Meta-analysis of gene-level associations for rare variants based on single-variant statistics

Meta-analysis of genome-wide association studies (GWASs) has led to the discoveries of many common variants associated with complex human diseases. There is a growing recognition that identifying "causal" rare variants also requires large-scale meta-analysis. The fact that association tests with rare variants are performed at the gene level rather than at the variant level poses unprecedented challenges in the meta-analysis. First, different studies may adopt different gene-level tests, so the results are not compatible. Second, gene-level tests require multivariate statistics (i.e., components of the test statistic and their covariance matrix), which are difficult to obtain. To overcome these challenges, we propose to perform gene-level tests for rare variants by combining the results of single-variant analysis (i.e., p values of association tests and effect estimates) from participating studies. This simple strategy is possible because of an insight that multivariate statistics can be recovered from single-variant statistics, together with the correlation matrix of the single-variant test statistics, which can be estimated from one of the participating studies or from a publicly available database. We show both theoretically and numerically that the proposed meta-analysis approach provides accurate control of the type I error and is as powerful as joint analysis of individual participant data. This approach accommodates any disease phenotype and any study design and produces all commonly used gene-level tests. An application to the GWAS summary results of the Genetic Investigation of ANthropometric Traits (GIANT) consortium reveals rare and low-frequency variants associated with human height. The relevant software is freely available.

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture

Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.

Genetic risks and childhood-onset asthma

Recent large-scale genome-wide association studies have successfully identified several genetic loci that influence asthma susceptibility. The loci thus far identified confer a high population attributable risk for childhood-onset disease and have provided a better understanding of the primary mechanisms underlying asthma and a clear focus for new therapies to treat the disease. The loci are of limited utility for diagnostic or predictive genetic testing. This review considers different aspects of genetic risk, including individual, population, and familial risks, and explores how these different measures interact and how the next generation of genetic studies might be best designed.

Abstract 4730: Integrating pathway analysis and genetics of gene expression for genome-wide association study on basal cell carcinoma

Genome-wide association studies (GWASs) have primarily focused on marginal effects for individual markers and have only incorporated external functional information after identifying robust statistical associations. A pathway-based approach using the classification of genes into functionally-related pathways may identify pathways enriched for associations with diseases. However, there are some limitations of assigning all the single nucleotide polymorphisms (SNPs) into the pathways by their physical locations, as most SNPs in a gene region will not represent functional variants of the gene and a gene may be regulated in trans by DNA variants that are far away from the structural gene. Thus, we integrated genetics of gene expression and the pathway analysis for the GWAS on basal cell carcinoma (BCC), and aimed to discover potential important biological pathways involved in the etiology of BCC. Specifically, we first conducted the GWAS of global gene expression in lymphoblastoid cell lines among 1355 individuals of British descent and identified 322,324 expression-associated SNPs (eSNPs), and then evaluated the association between these functionally annotated SNPs and BCC risk among 2,045 BCC cases and 6,013 controls in Caucasians. The associations of all the genes with BCC were represented by the eSNPs associated with their expression accordingly, and all the genes were assigned into 99 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for the pathway enrichment analysis by using Kolmogorov-Smirnov statistic. We performed 1,000 permutations to access the significance of the pathway enrichment by shuffling the case-control status and repeating the association analysis. As a result, a total of 10 (10%) pathways out of the 99 KEGG pathways reached a nominal p-value ≤ 0.05, twice as high as the number expected by chance (0.05 × 99 = 4.95). After the correction for multiple test by the false discovery rate, three pathways were significantly associated with BCC risk, which were the autoimmune thyroid disease pathway (p-value < 0.001), and JAK-STAT signaling pathway (p-value = 0.02), and B cell receptor signaling pathway (p-value = 0.05). Of note, most of the genes enriched in the autoimmune thyroid disease pathway were the components of HLA-complex, which has been known to play an important role in tumor immunity. There is also some evidence of biological functions for the other two pathways on cancer immunity or oncogenesis from the reported studies. In conclusion, our approach which integrates the pathway information and gene expression-annotated SNP data may help identify biological pathways in the etiology of BCC, which may be missed in traditional GWAS approach focusing on marginal effects of individual markers.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4730. doi:10.1158/1538-7445.AM2011-4730

Gene expression in skin and lymphoblastoid cells: Refined statistical method reveals extensive overlap in cis-eQTL signals

Psoriasis, an immune-mediated, inflammatory disease of the skin and joints, provides an ideal system for expression quantitative trait locus (eQTL) analysis, because it has a strong genetic basis and disease-relevant tissue (skin) is readily accessible. To better understand the role of genetic variants regulating cutaneous gene expression, we identified 841 cis-acting eQTLs using RNA extracted from skin biopsies of 53 psoriatic individuals and 57 healthy controls. We found substantial overlap between cis-eQTLs of normal control, uninvolved psoriatic, and lesional psoriatic skin. Consistent with recent studies and with the idea that control of gene expression can mediate relationships between genetic variants and disease risk, we found that eQTL SNPs are more likely to be associated with psoriasis than are randomly selected SNPs. To explore the tissue specificity of these eQTLs and hence to quantify the benefits of studying eQTLs in different tissues, we developed a refined statistical method for estimating eQTL overlap and used it to compare skin eQTLs to a published panel of lymphoblastoid cell line (LCL) eQTLs. Our method accounts for the fact that most eQTL studies are likely to miss some true eQTLs as a result of power limitations and shows that ∼70% of cis-eQTLs in LCLs are shared with skin, as compared with the naive estimate of < 50% sharing. Our results provide a useful method for estimating the overlap between various eQTL studies and provide a catalog of cis-eQTLs in skin that can facilitate efforts to understand the functional impact of identified susceptibility variants on psoriasis and other skin traits.

Polymorphisms of PHF11 and DPP10 are associated with asthma and related traits in a Chinese population

BACKGROUND

Initial studies by positional cloning have identified the genes encoding the plant homeodomain zinc finger protein 11 (PHF11) and dipeptidyl-peptidase 10 (DPP10) as asthma susceptibility genes. The variants in the two genes have been associated with asthma in several populations of European or Latin American origin.

OBJECTIVE

The aim of this study was to assess the common PHF11 and DPP10 polymorphisms for associations to asthma and asthma-related traits in a Han Chinese population.

METHODS

We genotyped six polymorphic markers in PHF11 and five polymorphic markers in DPP10 in a Han Chinese case-control cohort consisting of 408 asthma patients and 288 unrelated disease-free controls recruited from the Northern region of China. We analyzed the association between these markers and asthma as well as a number of intermediate, asthma-related traits. Linkage disequilibrium and haplotype patterns were also evaluated.

RESULTS

Significant associations were identified between two makers in PHF11 (rs1046295 and rs16659) and asthma susceptibility (odds ratio, OR = 1.32, 95% con fidence interval, CI = 1.06-1.65, p = 0.0096, for rs1046295, and OR = 1.41, 95% CI = 1.12-1.75, p = 0.0026, for rs16659). A strong association was observed between an SNP in DPP10 (rs10208402) and log(e)-transformed total IgE (p = 0.0003) and the percentage of peripheral blood eosinophils (p = 0.0023). A weak association between rs1430090 in DPP10 and forced expiratory volume in 1 s was also observed (p = 0.048). Haplotype analysis revealed two protective haplotypes in PHF11 against asthma.

CONCLUSION

The results provide supporting evidence for genetic variants in PHF11 and DPP10 genes underlying asthma susceptibility and asthma-related quantitative traits in a Han Chinese population.

Mapping complex disease traits with global gene expression

Variation in gene expression is an important mechanism underlying susceptibility to complex disease. The simultaneous genome-wide assay of gene expression and genetic variation allows the mapping of the genetic factors that underpin individual differences in quantitative levels of expression (expression QTLs; eQTLs). The availability of systematically generated eQTL information could provide immediate insight into a biological basis for disease associations identified through genome-wide association (GWA) studies, and can help to identify networks of genes involved in disease pathogenesis. Although there are limitations to current eQTL maps, understanding of disease will be enhanced with novel technologies and international efforts that extend to a wide range of new samples and tissues.

Genome-wide scan on total serum IgE levels identifies FCER1A as novel susceptibility locus

High levels of serum IgE are considered markers of parasite and helminth exposure. In addition, they are associated with allergic disorders, play a key role in anti-tumoral defence, and are crucial mediators of autoimmune diseases. Total IgE is a strongly heritable trait. In a genome-wide association study (GWAS), we tested 353,569 SNPs for association with serum IgE levels in 1,530 individuals from the population-based KORA S3/F3 study. Replication was performed in four independent population-based study samples (total n = 9,769 individuals). Functional variants in the gene encoding the alpha chain of the high affinity receptor for IgE (FCER1A) on chromosome 1q23 (rs2251746 and rs2427837) were strongly associated with total IgE levels in all cohorts with P values of 1.85 x 10(-20) and 7.08 x 10(-19) in a combined analysis, and in a post-hoc analysis showed additional associations with allergic sensitization (P = 7.78 x 10(-4) and P = 1.95 x 10(-3)). The "top" SNP significantly influenced the cell surface expression of FCER1A on basophils, and genome-wide expression profiles indicated an interesting novel regulatory mechanism of FCER1A expression via GATA-2. Polymorphisms within the RAD50 gene on chromosome 5q31 were consistently associated with IgE levels (P values 6.28 x 10(-7)-4.46 x 10(-8)) and increased the risk for atopic eczema and asthma. Furthermore, STAT6 was confirmed as susceptibility locus modulating IgE levels. In this first GWAS on total IgE FCER1A was identified and replicated as new susceptibility locus at which common genetic variation influences serum IgE levels. In addition, variants within the RAD50 gene might represent additional factors within cytokine gene cluster on chromosome 5q31, emphasizing the need for further investigations in this intriguing region. Our data furthermore confirm association of STAT6 variation with serum IgE levels.

