title: MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.
abstract: Major histocompatibility complex (MHC) class I chain-related gene B (MICB) encodes a ligand for activating NKG2D that expressed in natural killer cells, γδ T cells, and αβ CD8+ T cells, which is associated with autoimmune diseases, cancer, and infectious diseases. Here, we have established a system for genotyping MICB alleles using allele-specific primer extension (ASPE) on microarrays. Thirty-six high quality, allele-specific extension primers were evaluated using strict and reliable cut-off values using mean fluorescence intensity (MFI), whereby an MFI >30,000 represented a positive signal and an MFI <10,000 represented a negative signal. Eight allele-specific extension primers were found to be false positives, five of which were improved by adjusting their length, and three of which were optimized by refractory modification. The MICB alleles (*002:01, *003, *005:02/*010, *005:03, *008, *009N, *018, and *024) present in the quality control panel could be exactly defined by 22 allele-specific extension primers. MICB genotypes that were identified by ASPE on microarrays were in full concordance with those identified by PCR-sequence-based typing. In conclusion, we have developed a method for genotyping MICB alleles using ASPE on microarrays; which can be applicable for large-scale single nucleotide polymorphism typing studies of population and disease associations.
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.
authors.forename: In-Cheol
authors.initials: IC
authors.lastname: Baek
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.
authors.forename: Jung-Pil
authors.initials: JP
authors.lastname: Jang
authors.affiliation: Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea.
authors.forename: Eun-Jeong
authors.initials: EJ
authors.lastname: Choi
authors.affiliation: Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea.|Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea.
authors.forename: Tai-Gyu
authors.initials: TG
authors.lastname: Kim
mesh_terms: D000483:Alleles; D044466:Asian People; D018414:CD8-Positive T-Lymphocytes / Q000276:immunology; D017931:DNA Primers / Q000235:genetics; D005091:Exons; D005189:False Positive Reactions; D005787:Gene Frequency; D060005:Genotyping Techniques / Q000379:methods*; D006239:Haplotypes; D064368:Healthy Volunteers; D015395:Histocompatibility Antigens Class I / Q000235:genetics*; D006801:Humans; D008024:Ligands; D020411:Oligonucleotide Array Sequence Analysis; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D056910:Republic of Korea; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; D015395:Histocompatibility Antigens Class I; D008024:Ligands; C098080:MICB antigen