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Asthma and genes encoding components of the vitamin D pathway Bossé, Yohan; Lemire, Mathieu; Poon, Audrey H; Daley, Denise; He, Jian-Qing; Sandford, Andrew; White, John H; James, Alan L; Musk, William A; Palmer, Lyle J; Raby, Benjamin A; Weiss, Scott T; Kozyrskyj, Anita L; Becker, Allan; Hudson, Thomas J; Laprise, Catherine Oct 24, 2009

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ralssBioMed CentRespiratory ResearchOpen AcceResearchAsthma and genes encoding components of the vitamin D pathwayYohan Bossé1,2, Mathieu Lemire3, Audrey H Poon4,5, Denise Daley6, Jian-Qing He6, Andrew Sandford6, John H White7, Alan L James8, Arthur William Musk9, Lyle J Palmer10, Benjamin A Raby4,5,11, Scott T Weiss4,5,12, Anita L Kozyrskyj13, Allan Becker13, Thomas J Hudson*3 and Catherine Laprise14,15Address: 1Institut universitaire de cardiologie et de pneumologie de Québec, Québec, Canada, 2Laval University Hospital Research Center (CRCHUL), Québec, Canada, 3Ontario Institute for Cancer Research, Toronto, Canada, 4The Channing Laboratory, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA, 5Harvard Medical School, Boston, MA, USA, 6James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia, Vancouver, Canada, 7Departments of Physiology and Medicine, McGill University, Montreal, Canada, 8West Australian Sleep Disorders Research Institute, Sir Charles Gairdner Hospital, Western Australia, 9Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Western Australia, 10UWA Centre for Genetic Epidemiology and Biostatistics, The University of Western Australia, Western Australia, 11Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA, 12The Center for Genomics Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA, 13Department of Pediatrics and Child Health, Faculty of Medicine, University of Manitoba, Winnipeg, Canada, 14Université du Québec à Chicoutimi, Chicoutimi, Canada and 15Community Genomic Medicine Centre, University of Montreal, Chicoutimi University Hospital, Chicoutimi, CanadaEmail: Yohan Bossé - yohan.bosse@crhl.ulaval.ca; Mathieu Lemire - mathieu.lemire@oicr.on.ca; Audrey H Poon - audrey.poon@channing.harvard.edu; Denise Daley - ddaley@mrl.ubc.ca; Jian-Qing He - JHe@mrl.ubc.ca; Andrew Sandford - ASandford@mrl.ubc.ca; John H White - john.white@mcgill.ca; Alan L James - Alan.James.SCGH@health.wa.gov.au; Arthur William Musk - Bill.Musk@uwa.edu.au; Lyle J Palmer - lyle@cyllene.uwa.edu.au; Benjamin A Raby - Benjamin.Raby@channing.harvard.edu; Scott T Weiss - Scott.Weiss@channing.harvard.edu; Anita L Kozyrskyj - Anita.Kozyrskyj@capitalhealth.ca; Allan Becker - becker@ms.umanitoba.ca; Thomas J Hudson* - tom.hudson@oicr.on.ca; Catherine Laprise - Catherine_Laprise@uqac.ca* Corresponding author    AbstractBackground: Genetic variants at the vitamin D receptor (VDR) locus are associated with asthmaand atopy. We hypothesized that polymorphisms in other genes of the vitamin D pathway areassociated with asthma or atopy.Methods: Eleven candidate genes were chosen for this study, five of which code for proteins inthe vitamin D metabolism pathway (CYP27A1, CYP27B1, CYP2R1, CYP24A1, GC) and six that areknown to be transcriptionally regulated by vitamin D (IL10, IL1RL1, CD28, CD86, IL8, SKIIP). Foreach gene, we selected a maximally informative set of common SNPs (tagSNPs) using the European-derived (CEU) HapMap dataset. A total of 87 SNPs were genotyped in a French-Canadian familysample ascertained through asthmatic probands (388 nuclear families, 1064 individuals) andevaluated using the Family Based Association Test (FBAT) program. We then sought to replicatethe positive findings in four independent samples: two from Western Canada, one from Australiaand one from the USA (CAMP).Published: 24 October 2009Respiratory Research 2009, 10:98 doi:10.1186/1465-9921-10-98Received: 2 June 2009Accepted: 24 October 2009This article is available from: http://respiratory-research.com/content/10/1/98© 2009 Bossé et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Page 1 of 21(page number not for citation purposes)Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98Results: A number of SNPs in the IL10, CYP24A1, CYP2R1, IL1RL1 and CD86 genes were modestlyassociated with asthma and atopy (p < 0.05). Two-gene models testing for both main effects andthe interaction were then performed using conditional logistic regression. Two-gene modelsimplicating functional variants in the IL10 and VDR genes as well as in the IL10 and IL1RL1 geneswere associated with asthma (p < 0.0002). In the replicate samples, SNPs in the IL10 and CYP24A1genes were again modestly associated with asthma and atopy (p < 0.05). However, the SNPs or theorientation of the risk alleles were different between populations. A two-gene model involving IL10and VDR was replicated in CAMP, but not in the other populations.Conclusion: A number of genes involved in the vitamin D pathway demonstrate modest levels ofassociation with asthma and atopy. Multilocus models testing genes in the same pathway arepotentially more effective to evaluate the risk of asthma, but the effects are not uniform acrosspopulations.BackgroundAsthma is a heterogeneous respiratory disease character-ized by chronic inflammation of the airways associatedwith recurrent symptoms that range from mild to debili-tating [1]. Asthma is in large part attributable to geneticfactors [2]. However, identifying the causal genes has beena daunting task due to the inherent complexity of the dis-ease as well as methodological issues related to findinggenes of complex diseases [3]. The emerging picture fromthe literature suggests hundreds of genes are associatedwith asthma or asthma-related phenotypes [4,5]. Majorefforts are currently underway to validate these genes inlarger populations as well as to identify novel genes usingnew technology-driven approaches such as genome-widesingle-nucleotide-polymorphism (SNP) association stud-ies [6-8].The innate and adaptive immune systems play an impor-tant role in the pathogenesis of asthma. Many genesinvolved in inflammation and immunoregulation path-ways have been associated with asthma [3]. The immunesystem is complex in nature with multiple redundant andinterfering pathways. Recently, the vitamin D pathway hasemerged as a new pathway contributing to the outcome ofimmune responses [9-12]. The vitamin D pathway haslong been recognized for its endocrine actions on boneand mineral homeostasis. However, growing knowledgehas elucidated autocrine and paracrine roles for the vita-min D system with respect to cell growth, proliferationand differentiation as well as in immune regulation [13].The biologically active form of vitamin D (1α,25-dihy-droxyvitamin D3), also known as calcitriol, mediates itseffect by binding to the nuclear vitamin D receptor (VDR).Upon activation, the VDR ligand/receptor complex altersthe transcription rate of many genes involved in a widespectrum of biological responses [14].The hypothesis that the vitamin D pathway plays a role inincluding antigen-presenting cells and activated T lym-phocytes [15,16]. How VDR affects immune cell popula-tions, cytokine secretion, and production is not entirelyknown, but previous evidence suggests that VDR activa-tion may cause a developmental shift of T helper (Th) cellstoward type 2 [17,18]. The hypothesis that VDR plays arole in asthma was also reinforced by the resistance ofVDR knock-out mice to experimentally induced asthma[19]. These mice fail to develop airway inflammation,eosinophilia, or airway hyperresponsiveness, despite highIgE concentration and elevated Th2 cytokines. Recently, afunctional polymorphism (FokI, rs2228570) in the VDRgene was shown to have a functional impact on theimmune system by interfering with the signaling of tran-scription factors important in immune-mediated diseasessuch as NF-κB and NFAT [20]. Taken together, these stud-ies clearly support VDR as a possible candidate gene forasthma.Two groups co-reported that genetic variants within theVDR gene were associated with asthma [21,22]. In aFrench-Canadian founder population, Poon et al. [21]demonstrated that six SNPs located between intron 2 andexon 9 spanning 28 kb of the VDR gene were associatedwith asthma. Linkage disequilibrium (LD) patterns withinthis population revealed the presence of two blocks(block 1 and 2) containing 3 and 4 common haplotypes,respectively. One haplotype within each block was over-transmitted to affected offspring. By sequencing the pro-moter, exons and surrounding regions, they excludednovel missense mutations that could explain the observedassociation. In a second study, Raby et al. [22] found sig-nificant associations between VDR variants and asthma intwo independent studies. They first screened seven candi-date genes that map to the centromeric region of chromo-some 12 in the Childhood Asthma Management Program(CAMP) study. Only one SNP located in the VDR genedemonstrated evidence of association