scholarly journals Gene-Based Meta-Analysis of Genome-Wide Association Study Data Identifies Independent Single-Nucleotide Polymorphisms inANXA6as Being Associated With Systemic Lupus Erythematosus in Asian Populations

2015 ◽  
Vol 67 (11) ◽  
pp. 2966-2977 ◽  
Author(s):  
Jing Zhang ◽  
Lu Zhang ◽  
Yan Zhang ◽  
Jing Yang ◽  
Mengbiao Guo ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Study Data ◽  
Genome Wide Association ◽  
Nucleotide Polymorphisms ◽  
Systemic Lupus ◽  
Single Nucleotide ◽  
Asian Populations ◽  
Genome Wide

scholarly journals Meta-analysis of Genome-wide Association Study Identifies FBN2 as a Novel Locus Associated With Systemic Lupus Erythematosus in Thai Population

2020 ◽  
Author(s):  
Pattarin Tangtanatakul ◽  
Chisanu Thumarat ◽  
Nusara Satproedprai ◽  
Punna Kunhapan ◽  
Tassamonwan Chaiyasung ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Chinese Population ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Disease Risk ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Systemic Lupus ◽  
Thai Population ◽  
Genome Wide

Abstract Background: Differences in the expression of variants across ethnic groups in the Systemic Lupus Erythematosus (SLE) patients have been well documented. However, the genetic architecture in the Thai population has not been thoroughly examined. In this study, we carried out genome-wide association study (GWAS) in Thai population.Methods: Two GWAS cohorts were independently collected and genotyped: discovery dataset (487 SLE cases and 1,606 healthy controls) and replication dataset (405 SLE cases and 1,590 unrelated-disease controls). Data were imputed to the density of the 1,000 Genomes Project Phase 3. Association studies were performed based on different genetic models, and pathway enrichment analysis was further examined. In addition, the performance of disease risk estimation for individuals in Thai GWAS was assessed based on the polygenic risk score (PRS) model trained by other Asian populations.Results: Previous findings on SLE susceptible alleles were well replicated in the two GWAS. The SNPs on HLA-class II (rs9270970, A>G, OR=1.82, p-value = 3.61E-26), STAT4 (rs7582694, C>G, OR=1.57, p-value = 8.21E-16), GTF2I (rs73366469, A>G, OR=1.73, p-value = 2.42E-11) and FAM167A-BLK allele (rs13277113, A>G, OR=0.68, p-value = 1.58E-09) were also significantly associated with SLE in Thai population. Meta-analysis of the two GWAS identified a novel locus at the FBN2 that was specifically associated with SLE in the Thai population (rs74989671, A>G, OR=1.54, p-value = 1.61E-08). Functional analysis showed that rs74989671 resided in a peak of H3K36me3 derived from CD14+ monocytes and H3K4me1 from T-lymphocytes. In addition, we showed that the PRS model trained from the Chinese population could be applied in individuals of Thai ancestry, with the area under the receiver-operator curve (AUC) achieving 0.76 for this predictor.Conclusions: We demonstrated the genetic architecture of SLE in the Thai population and identified a novel locus associated with SLE. Also, our study suggested a potential use of the PRS model from Chinese population to estimate the disease risk for individuals of Thai ancestry.

scholarly journals Meta-analysis of genome-wide association study identifies FBN2 as a novel locus associated with Systemic Lupus Erythematosus in Thai population

2020 ◽  
Author(s):  
Pattarin Tangtanatakul ◽  
Chisanu Thumarat ◽  
Nusara Satproedprai ◽  
Punna Kunhapan ◽  
Tassamonwan Chaiyasung ◽  
...  
Keyword(s):  
Lupus Erythematosus ◽  
Chinese Population ◽  
Genetic Architecture ◽  
Genome Wide Association Study ◽  
Disease Risk ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Systemic Lupus ◽  
Thai Population ◽  
Genome Wide

Abstract Background: Differences in the expression of variants across ethnic groups in the Systemic Lupus Erythematosus (SLE) patients have been well documented. However, the genetic architecture in the Thai population has not been thoroughly examined. In this study, we carried out genome-wide association study (GWAS) in the Thai population. Methods: Two GWAS cohorts were independently collected and genotyped: discovery dataset (487 SLE cases and 1,606 healthy controls) and replication dataset (405 SLE cases and 1,590 unrelated-disease controls). Data were imputed to the density of the 1,000 Genomes Project Phase 3. Association studies were performed based on different genetic models, and pathway enrichment analysis was further examined. In addition, the performance of disease risk estimation for individuals in Thai GWAS was assessed based on the polygenic risk score (PRS) model trained by other Asian populations. Results: Previous findings on SLE susceptible alleles were well replicated in the two GWAS. The SNPs on HLA-class II (rs9270970, A>G, OR=1.82, p-value = 3.61E-26), STAT4 (rs7582694, C>G, OR=1.57, p-value = 8.21E-16), GTF2I (rs73366469, A>G, OR=1.73, p-value = 2.42E-11) and FAM167A-BLK allele (rs13277113, A>G, OR=0.68, p-value = 1.58E-09) were significantly associated with SLE in Thai population. Meta-analysis of the two GWAS identified a novel locus at the FBN2 that was specifically associated with SLE in the Thai population (rs74989671, A>G, OR=1.54, p-value = 1.61E-08). Functional analysis showed that rs74989671 resided in a peak of H3K36me3 derived from CD14+ monocytes and H3K4me1 from T-lymphocytes. In addition, we showed that the PRS model trained from the Chinese population could be applied in individuals of Thai ancestry, with the area under the receiver-operator curve (AUC) achieving 0.76 for this predictor. Conclusions: We demonstrated the genetic architecture of SLE in the Thai population and identified a novel locus associated with SLE. Also, our study suggested a potential use of the PRS model from the Chinese population to estimate the disease risk for individuals of Thai ancestry.

scholarly journals Genome-wide association study meta-analysis identifies five new loci for systemic lupus erythematosus

2018 ◽  
Vol 20 (1) ◽  
Author(s):  
Antonio Julià ◽  
Francisco Javier López-Longo ◽  
José J. Pérez Venegas ◽  
Silvia Bonàs-Guarch ◽  
Àlex Olivé ◽  
...  
Keyword(s):  
Systemic Lupus Erythematosus ◽  
Association Study ◽  
Lupus Erythematosus ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
Genome Wide Association ◽  
Systemic Lupus ◽  
Genome Wide
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