Collaborative Study On The Genetics Of Asthma Research Articles

The IL6R variation Asp358Ala is a potential modifier of lung function in subjects with asthma

The IL6R single nucleotide polymorphism (SNP) rs4129267 has recently been identified as an asthma susceptibility locus in subjects of European ancestry but has not been characterized with respect to asthma severity. The SNP rs4129267 is in linkage disequilibrium (r(2) = 1) with the IL6R coding SNP rs2228145 (Asp(358)Ala). This IL6R coding change increases IL-6 receptor (IL-6R) shedding and promotes IL-6 transsignaling. We sought to evaluate the IL6R SNP rs2228145 with respect to asthma severity phenotypes. The IL6R SNP rs2228145 was evaluated in subjects of European ancestry with asthma from the Severe Asthma Research Program (SARP). Lung function associations were replicated in the Collaborative Study on the Genetics of Asthma (CSGA) cohort. Serum soluble IL-6R levels were measured in subjects from SARP. Immunohistochemistry was used to qualitatively evaluate IL-6R protein expression in bronchoalveolar lavage cells and endobronchial biopsies. The minor C allele of IL6R SNP rs2228145 was associated with a lower percent predicted FEV(1) in the SARP cohort (P= .005), the CSGA cohort (P= .008), and in a combined cohort analysis (P= .003). Additional associations with percent predicted forced vital capacity (FVC), FEV(1)/FVC ratio, and PC(20) were observed. The rs2228145 C allele (Ala(358)) was more frequent in severe asthma phenotypic clusters. Elevated serum soluble IL-6R levels were associated with lower percent predicted FEV(1) (P= .02) and lower percent predicted FVC (P= .008) (n= 146). IL-6R protein expression was observed in bronchoalveolar lavage macrophages, airway epithelium, vascular endothelium, and airway smooth muscle. The IL6R coding SNP rs2228145 (Asp(358)Ala) is a potential modifier of lung function in subjects with asthma and might identify subjects at risk for more severe asthma. IL-6 transsignaling might have a pathogenic role in the lung.

Multipoint linkage disequilibrium mapping for complex diseases.

Linkage disequilibrium (LD) or association studies using case-parent trios have become a common approach to locate unobserved susceptibility genes underlying complex diseases. With the availability of ever more dense marker maps, how to utilize the information carried by multiple markers simultaneously remains challenging. Recently, Liang et al. ([2001a] Am. J. Hum. Genet. 68: 937-950) proposed a multipoint LD method to estimate the location of a susceptibility gene within a framework map along with its sampling uncertainty. Two important features of this method are that 1) it uses all trios whether parents are heterozygous for a given marker or not, and 2) it provides a single test statistic for the null hypothesis of no linkage or no LD to the region, avoiding the multiple testing problem encountered when performing individual transmission disequilibrium tests (TDT) for each marker individually. In this paper, we discuss how this method can be expanded to address important issues pertaining to complex diseases in a unified fashion. These issues include, among others, gene-gene and gene-environment interactions, genetic heterogeneity, phenotypic refinement, and paternal vs. maternal transmission. We applied this method to asthmatic case-parent trios from the Collaborative Study on the Genetics of Asthma (CSGA), and found that the previous evidence for linkage and LD in a 13.6 cM region of chromosome 11 can be attributed to maternal transmission, while there was no evidence of excess paternal transmission. Furthermore, such discrepancy in preferential transmission was most evident among probands with early onset age (6 years old or younger).

A genome-wide search for allergic response (atopy) genes in three ethnic groups: Collaborative Study on the Genetics of Asthma.

