Ultraspecific probes for high throughput HLA typing

Chen Feng, Catherine Putonti, Meizhuo Zhang, Rick Eggers, Rahul Mitra, Mike Hogan, Krishna Jayaraman, Yuriy Fofanov

Research output: Contribution to journalArticle

6 Citations (Scopus)

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.

Original languageEnglish (US)
Article number85
JournalBMC Genomics
Volume10
DOIs
StatePublished - Feb 20 2009
Externally publishedYes

Fingerprint

HLA Antigens
Alleles
Computer Simulation
Transplants
Disease Susceptibility
Human Genome
Genes
Single Nucleotide Polymorphism
Vaccines
Costs and Cost Analysis
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Feng, C., Putonti, C., Zhang, M., Eggers, R., Mitra, R., Hogan, M., ... Fofanov, Y. (2009). Ultraspecific probes for high throughput HLA typing. BMC Genomics, 10, [85]. https://doi.org/10.1186/1471-2164-10-85

Ultraspecific probes for high throughput HLA typing. / Feng, Chen; Putonti, Catherine; Zhang, Meizhuo; Eggers, Rick; Mitra, Rahul; Hogan, Mike; Jayaraman, Krishna; Fofanov, Yuriy.

In: BMC Genomics, Vol. 10, 85, 20.02.2009.

Research output: Contribution to journalArticle

Feng, C, Putonti, C, Zhang, M, Eggers, R, Mitra, R, Hogan, M, Jayaraman, K & Fofanov, Y 2009, 'Ultraspecific probes for high throughput HLA typing', BMC Genomics, vol. 10, 85. https://doi.org/10.1186/1471-2164-10-85
Feng C, Putonti C, Zhang M, Eggers R, Mitra R, Hogan M et al. Ultraspecific probes for high throughput HLA typing. BMC Genomics. 2009 Feb 20;10. 85. https://doi.org/10.1186/1471-2164-10-85
Feng, Chen ; Putonti, Catherine ; Zhang, Meizhuo ; Eggers, Rick ; Mitra, Rahul ; Hogan, Mike ; Jayaraman, Krishna ; Fofanov, Yuriy. / Ultraspecific probes for high throughput HLA typing. In: BMC Genomics. 2009 ; Vol. 10.
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