Asthma, hay fever (or allergic rhinitis) and eczema (or atopic
dermatitis) often coexist in the same individuals1, partly because of a shared genetic origin2–4. To
identify shared risk variants, we performed a genome-wide association study
(GWAS, n=360,838) of a broad allergic disease phenotype that
considers the presence of any one of these three diseases. We identified 136
independent risk variants (P<3x10-8),
including 73 not previously reported, which implicate 132 nearby genes in
allergic disease pathophysiology. Disease-specific effects were detected for
only six variants, confirming that most represent shared risk factors.
Tissue-specific heritability and biological process enrichment analyses suggest
that shared risk variants influence lymphocyte-mediated immunity. Six target
genes provide an opportunity for drug repositioning, while for 36 genes CpG
methylation was found to influence transcription independently of genetic
effects. Asthma, hay fever and eczema partly coexist because they share many
genetic risk variants that dysregulate the expression of immune-related
genes.
Vitamin D deficiency is a candidate risk factor for a range of adverse health outcomes. In a genome-wide association study of 25 hydroxyvitamin D (25OHD) concentration in 417,580 Europeans we identify 143 independent loci in 112 1-Mb regions, providing insights into the physiology of vitamin D and implicating genes involved in lipid and lipoprotein metabolism, dermal tissue properties, and the sulphonation and glucuronidation of 25OHD. Mendelian randomization models find no robust evidence that 25OHD concentration has causal effects on candidate phenotypes (e.g. BMI, psychiatric disorders), but many phenotypes have (direct or indirect) causal effects on 25OHD concentration, clarifying the epidemiological relationship between 25OHD status and the health outcomes examined in this study.
Twenty-five genome-wide association studies (GWAS) of asthma were published between 2007 and 2016, the largest with a sample size of 157242 individuals. Across these studies, 39 genetic variants in low linkage disequilibrium (LD) with each other were reported to associate with disease risk at a significance threshold of P<5 × 10−8, including 31 in populations of European ancestry. Results from analyses of the UK Biobank data (n=380 503) indicate that at least 28 of the 31 associations reported in Europeans represent true-positive findings, collectively explaining 2.5% of the variation in disease liability (median of 0.06% per variant). We identified 49 transcripts as likely target genes of the published asthma risk variants, mostly based on LD with expression quantitative trait loci (eQTL). Of these genes, 16 were previously implicated in disease pathophysiology by functional studies, including TSLP, TNFSF4, ADORA1, CHIT1 and USF1. In contrast, at present, there is limited or no functional evidence directly implicating the remaining 33 likely target genes in asthma pathophysiology. Some of these genes have a known function that is relevant to allergic disease, including F11R, CD247, PGAP3, AAGAB, CAMK4 and PEX14, and so could be prioritized for functional follow-up. We conclude by highlighting three areas of research that are essential to help translate GWAS findings into clinical research or practice, namely validation of target gene predictions, understanding target gene function and their role in disease pathophysiology and genomics-guided prioritization of targets for drug development.
Background: Polygenic scores (PGSs), which assess the genetic risk of individuals for a disease, are calculated as a weighted count of risk alleles identified in genome-wide association studies (GWASs). PGS methods differ in which DNA variants are included and the weights assigned
AbstractVitamin D deficiency is a candidate risk factor for a range of adverse health outcomes. In a genome-wide association study of 25 hydroxyvitamin D (25OHD) concentration in 417,580 Europeans we identified 143 independent loci in 112 1-Mb regions providing new insights into the physiology of vitamin D and implicating genes involved in (a) lipid and lipoprotein metabolism, (b) dermal tissue properties, and (c) the sulphonation and glucuronidation of 25OHD. Mendelian randomization models found no robust evidence that 25OHD concentration had causal effects on candidate phenotypes (e.g. BMI, psychiatric disorders), but many phenotypes had (direct or indirect) causal effects on 25OHD concentration, clarifying the relationship between 25OHD status and health.
Background
Hundreds of genetic variants are thought to contribute to variation
in asthma risk by modulating gene expression. Methods that increase the
power of genome wide association studies (GWAS) to identify risk-associated
variants are needed.
Objective
To develop a method that aggregates the evidence for association with
disease risk across expression quantitative trait loci (eQTLs) of a gene and
use this approach to identify asthma risk genes.
Methods
We developed a gene-based test and software package called EUGENE
that (1) is applicable to GWAS summary statistics; (2) considers both
cis- and trans-eQTLs; (3) incorporates
eQTLs identified in different tissues; and (4) uses simulations to account
for multiple testing. We applied this approach to two published asthma GWAS
(combined N=46,044) and used mouse studies to provide initial
functional insights into two genes with novel genetic associations.
Results
We tested the association between asthma and 17,190 genes which were
found to have cis-and/or trans-eQTLs
across 16 published eQTL studies. At an empirical false discovery rate of
5%, 48 genes were associated with asthma risk. Of these, for 37 the
association was driven by eQTLs located in established risk loci for
allergic disease, including six genes not previously implicated in disease
aetiology (eg. LIMS1, TINF2 and
SAFB). The remaining 11 significant genes represent
potential novel genetic associations with asthma. The association with four
of these replicated in an independent GWAS: B4GALT3,
USMG5, P2RY13 and
P2RY14, which are genes involved in nucleotide
synthesis or nucleotide-dependent cell activation. In mouse studies, P2ry13
and P2ry14 – purinergic receptors activated by ADP and UDP-sugars,
respectively – were up-regulated after allergen challenge, notably
in airway epithelial cells, eosinophils and neutrophils. Intranasal exposure
with the receptor agonists induced the release of IL-33 and subsequent
eosinophil infiltration into the lungs.
Conclusion
We identified novel associations between asthma and eQTLs for four
genes related to nucleotide synthesis/signaling, and demonstrate the power
of gene-based analyses of GWAS.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.