Dataset Information

Genome-Wide Association Study of Korean Asthmatics: A Comparison With UK Asthmatics.

ABSTRACT:

Purpose

Although genome-wide association studies (GWASs) represent the most powerful approach for identifying genes that influence asthma, to date, no studies have established genetic susceptibility to asthma in the Korean population. This study aimed to identify genetic variants associated with adult Korean asthmatics and compare them with the significant single nucleotide polymorphisms (SNPs) of UK asthmatics from the UK Biobank.

Methods

Patients were defined as having asthma if they were diagnosed by a doctor or taking medications for asthma. Controls were defined as individuals without asthma or chronic obstructive pulmonary disease. We performed quality control, genotype imputation, GWAS, and PrediXcan analyses. In the GWAS, a P value of < 5 × 10^-8 was considered significant. We compared significant SNPs between Korean and UK patients with asthma.

Results

A total of 1,386 asthmatic patients and 5,205 controls were analyzed. The SNP rs1770, located near the human leukocyte antigen (HLA)-DQB1, was the most significant SNP (P = 4.5 × 10^-10). In comparison with 24 SNPs in a GWAS of UK asthmatics, six SNPs were significant with the same odds ratio (OR) direction, including signals related to type 2 inflammation (e.g., IL1RL1, TSLP, and GATA3) and mucus plugging (e.g., MUC5AC). HLA-DQA1 showed an opposite OR direction. The HLA-DQB1 gene demonstrated significantly imputed mRNA expression in the lung tissue and whole blood.

Conclusions

The SNP rs1770 of HLA-DQB1 was the most significant in Korean asthmatics. Similarities and discrepancies were found in the genetic variants between Korean and UK asthmatics. GWAS of Korean asthmatics should be replicated and compared with those of GWAS of other ethnicities.

SUBMITTER: An J

PROVIDER: S-EPMC8255356 | biostudies-literature | 2021 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genome-Wide Association Study of Korean Asthmatics: A Comparison With UK Asthmatics.

An Jin J Do Ah Ra AR Kang Hae Yeon HY Kim Woo Jin WJ Lee Sanghun S Lee Ji Hyang JH Song Woo Jung WJ Kwon Hyouk Soo HS Cho You Sook YS Moon Hee Bom HB Hu Sile S Adcock Ian M IM Chung Kian Fan KF Won Sungho S Kim Tae Bum TB

Allergy, asthma & immunology research 20210701 4

<h4>Purpose</h4>Although genome-wide association studies (GWASs) represent the most powerful approach for identifying genes that influence asthma, to date, no studies have established genetic susceptibility to asthma in the Korean population. This study aimed to identify genetic variants associated with adult Korean asthmatics and compare them with the significant single nucleotide polymorphisms (SNPs) of UK asthmatics from the UK Biobank.<h4>Methods</h4>Patients were defined as having asthma if ...[more]

PMID: 34212547

Similar Datasets

Project description:BackgroundAnalyses of the hereditary propensity to dermatophytosis have revealed several proven genetic relationships. They include CARD9 deficiency, HLA-DR4 and HLA-DR8 type and genes encoding interleukin-22, defensin 2 and 4, and genetic defects in dectin-1, which increased the prevalence of dermatophytosis in families and were involved in the inheritance of susceptibility in their members.MethodsTo further investigate the genetic basis of dermatophytosis, we performed a genome-wide association study (GWAS) of the UK Biobank cohort. To identify cases of dermatophytosis, we used ICD10 code B35, which covers Tinea barbae, Tinea capitis, Tinea unguium, Tinea manuum, Tinea pedis, Tinea corporis, Tinea imbricata, Tinea cruris, other dermatophytoses and dermatophytosis, unspecified. Data processing was performed on Minerva, a Linux mainframe with Centos 7.6, at the Icahn School of Medicine at Mount Sinai. We used PLINK, a whole-genome association analysis toolset, to analyse the UKB chromosome files and the UK Biobank Data Parser (ukbb parser), a python-based package that allows easy interfacing with the large UK Biobank dataset. We used LocusZoom for the Manhattan and q-q plots. Other statistical analyses were done with R and SPSS 25.ResultsGenome-wide association study (GWAS) and meta-analysis association statistics highlighted one susceptibility locus, Tubulointerstitial Nephritis Antigen (TINAG), with genome-wide significance for dermatophytosis. The top SNP was rs16885197, a missense variant within TINAG, position chr6:54308557, alleles A > G, minor allele frequency (MAF) 0.014. Multivariate logistic regression indicated that the minor G allele increased odds ratio of dermatophytosis by 7.8. Carrying two G alleles raised dermatophytosis odds ratio by a factor of 14.ConclusionMore research into genetic and other predisposing factors for dermatophytosis is critical because of the implications for prophylaxis and therapy. It might be possible to prevent infection and recurrence by identifying people who are vulnerable to chronic dermatophytosis. Identifying high-risk families would enable their members to be educated about the dangers of fungal diseases. New therapeutic techniques to target altered hormonal and immune response pathways might be created. TINAG is a prospective target that should be investigated, based on the findings of this article.

Project description:Chronic pain is highly prevalent worldwide and represents a significant socioeconomic and public health burden. Several aspects of chronic pain, for example back pain and a severity-related phenotype 'chronic pain grade', have been shown previously to be complex heritable traits with a polygenic component. Additional pain-related phenotypes capturing aspects of an individual's overall sensitivity to experiencing and reporting chronic pain have also been suggested as a focus for investigation. We made use of a measure of the number of sites of chronic pain in individuals within the UK general population. This measure, termed Multisite Chronic Pain (MCP), is a complex trait and its genetic architecture has not previously been investigated. To address this, we carried out a large-scale genome-wide association study (GWAS) of MCP in ~380,000 UK Biobank participants. Our findings were consistent with MCP having a significant polygenic component, with a Single Nucleotide Polymorphism (SNP) heritability of 10.2%. In total 76 independent lead SNPs at 39 risk loci were associated with MCP. Additional gene-level association analyses identified neurogenesis, synaptic plasticity, nervous system development, cell-cycle progression and apoptosis genes as enriched for genetic association with MCP. Genetic correlations were observed between MCP and a range of psychiatric, autoimmune and anthropometric traits, including major depressive disorder (MDD), asthma and Body Mass Index (BMI). Furthermore, in Mendelian randomisation (MR) analyses a causal effect of MCP on MDD was observed. Additionally, a polygenic risk score (PRS) for MCP was found to significantly predict chronic widespread pain (pain all over the body), indicating the existence of genetic variants contributing to both of these pain phenotypes. Overall, our findings support the proposition that chronic pain involves a strong nervous system component with implications for our understanding of the physiology of chronic pain. These discoveries may also inform the future development of novel treatment approaches.

Dataset Information

Genome-Wide Association Study of Korean Asthmatics: A Comparison With UK Asthmatics.

Purpose

Methods

Results

Conclusions

Publications

Genome-Wide Association Study of Korean Asthmatics: A Comparison With UK Asthmatics.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets