[Show abstract][Hide abstract] ABSTRACT: Not accounting for interaction in association analyses may reduce the power to detect the variants involved. We investigate the powers of different designs to detect under two-locus models the effect of disease-causing variants among several hundreds of markers using family-based association tests by simulation. This setting reflects realistic situations of exploration of linkage regions or of biological pathways. We define four strategies: (S1) single-marker analysis of all Single Nucleotide Polymorphisms (SNPs), (S2) two-marker analysis of all possible SNPs pairs, (S3) lax preliminary selection of SNPs followed by a two-marker analysis of all selected SNP pairs, (S4) stringent preliminary selection of SNPs, each being later paired with all the SNPs for two-marker analysis. Strategy S2 is never the best design, except when there is an inversion of the gene effect (flip-flop model). Testing individual SNPs (S1) is the most efficient when the two genes act multiplicatively. Designs S3 and S4 are the most powerful for nonmultiplicative models. Their respective powers depend on the level of symmetry of the model. Because the true genetic model is unknown, we cannot conclude that one design outperforms another. The optimal approach would be the two-step strategy (S3 or S4) as it is often the most powerful, or the second best. Genet.
[Show abstract][Hide abstract] ABSTRACT: A previous genome-wide linkage scan in 295 families of the French Epidemiological Study on the Genetics and Environment of Asthma (EGEA) reported strong evidence of linkage of 11p14 to eczema.
Our purpose was to conduct fine-scale mapping of the 11p14 region to identify the genetic variants associated with eczema.
Association analyses were first conducted in the family sample from the French EGEA by using 2 methods: the family-based association method and logistic regression. Replication of the EGEA findings was sought in French Canadian and United Kingdom family samples, which, similarly to EGEA samples, were ascertained through asthma. We also tested for association in 2 German samples ascertained through eczema.
We found significant association of eczema with 11p14 genetic variants in the vicinity of the linkage peak in EGEA (P = 10(-4) for rs1050153 by using the family-based association method, which reached the multiple testing-corrected threshold of 10(-4); P = .003 with logistic regression). Pooled analysis of the 3 asthma-ascertained samples showed strong improvement in the evidence for association (P = 6 × 10(-6) for rs293974, P = 3 × 10(-5) for rs1050153, and P = 8 × 10(-5) for rs15783). No association was observed in the eczema-ascertained samples.
The significant single nucleotide polymorphisms are located within the overlapping anoctamin 3 (ANO3) and mucin 15 (MUC15) genes. Several lines of evidence suggest that MUC15 is a strong candidate for eczema. Further investigation is needed to confirm our findings and to better understand the role of the ANO3/MUC15 locus in eczema and its relationship with respect to asthma.
The Journal of allergy and clinical immunology 06/2012; 129(6):1547-53.e3. DOI:10.1016/j.jaci.2012.04.010 · 11.25 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Asthma, allergic rhinitis (AR) and atopic dermatitis also called eczema are allergic co-morbidites, which are likely to depend on pleiotropic genetic effects as well as on specific genetic factors. After a previous genome-wide linkage screen conducted for asthma and AR in a sample of 295 French EGEA families ascertained through asthmatic subjects, the aim here was to search for genetic factors involved in eczema and more particularly the ones shared by the three allergic diseases using the same EGEA data. In this sake, eczema and phenotypes of "allergic disease" accounting for the joint information on the presence/absence of the three diseases were examined by linkage analyses using the maximum likelihood binomial method. A fine mapping was carried out in regions detected for potential linkage, followed by association studies using the family-based association test (FBAT). Evidence for linkage to 11p14 region was shown for "allergic disease" and eczema. Linkage was also indicated between eczema and 5q13 and between "allergic disease" and both 5p15 and 17q21 regions. Fine mapping supported the evidence of linkage to 11p14 and FBAT analyses showed the association between "allergic disease" and a marker located at the linkage peak on 11p14. Further investigations in this region will allow identifying genetic factor(s) which could have pleiotropic effect in the three allergic diseases.
