 (1988).

  32. 32

    Purcell, S. et al. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81, 559–575 (2007).

  33. 33

    Price, A.L. et al. Principal components analysis corrects for stratification in genome-wide association studies. Nat. Genet. 38, 904–909 (2006).

  34. 34

    Browning, B.L. & Browning, S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am. J. Hum. Genet. 84, 210–223 (2009).

  35. 35

    Browning, S.R. & Browning, B.L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am. J. Hum. Genet. 81, 1084–1097 (2007).

Download references

Acknowledgements

We thank individuals with MS in Australia and New Zealand for supporting this research. We are grateful to M. Tanner for database management and J. Wright and C. Remediakis from Multiple Sclerosis Research Australia (MSRA) for expediting this research. J.P.R. and M.B. are supported by Career Development Awards from The National Health and Medical Research Council of Australia (NHMRC). M.A.B. is an NHMRC Principal Research Fellow. H.B. is an NHMRC Peter Doherty Post-doctoral Fellow. J.F. is an MSRA Post-doctoral Fellow. M.B.C. is supported by a grant from the John Hunter Hospital Charitable Trust Fund and a special grant from Macquarie Bank. Replication genotyping was conducted at the Murdoch Children's Research Institute Sequenom Platform Facility. This work was supported by MSRA, John T. Reid Charitable Trusts, Trish MS Research Foundation and the Australian Research Council, under the Linkage Projects Scheme (LP0776744).

Author information

Correspondence to Justin P Rubio or (Chair) Justin P Rubio or Justin P Rubio.

Additional information

A complete list of authors and affiliations is provided at the end of the article.

Supplementary information

Supplementary Text and Figures

Supplementary Tables 1–5, Supplementary Figures 1–3 and Supplementary Note (PDF 754 kb)

Rights and permissions

Reprints and Permissions

About this article

Further reading