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

Research output: Contribution to journalArticlepeer-review

2 Citations (Scopus)


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
Issue number2
Publication statusPublished - 08-2012
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Biochemistry
  • Immunology and Allergy
  • Immunology


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