Atopy is an IgE-mediated condition known to aggregate in families and is a major risk factor for asthma. As part of the Collaborative Study on the Genetics of Asthma (CSGA), a genome-wide scan for atopy, defined by skin sensitivity to one or more common environmental allergens, was conducted in 287 CSGA families (115 African American, 138 Caucasian and 34 Hispanic). Using a nonparametric genetic analysis approach, two regions were observed in the sample of all families that yielded multipoint lod scores >1.5 (chromosome 11q, lod=1.55 between D11S1986 and D11S1998; chromosome 20p between D20S473 and D20S604, lod=1.54). Modeling that included multiple genomic positions simultaneously indicated that four chromosomal regions accounted for the majority of evidence for linkage in the combined families. These four regions are on chromosomes 10p near D10S1412 (lod=0.94), 11q near D11S1986 (lod=1.76), 17q near D17S784 (lod=0.97) and 20p near D20S473 (lod=1.74). In the subset of pedigrees giving positive evidence for linkage on chromosome 11q, the evidence for linkage increased by lod scores greater than one in four other chromosomal regions: 5q (D5S1480, lod=1.65), 8p (D8S1113, lod=1.60), 12p (D12S372, lod=1.54) and 14q (D14S749, lod=1.70). These results suggest that several regions may harbor genes contributing to the risk for atopy and these may interact with one another in a complex manner.

Multipoint linkage disequilibrium mapping approach: incorporating evidence of linkage and linkage disequilibrium from unlinked region.

Gene mapping for complex diseases is still a challenge in genetic studies. For family-based studies, the single-locus methods for detecting linkage and linkage disequilibrium (LD) one at a time may not capture the assumed interaction between multiple causal genes efficiently. We propose a multipoint LD approach for assessing the evidence of linkage and LD in a targeted chromosomal region by incorporating evidence from an unlinked region using the case-parent trio design. The paternal and maternal preferential transmission statistics defined in Liang et al. ([2001] Am. J. Hum. Genet. 68:937-950) are the primary statistics for this approach. Our generalized estimating equation (GEE) method builds on a model using the expected preferential transmission statistic from the targeted region conditional on this same statistic from the unlinked region. The major assumption is that there is no more than one trait locus in both the targeted region and unlinked region. The map position of an unobserved trait locus and its confidence interval can be calculated. Finally, we apply this approach to the African-American families drawn from the Collaborative Study on the Genetics of Asthma (CSGA). Previous analysis using this GEE approach developed by Liang et al. ([2001] Am. J. Hum. Genet. 68:937-950) suggested strong evidence of linkage and LD on chromosome 11, but only marginal evidence on chromosome 8. While conditioning on marker D11S937 on chromosome 11, a separate trait locus on chromosome 8 was estimated at tau(2) empty set = 11.67 cM, with a 95% confidence interval of (8.75, 14.59), and the test statistic shows significant evidence of linkage and LD (P-value=0.0198) in this region of chromosome 8.

The Editors’ Choice

The Editors’ Choice

Genomewide Screen and Identification of Gene-Gene Interactions for Asthma-Susceptibility Loci in Three U.S. Populations: Collaborative Study on the Genetics of Asthma

The genomewide screen to search for asthma-susceptibility loci, in the Collaborative Study on the Genetics of Asthma (CSGA), has been conducted in two stages and includes 266 families (199 nuclear and 67 extended pedigrees) from three U.S. populations: African American, European American, and Hispanic. Evidence for linkage with the asthma phenotype was observed for multiple chromosomal regions, through use of several analytical approaches that facilitated the identification of multiple disease loci. Ethnicity-specific analyses, which allowed for different frequencies of asthma-susceptibility genes in each ethnic population, provided the strongest evidence for linkage at 6p21 in the European American population, at 11q21 in the African American population, and at 1p32 in the Hispanic population. Both the conditional analysis and the affected-sib-pair two-locus analysis provided further evidence for linkage, at 5q31, 8p23, 12q22, and 15q13. Several of these regions have been observed in other genomewide screens and linkage or association studies, for asthma and related phenotypes. These results were used to develop a conceptual model to delineate asthma-susceptibility loci and their genetic interactions, which provides a promising basis for initiation of fine-mapping studies and, ultimately, for gene identification.

Oligogenic approaches to the predisposition of asthma in ethnically diverse populations.

