Development of rheumatoid arthritis specific HLA-DRB1 genotyping microarray

• Published in: Biochip journal Vol. 8; no. 3; pp. 187 - 198
• Main Authors: Lee, Seung Yong, Yu, So Yeon, Bang, So-Young, Kim, Ji-Hoon, Kim, Seung Jun, Hong, Sung-Hyun, Kim, Kwangwoo, Lee, Hye-Soon, Bae, Sang-Cheol, Yoon, Young Ho, Hwang, Seung Yong
• Format: Journal Article
• Language: English
• Published: Heidelberg The Korean BioChip Society (KBCS) 01.09.2014; Springer Nature B.V; 한국바이오칩학회
• Subjects: Alleles; Amino acids; Arthritis; Biomedical Engineering and Bioengineering; Biotechnology; Chemistry; Chemistry and Materials Science; Clinical aspects; DNA microarrays; Drb1 protein; Epitopes; Genotypes; Genotyping; Histocompatibility antigen HLA; Hybridization; Original Article; Probes; Rheumatoid arthritis; Tissue typing; 생물공학; Risk allele; 4 digit; Genotyping; Rheumatoid arthritis; HLA-DRB1; Oligonucleotide microarray
• ISSN: 1976-0280; 2092-7843
• DOI: 10.1007/s13206-014-8305-x

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.