Human Genetics 02/2008; 122(6):605-14. DOI:10.1007/s00439-007-0439-7 · 4.52 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Plaque psoriasis is a chronic inflammatory disorder of the skin. It is inherited as a multifactorial trait, with a strong genetic component. Linkage studies have identified a large number of disease loci, but very few could be replicated in independent family sets. In this study, we present the results of a genome-wide scan carried out in 14 French extended families. Candidate regions were then tested in a second set of 32 families. Analysis of the pooled samples confirmed linkage to chromosomes 6p21 (Z(MLB) score=3.5, P=0.0002) and 20p13 (Z(MLB) score=2.9, P=0.002), although there was little contribution of the second family set to the 20p13 linkage signal. Moreover, we identified four additional loci potentially linked to psoriasis. The major histocompatibility complex region on 6p21 is a major susceptibility locus, referred to as PSORS1, which has been found in most of the studies published to date. The 20p13 locus segregates independently of PSORS1 in psoriasis families. It has previously been thought to be involved in the predisposition to psoriasis and other inflammatory disorders such as atopic dermatitis (AD) and asthma. Although psoriasis and AD rarely occur together, this reinforces the hypothesis that psoriasis is influenced by genes with general effects on inflammation and immunity.
[Show abstract][Hide abstract] ABSTRACT: Asthma and bronchial hyper-responsiveness (BHR), an asthma-related phenotype, result from many genetic (G) and environmental (E) factors. Passive exposure to tobacco smoke (ETS) in early life is one of these risk factors. Following a genome scan for asthma and associated phenotypes conducted in 295 French Epidemiological study on the Genetics and Environment of Asthma, our present aim was to investigate interactions between genetic susceptibility to asthma and to BHR with passive ETS using two different methods: the predivided sample test (PST) and the mean interaction test (MIT). PST and MIT consider the identical by descent (identity by descent) distribution at all markers in affected sib-pairs with 2, 1 or 0 sib(s) exposed to ETS. While the PST allows detection of both linkage and G x E interaction, the MIT tests for linkage by taking into account a possible interaction. Among the six regions detected at P</=0.005, three of them (1q43-q44, 4q34, 17p11) were revealed by both PST and MIT for BHR. The three other regions were detected by only one method: 5p15 for BHR using PST; 14q32 and 17q21 for asthma using MIT, underlying the importance of using concomitantly different approaches. None of these regions was revealed for asthma and bronchial responsiveness by previous linkage analyses of these data, supporting the idea that taking into account gene-environment interactions can substantially increase power of linkage detection. Our results also showed evidence for G x ETS interactions underlying BHR in all four regions detected by PST.
European Journal of HumanGenetics 07/2007; 15(7):810-5. DOI:10.1038/sj.ejhg.5201830 · 4.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A recent genome scan conducted in French EGEA families led to detect linkage of 1p31 to either asthma or allergic rhinitis (AR) and more significantly to asthma associated with AR. The goal of the present study was to assess formally whether 1p31 is a linkage region shared by two different diseases, asthma and AR, or whether it is specific to the co-morbidity asthma plus AR.
We used two different statistical approaches: the Triangle Test Statistic (TTS) and the Predivided Sample Test (PST), to search for heterogeneity of linkage to 1p31 according to the affection status being defined by either the presence of the two diseases (asthma plus AR) or the presence of only one disease ('asthma only' or 'AR only' or 'asthma only or AR only').
While no heterogeneity between the 'two diseases' phenotype and the 'one disease' phenotype was detected by the TTS, there was significant evidence for heterogeneity (p = 0.00007/0.002 after correction for multiple testing) using the PST. There was no indication of linkage in sib-pairs with 'one disease' only, while there was significant evidence for linkage in sib-pairs displaying asthma plus AR (p = 0.0002/0.0016 after correction).
The present analysis shows that the co-morbidity, asthma plus AR, represents a phenotypic entity, distinct from asthma only or AR only, controlled by a genetic factor located on 1p31.
Human Heredity 02/2007; 63(3-4):162-7. DOI:10.1159/000099828 · 1.64 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Identifying gene-environment (G x E) interactions has become a crucial issue in the past decades. Different methods have been proposed to test for G x E interactions in the framework of linkage or association testing. However, their respective performances have rarely been compared. Using Genetic Analysis Workshop 15 simulated data, we compared the power of four methods: one based on affected sib pairs that tests for linkage and interaction (the mean interaction test) and three methods that test for association and/or interaction: a case-control test, a case-only test, and a log-linear approach based on case-parent trios. Results show that for the particular model of interaction between tobacco use and Locus B simulated here, the mean interaction test has poor power to detect either the genetic effect or the interaction. The association studies, i.e., the log-linear-modeling approach and the case-control method, are more powerful to detect the genetic effect (power of 78% and 95%, respectively) and taking into account interaction moderately increases the power (increase of 9% and 3%, respectively). The case-only design exhibits a 95% power to detect G x E interaction but the type I error rate is increased.
[Show abstract][Hide abstract] ABSTRACT: In the sample of 295 French EGEA families with at least one asthmatic subject, a genome screen was conducted to identify potential linkage regions specific either to allergic rhinitis (AR) or to asthma as well as those shared by the two diseases. Two binary rhinitis phenotypes based on (1) diagnosis (ARbin1) and (2) symptoms (ARbin2) and a categorical ordered trait (ARcat) were considered. Asthma phenotype was based on answers to a standardized questionnaire plus the presence of bronchial hyper-responsiveness. Linkage analyses were conducted using the maximum likelihood binomial (MLB) method. These analyses provided potential evidence for linkage to three regions in the whole sample: 1p31 for the phenotype defined by ARbin2 plus asthma (P=0.00016), 2q32 for ARbin2 (P=0.00016) and 3p24-p14 for ARcat (P=0.001). Two other regions were detected in the subset of 185 families with at most one asthmatic sib: 9p22 and 9q22-q34 for ARbin1 (P=0.001 and 0.0007, respectively). No region showed evidence for linkage to asthma without being also linked to AR. While 1p31 may contain a genetic determinant common to asthma and AR, 2q32, 3p24-p14, 9p22 and 9q22-q34 are more likely to harbor genetic factors specific to AR.
Genes and Immunity 04/2005; 6(2):95-102. DOI:10.1038/sj.gene.6364163 · 3.79 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A genome-wide scan for asthma phenotypes was conducted in the whole sample of 295 EGEA families selected through at least one asthmatic subject. In addition to asthma, seven phenotypes involved in the main asthma physiopathological pathways were considered: SPT (positive skin prick test response to at least one of 11 allergens), SPTQ score being the number of positive skin test responses to 11 allergens, Phadiatop (positive specific IgE response to a mixture of allergens), total IgE levels, eosinophils, bronchial responsiveness (BR) to methacholine challenge and %predicted FEV(1). Four regions showed evidence for linkage (P</=0.001): 6q14 for %FEV(1), 12p13 for IgE, 17q22-q24 for SPT and 21q21 for both SPTQ and %FEV(1). Nine other regions indicated smaller linkage signals (0.001<P</=0.005). While most of these regions have been reported by previous asthma and lung function screens, 6q14 appears to be a new region potentially linked to %FEV(1). To determine which of these various asthma phenotypes are more likely to share common genetic determinants, a principal component analysis was applied to the genome-wide LOD scores. This analysis revealed clustering of LODs for asthma, SPT and Phadiatop on one axis and clustering of LODs for %FEV(1), BR and SPTQ on the other, while LODs for IgE and eosinophils appeared to be independent from all other LODs. These results provide new insights into the potential sharing of genetic determinants by asthma-related phenotypes.
Human Molecular Genetics 01/2005; 13(24):3103-13. DOI:10.1093/hmg/ddh340 · 6.68 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Using the sample of 107 families with at least two asthmatic siblings, as part of the EGEA study, we have investigated linkage to asthma (or atopy) and genetic heterogeneity according to the presence/absence of atopy (or asthma) using two approaches: (1) the triangle test statistic (TTS), which considers the identical by descent (IBD) distribution among affected sib-pairs discordant for another associated phenotype (eg asthmatic sib-pairs discordant for atopy) and (2) the predivided sample test (PST), which compares the IBD distribution of marker alleles between affected sib-pairs concordant and discordant for the associated phenotype. Two regions, 8p and 12q, already reported to be linked to both asthma and atopy, were examined here. A total of 20 asthmatic sib-pairs discordant for atopy and 24 atopic pairs discordant for asthma were analyzed by both TTS and PST methods and 83 pairs with atopic asthma by PST. Some evidence for linkage was observed for two markers in the 8p23.3-p23.2 region; D8S504 for asthma with genetic heterogeneity according to the presence/absence of atopy and D8S503 for atopy with genetic heterogeneity according to the presence/absence of asthma. In the 12q14.2-q21.33 region, there was also some evidence of linkage to two markers, D12S83 and D12S95, for atopy and asthma, respectively, with genetic heterogeneity according to the presence/absence of the associated trait. Provided the small distance between the two markers on either 8p (16 cM) or 12q (21 cM), it is unclear whether one or two genetic factors are involved in either region.