Using the genome-wide screening data of the Collaborative Study on the Genetics of Asthma (CSGA) (226 families, 1,461 genotyped subjects, 323 marker loci) and Hutterite studies (129 families, 690 genotyped subjects, 365 marker loci), we applied a genetic similarity function in order to quantify the inter-individual genetic distances d(xi,xj) between feature vectors xi, xj made up by the allelic patterns of subjects i,j with respect to loci li, l2,..., ln. Based on this similarity function, we structurally decomposed the genetic diversity of the CSGA population in order to address the question of ethnicity-related asthma vulnerability for genetically homogenous CSGA subgroups. The question of ethnicity-independent asthma vulnerability was investigated with all CSGA families as training and the Hutterite families as replication samples. We evaluated the between-sib similarities, which were expected to deviate from "0.5" in affected sib pairs if the region of interest contained markers close to disease-causing genes. The reference value 0.5 was derived by determining the parent-offspring similarities, which are always 0.5, irrespective of the affection status of parents and offspring. We found 18 vulnerability loci on chromosomes 1, 3, 4, 5, 6, 8, 12, 13, and 14, which were remarkably reproducible in the CSGA and the Hutterite data and constituted an ethnicity-independent oligogenic model.

Genome scan for linkage to asthma using a linkage disequilibrium-lod score test.

We report a genome-wide linkage study of asthma on the German and Collaborative Study on the Genetics of Asthma (CSGA) data. Using a combined linkage and linkage disequilibrium test and the nonparametric linkage score, we identified 13 markers from the German data, 1 marker from the African American (CSGA) data, and 7 markers from the Caucasian (CSGA) data in which the p-values ranged between 0.0001 and 0.0100. From our analysis and taking into account previous published linkage studies of asthma, we suggest that three regions in chromosome 5 (around D5S418, D5S644, and D5S422), one region in chromosome 6 (around three neighboring markers D6S1281, D6S291, and D6S1019), one region in chromosome 11 (around D11S2362), and two regions in chromosome 12 (around D12S351 and D12S324) especially merit further investigation.

Two-trait-locus linkage analyses of asthma susceptibility.

A genome-wide search was conducted to identify chromosomal regions likely to harbor genes for asthma susceptibility. One hundred and twelve Caucasian families ascertained through a proband with a diagnosis of asthma by the Collaborative Study on the Genetics of Asthma (CSGA) were used for this search. Genotype data on 323 polymorphic markers were analyzed via parametric and nonparametric linkage analysis in an initial genome scan to identify potential asthma susceptibility region(s). The regions where hold or nonparametric linkage scores were greater than 2.0 were selected for further investigation using two-trait-locus linkage analysis models.

Nonparametric linkage regression. II: Identification of influential pedigrees in tests for linkage.

We applied case-deletion-based diagnostics to the combined Caucasian genome scan data for asthma and IgE from the Collaborative Study on the Genetics of Asthma (CSGA) and German family studies in order to identify influential pedigrees in tests for linkage. These methods identified 12 pedigrees whose data appear not to fit the asthma linkage model and for whom alternative genetic and nongenetic explanations can be explored. The methods also identified four pedigrees for chromosome 1 and two pedigrees for chromosome 2 that provide strong evidence for linkage at their respective loci. Similarly, these methods helped identify four pedigrees that strongly influenced the linkage tests for IgE. From these data, we can construct an enriched subset of pedigrees to be used in further analysis for mapping region-specific putative trait predisposing loci.

Physician-derived asthma diagnoses made on the basis of questionnaire data are in good agreement with interview-based diagnoses and are not affected by objective tests