with asthma. Con-Page 2 of 21(page number not for citation purposes)autoimmune diseases such as asthma, originates from theidentification of VDR in immunological relevant cells,sistent with the French-Canadian population, two LDblocks were observed, each with three common haplo-Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98types. The 3' haplotype block in the CAMP study was sig-nificantly associated with asthma. To exclude thepossibility that neighboring genes cause the association,the authors genotyped 29 SNPs in a 330 kb region sur-rounding the VDR gene. None of these SNPs were associ-ated with asthma, leaving VDR as the most likely causalgene. Their finding was then replicated in the Nurses'Health Study (NHS) [22]. In that study, four of the sixgenotyped SNPs within the VDR gene were associatedwith asthma. However, it should be noted that the direc-tion of the association in NHS was opposite to the effectsseen in CAMP, but similar to the findings in the French-Canadian population. Taken together, these data sug-gested that the VDR locus harbors variants that contributeto asthma, but the orientation of the risk allele is incon-sistent across populations.Numerous metabolic pathways are likely to play a majorrole in complex diseases. It is necessary to study the com-ponents of these pathways to gain a more comprehensivegenetic view of the susceptibility conferred by variantslocated in closely related genes [23,24]. Accordingly, wehypothesized that polymorphisms in other genesinvolved in the vitamin D system are associated withasthma or atopy.MethodsPopulationSubjects were from the Saguenay_Lac-Saint-Jean (SLSJ)asthma study, which consists of French-Canadian familiesascertained through asthmatic probands. Probands wereincluded in the study if they fulfilled at least two of the fol-lowing criteria: 1) a minimum of three clinic visits foracute asthma within one year; 2) two or more asthma-related hospital admissions within one year; or 3) steroiddependency, defined by either six month's use of oral, orone year's use of inhaled corticosteroids. A total of 1064individuals from 388 nuclear families were included inthe present analyses. Families were included in the studyif at least one parent was available for phenotypic assess-ment, at least one parent was unaffected, and all fourgrandparents were of French-Canadian origin. Familymembers were considered asthmatics if both a self-reported history of asthma and a history of physician-diagnosed asthma were recorded, or by clinical evaluationfollowing a methacholine provocation test. Skin-pricktests were performed for 26 inhalant allergens and sub-jects were considered atopic if they had at least one posi-tive response (wheal diameter ≥ 3 mm at 10 min) [25].Spirometry, methacholine challenge and IgE measure-ments are described in detail elsewhere [21]. Table 1presents the characteristics of the subjects. The SLSJ localethics committee approved the study, and all subjects gaveinformed consent.Replication samplesData from the Canadian Asthma Primary PreventionStudy (CAPPS) study, the Study of Asthma Genes and theEnvironment (SAGE) birth cohort and the BusseltonHealth Study (BHS) were used to replicate the findings.The Childhood Asthma Management Program (CAMP)study was also used to replicate a specific gene-gene (VDR-IL10) interaction models. The CAPPS and SAGE studieshave been described elsewhere [26]. Briefly, the CAPPSstudy was initiated in 1995 to assess the effectiveness of amultifaceted intervention program in the primary preven-tion of asthma in high-risk infants [27,28]. High-riskinfants were identified before birth as having at least onefirst-degree relative with asthma or two first-degree rela-tives with other IgE-mediated allergic diseases. A total of549 children and their parents forming 545 families wereenrolled in the study during the second and third trimes-Table 1: Characteristics of the subjects in the Saguenay_Lac-Saint-Jean study.All subjects(n = 1064)Probands(n = 210)Affected members(n = 320)Unaffected members(n = 534)Age (years) 39.7 ± 22.1 17.6 ± 9.4 40.0 ± 19.5 48.3 ± 21.1Male: Female ratio 0.80 0.86 0.68 0.85Mean age of onset (years) 16.5 ± 17.0 7.4 ± 7.6 22.3 ± 18.7 NAFEV1 (% predicted) 94.1 ± 19.8 92.5 ± 16.1 88.9 ± 23.2 99.1 ± 17.2PEFR (%) 6.4 ± 4.6 7.3 ± 4.2 7.4 ± 5.9 5.0 ± 2.9PC20 (mg/ml) 21.1 ± 24.9 5.1 ± 8.5 8.8 ± 15.4 39.4 ± 24.9Serum IgE (mg/L) 452.7 ± 1619.2 720.3 ± 1919.9 531.4 ± 1960.8 244.8 ± 1005.9Atopy (n) 593 (56.3%) 171 (81.8%) 218 (69.2%) 204 (38.6%)Smoking Status (n)Never 551 (52.6%) 173 (84.0%) 154 (48.7%) 224 (42.7%)Ex-smoker 291 (27.8%) 11 (5.3%) 100 (31.7%) 180 (34.3%)Smoker 205 (19.6%) 22 (10.7%) 62 (19.6%) 121 (23.1%)Page 3 of 21(page number not for citation purposes)Values are means ± SD for quantitative variables.FEV1, Forced expiratory volume in one second; PC20, Concentration of methacholine inducing a 20% fall in FEV1; PEFR, Peak expiratory flow rate (morning-evening variation).Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98ter of pregnancy. The children were followed since birthand were assessed by a pediatric allergist for the presenceof asthma and allergies. Atopy was defined by skin-pricktest. A total of 16 allergens were tested and the diagnosiswas positive if at least one wheal ≥ 3 mm than the negativecontrol was observed. Children with 7 year follow-up dataand DNA were included in the current study (380 chil-dren/families). The SAGE study is a population-basedcohort of 16,320 children born in the province of Mani-toba, Canada, between January 1, 1995 and December 31,1995. Parents of these children were first survey by mail in2002. A subset of children was then invited to join thestudy at age 8-10 years. This subset included children withparent-declared asthma and children without asthma. Atotal of 723 families were recruited into the study. Allrecruited children underwent clinical assessment ofasthma by a pediatric allergist. Skin prick testing for 16allergens was used to define atopy. In the two latter stud-ies (SAGE and CAPPS), children affected with asthma/atopy and their parents were genotyped and analysed intrios. In contrast, the BHS was analysed using a case-con-trol design. This study comprised a series of six cross-sec-tional health surveys that took place every three yearsfrom 1966 to 1981 in all adults and children residing inthe Shire of Busselton, Western Australia and a follow-upstudy of all previous participants (residing within andoutside this Shire) in 1994/1995. Busselton is a coastaltown in the South West region of Western Australia with apopulation that is predominantly of European origin. Inthe present case-control study, all subjects (n = 1395, 751controls and 644 cases) who attended both the 1981 andthe 1994 survey and who had a diagnosis of asthma aswell as available DNA were included. Subjects were con-sidered to have asthma if they answered yes to the ques-tion "Has your doctor ever told you that you had asthma/bronchial asthma?" in a written questionnaire at eithersurvey. Subjects were considered controls if they answeredno at both surveys. Skin prick testing for 12 allergens wasused to define atopy. Finally, CAMP is a multicenteredNorth American clinical trial designed to investigate thelong-term effects of inhaled anti-inflammatory medica-tions in children with mild to moderate asthma [29,30].A total of 1625 individual members of 428 non-Hispanicwhite nuclear families were included in the present analy-ses. This represents the subset non-Hispanic with CAMPfamilies with available SNP genotype data at both theVDR and IL10 loci. The diagnosis of asthma was based ona methacholine provocation test and one or more of thefollowing criteria for at least 6 months in the year beforerecruitment: 1) asthma symptoms at least two times perweek, 2) at least two uses per week of an inhaled bron-chodilator, and 3) daily asthma medication. A local ethicscommittee approved the protocol independently in eachGene selectionEleven candidate genes were chosen for this study. Figure1 is a cartoon of the vitamin D pathway that illustrates theimplication of each gene selected. Briefly, genes encodingkey components of the vitamin D pathway were chosen,which include: enzymes responsible for the activation andinactivation vitamin D (CYP27A1, CYP27B1, CYP2R1and CYP24A1) [31,32]; the vitamin D binding protein(GC) that binds to vitamin D and its plasma metabolitesand transports them to target tissues; SKIIP, also known asNCoA62/SKIP, that serves as a coactivator a vitamin D-mediated transcription [33]; and five revevant genes forasthma that are known to be transcriptionally regulatedby vitamin D (IL10, IL1RL1, CD28, CD86 and IL8) [14].SNP selectionSNPs were selected using the CEPH genotype dataset fromphase 1 of the International HapMap project [34]. Thegenotype data were downloaded from the genomic regioncovering ten kilobases up- and downstream of each gene.A maximally informative set of SNPs was selected using apairwise tagging algorithm described by Carlson et al.