HapMap SNP Scanner: An online program to mine SNPs responsible for cell phenotype

T. Yamamura, J. Hikita, M. Bleakley, T. Hirosawa, A. Sato-Otsubo, H. Torikai, T. Hamajima, Y. Nannya, A. Demachi-Okamura, E. Maruya, H. Saji, Y. Yamamoto, T. Takahashi, N. Emi, Y. Morishima, Y. Kodera, K. Kuzushima, S. R. Riddell, S. Ogawa, Y. Akatsuka

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Abstract

Minor histocompatibility (H) antigens are targets of graft-vs-host disease and graft-vs-tumor responses after human leukocyte antigen matched allogeneic hematopoietic stem cell transplantation. Recently, we reported a strategy for genetic mapping of linkage disequilibrium blocks that encoded novel minor H antigens using the large dataset from the International HapMap Project combined with conventional immunologic assays to assess recognition of HapMap B-lymphoid cell line by minor H antigen-specific T cells. In this study, we have constructed and provide an online interactive program and demonstrate its utility for searching for single-nucleotide polymorphisms (SNPs) responsible for minor H antigen generation. The website is available as 'HapMap SNP Scanner', and can incorporate T-cell recognition and other data with genotyping datasets from CEU, JPT, CHB, and YRI to provide a list of candidate SNPs that correlate with observed phenotypes. This method should substantially facilitate discovery of novel SNPs responsible for minor H antigens and be applicable for assaying of other specific cell phenotypes (e.g. drug sensitivity) to identify individuals who may benefit from SNP-based customized therapies.

Original languageEnglish
Pages (from-to)119-125
Number of pages7
JournalTissue Antigens
Volume80
Issue number2
DOIs
Publication statusPublished - 01-08-2012

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All Science Journal Classification (ASJC) codes

  • Immunology and Allergy
  • Immunology
  • Biochemistry
  • Genetics

Cite this

Yamamura, T., Hikita, J., Bleakley, M., Hirosawa, T., Sato-Otsubo, A., Torikai, H., Hamajima, T., Nannya, Y., Demachi-Okamura, A., Maruya, E., Saji, H., Yamamoto, Y., Takahashi, T., Emi, N., Morishima, Y., Kodera, Y., Kuzushima, K., Riddell, S. R., Ogawa, S., & Akatsuka, Y. (2012). HapMap SNP Scanner: An online program to mine SNPs responsible for cell phenotype. Tissue Antigens, 80(2), 119-125. https://doi.org/10.1111/j.1399-0039.2012.01883.x