Background: Defining the phenotype is critical for investigating the genetic etiology of asthma. As part of the Collaborative Study on the Genetics of Asthma (CSGA), the primary objective of which is to identify asthma susceptibility loci, an algorithm was designed to determine diagnoses of definite asthma, probable asthma, less than probable asthma, or no asthma. A respiratory questionnaire was designed to assist in the process of characterizing the asthma phenotype. Objective: This study was designed to determine the validity of the CSGA algorithm for the diagnosis of asthma, to determine agreement in assessing an asthma diagnosis between the information obtained by the CSGA questionnaire versus a patient interview by a panel of specialist physicians, and to determine the degree to which objective tests would alter the questionnaire-based certainty of asthma diagnosis. Methods: An expert panel of asthma clinicians (n = 4) indicated to what degree they were certain that a subject (n = 48) had asthma as determined by using a 6-point Likert scale based on a 20-minute interview (phase I), a review of the CSGA questionnaire (phase II), a review of the questionnaire plus skin test and peripheral blood eosinophilia data (phase III), and a review of phase III information plus pulmonary data (spirometry and methacholine-reversibility testing; IV). Intraclass correlation coefficients (ICCs) were calculated between the physicians’ interpretation of the likelihood of asthma based on the information they received during each of the phases and between the CSGA algorithm and each of the phases. Results: Interjudge reliability with regard to the degree of certainty with which an asthma diagnosis could be made by interview was excellent (ICC, 98; 95% confidence intervals [95% CIs], 0.87–0.99). We also found that the agreement between the physicians’ interview with the patients (phase I) and the CSGA algorithm was good and at least as good with the addition of the CSGA questionnaire data and objective data (ICC, 0.65–0.75). Good agreement was also observed between the average certainty score from the interview and the CSGA questionnaire (ICC, 92; 95% CI, 0.76–0.93), and ICCs determining the agreement on asthma diagnosis between phase I and phases III and IV, in which objective data were introduced, did not change from the ICCs comparing phase I with phase II (ICC of 0.93 [95% CI, 0.79–0.96] and ICC of 0.91 [95% CI 0.73–0.95], respectively). Conclusion: We conclude that the CSGA algorithm is a valid tool for which the diagnosis of asthma can be made at an acceptable level of certainty and that the CSGA questionnaire, interpreted by an asthma specialist, is a useful tool for the diagnosis of asthma in clinical or epidemiologic studies. (J Allergy Clin Immunol 1999;104:791-6.)

Linkage analysis of Dermatophagoides pteronyssinus–specific IgE responsiveness with polymorphic markers on chromosome 6p21 ( HLA-D region) in Caucasian families by the transmission/disequilibrium test

Background: Recently, we have obtained evidence for linkage between Der p 1–specific IgE antibodies and markers on chromosome 6p21 ( HLA-D region) in a genome-wide screening in Caucasian families recruited as a part of the Collaborative Study on the Genetics of Asthma (CSGA). Objective: Specific IgE antibodies toward different Dermatophagoides pteronyssinus (Der p) polypeptides were detected by immunoblotting analysis, and the transmission/disequilibrium test (TDT) was performed between specific IgE responsiveness toward each different Der p polypeptide and markers on chromosome 6p21 to better clarify the genetic contribution of HLA-D genes. Methods: We studied 299 individuals in 45 Caucasian families participating in the CSGA. Serum samples from 137 individuals that showed elevated specific IgE antibodies toward the Der p crude allergen (> –0.5 log IU/mL) by ACCESS immunoassay were subjected to immunoblotting analysis. TDT was conducted between the presence of specific IgE antibodies toward each of 12 different Der p polypeptides and 4 polymorphic markers on chromosome 6p21. Results: The 196-bp allele of D6S1281 and the 104-bp allele of DQCAR showed significant excess transmission to specific IgE responders toward a particular Der p polypeptide (120 kd, 55 kd, 45 kd, or 37 kd). In contrast, the 200-bp allele of D6S1281 and the 204-bp allele of D6S291 showed significantly decreased transmission to specific IgE responders toward a particular Der p polypeptide (120 kd, 90 kd, 52 kd, or 45 kd). Deviation from the expected 50% transmission in heterozygous parents was statistically significant after correcting for multiple comparisons. Conclusion: This study supported our previous findings that genes on chromosome 6p21 ( HLA-D region) may influence the expression of Der p–specific IgE responsiveness in this Caucasian population. Our results, however, reveal the complexity of genetic regulations of Der p–specific IgE responsiveness by HLA-D genes, suggesting the strong influence of non- HLA loci and perhaps environmental factors for the development of Der p–specific IgE responsiveness. (J Allergy Clin Immunol 1998;102:443-8.)