European Journal of HumanGenetics 09/2003; 11(8):590-6. DOI:10.1038/sj.ejhg.5201014 · 4.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We studied the possible involvement of ten candidate genes in autism: proenkephalin, prodynorphin, and proprotein convertase subtilisin/kexin type 2 (opioid metabolism); tyrosine hydroxylase, dopamine receptors D2 and D5, monoamine oxidases A and B (monoaminergic system); brain-derived neurotrophic factor, and neural cell adhesion molecule (involved in neurodevelopment). Thirty-eight families with two affected siblings and one family with two affected half-siblings, recruited by the Paris Autism Research International Sibpair Study (PARIS), were tested using the transmission disequilibrium test and two-point affected sib-pair linkage analysis. We found no evidence for association or linkage with intragenic or linked markers. Our family sample has good power for detecting a linkage disequilibrium of 0.80. Thus, these genes are unlikely to play a major role in the families studied, but further studies in a much larger sample would be needed to highlight weaker genetic effects.
American Journal of Medical Genetics 04/2002; 114(2):125-8. · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It is generally believed that an early age at the onset of disease is associated with a stronger genetic component. Our aim here was to investigate both linkage and genetic heterogeneity of asthma, the latter corresponding to different genotype relative risks of a putative linked gene according to age at onset of asthma. This analysis was conducted in 107 French EGEA families with at least two asthmatic siblings, considering 157 markers that were part of our previous genome screen, using the TTS (the Triangle Test Statistic) which has been developed to detect both linkage and intra-sibpair genetic heterogeneity. This test has been applied to 38 asthmatic sib-pairs discordant for age at the onset of asthma. To confirm the existence of genetic heterogeneity, we also used the predivided sample test (PST) which compares the IBD (identity by descent) distribution of marker alleles between asthmatic sib-pairs concordant (67) and discordant (38) for the age at onset. The cutoff point used for the age at onset was 4 years, the median age at onset in our sample of asthmatic sibs. Linkage and genetic heterogeneity for a region located on chromosome 7q (at 109 cM from pter) were indicated by both tests, TTS (P=0.005, P>0.5 after correction for multiple testing) and PST (P=0.0001, 0.015 after correction). These results suggest a genetic factor on 7q involved in asthma with genotype relative risks differing according to age at onset of disease.
European Journal of HumanGenetics 11/2001; 9(11):867-72. DOI:10.1038/sj.ejhg.5200732 · 4.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Chronic liver disease is a major complication of cystic fibrosis. Its incidence and severity show marked heterogeneity, even among the homogeneous group of homozygous DeltaF508 patients, suggesting that environmental or genetic factors other than the deletion DeltaF508 may influence the development of cystic fibrosis related liver disease. We investigated whether the allelic variants of mannose binding lectin, an important protein of the immune system, could be associated with the presence of cirrhosis in a population of 216 homogeneous homozygous DeltaF508 patients. Analysis of the data shows that the presence of cirrhosis in cystic fibrosis patients is significantly associated with a mutated mannose binding lectin genotype (homozygous or compound heterozygous for mannose binding lectin variants). The modulating role of mannose binding lectin in the occurrence of cirrhosis in cystic fibrosis could be explained by the fact that hepatotoxic damage from viruses or bacteria might be increased by the immunodeficiency associated with mannose binding lectin variants and might facilitate the degradation of liver status. These data highlight the crucial role of mannose binding lectin in the clinical outcome of cystic fibrosis, as it has recently been shown that the mannose binding lectin gene is a modulating gene of the respiratory involvement in cystic fibrosis patients.
Journal of Medical Genetics 06/2001; 38(5):310-1. · 5.64 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A genome-wide search was conducted in 107 nuclear families with at least two siblings with asthma, as part of the French EGEA study. A two-stage analysis strategy was applied to the 107 families divided into two independent subsets of 46 and 61 families, where all regions detected in the first set of families were tested for replication in the second set. In addition, all regions reported by published genome scans in different populations were examined in the total sample. A total of 254 markers were typed in the first set of families and 70% of them in the second set. Linkage was investigated by model-free methods for asthma and four asthma-related phenotypes: bronchial responsiveness (BR), skin test response, total immunoglobulin E (IgE) levels, and eosinophil count. The two-stage analysis led to the detection of three regions: 11p13 for IgE, 12q24 for eosinophils, and 17q12-21 for asthma and skin tests. Among the regions reported by published genome screens, seven were found in the 107 French EGEA families: three being already detected by the two-stage analysis, 11p13 (p = 0.005), 12q24 (p = 0.0008), and 17q12-21 (p = 0.001), and four additional ones, 1p31 (p = 0.005) for asthma, 11q13 (p = 0.006) for IgE, 13q31 (p = 0.001) for eosinophils, and 19q13 (p = 0.02) for BR.
