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| 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
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| 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.
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| 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).
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| Contributor(s) |
Ricci G, Astolfi A |
| Citation(s) |
21359210 |
| |
| Submission date |
Oct 01, 2010 |
| Last update date |
May 17, 2017 |
| Contact name |
Giampaolo Ricci |
| E-mail(s) |
giampaolo.ricci@unibo.it
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| Phone |
00390516363075
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| Organization name |
University of Bologna
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| Department |
Pediatric Allergologic Center
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| Lab |
Gynecologic, Obstetric and Pediatric Sciences
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| Street address |
Massarenti 9
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| City |
Bologna |
| State/province |
BO |
| ZIP/Postal code |
40138 |
| Country |
Italy |
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| Platforms (2) |
| 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 |
PRJNA132513 |
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