SNP analysis of the PHF11 gene in italian families with allergic asthma

Asthma is a disease of the lungs characterized by reversible airway obstruction and bronchial hyper-reactivity and is associated with pulmonary inflammation. Asthma has an important genetic component but no clear pattern of inheritance; its phenotypes, including bronchial hyper-responsiveness (BHR), atopy, and increased IgE, result from the interaction of multiple gene variants, each having a modest effect, and the environment. In a previous genomic screen for asthma, conducted on 123 families from north east Italy, characterized for clinical asthma, rhinitis, elevated total serum IgE, positive Skin Prick Test, and bronchial hyper-responsiveness (BHR) to methacholine, it has been observed the presence of linkage between region 13q14 and elevated total serum IgE. Two studies, recently reported in literature, Zhang et al., 2003, and Jang et al., 2005, identified an association of the PHF11 gene with elevated IgE and atopic dermatitis, respectively. The aim of this study was to develop a multiple genotyping technique and to perform an association study of the PHF11 gene in the 23 families, for a total of 144 individuals, which demonstrated positive linkage to elevated total serum IgE. 7 SNPs have been analyzed in the PHF11 gene, reported in literature associated with elevated IgE: rs2247119, in intron 3; rs2274276, in intron 4; rs2031532, in intron 2; rs1046295, in the 3’UTR zone; 185752b5_2, in intron 9; 185306b7_1, in intron 1; and 185752b4_2, in intron 5. The first four SNPs have also been associated to atopic dermatitis. The 7 polymorphisms have been first validated with 15 control samples of the same population by sequencing and enzymatic restriction. The SNPs rs2247119, and rs2274276 have been analyzed through PCR and enzymatic restriction with the enzymes Fnu4 HI and Nsp I, respectively. The other 5 SNPs have been analyzed in multiplex with the ddNTP Primer Extension technique, utilizing the SNaPshot Multiplex kit (Applied Biosystems) with the ABI PRISM 310 Genetic Analyzer using the Genescan program. The genotyped SNPs have been analyzed through TDT Test with the Merlin program. This analysis confirmed the presence of linkage between region 13q14 and IgE, but a presence of association between the analyzed SNPs and IgE in allergic asthma was not observed. No association was identified with other asthma related phenotypes. The analysis suggests that other polymorphisms or genes may be involved, and can interfere with the association. It may be appropriate to further extend the analyzed region to other neighbouring regions, which demonstrated positive linkage to asthma and related phenotypes.