SNP typing accurately discriminates HLA-Cw*06:02 in psoriasis patients
MedWire News: Researchers have developed a new technique for genotyping the main candidate gene HLA-C in patients with psoriasis, which allows discrimination of homozygotes and heterozygotes through typing of four single nucleotide polymorphisms.
"Considering the clinical and genetic heterogeneity of psoriasis which may translate into distinct disease pathology and treatment response, correct typing of the main candidate gene HLA-C is critical," say Pernilla Nikamo and Mona Ståhle, both from the Karolinska Institute in Stockholm, Sweden.
Currently available methods for genotyping either do not distinguish between homozygotes and heterozygotes (Bunce et al's gold standard) or are time consuming, expensive, and require substantial amounts of DNA (PCR-SSP Olerup HLA-C low resolution kit).
"Typing of the single nucleotide polymorphisms (SNPs)… proved to be precise, reliable, time and cost-effective, and requiring a low amount of DNA," say the authors.
For the study, the team performed genotyping in 1591 patients with psoriasis, aged 31 years on average, and 1809 controls using methods devised by Bunce et al, PCR-SSP Olerup, or typing of a combination of four HLA-C SNPs rs10484554, rs3130457, rs6904246, and rs7745906.
All patients were Caucasian and were included in the study based on typing of three ethnicity-related SNPs, rs1426654, rs2555364, and rs16960620. A maximum of 20 ng DNA was used per sample when typing using the four HLA-C SNPs was performed.
Comparison of genotypes obtained through the Olerup SSP method with the newly proposed method showed complete concordance in the 261 genotyped patients.
Analysis of Bunce et al's HLA-C genotyping method revealed a 1.1% genotyping error compared with SNP typing. "This verifies that the combination of these four SNPs allows for correct typing of [the] HLA-Cw*06:02 [allele] including determination of zygosity," says the team.
Furthermore, all of the 133 HLA-Cw*06-positive individuals tested by the Olerup high resolution kit carried the HLA-Cw*06:02 allele. GWAS typing and SNP typing were found to correlate by 100%.
Writing in the journal Experimental Dermatology, the researchers conclude: "The SNP method… is a highly sensitive and specific method generating equal genotyping information compared with the commercial tool provided by Olerup... The low cost, high-throughput capacity, and requirement for limited amount of DNA makes this procedure useful for HLA-Cw*06:02 typing in clinical practice."
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By Ingrid Grasmo