Open AccessHapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype
Author(s) -
Yamamura T.,
Hikita J.,
Bleakley M.,
Hirosawa T.,
SatoOtsubo A.,
Torikai H.,
Hamajima T.,
Nannya Y.,
DemachiOkamura A.,
Maruya E.,
Saji H.,
Yamamoto Y.,
Takahashi T.,
Emi N.,
Morishima Y.,
Kodera Y.,
Kuzushima K.,
Riddell S. R.,
Ogawa S.,
Akatsuka Y.
Publication year - 2012
Publication title -
tissue antigens
Language(s) - English
Resource type - Journals
eISSN - 1399-0039
pISSN - 0001-2815
DOI - 10.1111/j.1399-0039.2012.01883.x
Subject(s) - international hapmap project , single nucleotide polymorphism , minor histocompatibility antigen , minor allele frequency , snp genotyping , biology , snp , linkage disequilibrium , antigen , genetics , computational biology , immunology , major histocompatibility complex , gene , genotype
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.