Development of rheumatoid arthritis specific HLA-DRB1 genotyping microarray

HLA-DRB1 is the most important gene for rheumatoid arthritis (RA) susceptibility. The HLADRB1 shared epitope (SE) alleles that share conserved amino acid sequences and non-SE *09:01 allele account for about one-third of the genetic contribution to RA. We aimed to develop RA specific HLA-DRB1 genotyping microarray kit to achieve a 4-digit high resolution typing for the essential set of the susceptible DRB1 alleles in the RA. Korean RA patients (n=172) and controls (n=13) who performed HLA-DRB1 genotyping at 4-digit resolution by standard PCR-SBT method were enrolled. A total of 14 probes were designed for the RA specific HLA-DRB1 genotyping microarray. PCR products were hybridized with the probes which were covalently linked with a silylated glass slide of microarrays. HLA-DRB1 genotype was assigned using a signal table based on the scanned hybridization patterns. Using the RA-specific HLA-DRB1 microarray chip, we accurately determined the RA susceptible alleles at 4-digit resolution (*01:01, *04:01, *04:04, *04: 05, *04:08, *04:10, *09:01, *10:10) and all the other subtypes of *04 in Korean population (n=185). Microarray results from 185 subjects showed high concordance with conventional PCR-SBT method irrespective of genotypes of risk or non-risk alleles (N=181), except for ambiguity in four cases of *01:01/*04:06 genotype, in which the microarray results were *01:01 /*04:03 or *01:01/*04:06. We developed a cost-effective RA-specific HLA-DRB1 genotyping microarray chip which is accurate and useful in clinical aspects as well as research purpose for RA.