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Series GSE24481 Query DataSets for GSE24481
Status Public on Mar 17, 2011
Title Pooled genome-wide analysis to identify novel risk loci for pediatric allergic asthma
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary We performed a pooled GWAS and individual genotyping in 269 children with allergic respiratory diseases comparing allergic children with and without asthma. We used a modular approach to identify the most significant loci associated with asthma by combining silhouette statistics and physical distance method with cluster-adapted thresholding. We found 97% concordance between pooled GWAS and individual genotyping, with 36 out of 37 top-scoring SNPs significant at individual genotyping level. The most significant SNP is located inside the coding sequence of C5, an already identified asthma susceptibility gene, while the other loci regulate functions that are relevant to bronchial physiopathology, as immune- or inflammation-mediated mechanisms and airway smooth muscle contraction. Integration with gene expression data (from mouse experimental asthma model taken from GSE6858 and GSE1301) showed that almost half of the putative susceptibility genes are differentially expressed in experimental asthma mouse models.
Overall design Affymetrix SNP arrays (Mapping 250K NspI and StyI) were performed according to the manufacturer's directions on pooled DNA extracted from peripheral blood samples.The design is a pooled-GWAS. DNA samples were assigned to the Asthma group if displaying symptoms of asthma, alone or associated to other allergic phenotypes, including rhinoconjunctivitis (RC), and assigned to the RC group if displaying rhinitis or rhinoconjunctivits alone or associated to other allergic phenotypes, excluding asthma. Each of the two groups was subdiveded into 4 independent groups of samples, each containing 31-36 individuals. Individual DNA samples were then added to their respective pools in equivalent molar amounts. Each pool was labeled and hybridized independently on three different arrays (3 technical replicates for each pool).
Contributor(s) Ricci G, Astolfi A
Citation(s) 21359210
Submission date Oct 01, 2010
Last update date May 17, 2017
Contact name Giampaolo Ricci
Phone 00390516363075
Organization name University of Bologna
Department Pediatric Allergologic Center
Lab Gynecologic, Obstetric and Pediatric Sciences
Street address Massarenti 9
City Bologna
State/province BO
ZIP/Postal code 40138
Country Italy
Platforms (2)
GPL3718 [Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array
GPL3720 [Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array
Samples (48)
GSM602951 Asthma_pool_A_r1_Nsp
GSM602952 Asthma_pool_B_r1_Nsp
GSM602953 Asthma_pool_C_r1_Nsp
BioProject PRJNA132513

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE24481_RAW.tar 1.1 Gb (http)(custom) TAR (of CEL)
Processed data included within Sample table

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