title: HapMap SNP Scanner: an online program to mine SNPs responsible for cell phenotype.
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.
authors.affiliation: Division of Immunology, Aichi Cancer Center Research Center, Nagoya, Aichi, Japan.
authors.forename: T
authors.initials: T
authors.lastname: Yamamura
authors.forename: J
authors.initials: J
authors.lastname: Hikita
authors.forename: M
authors.initials: M
authors.lastname: Bleakley
authors.forename: T
authors.initials: T
authors.lastname: Hirosawa
authors.forename: A
authors.initials: A
authors.lastname: Sato-Otsubo
authors.forename: H
authors.initials: H
authors.lastname: Torikai
authors.forename: T
authors.initials: T
authors.lastname: Hamajima
authors.forename: Y
authors.initials: Y
authors.lastname: Nannya
authors.forename: A
authors.initials: A
authors.lastname: Demachi-Okamura
authors.forename: E
authors.initials: E
authors.lastname: Maruya
authors.forename: H
authors.initials: H
authors.lastname: Saji
authors.forename: Y
authors.initials: Y
authors.lastname: Yamamoto
authors.forename: T
authors.initials: T
authors.lastname: Takahashi
authors.forename: N
authors.initials: N
authors.lastname: Emi
authors.forename: Y
authors.initials: Y
authors.lastname: Morishima
authors.forename: Y
authors.initials: Y
authors.lastname: Kodera
authors.forename: K
authors.initials: K
authors.lastname: Kuzushima
authors.forename: S R
authors.initials: SR
authors.lastname: Riddell
authors.forename: S
authors.initials: S
authors.lastname: Ogawa
authors.forename: Y
authors.initials: Y
authors.lastname: Akatsuka
mesh_terms: D001402:B-Lymphocytes / Q000276:immunology; D002460:Cell Line; D002874:Chromosome Mapping; D057225:Data Mining; D005838:Genotype; D060148:HapMap Project; D018380:Hematopoietic Stem Cell Transplantation; D006650:Histocompatibility Testing / Q000379:methods*; D006801:Humans; D020407:Internet; D015810:Linkage Disequilibrium; D015778:Minor Histocompatibility Antigens / Q000235:genetics / Q000276:immunology*; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D012984:Software; D013601:T-Lymphocytes / Q000276:immunology; D014184:Transplantation, Homologous
chemical_list: D015778:Minor Histocompatibility Antigens