A genome-wide association study suggests contrasting associations in ACPA-positive versus ACPA-negative rheumatoid arthritis

Abstract

Background: Rheumatoid arthritis (RA) can be divided into two major subsets based on the presence or absence of antibodies to citrullinated peptide antigens (ACPA). Until now, data from genome-wide association studies (GWAS) have only been published from ACPA-positive subsets of RA or from studies that have not separated the two subsets. The aim of the current study is to provide and compare GWAS data for both subsets.

Methods and results: GWAS using the Illumina 300K chip was performed for 774 ACPA-negative patients with RA, 1147 ACPA-positive patients with RA and 1079 controls from the Swedish population-based case-control study EIRA. Imputation was performed which allowed comparisons using 1,723,056 single nucleotide polymorphisms (SNPs). No SNP achieved genome-wide significance (2.9 × 10⁻⁸) in the comparison between ACPA-negative RA and controls. A case-case association study was then performed between ACPA-negative and ACPA-positive RA groups. The major difference in this analysis was in the HLA region where 768 HLA SNPs passed the threshold for genome-wide significance whereas additional contrasting SNPs did not reach genome-wide significance. However, one SNP close to the RPS12P4 locus in chromosome 2 reached a p value of 2 × 10⁶ and this locus can thus be considered as a tentative candidate locus for ACPA-negative RA.

Conclusions: ACPA-positive and ACPA-negative RA display significant risk allele frequency differences which are mainly confined to the HLA region. The data provide further support for distinct genetic aetiologies of RA subsets and emphasise the need to consider them separately in genetic as well as functional studies of this disease.

Figure 1

Work flow for genome-wide analysis (GWAS) of two subgroups of rheumatoid arthritis (RA). Three different Caucasian study populations represented in different colours (blue, green and red: Swedish, US, UK). Selection of data from previously published studies indicated by dashed rectangles with subsequent reference. Difference in sums is due to QC procedures at each stage of analysis. ACPA, antibodies to citrullinated peptide antigens.

Figure 2

Probability plot for association with ACPA-negative rheumatoid arthritis (774 cases) versus 1079 controls, λ_GC = 1.0132 based on 1 723 056 single nucleotide polymorphisms. ACPA, antibodies to citrullinated peptide antigens.

Figure 3

Quintile-quintile probability plots for observed versus expected distribution of p values for χ² statistics for (A) ACPA-negative RA versus controls and (B) ACPA-positive RA versus controls. ACPA, antibodies to citrullinated peptide antigens; RA, rheumatoid arthritis; SNP, single nucleotide polymorphism.

Figure 4

Probability plot for association with ACPA-positive rheumatoid arthritis (1147 cases) versus 1079 controls, λ_GC = 1.0263 based on 1 723 056 single nucleotide polymorphisms (SNPs). Upper figure represents data for all SNPs including MHC locus and lower figure is without data for SNPs from MHC locus. ACPA, antibodies to citrullinated peptide antigens.

Figure 5

Probability plot for association for ACPA-positive RA (1147 cases) versus ACPA-negative RA (774 cases). λ_GC = 1.0029 based on 1 723 056 single nucleotide polymorphisms. ACPA, antibodies to citrullinated peptide antigens; RA, rheumatoid arthritis.