The PHF11 gene is not associated with asthma or asthma phenotypes in two independent populations J McClenaghan, 1 N M Warrington, 1 E F Jamrozik, 1 J Hui, 2,3 J P Beilby, 2,3 J Hansen, 4 N H de Klerk, 4 A L James, 5,6 A W Musk, 5,6 L J Palmer 1,7,8 c Additional details are published online only at http:// thorax.bmj.com/content/vol64/ issue7 1 Centre for Genetic Epidemiology and Biostatistics, University of Western Australia, Nedlands, Australia; 2 Clinical Biochemistry, PathWest Laboratory Medicine, Perth, Australia; 3 School of Surgery and Pathology, University of Western Australia, Perth, Australia; 4 Division of Biostatistics and Genetic Epidemiology, Telethon Institute for Child Health Research, Centre for Child Health Research, University of Western Australia, Perth, Australia; 5 West Australian Sleep Disorders Research Institute, Sir Charles Gardner Hospital, Nedlands, Australia; 6 School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia; 7 Western Australian Institute for Medical Research and UWA Centre for Medical Research, University of Western Australia, Nedlands, Australia; 8 School of Population Health, University of Western Australia, Crawley, Australia Correspondence to: Professor L J Palmer, University of Western Australia, Nedlands, WA 6009, Australia; lyle@ cyllene.uwa.edu.au Received 11 October 2008 Accepted 26 March 2009 Published Online First 20 April 2009 ABSTRACT Background: Numerous areas of the human genome have previously been associated with asthma and asthma-related phenotypes, but few positive findings have been successfully replicated in independent popu- lations. Initial studies have reported strong associations of variants in the plant homeodomain zinc finger protein 11 (PHF11) gene with serum IgE levels, asthma, airway hyper-responsiveness and childhood atopic dermatitis. Objectives: To investigate the association of variants in the PHF11 gene with asthma and associated intermediate phenotypes in two independent Western Australian population-based samples. Methods: A linkage-disequilibrium (LD)-tagging set of 20 single nucleotide polymorphisms (SNPs) was genotyped in PHF11 in two separate populations (total n = 2315), a family-based twin study consisting of 230 families (n = 992 subjects) and a population-based nested case- control study consisting of 617 asthma cases and 706 controls. Information regarding asthma, respiratory phy- siology, atopy and environmental exposures was col- lected. Transmission disequilibrium tests, variance components models and generalised linear models were used to test for association between PHF11 SNPs and selected asthma outcomes (including longitudinal change in lung function). Results: After correction for multiple testing, no statistically significant (p,0.05) associations were found between PHF11 and either asthma or total serum IgE levels in either population. No statistically significant associations were found with any other asthma-asso- ciated phenotypes in either population. Conclusions: Previously reported associations of PHF11 with asthma outcomes were not replicated in this study. This study suggests that PHF11 is unlikely to contain polymorphic loci that have a major impact on asthma susceptibility in our populations. Asthma is a chronic inflammatory disease of the airways which results in variable airway obstruc- tion and episodes of wheezing and breathlessness due to widespread narrowing of the airways in the lung. 1 The prevalence of asthma in the general population of Australia varies depending on the definition of asthma diagnosis, but is generally accepted to be around 10–12% of adults and 12–15% of children in Australia, 2 both of which are high by international standards. 3 Asthma is a complex disease caused by intricate interactions among genetic and environmental influences. 4 The heterogeneous and complex nat- ure of the aetiology of asthma has made it difficult to pinpoint precisely the extent of attribution of individual genetic and environmental influences, and can be further complicated by incomplete penetrance, epistasis and phenotypic pleiotrophy. 5 Difficulties in defining asthma, and the complex- ities of the pathogenic mechanisms underlying the disease, mean that intermediate asthma pheno- types are commonly used in genetic studies. 6 Commonly measured intermediate phenotypes for asthma include raised total serum IgE levels, increased exhaled nitric oxide (eNO), decreased spirometric indices (eg, forced expiratory volume in 1 s, FEV 1 ) and airway hyper-responsiveness (AHR) to inhaled spasmogens. All of these phenotypes are highly heritable. 7 There have been many genome-wide linkage scans for asthma, and several genes have been claimed as positionally cloned susceptibility loci. 8–12 The 13q14 region, in which the plant homeo- domain zinc finger protein 11 (PHF11) gene resides, has demonstrated significant linkage (p,0.05) with asthma, atopy and IgE levels in a number of studies. 13–17 The genome-wide linkage scan of Zhang et al 18 narrowed down this region of association with IgE levels to the PHF11 gene and two flanking genes on either side, with three SNPs identified as having independent associations with total serum IgE levels. In an independent study in children, Hersh et al 19 reported marginal associa- tions between PHF11 and asthma, as well as AHR, but found limited association with IgE levels. The current interest in PHF11 as a potential candidate gene has arisen from positional approaches. Until recently there was no clearly defined biological mode of action for PHF11 in relation to asthma, although it has been suggested to play a role in chromatin-mediated transcrip- tional regulation and immunoregulation, especially of B lymphocytes. 18 20 A recent study by Clark et al 21 found a higher expression of PHF11 in Th1 cells than Th2 cells, as well as a marked increase in PHF11 expression in basophils and mature dendri- tic cells, although there was low expression in mast cells and eosinophils. Given the complex nature of the aetiology of asthma and the frequent inability of secondary studies to replicate a positive result in a primary study, comprehensive replication of initial positive findings in gene-disease association studies has become critical for determining the validity of a candidate gene for a specific trait. 22 23 To investi- gate the association of PHF11 with asthma phenotypes, we identified a linkage-disequilibrium (LD)-tagging set of SNPs in the gene and conducted genetic association studies in two independent comprehensively phenotyped Western Australian (WA) samples. The potential pathway(s) through Asthma 620 Thorax 2009;64:620–625. doi:10.1136/thx.2008.108985 group.bmj.com on February 11, 2016 - Published by http://thorax.bmj.com/ Downloaded from