[35]. A Perl program, called ldSelect http://droog.gs.washington.edu/ldSelect.html, was used to select the SNPs ineach gene. Briefly, this program analyzes the pattern of LDbetween SNPs and forms bins of SNPs in LD based on anr2 threshold. The algorithm ensures that all pairwise LDvalues between SNPs in the same bin exceed the r2 thresh-old. Accordingly, any SNP in a bin can serve as a proxy(tagSNP) for all other SNPs in the same bin. Only one tag-SNP needs to be typed per bin. At this level, nonsynony-mous SNPs genotyped in the HapMap dataset wereprioritized using the "-required" option. Similarly, someSNPs were prioritized based on the type of variation (A/T,C/T, etc) to meet the genotyping technology requirement.The minor allele frequency and the r2 thresholds were setat 0.05 and 0.8, respectively, using the "-freq" and "-r2"options. Known nonsynonymous SNPs or functional var-iants not genotyped in the HapMap dataset were alsoselected for genotyping. Selected SNPs and their character-istics are shown in additional file (see Additional file 1).The location of SNPs relative to the gene structure is illus-trated in Additional file 2.GenotypingIn the SLSJ study, a total of 87 SNPs were genotyped usingthe SNP stream® UHT technology [36]. Primers weredesigned using FastPCR version 3.8.78 for multiplex PCR[37]. Single base extension primers were designed usingAutoprimer.com (Beckman Coulter). The protocol andreaction conditions were performed in accordance withthe manufacturer [36]. SNPs were genotyped in differentpanels that were organized by grouping SNPs with thePage 4 of 21(page number not for citation purposes)study. Written informed consent was obtained from allstudy participants.same type of variation (A/T, C/T, etc) and by respectingthe 12-plex maximum capacity of the system. For the rep-Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98lication studies (CAPPS, SAGE and BHS), 52 SNPs locatedin five genes were genotyped using the Illumina Golden-Gate assay [38] as part of a larger SNP genotyping panelhttp://www.genapha.ca. SNP genotypes in CAMP availa-ble from prior analyses were generated for VDR [22] andIL10 [39] using the MassARRAY platform (Sequenom, SanDiego, CA) and SNaPShot (Applied Biosystems, ForrestCity, CA), respectively, as previously described.Statistical analysesMendelian inheritance incompatibilities were inspectedusing Pedmanager version 0.9 and Hardy-Weinberg equi-librium was evaluated using a χ2 test among parents. Forthe SLSJ, CAPPS and SAGE studies the Family Based Asso-ciation Test (FBAT) program was used to test associationwith single SNPs [40]. All tests were performed with anadditive model using the empirical variance-covarianceestimator that adjusts for the correlation among siblingGenes involved in the vitamin D pathwayFigure 1Genes involved in the vitamin D pathway. Vitamin D3 comes from the diet but is mostly produced in the skin by the pho-tolytic cleavage of 7-dehydrocholesterol. From vitamin D3, two enzymatic activation steps are required to produce the biolog-ically active form of vitamin D [1α,25-(OH)2 D3]. CYP27A1 and CYP2R1 genes encode enzymes with 25-hydroxylase activity that catalyze the C-25 hydroxylation of vitamin D3. A final activation enzyme encoded by CYP27B1 subsequently catalyzes the rate-limiting C-1 hydroxylation step in 1α,25-(OH)2 D3 synthesis. The later enzyme is tightly-regulated in the kidney by calcium homeostatic signals, but also strongly induced by immune inputs (e.g. TLR signaling) in many cells of the immune system [12] (not depicted). The active form of vitamin D, 1α,25-(OH)2 D3 (orange triangle), is then transport to vitamin D target cells by the vitamin D binding protein (encoded by the GC locus) or is metabolically inactivated by the 24-hydroxylase enzyme (encoded by the CYP24A1 locus). In vitamin D target cells, 1α,25-(OH)2 D3 translocates to the nucleus and binds to the vitamin D receptor (VDR). The ligand/receptor complex binds vitamin D response element (VDRE) located in the promoter region of target genes. The DNA-bound complex interacts with nuclear coregulators, such as SKIIP [33], and alters the rate of gene transcription. Five genes having a VDRE or/and being transcriptionally regulated by vitamin D stimulation are shown (blue square). Genes selected for genotyping in the SLSJ study are circled in blue.Page 5 of 21(page number not for citation purposes)genotypes and for multiple nuclear families within a sin-gle pedigree. The FBAT test provides a Z-statistic with theRespiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98corresponding p value. A positive Z-statistic is indicativeof a high-risk allele and a negative Z-statistic is indicativeof a protective allele. In the BHS, the single SNP associa-tions were evaluated using the Cochran-Armitage test fortrend with additive coding of alleles. Genes showing atleast one SNP with a p < 0.05 in the SLSJ collection wereconsidered for validation in the other populations. Ourstrategy to deal with multiple testing was to replicate theassociations in independent populations instead of usingan adjusted p value. LD values were evaluated using the r2metrics and calculated with Haploview 3.32 [41]. Powercalculations for the four study populations were recentlydescribed [42].Gene-gene interactions were evaluated for asthma andatopy using a multilocus analysis method following theframework described in Millstein et al. [23]. This strategyis based on likelihood-ratio tests that used a log-additivecoding scheme, where genotypes aa, Aa, and AA are codedas 0, 1, and 2, respectively. Briefly, the analyses were per-formed in two stages. In stage one, single SNP tests ofassociations were evaluated by contrasting the nullhypothesis of no association with the alternative hypoth-esis. The threshold for significance for stage one of thegene-gene interaction tests was then adjusted for multipletesting using the Bonferroni correction. In stage two, a fulltwo-gene interaction model, including the two maineffects and the interaction term, was tested against thereduced model that includes only the main effects thatwere declared significant in the first stage, if any. Thisstrategy avoids retesting the same effects detected in stageone. While the framework of Millstein et al. [23] wasdescribed for a case-control dataset, it can easily beadapted to a case-parent design by following the case/pseudocontrol design described by Cordell et al. [43],where each case is matched with three pseudocontrolsderived from the untransmitted parental alleles. Follow-ing this, conditional logistic regression is used to assessthe significance of the main and interaction terms. Sincetransmission to multiple affected siblings cannot beassumed to be independent events, and since the familiesin our sample may contain more than one case, robustestimates for the variance and Wald tests were usedinstead of likelihood ratio tests for the SLSJ, CAPPS andSAGE studies. Considering the number of SNPs geno-typed in genes involved in the vitamin D pathway, a totalof 5003 two-gene interaction models were evaluated.Post hoc analyses were performed with the combined data-set (SLSJ, CAPPS, SAGE, and BHS). Tests of associationwere performed using the likelihood method imple-mented in UNPHASE v3.0.10 [44], which allow data fromfamily studies and case-control individuals to be analyzedResultsResults from the SLSJ populationAdditional file 1 presents the 87 genotyped SNPs andtheir characteristics in the SLSJ study. Two SNPs failed theassay design including one in the CD86 gene (rs1915087)and another in the GC gene (rs1491711). Both of theseSNPs are singletons and are not tagging other SNPs in thegenes. A third SNP (rs8176353) located in the CYP27B1gene was monomorphic. Additional file 1 also showedthe minor allele frequencies for a reference population(CEPH from HapMap) and for the SLSJ study. In mostcases, the minor allele frequencies were very similarbetween the two populations with a mean difference of2% and the largest difference was 16% for SNP rs4308217located in the CD86 gene. After Bonferroni correction,only one SNP was out of Hardy-Weinberg equilibrium(see Additional file 1). This SNP (rs4809960) is a single-ton in the CYP24A1 gene and was removed from furtheranalyses. Accordingly, a total of 83 SNPs were tested forassociation with asthma and atopy. Additional file 2shows the exon-intron structure of each gene and the loca-tion of genotyped SNPs.The overall distribution of single marker FBAT associationtests shows a greater number of small p values for asthmacompared to what was expected by chance (see Additionalfile 3). Results for genes with at least one significant pvalue for asthma and atopy are illustrated in Figure 2(results for all genes are illustrated in Additional file 2).The details of these tests are shown in Table 2 for SNPshaving at least one p value < 0.1 for asthma or atopy(FBAT results for all SNPs can be found