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Logo of bmcgenoBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Genomics
 
BMC Genomics. 2009; 10: 85.
Published online Feb 20, 2009. doi:  10.1186/1471-2164-10-85
PMCID: PMC2661095
Ultraspecific probes for high throughput HLA typing
Chen Feng,#1 Catherine Putonti,#2,3 Meizhuo Zhang,4 Rick Eggers,5 Rahul Mitra,5 Mike Hogan,5 Krishna Jayaraman,5 and Yuriy Fofanovcorresponding author1,6
1Department of Computer Science, University of Houston, Houston, TX, USA
2Department of Computer Science, Loyola University Chicago, Chicago, IL, USA
3Department of Biology, Loyola University Chicago, Chicago, IL, USA
4Collaborative Center for Statistics in Science, Yale University, New Haven, CT, USA
5Genomics USA, Inverness, IL, USA
6Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
corresponding authorCorresponding author.
#Contributed equally.
Chen Feng: cfeng/at/bioinfo.uh.edu; Catherine Putonti: cputonti/at/luc.edu; Meizhuo Zhang: meizhuo.zhang/at/yale.edu; Rick Eggers: rik/at/email.arizona.edu; Rahul Mitra: mitradna/at/gmail.com; Mike Hogan: mikehogan12751/at/earthlink.net; Krishna Jayaraman: kjayaraman3/at/gmail.com; Yuriy Fofanov: yfofanov/at/bioinfo.uh.edu
Received July 14, 2008; Accepted February 20, 2009.
Abstract
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.
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