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

Tissue Antigens
T YamamuraYoshiki Akatsuka

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.

References

Jan 20, 1999·The Journal of Experimental Medicine·H DolstraE van de Wiel-van Kemenade
Dec 22, 1999·Immunogenetics·H RammenseeS Stevanović
Jan 10, 2001·The Journal of Experimental Medicine·A G BricknerS R Riddell
May 29, 2003·The Journal of Experimental Medicine·Yoshiki AkatsukaToshitada Takahashi
Dec 20, 2003·Nature·UNKNOWN International HapMap Consortium
May 4, 2004·Nature Reviews. Cancer·Marie Bleakley, Stanley R Riddell
Oct 29, 2005·Nature·UNKNOWN International HapMap Consortium
Dec 3, 2005·The Journal of Clinical Investigation·Eric Spierings, Els Goulmy
Jun 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·R Stephanie HuangM Eileen Dolan
Oct 19, 2007·Nature·UNKNOWN International HapMap ConsortiumJohn Stewart
Sep 24, 2008·Blood·Michi KameiYoshiki Akatsuka
Nov 26, 2009·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Robbert M SpaapenTuna Mutis

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