in Additional file4). Five SNPs in the IL10 gene, three located in the pro-moter (rs1800872, rs1800871, rs1800896), one in intron1 (rs3024490), and the other located in the 3' region(rs4844553) were significantly associated with asthma.Three of them (rs1800871, rs1800872, and rs3024490)were in tight LD (r2 > 0.97), while the others were in lowto modest LD (Figure 3). Haplotype analysis for the threetightly linked SNPs revealed the presence of only two hap-lotypes with an allele frequency above 1% in the SLSJ pop-ulation. The TAA haplotype had a frequency of 0.268 andwas overtransmitted to asthma patients (p = 0.024), whilethe CCC haplotype had a frequency of 0.726 and wasundertransmitted (p = 0.013). Four out of the eight geno-typed SNPs in the CYP24A1 gene were also modestly asso-ciated with asthma or atopy (range of p values = 0.051 to0.015). The two intronic SNPs associated with atopy(rs912505 and rs927650) were in modest LD (r2 = 0.36)and the two SNPs associated with asthma (rs2248359 andrs8124792) located in the promoter and the 3' region ofthe gene were in complete equilibrium (r2 = 0) (Figure 3).Three intronic SNPs in the IL1RL1 gene were also associ-Page 6 of 21(page number not for citation purposes)together. ated with asthma. Two of them (rs1420089 andrs1861245) were in modest LD (r2 = 0.28) and the thirdRespiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98Page 7 of 21(page number not for citation purposes)Table 2: Single SNP association results for asthma and atopy in the Saguenay_Lac-Saint-Jean study.Asthma AtopyGene SNP Allele Allele frequency # of families* Z P value Allele frequency # of families* Z P valueIL10 rs4844553 C 0.94 39 2.10 0.036 0.94 33 0.15 0.881T 0.06 39 -2.10 0.036 0.06 33 -0.15 0.881rs3024490 A 0.28 105 2.42 0.016 0.28 94 0.80 0.423C 0.72 105 -2.42 0.016 0.72 94 -0.80 0.423rs1800872 A 0.28 105 2.42 0.016 0.28 94 0.80 0.423C 0.72 105 -2.42 0.016 0.72 94 -0.80 0.423rs1800871 C 0.71 95 -2.52 0.012 0.71 84 -1.22 0.221T 0.29 95 2.52 0.012 0.29 84 1.22 0.221rs1800896 C 0.46 117 -2.47 0.014 0.46 101 -1.49 0.137T 0.54 117 2.47 0.014 0.54 101 1.49 0.137IL1RL1 rs950880 A 0.39 126 1.73 0.084 0.39 105 1.64 0.100C 0.61 126 -1.73 0.084 0.61 105 -1.64 0.100rs1420089 C 0.18 72 -2.14 0.033 0.18 60 -0.21 0.832T 0.82 72 2.14 0.033 0.82 60 0.21 0.832rs1946131 C 0.92 53 -2.44 0.015 0.92 42 -1.96 0.050T 0.09 53 2.44 0.015 0.09 42 1.96 0.050rs1921622 C 0.54 75 -1.65 0.099 0.54 65 -1.39 0.165T 0.46 75 1.65 0.099 0.46 65 1.39 0.165rs1861245 A 0.43 101 -2.14 0.032 0.43 74 -1.19 0.235G 0.57 101 2.14 0.032 0.57 74 1.19 0.235CD28 rs6435203 C 0.34 120 -1.97 0.049 0.34 104 -1.17 0.243T 0.67 120 1.97 0.049 0.67 104 1.17 0.243CYP27A1 rs4674338 C 0.60 96 1.85 0.064 0.60 82 1.72 0.085T 0.41 96 -1.85 0.064 0.41 82 -1.72 0.085CD86 rs2715267 A 0.64 102 -1.82 0.069 0.64 91 -2.86 0.004C 0.37 102 1.82 0.069 0.37 91 2.86 0.004rs2715273 A 0.82 79 1.75 0.081 0.82 65 1.67 0.096T 0.18 79 -1.75 0.081 0.18 65 -1.67 0.096rs6805035 A 0.88 51 1.74 0.083 0.88 43 1.43 0.154C 0.12 51 -1.74 0.083 0.12 43 -1.43 0.154rs2332096 A 0.46 117 -1.39 0.164 0.46 108 -1.79 0.074C 0.54 117 1.39 0.164 0.54 108 1.79 0.074CYP2R1 rs11023374 C 0.33 105 2.38 0.017 0.33 88 1.33 0.183T 0.67 105 -2.38 0.017 0.67 88 -1.33 0.183CYP24A1 rs8124792 C 0.95 22 2.18 0.030 0.95 24 1.89 0.058T 0.05 22 -2.18 0.030 0.05 24 -1.89 0.058rs927650 C 0.55 108 -1.65 0.100 0.55 91 -1.95 0.051T 0.45 108 1.65 0.100 0.45 91 1.95 0.051rs912505 C 0.29 89 -1.63 0.104 0.29 80 -2.44 0.015T 0.71 89 1.63 0.104 0.71 80 2.44 0.015rs2248359 C 0.58 112 2.15 0.032 0.58 97 0.56 0.577T 0.42 112 -2.15 0.032 0.42 97 -0.56 0.577*Number of informative families to conduct the test.P values < 0.05 are shown in bold.Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98one (rs1946131) showed no LD with the other (Figure 3).Also worth mentioning is a SNP (rs2715267) in the pro-moter region of the CD86 gene that was significantly asso-ciated with atopy (p = 0.004). A trend for this SNP wasalso observed for asthma (p = 0.069). Finally, one SNP(rs11023374) in intron 2 of the CYP2R1 gene was associ-ated with asthma (p = 0.017). LD plots for all genes areillustrated in Additional file 5.Interaction among functionally related genes may not besurprising. Hence, all possible two-gene interactions weretested for asthma in the SLSJ study for the 11 genes understudy plus the VDR gene (Figure 4). Two concentratedspots of significant two-gene models for asthma areobserved in this figure. The one at the bottom representstwo-gene models involving SNPs in the IL10 and VDRgenes. The second spot located in the center of Figure 4significant between SNPs in the IL10 and CD86 genes.Additional file 6 shows the two-gene models for atopy inthe SLSJ study. Overall, gene-gene interactions were mod-est for atopy.To understand the impact of these two-gene models onthe risk of asthma, the genotype by genotype odds ratiomatrix was calculated and some representative and mostsignificant two-gene models are illustrated in Figure 5.Figure 5a, b and 5c show two-gene models between SNPsin the IL10 and VDR genes. Figure 5a shows that the riskof having asthma is similar for carriers of two rare IL10alleles irrespective of the VDR genotypes. However, therisk increases with the increasing number of commonIL10 alleles for individuals who are homozygous for thecommon VDR allele. In contrast, the risk tends to decreasewith the increasing number of common IL10 alleles forGenetic association of SNPs in the vitamin D pathway genes with asthma and atopy in the SLSJ studyFigure 2Genetic association of SNPs in the vitamin D pathway genes with asthma and atopy in the SLSJ study. Only genes with a least one significant p value (p < 0.05) are illustrated. Each subfigure presents the result of one gene. The top line indicates the gene name and symbol. The upper part of each subfigure shows the exon-intron structure of the gene and the localization of the genotyped SNPs. The coding exons are shown in black and the untranslated regions are shown in grey. The lower part of each subfigure illustrates the association results for asthma (solid circles) and atopy (open circles). The x-axis shows the localization of the gene and SNPs on NCBI Human Genome build 35. The y-axis shows the FBAT empirical p values on a log10 scale. The lower and upper dashed lines represent p value thresholds of 0.05 and 0.001, respectively. The upper and lower parts of each subfigure are shown on the same scale.Page 8 of 21(page number not for citation purposes)represents two-gene models involving SNPs in the IL10and IL1RL1 genes. Multiple two-gene models were alsoindividuals who are homozygous for the rare VDR allele.Figure 5b shows that the risk of asthma increases with theRespiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98number of rare IL10 alleles, but the effect is greater withan increasing number of common alleles at the VDRlocus. Figure 5a and 5b show representative interactionsbetween SNPs located in the promoter region of IL10 andthe 3'UTR region of VDR. However, more complex inter-actions between these two genes were observed betweenSNPs located in the 3'UTR region of both genes. Figure 5cshows that the effect of the IL10 rare allele goes in theopposite directions depending on whether subjects arehomozygous for the common or the rare VDR alleles. Fig-ure 5d shows a representative interaction between pro-moter polymorphisms in the IL10 gene andnonsynonymous SNPs located in the IL1RL1 gene. In thismodel, the rare IL10 alleles increase the risk, but the mag-nitude of the effect is greater with the number of rare alle-and CD86 genes. In this model, the risk of asthma is sim-ilar for carriers of two common CD86 alleles irrespectiveof the IL10 genotypes, however, the risk increases addi-tively with the number of rare alleles in the two genes.Replication samplesFor all the single SNP associations observed in the SLSJpopulation, the statistical significance was modest anddid not survive multiple correction procedures. Accord-ingly, an effort was made to replicate these findings inthree additional studies. A comprehensive set of taggingSNPs in the IL10, CYP24A1, IL1RL1, CD86, and CYP2R1genes plus the significant (p < 0.05) SNPs in the SLSJ studywere genotyped in the CAPPS, SAGE and BHS studies.Table 3 shows SNPs with at least one p value < 0.05 forLinkage disequilibrium (LD) plots surrounding five genes involved in the vitamin D pathway in the SLSJ studyFigur 3Linkage disequilibrium (LD) plots surrounding five genes involved in the vitamin D pathway in the SLSJ study. The LD plots were generated by Haploview 3.32 [41]. Gene symbols are indicated at the top of each graph. The top horizontal bar illustrates the location of SNPs on a physical scale. The color of squares illustrates the strength of pairwise r2 values on a black and white scale where black indicates perfect LD (r2 = 1.00) and white indicates perfect equilibrium (r2 = 0). The r2 LD value is also indicated within each square. Blocks are defined using the Gabriel et al [71] definition. Failed and monomorphic SNPs as well as SNPs not in Hardy-Weinberg equilibrium are not illustrated.  