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.
| Original language | English |
|---|---|
| Pages (from-to) | 119-125 |
| Number of pages | 7 |
| Journal | Tissue Antigens |
| Volume | 80 |
| Issue number | 2 |
| DOIs | |
| Publication status | Published - 01-08-2012 |
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All Science Journal Classification (ASJC) codes
- Immunology and Allergy
- Immunology
- Biochemistry
- Genetics
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HapMap SNP Scanner : An online program to mine SNPs responsible for cell phenotype. / 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, Yoshiki.
In: Tissue Antigens, Vol. 80, No. 2, 01.08.2012, p. 119-125.Research output: Contribution to journal › Article
TY - JOUR
T1 - HapMap SNP Scanner
T2 - An online program to mine SNPs responsible for cell phenotype
AU - Yamamura, T.
AU - Hikita, J.
AU - Bleakley, M.
AU - Hirosawa, T.
AU - Sato-Otsubo, A.
AU - Torikai, H.
AU - Hamajima, T.
AU - Nannya, Y.
AU - Demachi-Okamura, A.
AU - Maruya, E.
AU - Saji, H.
AU - Yamamoto, Y.
AU - Takahashi, T.
AU - Emi, N.
AU - Morishima, Y.
AU - Kodera, Y.
AU - Kuzushima, K.
AU - Riddell, S. R.
AU - Ogawa, S.
AU - Akatsuka, Yoshiki
PY - 2012/8/1
Y1 - 2012/8/1
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84864335470&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84864335470&partnerID=8YFLogxK
U2 - 10.1111/j.1399-0039.2012.01883.x
DO - 10.1111/j.1399-0039.2012.01883.x
M3 - Article
C2 - 22568758
AN - SCOPUS:84864335470
VL - 80
SP - 119
EP - 125
JO - HLA
JF - HLA
SN - 2059-2302
IS - 2
ER -