Gene mapping and functional annotation of GWAS of oral ulcers using FUMA software

Xiaoye Jin,Yijie Wang,Xingru Zhang,Chuanliang Chen,Wenqing Zhang,Hongdan Wang

doi:10.1038/s41598-020-68976-2

Abstract

Oral ulcers not only influence the physical health of patients, but they also interfere with their quality of life. However, the exact etiology of oral ulcers is not clear. To explore the roles of genetic factors in oral ulcers, a genome-wide association study of the condition in European individuals was re-evaluated by the FUMA v1.3.5e online tool. A total of 380 independent significant single nucleotide polymorphisms (SNPs) and 89 lead SNPs were identified in 34 genomic risk loci. Out of these identified genomic risk loci, 280 possible causal genes were pinpointed by positional mapping and expression quantitative trait locus mapping. Among these genes, 216 novel genes were identified. Furthermore, some genomic loci were mapped to a single gene. Functional annotation of these prioritized genes revealed that the immune response pathway was implicated in the onset of oral ulcers. Overall, our findings revealed novel possible causal genes and demonstrated that the immune response has a crucial role in the occurrence of oral ulcers.

Highlights

Oral ulcers influence the physical health of patients, but they interfere with their quality of life
A total of 380 independent significant single nucleotide polymorphisms (SNPs) and 89 lead SNPs were identified from GWAS of oral ulcers by FUMA (Supplementary Tables 3, 4)
Dudding et al conducted GWAS of oral ulcers based on the UK Biobank Project, and found 97 independent lead variants[4]

Summary

Introduction

Oral ulcers influence the physical health of patients, but they interfere with their quality of life. To explore the roles of genetic factors in oral ulcers, a genome-wide association study of the condition in European individuals was re-evaluated by the FUMA v1.3.5e online tool. Some genomic loci were mapped to a single gene Functional annotation of these prioritized genes revealed that the immune response pathway was implicated in the onset of oral ulcers. Wu et al conducted integration analyses of GWAS results and expression quantitative trait locus (eQTL) data for schizophrenia They found that some pathways could provide novel insights into the genetic architecture of schizophrenia[11]. Posthuma and colleagues re-analysed the GWAS results for Crohn’s disease, schizophrenia and body mass index by FUMA They found that FUMA validated known candidate genes in these traits, it identified some additional putative causal genes by eQTL mapping and chromatin interaction mapping[18]. FUMA could undertake robust and reliable post-GAWS analyses and provide valuable clues for understanding the genetic mechanism of traits/diseases

Methods

Results

Conclusion