CYP24A1 IL10 CYP2R1CD86 IL1RL1 Page 9 of 21(page number not for citation purposes)les at the IL1RL1 gene. Figure 5e shows a representativeinteraction between promoter polymorphisms in the IL10asthma or atopy in the three studies as well as SNPs withp value < 0.05 in the SLSJ study. Complete results for theRespiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98Figure 4 (see legend on next page)Page 10 of 21(page number not for citation purposes)Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98replicate samples can be found in Additional file 7. ForIL10, none of the SNPs associated with asthma in the SLSJstudy were significant in the other studies except the pro-moter polymorphism rs1800896, with a marginal p valueof 0.022 in CAPPS. However, the C allele that was protec-tive in the SLSJ study was the risk allele in the CAPPSstudy. The direction of the risk allele in the SAGE studywas similar to the one observed in the SLSJ, but the effectwas not significant. Similar flip-flop phenomena wereobserved between the SAGE and CAPPS studies for SNPsthat were not significant in the SLSJ study. Two SNPs intight LD, rs3024498 located in the 3'UTR and rs3024492located in intron 3, showed p values > 0.01 in both repli-cate samples, but the orientation of the risk allele wasreversed. For most IL10 SNPs, it was noticeable that theorientation of the risk alleles is in agreement between theSLSJ and SAGE studies and in the opposite direction forCAPPS. No SNP in the IL10 gene was significantly associ-ated with asthma or atopy in the BHS. Taken together, sig-nificant associations in the IL10 gene were observed inthree studies. However, different SNPs were associated indifferent populations and the direction of the risk allele inthe CAPPS study was reversed compared with the SLSJ andSAGE studies.The associations observed for the IL1RL1 and CYP2R1genes in the SLSJ study were not validated in the replica-tion samples (Table 3). No other SNP in the IL1RL1 genewas associated with asthma or atopy in the replicationstudies except a non-synonymous coding SNP(rs1041973, Glu78Ala) that was borderline significant foratopy in SAGE. For CYP2R1, two additional SNPs locatedin the promoter and intron 1 were associated with asthmain the BHS. However, none of these SNPs were replicatedin the other studies. For CD86, the promoter SNP(rs2715267) that was associated with atopy in the SLSJ (p= 0.004) could not be assessed in the other studies due tofailure of the genotyping assay. However, two othersignificantly associated with asthma in CAPPS. A differentSNP (rs9282641) located in non-coding exon 1 was sig-nificantly associated with asthma in the BHS. This latterSNP was not in LD with any of the three SNPs associatedwith asthma in CAPPS and SLSJ. Accordingly, differentCD86 polymorphims were associated with asthma inthree populations. Finally, significant SNPs were observedin the CYP24A1 gene in all studies. However, there was noconsistency with the SLSJ study in terms of phenotype andorientation of the risk alleles.The two-gene models were also performed in the replica-tion samples for the five genes that were genotyped inCAMP, SAGE and BHS. The significant two-gene modelsinvolving IL10 and VDR as well as IL10 and IL1RL1observed in the SLSJ study is not replicated in the CAPPS,SAGE and BHS. It should be noted that the sample sizesin the SAGE and CAPPS studies limit our ability to repli-cate the findings. For example, the number of cases con-tributing to the two-gene model involving IL10-rs1800896 and VDR-rs1544410 (Figure 5a) was approxi-mately halved in SAGE and reduced to a quarter in CAPPScompared with the SLSJ study. However, even with similarpower, the significant two-gene models observed in theSLSJ are not replicated in the BHS (see Additional file 8).Taken together, none of the significant two-gene modelsobserved in the SLSJ study were properly replicated inCAPPS, SAGE and BHS.The significant two-gene models involving IL10 and VDRwere also tested in the CAMP study. A different panel ofSNPs was genotyped in CAMP and some of the two-genemodels are significant (p < 0.05). The most significanttwo-gene models is observed between VDR-rs7975232and IL10-rs1800896 (Wald test p = 0.018) or IL10-rs1800872 (Wald-test p = 0.016). Figure 6 shows the com-parison of two-gene models observed in the SLSJ andCAMP studies. VDR-rs1544410 is not genotyped inTwo-gene model analyses on asthma in the SLSJ study for genes involved in the vitamin D pathwayFigur  4 (see previous page)Two-gene model analyses on asthma in the SLSJ study for genes involved in the vitamin D pathway. The plot illustrates the p values for single SNP association and all possible two-SNP combinations. Each line represents a SNP listed at the left of the figure. Each column represents a SNP listed in the same order but from left to right. The white horizontal and vertical lines break up the figure by genes. Gene names are indicated at the right of the figure. P values are illustrated using the following color scheme: grey, p > 0.05; blue, 0.05 > p > 0.01; yellow, 0.01 > p > 0.001; orange, 0.001 > p > 0.0001, red, 0.0001 > p > 0.00001. The squares forming the diagonal (upper-left to lower-right) depict p values for single SNP association based on a Wald test (see materials and methods). Two-gene models for SNPs located in the same gene were not assessed and were not coloured, which created the large white square patterns along the diagonal. Illustrated above the diagonal are p values for the interaction term only, which are the results of Wald tests contrasting the full model (two main effects and the interaction) to the reduced model (two main effects only). Illustrated below the diagonal are p values testing the full model (two main effects and the interaction) against a reduced model that is conditional on single SNPs declared significant when taken individu-ally, if any (see materials and methods). White squares illustrate tests for which the model failed to converge.intronic SNPs (rs9831894 and rs2332096, r2 = 0.48 in the CAMP, but rs7975232 was in moderately high LD with itPage 11 of 21(page number not for citation purposes)European HapMap data), not in LD with rs2715267, were (D' = 1.0 and r2 = 0.59, based on the HapMap CEU geno-Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98Page 12 of 21(page number not for citation purposes)Combined genotypic effects of selected two-gene models on asthma in the SLSJ studyFigure 5Combined genotypic effects of selected two-gene models on asthma in the SLSJ study. Each subfigure illustrates the risk of asthma according to two SNPs located in different genes. The genes and SNPs named are indicated above each sub-figure representing SNP 1 and SNP 2, respectively. With two bi-allelic SNPs (3 genotypes per SNP), a 3 by 3 odds ratio matrix is calculated and visually represented. All risks are evaluated relative to homozygotes for the common allele at both SNPs. The y-axis shows the odds ratio on a log2 scale, which makes the odds ratio above and below 1 on the same visual scale. The x-axis indicates the genotypes for SNP number 1. By drawing a line that joins the dots representing the genotypes for SNP number 2, the genotypic effect of SNP number 1 can be observed on different genotypic backgrounds of SNP number 2. The first three p values come from a model testing the main effect of both SNPs and the interaction term. The Wald test p value is the result of the full two-gene model tested against a reduced model (see materials and methods).Page 13 of 21(page number not for citation purposes)AtopyCAPPS BHSAF Fa Z p AFcaseAFctrlX2 p3 0.05 22 -1.88 0.061 0.05 0.06 0.12 0.7293 0.95 22 1.88 0.0613 0.78 70 -0.54 0.592 0.71 0.72 0.26 0.6083 0.22 70 0.54 0.5920.78 69 -0.75 0.453 0.71 0.72 0.20 0.6550.22 69 0.75 0.4537 0.29 78 0 1 0.23 0.23 0.07 0.7887 0.71 78 0 19 0.3 78 -0.1 0.922 0.23 0.23 0.07 0.7869 0.7 78 0.1 0.9223 0.43 83 0.29 0.772 0.50 0.50 0.06 0.8043 0.58 83 -0.29 0.7728 0.64 82 -1.18 0.239 0.55 0.56 0.13 0.7178 0.36 82 1.18 0.2397 0.09 40 0 1 0.12 0.12 0.03 0.8747 0.91 40 0 16 0.23 73 0.11 0.9156 0.77 73 -0.11 0.9154 0.1 37 0.78 0.435 0.10 0.09 1.61 0.2054 0.9 37 -0.78 0.4350.93 35 -0.16 0.873 0.91 0.90 0.82 0.3650.07 35 0.16 0.8737 0.4 96 -0.26 0.792 0.39 0.40 0.21 0.6457 0.6 96 0.26 0.792Respiratory Research 2009, 10:98http://respiratory-research.com/content/10/1/98Table 3: Single SNP association results for asthma and atopy in the replication samples.AsthmaSAGE CAPPS BHS SAGEGenes SNPs Allele AF Fa Z p AF Fa Z p AFcaseAFctrlX2 p AF Fa Z pIL10 rs4844553 A 0.07 25 0.96 0.336 0.05 11 0.3 0.763 0.05 0.06 1.21 0.272 0.07 35 -0.16 0.87G 0.93 25 -0.96 0.336 0.95 11 -0.3 0.763 0.93 35 0.16 0.87rs3024498 A 0.78 83 3.06 0.002 0.78 40 -2.56 0.01 0.70 0.72 1.74 0.187 0.78 108 1.22 0.22G 0.23 83 -3.06 0.002 0.22 40 2.56 