American Journal of Respiratory and Critical Care Medicine 12/2000; 162(5):1812-8. DOI:10.1164/ajrccm.162.5.2002113 · 11.99 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A subset of 299 patients with homozygous sickle cell anaemia, enrolled in the cohort of the French Study Group on sickle cell disease (SCD), was investigated in this study. The majority of patients were children (mean age 10.1 +/- 5.8 yr) of first generation immigrants from Western and Central Africa, the others originated from the French West Indies (20.2%). We report the frequency of the main clinical events (mean follow-up 4.2 +/- 2.2 yr). The prevalence of meningitis-septicaemia and osteomyelitis was, respectively, 11.4% and 12% acute chest syndrome was observed in 134 patients (44.8%). Twenty patients (6.7%) developed stroke with peak prevalence at 10-15 yr of age. One hundred and seventy-two patients (58%) suffered from one or more painful sickle cell crises, while the others (42.5%) never suffered from pain. The overall frequency of acute anaemic episodes was 50.5%, (acute aplastic anaemia 46%; acute splenic sequestration 26%). A group of 27 patients were asymptomatic (follow-up > 3 yr). Epistatic mechanisms influencing SCD were studied. Coinherited alpha-thalassemia strongly reduced the risk of stroke (p <0.001) and increased that of painful crises (p < 0.02). There was a low prevalence of Senegal and Bantu (CAR) betas-chromosomes in patients with meningitis (p <0.04) and osteomyelitis (p < 0.03). Prevalence of Senegal betas-chromosomes was lower in the asymptomatic group of 27 patients (p < 0.02). The patients come from a population of unmixed immigrants in whom the beta-globin gene haplotype strongly reflects the geographic origin and identifies subgroups with a homogenous genetic background. Thus the observed effects might result more from differences in as yet unidentified determinants in the genetic background than from the direct linkage with differences in the beta-globin gene locus.
European Journal Of Haematology 10/2000; 65(3):155-64. · 2.41 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Besides melanoma susceptibility genes and shared environmental exposures, part of the familial clustering of cutaneous malignant melanoma (CMM) might be due to familial aggregation of melanoma-associated phenotypes. Our goal was to assess the patterns of familial aggregation of three melanoma risk factors: great number of naevi (GNN), light phototype (LP) and high degree of sun exposure (HDSE).
Familial aggregation of GNN, LP and HDSE was investigated in 66 French families with at least two CMM cases and was measured by the asssociation of the relatives' traits with the probands' traits, using the generalized estimating equations approach. The probands were the melanoma cases leading to ascertainment of the families, subdivided into cases (with the trait studied) and controls (without the trait).
We found significant evidence for familial aggregation of GNN only among sibs (OR = 3.7, 95% CI : 1.4-10.5, P = 0.01), of LP among blood relatives (OR = 3.8, 95% CI : 1.8-8.0, P = 0.004) and of HDSE among blood relatives (OR = 4.5, 95% CI : 2.1-9.9, P < 0.001) and spouses (OR = 44.3, 95% CI : 5.1-382.2, P < 10(-3)). These results suggest that genetic factors might account for the clustering of GNN and LP and shared environment for the aggregation of HDSE. The GNN clustering was lower in families with increasing numbers of CMM (>/=3 cases) or presence of p16 mutations, the opposite being observed for LP and HDSE. Moreover, the familial aggregation of LP was significantly lower in families with highly sun-exposed members.
Melanoma might not only result from specific genetic and environmental factors but also from those underlying melanoma-associated traits involving complex gene-gene and gene-environment interactions.
International Journal of Epidemiology 06/2000; 29(3):408-15. DOI:10.1093/ije/29.3.408 · 9.20 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Data from 2,666 patients with cystic fibrosis (CF) born in France, submitted during the period of 1992-1996 to the French registry for CF, were used to describe the different mutations, their frequency and their regional distribution. A total of 5,332 CF chromosomes have been analyzed, demonstrating 229 different mutations and accounting for 87% of CF genes in the French population. DeltaF508 is the most common mutation at 67.9% of CF mutations, followed by G542X (2.5%), N1303K (2.0%), 1717-1G-->A (1.2%), R553X (0.8%) and G551D (0.7%). The data show a clear geographical variation in the distribution of many of the mutations. Given the geographical heterogeneity of these mutations, carrier screening does not appear to be feasible in most French regions.
Human Heredity 03/2000; 50(2):142-5. · 1.64 Impact Factor