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

• Published in: Tissue antigens Vol. 80; no. 2; pp. 119 - 125
• Main Authors: 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.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01.08.2012
• Subjects: B-Lymphocytes - immunology; Cell Line; Chromosome Mapping; Data Mining; Data processing; Drugs; Gene mapping; genome-wide association study; Genotype; Genotyping; H antigen; HapMap; HapMap Project; Hematopoietic Stem Cell Transplantation; Histocompatibility antigen HLA; Histocompatibility Testing - methods; Humans; Internet; Linkage Disequilibrium; Lymphocytes T; Mines; minor histocompatibility antigen; Minor Histocompatibility Antigens - genetics; Minor Histocompatibility Antigens - immunology; online software; Phenotype; Polymorphism, Single Nucleotide; Single-nucleotide polymorphism; Software; stem cell transplantation; T-Lymphocytes - immunology; Transplantation, Homologous
• ISSN: 0001-2815; 1399-0039
• DOI: 10.1111/j.1399-0039.2012.01883.x

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.