Abstract
Several studies have identified the PTPN22 allelic variant 1858 C/T that encodes the R620W amino-acid change as a putative susceptibility factor in autoimmune diseases. The current study was undertaken to examine a large cohort of Finnish rheumatoid arthritis ( RA) and juvenile idiopathic arthritis (JIA) subjects using both population control and, importantly, family-based association methods. The latter is particularly important when, as is the case for the 1858 C/ T polymorphism, the frequency of the variant allele ( T) differs in both major ancestral populations and in subpopulations. The analysis of rheumatoid factor-positive 1030 RA probands from Finland provides strong support for association of this variant in both population studies ( allele specific odds ratio (OR) = 1.47, 95% confidence interval (CI) = 1.27 - 1.70, P = 3 x 10(-7)) and in family studies (P<10(-6)). In contrast, no allelic association was seen with JIA ( 230 probands) and only weak evidence for a genotypic effect of 1858T homozygotes was observed in this population.