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Immunogenetic profiling of 23 SNP s of cytokine and chemokine receptor genes through a minisequencing technique: Design, development and validation
Author(s) -
ValverdeVillegas J. M.,
Medeiros R. M.,
Almeida S. E. M.,
Chies J. A. B.
Publication year - 2017
Publication title -
international journal of immunogenetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.41
H-Index - 47
eISSN - 1744-313X
pISSN - 1744-3121
DOI - 10.1111/iji.12314
Subject(s) - biology , multiplex , genotyping , snp , genetics , single nucleotide polymorphism , sanger sequencing , genotype , snp genotyping , gene , immunology , dna sequencing
Summary The minisequencing technique offers accuracy and robustness to genotyping of polymorphic DNA variants, being an excellent option for the identification and analyses of prognostic/susceptibility markers in human diseases. Two multiplex minisequencing assays were designed and standardized to screen 23 candidate SNP s in cytokine, chemokine receptor and ligand genes previously associated with susceptibility to cancer and autoimmune disorders as well as to infectious diseases outcome. The SNP s were displayed in two separate panels (panel 1— IL 2 rs2069762, TNF α rs1800629, rs361525; IL 4 rs2243250; IL 6 rs1800795; IL 10 rs1800896, rs1800872; IL 17A rs8193036, rs2275913 and panel 2— CCR 3 rs309125, CCR 4 rs6770096, rs2228428; CCR 6 rs968334; CCR 8 rs2853699; CXCR 3 rs34334103, rs2280964 ; CXCR 6 rs223435, rs2234358; CCL 20 rs13034664, rs6749704; CCL 22 rs4359426; CXCL 10/ IP ‐10 rs3921, rs56061981). A total of 305 DNA samples from healthy individuals were genotyped by minisequencing. To validate the minisequencing technique and to encompass the majority of the potential genotypes for all 23 SNP s, 20 of these samples were genotyped by Sanger sequencing. The results of both techniques were 100% in agreement. The technique of minisequencing showed high accuracy and robustness, avoiding the need for high quantities of DNA template samples. It was easily to be conducted in bulk samples derived from a highly admixed human population, being therefore an excellent option for immunogenetic studies.