0.01 0.23 108 -1.22 0.22rs3024492 A 0.78 81 2.89 0.004 0.78 40 -2.56 0.01 0.70 0.72 1.55 0.213 0.78 108 1.13 0.26T 0.22 81 -2.89 0.004 0.22 40 2.56 0.01 0.22 108 -1.13 0.26rs3024490 A 0.28 69 0.63 0.527 0.29 34 -1.64 0.101 0.24 0.22 1.63 0.202 0.28 99 0.36 0.71C 0.72 69 -0.63 0.527 0.71 34 1.64 0.101 0.72 99 -0.36 0.71rs1800872 A 0.28 70 0.73 0.463 0.3 34 -1.64 0.101 0.24 0.22 1.64 0.200 0.28 98 0.46 0.64C 0.72 70 -0.73 0.463 0.7 34 1.64 0.101 0.72 98 -0.46 0.64rs1800896 C 0.43 87 -1.22 0.221 0.43 40 2.29 0.022 0.50 0.50 0.02 0.889 0.43 124 -0.55 0.58T 0.57 87 1.22 0.221 0.58 40 -2.29 0.022 0.57 124 0.55 0.58rs10494879 C 0.63 93 1.44 0.151 0.64 42 -2.07 0.039 0.55 0.56 0.51 0.476 0.63 127 0.08 0.93G 0.37 93 -1.44 0.151 0.36 42 2.07 0.039 0.37 127 -0.08 0.93IL1RL1 rs1420089 C 0.09 39 1.41 0.16 0.09 19 -0.23 0.819 0.11 0.11 0.08 0.782 0.09 50 1.91 0.05T 0.91 39 -1.41 0.16 0.91 19 0.23 0.819 0.91 50 -1.91 0.05rs1041973 A 0.22 80 -0.1 0.921 0.23 35 0.16 0.876 0.22 98 -1.99 0.04C 0.78 80 0.1 0.921 0.77 35 -0.16 0.876 0.78 98 1.99 0.04rs1946131 A 0.11 43 -0.3 0.768 0.1 16 -0.23 0.819 0.10 0.10 0.36 0.55 0.11 52 -1.05 0.29G 0.9 43 0.3 0.768 0.9 16 0.23 0.819 0.9 52 1.05 0.29CD86 rs9282641 C 0.93 36 0.8 0.423 0.93 14 -0.78 0.439 0.89 0.92 7.34 0.007 0.93 42 0 1T 0.07 36 -0.8 0.423 0.07 14 0.78 0.439 0.07 42 0 1rs9831894 G 0.42 88 -1.12 0.261 0.4 40 -2.61 0.009 0.39 0.39 0.00 0.952 0.42 124 -0.23 0.81T 0.58 88 1.12 0.261 0.6 40 2.61 0.009 0.58 124 0.23 0.81Page 14 of 21(page number not for citation purposes).56 94 -0.92 0.357 0.54 0.54 0.00 0.958.44 94 0.92 0.357.27 72 1.05 0.292 0.28 0.27 0.08 0.775.73 72 -1.05 0.292.44 94 0.81 0.421 0.42 0.43 0.30 0.582.56 94 -0.81 0.421.42 93 -0.62 0.538 0.46 0.43 2.38 0.123.58 93 0.62 0.538.08 40 0.15 0.881 0.07 0.05 4.65 0.031.93 40 -0.15 0.881.57 1000.78 0.439 0.54 0.52 0.89 0.344.43 100-0.78 0.439.73 86 -0.2 0.843 0.77 0.79 1.64 0.200.27 86 0.2 0.843.44 97 2.51 0.012 0.42 0.40 1.14 0.287.56 97 -2.51 0.012.87 61 0.25 0.806 0.86 0.87 0.06 0.814.13 61 -0.25 0.806.45 96 1.17 0.241 0.42 0.40 1.07 0.302.55 96 -1.17 0.241cy; Fa, Number of informative families to conduct the at study. Coding non-synonymous SNPs are shown in Respiratory Research 2009, 10:98http://respiratory-research.com/content/10/1/98rs2332096 G 0.57 87 -1.53 0.127 0.56 43 -2.36 0.018 0.53 0.55 0.47 0.491 0.57 129 -1.08 0.28 0T 0.44 87 1.53 0.127 0.44 43 2.36 0.018 0.44 129 1.08 0.28 0CYP2R1 rs11023374 C 0.27 72 -0.63 0.532 0.27 35 0.44 0.662 0.27 0.28 0.07 0.793 0.27 91 0.38 0.703 0T 0.73 72 0.63 0.532 0.73 35 -0.44 0.662 0.73 91 -0.38 0.703 0rs10500804 G 0.4 92 1.81 0.07 0.44 40 -0.41 0.68 0.41 0.44 4.25 0.039 0.4 119 0.72 0.47 0T 0.6 92 -1.81 0.07 0.56 40 0.41 0.68 0.6 119 -0.72 0.47 0rs1562902 C 0.46 93 -0.83 0.405 0.42 39 -0.42 0.674 0.47 0.43 4.71 0.03 0.46 126 0.16 0.874 0T 0.54 93 0.83 0.405 0.58 39 0.42 0.674 0.54 126 -0.16 0.874 0CYP24A1 rs8124792 A 0.06 30 0.17 0.862 0.08 12 -0.26 0.796 0.06 0.06 0.29 0.591 0.06 42 1.18 0.238 0G 0.94 30 -0.17 0.862 0.93 12 0.26 0.796 0.94 42 -1.18 0.238 0rs927650 C 0.54 94 0.81 0.417 0.57 41 -0.69 0.492 0.55 0.50 6.75 0.009 0.54 127 0.23 0.816 0T 0.46 94 -0.81 0.417 0.43 41 0.69 0.492 0.46 127 -0.23 0.816 0rs912505 A 0.75 75 0.53 0.596 0.73 29 0.69 0.493 0.78 0.79 0.41 0.521 0.75 106 0.83 0.409 0G 0.25 75 -0.53 0.596 0.27 29 -0.69 0.493 0.25 106 -0.83 0.409 0rs2248359 A 0.35 87 1.04 0.296 0.44 41 1.82 0.069 0.41 0.41 0.02 0.889 0.35 133 0.54 0.588 0G 0.65 87 -1.04 0.296 0.56 41 -1.82 0.069 0.65 133 -0.54 0.588 0rs2426498 C 0.87 49 -1.39 0.166 0.87 24 0.82 0.414 0.86 0.87 0.03 0.859 0.87 58 -2.14 0.032 0G 0.13 49 1.39 0.166 0.13 24 -0.82 0.414 0.13 58 2.14 0.032 0rs6068821 A 0.41 95 2.32 0.021 0.45 39 0.27 0.785 0.41 0.39 1.15 0.283 0.41 126 2.24 0.025 0G 0.59 95 -2.32 0.021 0.55 39 -0.27 0.785 0.59 126 -2.24 0.025 0CAPPS, Canadian Asthma Primary Prevention Study; SAGE, Study of Asthma Genes and the Environment; BHS, Busselton Health Study; AF, allele frequentest.P values below 0.05 are shown in bold. SNPs that are significant in the SLSJ study (Table 2) are underlined as well as the allele that increases the risk in thbold.Table 3: Single SNP association results for asthma and atopy in the replication samples. (Continued)Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98typing dataset). The gene-gene interaction models weresimilar between the two studies. The effect of the IL10 var-iant on asthma seemed dependent on the VDR variant.This can be appreciated in Figure 6 by comparing thesolid, dotted and dashed lines between studies. The flip-flop phenomenon previously observed in the VDR genebetween the SLSJ and CAMP studies [21,22] can also beappreciated in Figure 6 (the solid line is at the top in theSLSJ study and at the bottom in the CAMP study).Combined analysesSingle SNP association tests and two-gene models weretested in the combined dataset. Overall, none of the SNPsare significantly associated with asthma or atopy after cor-rections for multiple testing (see Additional file 9). Simi-larly, the two-gene models for asthma and atopy were notsignificant (see Additional files 10 and 11, respectively).DiscussionWe performed a genetic association study between asthmaand genes involved in the vitamin D pathway. SNPslocated in five genes, including IL10, CYP24A1, IL1RL1,CYP2R1 and CD86, showed modest association withasthma or atopy in an asthma family study derived fromthe Saguenay_Lac-Saint-Jean population. Exploring gene-gene interactions in this pathway revealed significant two-gene models that refined risk evaluation for asthma. In anAustralian study. Again modest associations wereobserved for the IL10, CYP24A1 and CD86 genes forasthma or atopy. In general, SNPs showing associationwere different between studies or the orientation of therisk allele was reversed. Similarly, the significant two-genemodels found in the original study were not replicated inthe two additional Canadian studies and the Australianstudy. However, a significant two-gene model involvingthe IL10 and VDR gene was replicated in the Americanstudy.Overall, no genes or gene-gene interactions in the vitaminD pathway were consistently associated with asthma oratopy across all populations. This can be explained bymultiple factors as discussed previously [3,42]. Briefly,asthma was defined differently between populations,including patient self-reported, physician's diagnosis, or acombination of clinical characteristics and objectivethreshold from methacholine challenges. In addition, theindividual studies are either early or late-onset asthma.More specific for the current study, many environmentalfactors such as sun exposure and dietary vitamin D intakemay differ between studies and explained some of thecontroversies and flip-flop observations. Considering thedifferences among populations, our replication effort maybe more properly labeled as a descriptive study.Two-gene models on asthma involving the IL10 and VDR genes in the SLSJ and the CAMP studiesFigur  6Two-gene models on asthma involving the IL10 and VDR genes in the SLSJ and the CAMP studies. With two bi-allelic SNPs (3 genotypes per SNP), a 3 by 3 odds ratio matrix is calculated and visually represented. The y-axis shows the odds ratio on a log2 scale, which makes the odds ratio above and below 1 on the same visual scale. The IL10 genotypes are illustrated on the x-axis. Different panels of SNPs were genotyped between the two studies and the comparison for the VDR gene is made with different SNPs that are in LD (D' = 1.0 and r2 = 0.59, based on the HapMap CEU genotyping dataset). In the SLSJ study, the risks are evaluated relative to the VDR-GG and IL10-TT genotypes. In CAMP, the risks are evaluated relative to the VDR-CC and IL10-TT genotypes.Page 15 of 21(page number not for citation purposes)attempt to replicate these findings, we evaluated the sig-nificant genes in two additional Canadian studies and oneA number of SNPs in the IL10 gene surrounding the pro-moter region and extending up to intron 1 were signifi-Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98cantly associated with asthma in the SLSJ collection. Allthese SNPs were in tight LD and most of the genetic diver-sity at this locus was captured by only two haplotypes.Based on functional studies [45-50], the three-SNP pro-moter haplotypes formed by rs180096, rs1800871, andrs1800872 have been referred as the high and low IL10-producing haplotypes. IL10 is known as an anti-inflam-matory cytokine [51]. Accordingly, it makes biologicalsense that a low IL10-producing haplotype would be asso-ciated with asthma, which is consistent with most of theliterature [39,52-54]. Surprisingly, none of the promoterpolymorphisms in IL10 were associated with asthma oratopy in the SAGE and CAPPS populations with the excep-tion of rs1800896, which was associated with asthma inCAPPS. However, the orientation of the risk allele wasreversed compared to what was observed in the SLSJ studyand the vast majority of the scientific