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Ultraspecific probes for high throughput HLA typing
BACKGROUND: The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to...
Autores principales: | , , , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2009
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661095/ https://www.ncbi.nlm.nih.gov/pubmed/19232123 http://dx.doi.org/10.1186/1471-2164-10-85 |
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author | Feng, Chen Putonti, Catherine Zhang, Meizhuo Eggers, Rick Mitra, Rahul Hogan, Mike Jayaraman, Krishna Fofanov, Yuriy |
author_facet | Feng, Chen Putonti, Catherine Zhang, Meizhuo Eggers, Rick Mitra, Rahul Hogan, Mike Jayaraman, Krishna Fofanov, Yuriy |
author_sort | Feng, Chen |
collection | PubMed |
description | BACKGROUND: The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to achieve high-resolution typing, this has yet to be attained due to inefficiencies of current probe design strategies. RESULTS: We present a novel three-step approach for the design of high-throughput microarray assays for HLA typing. This approach first selects sequences containing the SNPs present in all alleles of the locus of interest and next calculates the number of base changes necessary to convert a candidate probe sequences to the closest subsequence within the set of sequences that are likely to be present in the sample including the remainder of the human genome in order to identify those candidate probes which are "ultraspecific" for the allele of interest. Due to the high specificity of these sequences, it is possible that preliminary steps such as PCR amplification are no longer necessary. Lastly, the minimum number of these ultraspecific probes is selected such that the highest resolution typing can be achieved for the minimal cost of production. As an example, an array was designed and in silico results were obtained for typing of the HLA-B locus. CONCLUSION: The assay presented here provides a higher resolution than has previously been developed and includes more alleles than previously considered. Based upon the in silico and preliminary experimental results, we believe that the proposed approach can be readily applied to any highly polymorphic gene system. |
format | Text |
id | pubmed-2661095 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2009 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-26610952009-03-26 Ultraspecific probes for high throughput HLA typing Feng, Chen Putonti, Catherine Zhang, Meizhuo Eggers, Rick Mitra, Rahul Hogan, Mike Jayaraman, Krishna Fofanov, Yuriy BMC Genomics Research Article BACKGROUND: The variations within an individual's HLA (Human Leukocyte Antigen) genes have been linked to many immunological events, e.g. susceptibility to disease, response to vaccines, and the success of blood, tissue, and organ transplants. Although the microarray format has the potential to achieve high-resolution typing, this has yet to be attained due to inefficiencies of current probe design strategies. RESULTS: We present a novel three-step approach for the design of high-throughput microarray assays for HLA typing. This approach first selects sequences containing the SNPs present in all alleles of the locus of interest and next calculates the number of base changes necessary to convert a candidate probe sequences to the closest subsequence within the set of sequences that are likely to be present in the sample including the remainder of the human genome in order to identify those candidate probes which are "ultraspecific" for the allele of interest. Due to the high specificity of these sequences, it is possible that preliminary steps such as PCR amplification are no longer necessary. Lastly, the minimum number of these ultraspecific probes is selected such that the highest resolution typing can be achieved for the minimal cost of production. As an example, an array was designed and in silico results were obtained for typing of the HLA-B locus. CONCLUSION: The assay presented here provides a higher resolution than has previously been developed and includes more alleles than previously considered. Based upon the in silico and preliminary experimental results, we believe that the proposed approach can be readily applied to any highly polymorphic gene system. BioMed Central 2009-02-20 /pmc/articles/PMC2661095/ /pubmed/19232123 http://dx.doi.org/10.1186/1471-2164-10-85 Text en Copyright © 2009 Feng et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Feng, Chen Putonti, Catherine Zhang, Meizhuo Eggers, Rick Mitra, Rahul Hogan, Mike Jayaraman, Krishna Fofanov, Yuriy Ultraspecific probes for high throughput HLA typing |
title | Ultraspecific probes for high throughput HLA typing |
title_full | Ultraspecific probes for high throughput HLA typing |
title_fullStr | Ultraspecific probes for high throughput HLA typing |
title_full_unstemmed | Ultraspecific probes for high throughput HLA typing |
title_short | Ultraspecific probes for high throughput HLA typing |
title_sort | ultraspecific probes for high throughput hla typing |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2661095/ https://www.ncbi.nlm.nih.gov/pubmed/19232123 http://dx.doi.org/10.1186/1471-2164-10-85 |
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