Is eczema really on the increase worldwide?

BACKGROUND

It is unclear whether eczema prevalence is truly increasing worldwide.

OBJECTIVE

We sought to investigate worldwide secular trends in childhood eczema.

METHODS

Children (n = 302,159) aged 13 to 14 years in 105 centers from 55 countries and children aged 6 to 7 years (n = 187,943) in 64 centers from 35 countries were surveyed from the same study centers taking part in Phase One and Three of the International Study of Asthma and Allergies in Childhood by using identical validated and translated questionnaires. Eczema was defined as an itchy, relapsing, flexural skin rash in the last 12 months, and it was termed severe eczema when it was associated with 1 or more disturbed nights per week.

RESULTS

Annual prevalence changes in relation to average prevalence across Phase One and Three were generally small and differed in direction according to the age of the participants and world region. For children 13 to 14 years old, eczema symptom prevalence decreased in some previously high-prevalence centers from the developed world, such as the United Kingdom and New Zealand, whereas centers with previously high prevalence rates from developing countries continued to increase. In the children 6 to 7 years old, most centers showed an increase in current eczema symptoms. Similar patterns to these were present for severe eczema at both ages.

CONCLUSION

The epidemic of eczema seems to be leveling or decreasing in some countries with previously high prevalence rates. The picture elsewhere is mixed, with many formerly low-prevalence developing countries experiencing substantial increases, especially in the younger age group.

The immunogenetics of asthma and eczema: a new focus on the epithelium

Asthma and eczema (atopic dermatitis) are the most common chronic diseases of childhood. These diseases are characterized by the production of high levels of immunoglobulin E in response to common allergens. Their development depends on both genetic and environmental factors. Over the past few years, several genes and genetic loci that are associated with increased susceptibility to asthma and atopic dermatitis have been described. Many of these genes are expressed in the mucosa and epidermis, indicating that events at epithelial-cell surfaces might be driving disease processes. This review describes the mechanisms of innate epithelial immunity and the role of microbial factors in providing protection from disease development. Understanding events at the epithelial-cell surface might provide new insights for the development of new treatments for inflammatory epithelial disease.

A new gene for asthma: would you ADAM and Eve it?

Recently, a novel gene was reported to underlie asthma. Linkage to the short arm of chromosome 20 in a genome screen was followed by positive tests of association that centre on the gene for a membrane-anchored zinc-dependent metalloproteinase known as ADAM33. The domain structure of the ADAM33 protein gives capabilities of proteolysis, adhesion, cell fusion and intracellular signalling. Although its function is at present unknown, these potential actions of ADAM33 provide many possibilities for further research.

Genetics and genomics of asthma and allergic diseases

Asthma and eczema (atopic dermatitis) are characterized by a number of unexplained phenomena: the familial aggregation of disease, the initiation of disease by apparently trivial exposure to allergens, the preferential transmission of disease from affected mothers and the large increase in prevalence of disease in Westernized societies in the last century. A number of genes and chromosomal regions have been identified that consistently show linkage to asthma and its related phenotypes. Known loci modify the strength of the atopic response, nonspecific inflammation, the ability to respond to particular allergens and nonspecific airway reactivity. Eczema has been shown to be due to a different set of genetic loci that are shared with other skin diseases such as psoriasis and leprosy. Genetic and genomic studies both provide evidence that epithelial surfaces are active in the induction of allergic disease.

Allergy to dermatophagoides in a group of Spanish gypsies: genetic restrictions

BACKGROUND

Spanish gypsies have traditionally lived as nomads, a reason why few epidemiological studies were done in this ethnic group. However, the high prevalence of asthmatic diseases demonstrated in a population residing in the North of Spain induces us to analyse whether it was due to the influence of genetic loci previously implicated in other population studies as causing the disorders.

METHODS

DRB1* and DQB1* HLA class II, TCR-Valpha8.1, FcepsilonRI-beta Rsa I exon 7 and intron 2, TNF-beta (LTalpha-Nco I) and CD14, were tested for association with asthma and atopy by multiple regression analysis, in 5 families comprising 87 individuals.