literature. In con-trast, SNPs located in the 3' end of the IL10 gene(rs3024498 and rs3024492) were associated with asthmain the replicate samples. The functional consequences ofthese SNPs are unknown but they were previously associ-ated with serum levels of calcidiol (25-OH-D3), the pre-hormone form of vitamin D [55], and with longitudinaldecline rate of lung function [56].Other genes in the vitamin D pathway tested in the cur-rent study have been previously associated with asthma orasthma-related phenotypes. In the German Asthma Fam-ily Study, Wjst et al. [55] identified SNPs in the IL10 genebut also in the GC, CYP2R1 and CYP24A1 genes that weresignificantly associated with asthma or IgE levels. Interest-ingly, SNPs in these genes were also associated with serumlevels of calcidiol (25-OH-D3) and calcitriol[1α,25(OH)2D3]. In the SLSJ population, three SNPs inthe CYP24A1 gene showed modest evidence of associa-tion with asthma or atopy (p < 0.05). In addition, the onlyCYP24A1 SNP (rs2248359) genotyped in commonbetween the German and SLSJ population showed a con-sistent result with an increase risk of asthma associatedwith the C allele. SNPs in the CYP2R1 gene, encoding anenzyme implicated in earlier steps of the vitamin D meta-bolic pathway, were also associated with asthma in boththe German and the SLSJ studies. Only one SNP in theCD86 and CD28 genes reached significance in the SLSJpopulation. The CD28 and CD86 interaction representsan important costimulatory signaling pathway for CD4positive T cell activation and Th2 cytokine production[57]. The association between atopy and the CD86 pro-moter polymorphism rs2715267 was relatively strong inthe SLSJ collection (p = 0.004). Different SNPs in theCD86 gene were also associated with asthma in the CAPPSand BHS studies. Thus, evidence is building to implicateCD86 as a susceptibility gene for asthma, but independentwith the previous studies showing the lack of associationwith asthma [58-60]. Many SNPs in the IL1RL1 gene wereassociated with asthma in the SLSJ study. This receptor isrequired for the development of an effective Th2 response[61,62] and mediates the biological effects of IL-33 [63].A functional promoter polymorphism (rs6543116) in theIL1RL1 gene was previously associated with atopic derma-titis and high total IgE levels in the sera from the samepatients [64]. More recently, a genome-wide associationscan for blood eosinophil count identified a strong asso-ciation with an intronic SNP (rs1420101) in this gene[65]. The same SNP was then associated with asthma in acollection of ten different populations (7,996 cases and44,890 controls). This SNP was not genotyped in the cur-rent study, but rs950880 can be used as a surrogate (r2 =0.96 based on the European HapMap data). rs950880 wasnot associated with asthma or atopy in any of the fourpopulations evaluated in the current study. However, atrend (p ≤ 0.10) in the same direction as the eosinophil/asthma study [65] was observed for asthma and atopy inthe SLSJ study as well as for atopy in the BHS. Finally, theSLSJ results do not support previous observations with theGC and IL8 genes [55,66,67].It is reasonable to expect interactions among functionallyrelated genes. In the SLSJ study, some two-gene modelswere more efficient at evaluating the risk of asthma com-pared with single SNP models. The models implicatingfunctional variants in the VDR and IL10 genes are partic-ularly interesting. We previously demonstrated thatgenetic variants in the VDR gene are associated withasthma [21]. Since the latter publication [21], we havegenotyped more SNPs in the VDR gene in the same popu-lation and many SNPs between intron 2 and exon 9 areassociated with asthma (see Additional file 12). Themechanism explaining this association is still unclear, butallele-specific expression at this locus implicates the pres-ence of genetic variants that influence VDR expression[68]. In fact, we observed that the highly expressed haplo-type was overtransmitted to asthmatic individuals, whilethe low expressed haplotype was undertransmitted [3].These VDR haplotypes can be tagged by the SNPrs1544410 with the G allele being associated with thehigh-risk/high-expressed haplotype and the A allele beingassociated with the low-risk/low-expressed haplotype. Asmentioned above, the low IL10-producing haplotype wasassociated with asthma in the same population (SLSJ).These IL10 haplotypes can be tagged by the SNPrs1800871 with the T allele being associated with thehigh-risk/low-producing haplotype and the C allele beingassociated with the low-risk/high-production haplotype.By combining the information of both SNPs (IL10-rs1800871 and VDR-rs1544410) we obtained the two-Page 16 of 21(page number not for citation purposes)replications in larger population samples are required. Incontrast, the overall results for CD28 are more consistentgene model shown in Figure 5b and that was a significant(p = 0.00018) predictor of the risk of asthma. In thisRespiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98model, the risk of asthma increased additively with thenumber of G alleles (tagging the high-risk/high-expressedhaplotype) at the VDR locus and with the number of Talleles (tagging the high-risk/low-producing haplotype) atthe IL10 locus. Similarly, other intriguing interactionsbetween plausible candidate genes were observed in theSLSJ population, including IL10 and IL1RL1 (Figure 5d)as well as IL10 and CD86 (Figure 5e). Although interest-ing, the large majority of these two-gene models were notreplicated in the other populations. In the CAMP study, atwo gene-model involving IL10 and VDR variants mir-rored the observation made in the SLSJ sample. However,further work will be required to demonstrate the relevanceof these two-gene models in asthma.The cascade of enzymatic reactions that lead to the bio-synthesis of 1α,25(OH)2D3 is complex and requires theparticipation of many gene products (Figure 1). It is con-ceivable that polymorphisms in any of several genes inthis pathway could lead to differences in endogenous bio-synthesis and bioavailability of 1α,25(OH)2D3. At a moredownstream step in the pathway, genetic variants in theVDR itself or in genes implicated in the transcriptionalmachinery, can influence the sensitivity of the1α,25(OH)2D3 stimulus. Further downstream are tran-scriptionally regulated genes, or vitamin responsive genes,that mediate the broad physiological actions of1α,25(OH)2D3. Again, polymorphisms in these genes areprime candidates to influence the vitamin D response.However, at this level the task is rather challenging owingto the large number of genes regulated by 1α,25(OH)2D3[14]. An extra layer of complexity exists, knowing that theregulation of gene expression by 1α,25(OH)2D3 is highlycell-specific [69,70]. Accordingly, a large number of genescan determine the overall response to the vitamin D path-way. With this in perspective, gene selection in the currentstudy was not comprehensive. On the other hand, theresults of the current study may have implications in awider scope than the field of asthma and asthma-relatedphenotypes. SNPs associated with asthma in the vitaminD pathway genes may influence the overall vitamin D sen-sitivity and consequently influence many other diseases[55].ConclusionCumulative observations implicate the vitamin D path-way in immune responses. By studying genes involved inthis pathway, we identified genetic polymorphisms mod-estly associated with asthma and atopy in asthmatic fam-ilies from the Saguenay_Lac-Saint-Jean region. Significanttwo-gene models that include interactions between com-ponents of the pathway were also identified. We thenattempted to replicate the findings in two additionalwere modestly associated with asthma or atopy. However,the SNPs or the orientation of the risk alleles were differ-ent between populations. It is conceivable that the effectof the VDR system in immune responses can be overruledby more potent immune pathways. Accordingly, the effectof the vitamin D pathway might be detectable only in spe-cific environments or age-related contexts. Further studiesare warranted to confirm the single SNP and the multilo-cus models associated with asthma in the current study.List of abbreviations usedBHS: Busselton Health Study; CAMP: Childhood AsthmaManagement Program; CAPPS: Canadian Asthma PrimaryPrevention Study; CD28: CD28 molecule; CD86: CD86molecule; CYP24A1: cytochrome P450, family 24, sub-family A, polypeptide 1; CYP27A1: cytochrome P450,family 27, subfamily A, polypeptide 1; CYP27B1: cyto-chrome P450, family 27, subfamily B, polypeptide 1;CYP2R1: cytochrome P450, family 2, subfamily R,polypeptide 1; FBAT: family based association test; FEV1:forced expiratory volume in 1 second; GC: vitamin Dbinding protein; IL10: interleukin 10; IL1RL1: interleukin1 receptor-like 1; IL8: interleukin 8; LD: linkage disequi-librium; NHS: Nurses' Health Study; PC20: the concentra-tion of methacholine that causes a 20% decline in FEV1;SAGE: Study of Asthma Genes and the Environment;SKIIP: SKI interacting protein; SLSJ: Saguenay_Lac-Saint-Jean; SNP: single-nucleotide-polymorphism; VDR: vita-min D receptor.Competing interestsThe authors declare that they have no competing interests.Authors' contributionsYB carried out gene/SNP selection, genotyping in the SLSJstudy, integration of datasets and was primary author ofthe manuscript. ML performed statistical analyses in SLSJ,SAGE, CAPPS, and BHS. AHP carried out statistical analy-ses in CAMP. DD, JQH and AS provided statistical, geno-typing and genetics expertise to replicate the findings inthe AllerGen study samples. JHW made substantial intel-lectual contribution in gene selection. ALJ, AWM and LJPparticipated in the conception and coordination of theBHS. BAR and STW participated in the conception andcoordination of CAMP. ALK participated in the coordina-tion of the SAGE study. AB conceived and acquired fund-ing for the SAGE and CAPPS studies. TJH and CLconceived and acquired funding for the SLSJ study. TJHalso provided general supervision of the research group.All authors read and approved the final manuscript.Page 17 of 21(page number not for citation purposes)Canadian studies and one Australian study. Similar to theSLSJ study, some SNPs in the IL10 and CYP24A1 genesRespiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98Additional materialAdditional file 1SNP characteristics. Table showing the SNPs selected for genotyping and their characteristics including chromosomal location, type of variation, minor allele, minor allele frequency, and Hardy-Weinberg p value.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S1.DOC]Additional file 2Genetic association of SNPs in the vitamin D pathway genes with asthma and atopy in the SLSJ study. Each subfigure presents the result of one gene. The top line indicates the gene name and symbol. The upper part of each subfigure shows the exon-intron structure of the gene and the localization of the genotyped SNPs. The coding exons are shown in black and the untranslated regions are shown in grey. The lower part of each subfigure illustrates the association results for asthma (solid circles) and atopy (open circles). The x-axis shows the localization of the gene and SNPs on NCBI Human Genome build 35. The y-axis shows the FBAT empirical p values on a log10 scale. The lower and upper dashed lines rep-resent p value thresholds of 0.05 and 0.001, respectively. The upper and lower parts of each subfigure are shown on the same scale.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S2.JPEG]Additional file 3The overall distribution of p values derived from single marker FBAT association tests in the SLSJ study. The top panels are Q-Q plots showing the distribution of observed p values against the expected distribution for asthma and atopy. The bottom panels are histograms showing the distri-bution of p values for asthma and atopy. The dashed lines represent the mean number of p values that is expected by chance. Association test results for 83 SNPs located in 11 genes are illustrated.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S3.JPEG]Additional file 4Single SNP association results for asthma and atopy in the Saguenay_Lac-Saint-Jean study. Table showing the FBAT results for all SNPs in the Saguenay_Lac-Saint-Jean study.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S4.DOC]Additional file 5Linkage disequilibrium (LD) plots surrounding eleven genes involved in the vitamin D pathway in the SLSJ study. The LD plots were gener-ated by Haploview 3.32 [41]. Gene symbols are indicated at the top of each graph. The top horizontal bar illustrates the location of SNPs on a physical scale. The color of squares illustrates the strength of pairwise r2 values on a black and white scale where black indicates perfect LD (r2 = 1.00) and white indicates perfect equilibrium (r2 = 0). The r2 LD value is also indicated within each square. Blocks are defined using the Gabriel et al [71] definition. Failed and monomorphic SNPs as well as SNPs not in Hardy-Weinberg equilibrium are not illustrated.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-Additional file 6Two-gene model analyses on atopy in the SLSJ study. Visual represen-tation of results is explained in Figure 4.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S6.JPEG]Additional file 7Single SNP association results for asthma and atopy in the replication samples. Table showing the results for all SNPs in the replication samples.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S7.DOC]Additional file 8Two-gene model analyses on asthma in the BHS. Visual representation of results is explained in Figure 4.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S8.JPEG]Additional file 9Single SNP association results for asthma and atopy in combined analyses (SLSJ, CAPPS, SAGE, and BHS). Table showing the results for the combined analyses.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S9.DOC]Additional file 10Two-gene model analyses on asthma in the combined dataset for genes involved in the vitamin D pathway. Visual representation of results is explained in Figure 4.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S10.JPEG]Additional file 11Two-gene model analyses on atopy in the combined dataset for genes involved in the vitamin D pathway. Visual representation of results is explained in Figure 4.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S11.JPEG]Additional file 12Genetic association between SNPs in the vitamin D receptor gene and asthma in the SLSJ study. The upper part of the figure shows the exon-intron structure of the gene and the localization of the genotyped SNPs. The coding exons are shown in black and the untranslated regions are shown in grey. The lower part of the figure illustrates the association results for asthma. The x-axis shows the localization of the gene and SNPs on NCBI Human Genome build 35. The y-axis shows the FBAT empirical p values on a log10 scale. The lower and upper dashed lines represent p value thresholds of 0.05 and 0.001, respectively. The upper and lower parts of the figure are shown on the same scale.Click here for file[http://www.biomedcentral.com/content/supplementary/1465-9921-10-98-S12.JPEG]Page 18 of 21(page number not for citation purposes)9921-10-98-S5.DOC]Respiratory Research 2009, 10:98 http://respiratory-research.com/content/10/1/98AcknowledgementsWe gratefully acknowledge Peter D Paré for in-depth review of the manu-script. Y. Bossé was the recipient of a fellowship award from the Canadian Institutes of Health and Research (CIHR) and is currently a research scholar from the Heart and Stroke Foundation of Canada. A.H. Poon is recipient of a fellowship award from the Croucher Foundation. D. Daley was the recipient of a fellowship award from the CIHR and is currently holding a Canada Research Chair on the Genetic Epidemiology of Complex Diseases and a Michael Smith Career Scholar Award. A. Sandford is the recipient of a Canada Research Chair in genetics. J.H. White is supported by a National Scientist Award from the "Fonds de la Recherche en Santé du Québec" (FRSQ). B.A. Raby is a recipient of a Mentored Clinical Scientist Development Award from NIH/NHLBI (K08 HL074193). T.J. Hudson is currently funded by a Senior Investigator Award of the Ontario Institute for Cancer Research and was the recipient of a Clinician-Scientist Award in Translational Research by the Burroughs Wellcome Fund and an Investiga-tor Award from the Canadian Institutes of Health Research. C. Laprise is the chairholder of the Canada Research Chair on genetic determinants in asthma and the director of the Inflammation and Remodeling Strategic Group of the Respiratory Health Network of the FRSQ, which partially support the French Canadian study. Additional support for this study came from the Networks of Centres of Excellence, Allergy, Genes and Environ-ment Network (AllerGen). We acknowledge the CAMP investigators and research team, supported by NHLBI, for collection of CAMP Genetic Ancil-lary Study data. All work on data collected from the CAMP Genetic Ancil-lary Study was conducted at the Channing Laboratory of the Brigham and Women's Hospital under appropriate CAMP policies and human subject's protections. The CAMP Genetics Ancillary Study is supported by U01 HL075419, U01 HL65899, P01 HL083069, R01 HL 086601, and T32 HL07427 from the National Heart, Lung and Blood Institute, National Insti-tutes of Health. Additional support for this research came from AllerGen. A. Becker, Y. Bossé, D. Daley, J.-Q. He, T.J. Hudson, A.L. James, A.L. Kozyr-skyj, C. Laprise, M. Lemire, A.W. Musk, L.J. Palmer, P.D. Paré and A. Sand-ford are members of AllerGen. The Busselton Health Study received support from Healthway, Western Australia for the 1994 re-survey. The Busselton Health Study acknowledges the study participants and local vol-untary survey staff.References1. 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