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| Status |
Public on Jan 01, 2008 |
| Title |
Identification of human minor H antigens based on genotyping of pooled DNA |
| Organism |
Homo sapiens |
| Experiment type |
SNP genotyping by SNP array
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| Summary |
Minor histocompatibility (H) antigens are the molecular targets of allo-immunity responsible both for the development of anti-tumor effects and for graft-versus-host disease (GVHD) in allogeneic hematopoietic stem cell transplantation (allo-HSCT). However, despite their potential clinical use, our knowledge of human minor H antigens is largely limited by the lack of efficient methods of their characterization. Here we report a robust and efficient method of minor H gene discovery that combines whole genome association scans (WGAS) with cytotoxic T-lymphocyte (CTL) assays, in which the genetic loci of minor H genes recognized by the CTL clones are precisely identified using pooled-DNA analysis of immortalized lymphoblastoid cell lines with/without susceptibility to those CTLs. Using this method, we have successfully mapped two loci: one previously characterized (HMSD encoding ACC-6), and one novel. The novel minor H antigen encoded by the BCL2A1 was identified within a 26 kb linkage disequilibrium block on chromosome 15q25, which had been directly mapped by WGAS. The pool size required to identify these regions was no more than 100 individuals. Thus, once CTL clones are generated, this method should substantially facilitate discovery of minor H antigens applicable to targeted allo-immune therapies and also contribute to our understanding of human allo-immunity.
Keywords: pooled DNA, minor histocompatibility antigen, genotype array
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| Overall design |
For CTL-2A12, we collected 44 cytotoxicity-positive (CTX+) and 44 cytotoxicity-negative (CTX-) B-LCLs. For CTL-1B9, 57 CTX+ and 38 CTX- B-LCLs were collected. Pools of DNA were generated and subjected to analysis on Affymetrix® GeneChip® 100K and 500K microarrays in duplicates.Genetic mapping of the minor H locus was performed by identifying marker SNPs that showed statistically significant deviations in allele-frequencies between CTX+ and CTX- pools based on the observed allele-specific signals in the microarray experiments.
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| Contributor(s) |
Kawase T, Nannya Y, Torikai H, Yamamoto G, Onizuka M, Morishima S, Tsujimura K, Miyamura K, Kodera Y, Morishima Y, Takahashi T, Kuzushima K, Ogawa S, Akatsuka Y |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Dec 31, 2007 |
| Last update date |
Dec 22, 2017 |
| Contact name |
Yasuhito Nannya |
| E-mail(s) |
ynanya-tky@umin.ac.jp
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| Phone |
+81-3-3815-5411
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| Organization name |
Tokyo University
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| Department |
Department of Hematology/Oncology
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| Lab |
Genome Laboratory
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| Street address |
BUnkyo-ku Hongo 7-3-1
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| City |
Tokyo |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
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| Platforms (4)
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| GPL2004 |
[Mapping50K_Hind240] Affymetrix Human Mapping 50K Hind240 SNP Array |
| GPL2005 |
[Mapping50K_Xba240] Affymetrix Human Mapping 50K Xba240 SNP Array |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL3720 |
[Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array |
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| Samples (48)
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| Relations |
| BioProject |
PRJNA108615 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE10044_RAW.tar |
1021.6 Mb |
(http)(custom) |
TAR (of CEL, CHP) |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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