MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.
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...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2015-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC4646348?pdf=render |
| _version_ | 1811193955845406720 |
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| author | In-Cheol Baek Jung-Pil Jang Eun-Jeong Choi Tai-Gyu Kim |
| author_facet | In-Cheol Baek Jung-Pil Jang Eun-Jeong Choi Tai-Gyu Kim |
| author_sort | In-Cheol Baek |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T00:19:21Z |
| format | Article |
| id | doaj.art-a6a7269f4ac54335a2845054a7e90c2d |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-12T00:19:21Z |
| publishDate | 2015-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a6a7269f4ac54335a2845054a7e90c2d2022-12-22T03:55:46ZengPublic Library of Science (PLoS)PLoS ONE1932-62032015-01-011011e014246710.1371/journal.pone.0142467MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers.In-Cheol BaekJung-Pil JangEun-Jeong ChoiTai-Gyu KimMajor 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.http://europepmc.org/articles/PMC4646348?pdf=render |
| spellingShingle | In-Cheol Baek Jung-Pil Jang Eun-Jeong Choi Tai-Gyu Kim MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. PLoS ONE |
| title | MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. |
| title_full | MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. |
| title_fullStr | MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. |
| title_full_unstemmed | MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. |
| title_short | MICB Allele Genotyping on Microarrays by Improving the Specificity of Extension Primers. |
| title_sort | micb allele genotyping on microarrays by improving the specificity of extension primers |
| url | http://europepmc.org/articles/PMC4646348?pdf=render |
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