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

T. Yamamura, J. Hikita, M. Bleakley, T. Hirosawa, A. Sato-Otsubo, H. Torikai, T. Hamajima, Y. Nannya, A. Demachi-Okamura, E. Maruya, H. Saji, Y. Yamamoto, T. Takahashi, N. Emi, Y. Morishima, Y. Kodera, K. Kuzushima, S. R. Riddell, S. Ogawa, Yoshiki Akatsuka

Research output: Contribution to journalArticle

1 Citation (Scopus)

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 languageEnglish
Pages (from-to)119-125
Number of pages7
JournalTissue Antigens
Volume80
Issue number2
DOIs
Publication statusPublished - 01-08-2012

Fingerprint

HapMap Project
Polymorphism
Single Nucleotide Polymorphism
Nucleotides
Phenotype
T-cells
Graft vs Tumor Effect
Grafts
Minor Histocompatibility Antigens
T-Lymphocytes
Genetic Linkage
Hematopoietic Stem Cell Transplantation
Linkage Disequilibrium
Graft vs Host Disease
HLA Antigens
Stem cells
Websites
Tumors
Assays
Cells

All Science Journal Classification (ASJC) codes

  • Immunology and Allergy
  • Immunology
  • Biochemistry
  • Genetics

Cite this

Yamamura, T., Hikita, J., Bleakley, M., Hirosawa, T., Sato-Otsubo, A., Torikai, H., ... Akatsuka, Y. (2012). HapMap SNP Scanner: An online program to mine SNPs responsible for cell phenotype. Tissue Antigens, 80(2), 119-125. https://doi.org/10.1111/j.1399-0039.2012.01883.x
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. / HapMap SNP Scanner : An online program to mine SNPs responsible for cell phenotype. In: Tissue Antigens. 2012 ; Vol. 80, No. 2. pp. 119-125.
@article{8313007fc34041638d00946b4eed79a6,
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.",
author = "T. Yamamura and J. Hikita and M. Bleakley and T. Hirosawa and A. Sato-Otsubo and H. Torikai and T. Hamajima and Y. Nannya and A. Demachi-Okamura and E. Maruya and H. Saji and Y. Yamamoto and T. Takahashi and N. Emi and Y. Morishima and Y. Kodera and K. Kuzushima and Riddell, {S. R.} and S. Ogawa and Yoshiki Akatsuka",
year = "2012",
month = "8",
day = "1",
doi = "10.1111/j.1399-0039.2012.01883.x",
language = "English",
volume = "80",
pages = "119--125",
journal = "HLA",
issn = "2059-2302",
publisher = "Wiley-Blackwell",
number = "2",

}

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, SR, Ogawa, S & Akatsuka, Y 2012, 'HapMap SNP Scanner: An online program to mine SNPs responsible for cell phenotype', Tissue Antigens, vol. 80, no. 2, pp. 119-125. https://doi.org/10.1111/j.1399-0039.2012.01883.x

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 journalArticle

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 -

Yamamura T, Hikita J, Bleakley M, Hirosawa T, Sato-Otsubo A, Torikai H et al. HapMap SNP Scanner: An online program to mine SNPs responsible for cell phenotype. Tissue Antigens. 2012 Aug 1;80(2):119-125. https://doi.org/10.1111/j.1399-0039.2012.01883.x