DESCRIPTION:

List of positional candidate genes after correcting for multiple testing and controlling the false discovery rate from genome wide association studies (GWAS) retrieved from the NHGRI-EBI Catalog of published genome-wide association studies (http://www.ebi.ac.uk/gwas/). The disease/trait examined in this study, as reported by the authors, was Systemic sclerosis. The EFO term systemic scleroderma was annotated to this set after curation by NHGRI-EBI. Intergenic SNPS were mapped to both the upstream and downstream gene. P-value uploaded. This gene set was generated using gwas2gs v. 0.1.8 and the GWAS Catalog v. 1.0.1.

LABEL:

GWAS: systemic scleroderma

SCORE TYPE:

P-Value

DATE ADDED:

2017-05-02

DATE UPDATED:

2024-04-25

SPECIES:

AUTHORS:

O Gorlova, JE Martin, B Rueda, BP Koeleman, J Ying, M Teruel, LM Diaz-Gallo, JC Broen, MC Vonk, CP Simeon, BZ Alizadeh, MJ Coenen, AE Voskuyl, AJ Schuerwegh, PL van Riel, M Vanthuyne, R van 't Slot, A Italiaander, RA Ophoff, N Hunzelmann, V Fonollosa, N Ortego-Centeno, MA González-Gay, FJ García-Hernández, MF González-Escribano, P Airo, J van Laar, J Worthington, R Hesselstrand, V Smith, F de Keyser, F Houssiau, MM Chee, R Madhok, PG Shiels, R Westhovens, A Kreuter, E de Baere, T Witte, L Padyukov, A Nordin, R Scorza, C Lunardi, BA Lie, AM Hoffmann-Vold, O Palm, P García de la Peña, P Carreira, J Varga, M Hinchcliff, AT Lee, P Gourh, CI Amos, FM Wigley, LK Hummers, JL Nelson, G Riemekasten, A Herrick, L Beretta, C Fonseca, CP Denton, PK Gregersen, S Agarwal, S Assassi, FK Tan, FC Arnett, TR Radstake, MD Mayes, J Martin

TITLE:

Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.

JOURNAL:

PLoS genetics Jul 2011, Vol 7, pp. e1002178

ABSTRACT:

The aim of this study was to determine, through a genome-wide association study (GWAS), the genetic components contributing to different clinical sub-phenotypes of systemic sclerosis (SSc). We considered limited (lcSSc) and diffuse (dcSSc) cutaneous involvement, and the relationships with presence of the SSc-specific auto-antibodies, anti-centromere (ACA), and anti-topoisomerase I (ATA). Four GWAS cohorts, comprising 2,296 SSc patients and 5,171 healthy controls, were meta-analyzed looking for associations in the selected subgroups. Eighteen polymorphisms were further tested in nine independent cohorts comprising an additional 3,175 SSc patients and 4,971 controls. Conditional analysis for associated SNPs in the HLA region was performed to explore their independent association in antibody subgroups. Overall analysis showed that non-HLA polymorphism rs11642873 in IRF8 gene to be associated at GWAS level with lcSSc (P = 2.32×10(-12), OR = 0.75). Also, rs12540874 in GRB10 gene (P = 1.27 × 10(-6), OR = 1.15) and rs11047102 in SOX5 gene (P = 1.39×10(-7), OR = 1.36) showed a suggestive association with lcSSc and ACA subgroups respectively. In the HLA region, we observed highly associated allelic combinations in the HLA-DQB1 locus with ACA (P = 1.79×10(-61), OR = 2.48), in the HLA-DPA1/B1 loci with ATA (P = 4.57×10(-76), OR = 8.84), and in NOTCH4 with ACA P = 8.84×10(-21), OR = 0.55) and ATA (P = 1.14×10(-8), OR = 0.54). We have identified three new non-HLA genes (IRF8, GRB10, and SOX5) associated with SSc clinical and auto-antibody subgroups. Within the HLA region, HLA-DQB1, HLA-DPA1/B1, and NOTCH4 associations with SSc are likely confined to specific auto-antibodies. These data emphasize the differential genetic components of subphenotypes of SSc. PUBMED: 21779181
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