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Respiratory Medicine

Identification of KIF3A as a Novel Candidate Gene for Childhood Asthma Using RNA Expression and Population Allelic Frequencies Differences
Published: Tuesday, August 30, 2011
Author: Melinda Butsch Kovacic et al.

by Melinda Butsch Kovacic, Jocelyn M. Biagini Myers, Ning Wang, Lisa J. Martin, Mark Lindsey, Mark B. Ericksen, Hua He, Tia L. Patterson, Tesfaye M. Baye, Dara Torgerson, Lindsey A. Roth, Jayanta Gupta, Umasundari Sivaprasad, Aaron M. Gibson, Anna M. Tsoras, Donglei Hu, Celeste Eng, Rocío Chapela, José R. Rodríguez-Santana, William Rodríguez-Cintrón, Pedro C. Avila, Kenneth Beckman, Max A. Seibold, Chris Gignoux, Salma M. Musaad, Weiguo Chen, Esteban González Burchard, Gurjit K. Khurana Hershey


Asthma is a chronic inflammatory disease with a strong genetic predisposition. A major challenge for candidate gene association studies in asthma is the selection of biologically relevant genes.

Methodology/Principal Findings

Using epithelial RNA expression arrays, HapMap allele frequency variation, and the literature, we identified six possible candidate susceptibility genes for childhood asthma including ADCY2, DNAH5, KIF3A, PDE4B, PLAU, SPRR2B. To evaluate these genes, we compared the genotypes of 194 predominantly tagging SNPs in 790 asthmatic, allergic and non-allergic children. We found that SNPs in all six genes were nominally associated with asthma (p<0.05) in our discovery cohort and in three independent cohorts at either the SNP or gene level (p<0.05). Further, we determined that our selection approach was superior to random selection of genes either differentially expressed in asthmatics compared to controls (p?=?0.0049) or selected based on the literature alone (p?=?0.0049), substantiating the validity of our gene selection approach. Importantly, we observed that 7 of 9 SNPs in the KIF3A gene more than doubled the odds of asthma (OR?=?2.3, p<0.0001) and increased the odds of allergic disease (OR?=?1.8, p<0.008). Our data indicate that KIF3A rs7737031 (T-allele) has an asthma population attributable risk of 18.5%. The association between KIF3A rs7737031 and asthma was validated in 3 independent populations, further substantiating the validity of our gene selection approach.


Our study demonstrates that KIF3A, a member of the kinesin superfamily of microtubule associated motors that are important in the transport of protein complexes within cilia, is a novel candidate gene for childhood asthma. Polymorphisms in KIF3A may in part be responsible for poor mucus and/or allergen clearance from the airways. Furthermore, our study provides a promising framework for the identification and evaluation of novel candidate susceptibility genes.