Genetic influences of chromosomes 5q31-q33 and 11q13 on specific IgE responsiveness to common inhaled allergens among African American families

Background: We have recently conducted a genome-wide screening for genes influencing Dermatophagoides pteronyssinus–specific IgE responsiveness as a part of the Collaborative Study on the Genetics of Asthma (CSGA), which showed evidence for linkage in some regions, including chromosomes 5q31-q33 and 11q13 in African American families. Objectives: To clarify relative contributions of these regions to atopy in the same African American population, we have conducted further genetic linkage studies of specific IgE responses toward common inhaled allergens. Methods: We studied 328 individuals in 58 African American families participating in the CSGA. Specific IgE responses toward Dermatophagoides farinae, cat, dog, American cockroach, rye grass, and Bermuda grass, as measured by skin tests, were used for multipoint linkage analysis with polymorphic markers on chromosomes 5q31-q33 and 11q13. Results: Specific IgE response toward American cockroach showed evidence for linkage to chromosomes 5q31-q33 ( P = .0050) and 11q13 ( P = .017). Specific IgE response toward dog showed evidence for linkage with chromosome 5q31-q33 ( P = .0043). Evidence for linkage with chromosome 11q13 was obtained for specific IgE responses toward Dermatophagoides farinae ( P = .012), cat (P = .035), and Bermuda grass ( P = .017). The presence of a positive ST response for at least 1 of 30 common allergens showed evidence for linkage to chromosomes 5q31-q33 ( P = .017) and 11q13 ( P = .00058). Conclusions: These data support that genes on both chromosomes 5q31-q33 and 11q13 confer susceptibility to upregulated IgE-mediated immune responses in this African American population. The putative genes on chromosomes 5q31-q33 and 11q13, however, showed contrasting effects on atopy, which may result from strong gene–environmental interactions. (J Allergy Clin Immunol 1998;102:449-53.)

Genetic regulation of Dermatophagoides pteronyssinus–specific IgE responsiveness: A genome-wide multipoint linkage analysis in families recruited through 2 asthmatic sibs

Background: Dermatophagoides pteronyssinus (Der p) is one of the most frequently implicated allergens in atopic diseases. Although HLA could play an important role in the development of the IgE response to the Der p allergens, genetic regulation by non- HLA genes influences certain HLA-associated IgE responses to complex allergens. Objective: To clarify genetic control for the expression of Der p–specific IgE responsiveness, we conducted a genome-wide search for genes influencing Der p–specific IgE antibody levels by using 45 Caucasian and 53 African American families ascertained as part of the Collaborative Study on the Genetics of Asthma (CSGA). Methods: Specific IgE antibody levels to the Der p crude allergen and to the purified allergens Der p 1 and Der p 2 were measured. Multipoint, nonparametric linkage analysis of 370 polymorphic markers was performed with the GENEHUNTER program. Results: The best evidence of genes controlling specific IgE response to Der p was obtained in 2 novel regions: chromosomes 2q21-q23 ( P = .0033 for Caucasian subjects) and 8p23-p21 ( P = .0011 for African American subjects). Three regions previously proposed as candidate regions for atopy, total IgE, or asthma also showed evidence for linkage to Der p–specific IgE responsiveness: 6p21 ( P = .0064) and 13q32-q34 ( P = 0.0064) in Caucasian subjects and 5q23-q33 ( P = 0.0071) in African American subjects. Conclusions: No single locus generated overwhelming evidence for linkage in terms of established criteria and guidelines for a genome-wide screening, which supports previous assertions of a heterogeneous etiology for Der p–specific IgE responsiveness. Two novel regions, 2q21-q23 and 8p23-p21, that were identified in this study merit additional study. (J Allergy Clin Immunol 1998;102:436-42.)

Do genetics play a role in the pathogenesis of asthma?

Asthma is a phenotypically heterogeneous disorder associated with intermittent respiratory symptoms, bronchial hyperresponsiveness (BHR), and reversible airflow obstruction. 1, 2 Most individuals with asthma have evidence of BHR and atopy, with elevated total serum IgE, allergen-specific IgE, or skin-test reactivity to common allergens. At present, it is not clear whether asthma, BHR, and atopy are clinical manifestations of the same underlying primary defect or whether they share common pathways with distinct primary molecular origins. A genetic component to asthma has long been suggested by studies demonstrating increased prevalences of asthma among first-degree relatives of asthmatic subjects and greater concordance rates among monozygotic compared with dizygotic twins. 3-7 Such “clustering” in families is consistent with a genetic cause but may also reflect the effects of shared environmental exposures. Thus familial clustering does not prove a genetic cause. Although segregation analyses in populations of asthmatic families have suggested the likelihood of a major