1. Demo data

The demo data is a GWAS of rheumatoid arthritis (RA) from WTCCC, 2007 [1]. The result of this GWAS includes ~ 455 K GWAS SNP P-values and 154 most significant SNPs with P-value < 10-5. 

 

So the input data for the demo run:

1) GWAS SNP P-value data: gz txt (required input) Download gz  Download txt

 

2) Most significant SNPs: txt (optional input, which can be exacted automatically from 1) by setting P-value < 10-5) Download

 

2. Demo run

1)     Parameters

Use the default parameters as shown in the homepage.

 

2)     Result

Utilizing the ~ 455 K GWAS SNP P-values as input and the 154 SNPs as the most significant SNPs, with default parameters, ICSNPathway identified two candidate causal SNPs (rs2476601 and rs2230926) and two candidate causal pathways (‘protein tyrosine phosphatase activity’ and ‘CD40L signaling pathway’) (Table 1-2). Both rs2476601 and rs2230926 were not presented in original GWAS for RA while both of them were proved to be associated with RA in additional GWASs for RA [2-5]. The two candidate causal SNPs and two candidate causal pathways indicate two hypotheses of biological mechanisms. One is [rs2476601 (non-synonymous, deleterious) -> PTPN22 -> protein tyrosine phosphatase activity] and the other is [rs2230926 (non-synonymous) -> TNFAIP3 -> CD40L signaling pathway]. Both are well supported by experimental results [6-7].

 

Hypotheses

[rs2476601 (non-synonymous, deleterious) -> PTPN22 -> protein tyrosine phosphatase activity]

[rs2230926 (non-synonymous) -> TNFAIP3 -> CD40L signaling pathway]

 

Table 1 Candidate causal SNPs of RA. 

Candidate causal SNP

Functional class

Gene

Candidate causal pathway a

-log10(P) b

In LD with

r2

D'

-log10(P) c

rs2476601

non-synonymous (deleterious)

PTPN22

1

-

rs6679677

1.0

1.0

25.5

rs2230926

non-synonymous

TNFAIP3

2

-

rs5029939

1.0

1.0

5.5

a The number indicates the index of pathways, which are ranked by their statistical significance (FDR).

b -log10(P) for candidate causal SNP in original GWAS. '-' denotes that this SNP is not represented in the original GWAS.

c -log10(P) for the SNP (which the candidate causal SNP is in LD with) in original GWAS.

 

Table 2 Candidate causal pathways of RA.

Index

Candidate pathway

Nominal P

FDR

1

protein tyrosine phosphatase activity (GO:0004725)

0.004

0.041

2

CD40L Signaling Pathway (cd40Pathway)

0.010

0.042

 

 

References

[1] WTCCC. (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 447, 661-678.

[2] Plenge, R.M., Seielstad, M., Padyukov, L., Lee, A.T., Remmers, E.F., Ding, B., Liew, A., Khalili, H., Chandrasekaran, A., Davies, L.R. et al. (2007) TRAF1-C5 as a risk locus for rheumatoid arthritis--a genomewide study. N Engl J Med, 357, 1199-1209.

[3] Gregersen, P.K., Amos, C.I., Lee, A.T., Lu, Y., Remmers, E.F., Kastner, D.L., Seldin, M.F., Criswell, L.A., Plenge, R.M., Holers, V.M. et al. (2009) REL, encoding a member of the NF-kappaB family of transcription factors, is a newly defined risk locus for rheumatoid arthritis. Nat Genet, 41, 820-823.

[4] Stahl, E.A., Raychaudhuri, S., Remmers, E.F., Xie, G., Eyre, S., Thomson, B.P., Li, Y., Kurreeman, F.A., Zhernakova, A., Hinks, A. et al. (2010) Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci. Nat Genet, 42, 508-514.

[5] Kochi, Y., Okada, Y., Suzuki, A., Ikari, K., Terao, C., Takahashi, A., Yamazaki, K., Hosono, N., Myouzen, K., Tsunoda, T. et al. (2010) A regulatory variant in CCR6 is associated with rheumatoid arthritis susceptibility. Nat Genet, 42, 515-519.

[6] Fiorillo, E., Orru, V., Stanford, S.M., Liu, Y., Salek, M., Rapini, N., Schenone, A.D., Saccucci, P., Delogu, L.G., Angelini, F. et al. (2010) Autoimmune-associated PTPN22 R620W variation reduces phosphorylation of lymphoid phosphatase on an inhibitory tyrosine residue. J Biol Chem, 285, 26506-26518.

[7] Musone, S.L., Taylor, K.E., Lu, T.T., Nititham, J., Ferreira, R.C., Ortmann, W., Shifrin, N., Petri, M.A., Kamboh, M.I., Manzi, S. et al. (2008) Multiple polymorphisms in the TNFAIP3 region are independently associated with systemic lupus erythematosus. Nat Genet, 40, 1062-1064.