RESULTS

Significant associations were found with DQB1*02 (p = 0.02) and DQB1*0301 (p = 0.008) and elevated levels of total serum IgE. A negative association (p = 0.02) was found between total serum IgE and DRB1*14. FcepsilonRI-beta Rsa I-In2 allele 1 was associated with high levels of total serum IgE (p = 0.04). Levels of Der p 1 IgE antibodies were negatively associated with DRB1*11-DQB1*0301 (p = 0.007), and positively with TCR Valpha-8 allele 1 (p = 0.04) and with FcepsilonRI-beta Rsa I-In2 allele 1 (p = 0.009).

CONCLUSIONS

Our results do not show any association between asthma and the genetic loci studied although they do suggest the existence of multiple genetic influences on the allergic response in these families.

Segregation analysis of the specific response to allergens: a recessive major gene controls the specific IgE response to Timothy grass pollen

Segregation analysis of the specific response to allergens (SRA) was performed in a sample of 234 randomly selected Australian families using the regressive models. Various SRA phenotypes were considered using broad and narrow definitions of these phenotypes, according to the type of test used, skin test or RAST test, and the specificity of the response to allergen. Strong evidence for familial dependencies among blood relatives was shown for most SRA phenotypes, especially when using a broad definition. There was no evidence for a Mendelian factor accounting for the familial transmission of these broadest phenotypes, which may involve multiple factors preventing the clear detection of a major effect with Mendelian transmission. However, segregation of a Mendelian recessive major gene was detected for one SRA sub-phenotype, the IgE response to a single allergen, Timothy grass pollen, measured by the RAST test. Identification of a specific SRA phenotype controlled by a major gene may have important implications for further linkage studies.

Indication of linkage of serum IgE levels to the interleukin-4 gene and exclusion of the contribution of the (-590 C to T) interleukin-4 promoter polymorphism to IgE variation

Previous segregation analysis of a sample of 234 randomly selected Australian families showed evidence for a recessive major gene controlling serum immunoglobulin E (IgE) levels independently of the specific response to allergens (SRA). Since linkage has been recently reported between serum IgE levels and the 5q candidate region spanning the interleukin-4 (IL-4) gene, we investigated whether the recessive major gene detected by segregation analysis was linked to the IL-4 region and whether polymorphisms within the IL-4 gene were associated with IgE levels. Both sib-pair method and combined segregation and linkage analysis using the regressive models were applied to our data. Whereas there was no evidence of linkage of total IgE levels to the IL-4 region, an indication of linkage (P values ranging between 0.01 and 0.03) was found between IgE levels adjusted for SRA and two IL-4 polymorphisms: one dinucleotide repeat in intron 2 of the IL-4 gene and a single nucleotide (-590 C to T) polymorphism in the IL-4 promoter. However, the putative IL-4 linked gene did not appear to be in linkage disequilibrium with either of these two polymorphisms. A contribution of the IL-4 promoter polymorphism, presumed to be a potential functional variant influencing IgE variation, was also excluded.

The alliance of genes and environment in asthma and allergy

The diseases of asthma, eczema and hay fever are typified by reactions to common allergens, which are mediated by immunoglobulin E. These allergic diseases are increasing in prevalence, and are now a major source of disability throughout the developed world. They are the result of complex interactions between largely unknown genetic and environmental mechanisms. The identification of the environmental factors offers the real possibility of prevention of disease, and unravelling the genetics of allergic illnesses is likely to change their classification and treatment. Early life seems particularly important, when the initiation of allergic disease may result from genetic and environmental modification of the immune interaction between mother and child.

Detection of a recessive major gene for high IgE levels acting independently of specific response to allergens

The genetic control of the total IgE, the immunoglobulins E involved in allergy, remains still unclear. Although high IgE levels were found to be determined by a recessive major gene in several studies, other modes of inheritance were also reported. Moreover, at least two different genetic mechanisms controlling the IgE regulation have been suggested: one involved in the specific IgE response and the other one in the nonspecific response. To better understand the genetic mechanisms controlling IgE variation, we performed segregation analysis of IgE levels by ignoring or taking into account the specific response to allergens (SRA). Analyses were conducted using the class D regressive model, in a sample of 234 Australian nuclear families randomly selected during the winter months, when IgE levels are the lowest (basal). SRA, when included as a covariate in the model, was defined by one of the three following criteria: (1) raised specific IgE level for one or more allergens, (2) positive skin test for one or more allergens, and (3) at least one of the (1) or (2) criteria. When the presence of SRA is ignored, the familial transmission of total IgE level is compatible with the segregation of a recessive major gene and residual familial correlations. When the presence of SRA is accounted for in the analysis, whether defined by criteria (1), (2), or (3), there is still evidence for a recessive major gene controlling IgE levels but residual familial correlations are no longer significant. In addition, no interaction between this major gene and SRA is shown here. Our results suggest that this gene, which accounts for 28% of the variation of the trait, may be involved in the control of basal IgE production, independently of specific response to allergens.