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

Publication Type:

Journal Article


Tissue antigens, Volume 80, Issue 2, p.119-25 (2012)


2012, B-Lymphocytes, Cell Line, Center-Authored Paper, Chromosome Mapping, Clinical Research Division, Data Mining, Genotype, HapMap Project, hematopoietic stem cell transplantation, Histocompatibility Testing, Humans, Internet, LINKAGE DISEQUILIBRIUM, Minor Histocompatibility Antigens, PHENOTYPE, Polymorphism, Single Nucleotide, Software, T-Lymphocytes, Transplantation, Homologous


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.