scholarly journals A Genome-Wide Association Study for Hypertensive Kidney Disease in Korean Men

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 751
Author(s):  
Hye-Rim Kim ◽  
Hyun-Seok Jin ◽  
Yong-Bin Eom
Keyword(s):  
Blood Pressure ◽  
Kidney Disease ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Integrated Analysis ◽  
Eqtl Analysis ◽  
Strong Linkage Disequilibrium ◽  
Genome Wide ◽  
A Genome

Hypertension is one of the major risk factors for chronic kidney disease (CKD), and the coexistence of hypertension and CKD increases morbidity and mortality. Although many genetic factors have been identified separately for hypertension and kidney disease, studies specifically focused on hypertensive kidney disease (HKD) have been rare. Therefore, this study aimed to identify loci or genes associated with HKD. A genome-wide association study (GWAS) was conducted using two Korean cohorts, the Health Examinee (HEXA) and Korean Association REsource (KARE). Consequently, 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with HKD in the discovery and replication phases (p < 5 × 10−8, p < 0.05, respectively). We further analyzed HKD-related traits such as the estimated glomerular filtration rate (eGFR), creatinine, blood urea nitrogen (BUN), systolic blood pressure (SBP) and diastolic blood pressure (DBP) at the 14q21.2 locus, which showed a strong linkage disequilibrium (LD). Expression quantitative trait loci (eQTL) analysis was also performed to determine whether HKD-related SNPs affect gene expression changes in glomerular and arterial tissues. The results suggested that the FANCM gene may affect the development of HKD through an integrated analysis of eQTL and GWAS and was the most significantly associated candidate gene. Taken together, this study indicated that the FANCM gene is involved in the pathogenesis of HKD. Additionally, our results will be useful in prioritizing other genes for further experiments.

scholarly journals A Genome-Wide Association Study of Hypertension and Blood Pressure in African Americans

PLoS Genetics ◽  
2009 ◽  
Vol 5 (7) ◽  
pp. e1000564 ◽  
Author(s):  
Adebowale Adeyemo ◽  
Norman Gerry ◽  
Guanjie Chen ◽  
Alan Herbert ◽  
Ayo Doumatey ◽  
...  
Keyword(s):  
Blood Pressure ◽  
African Americans ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals Metabolite Genome-Wide Association Study for Indoleamine 2,3-Dioxygenase Activity Associated with Chronic Kidney Disease

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1905
Author(s):  
Hye-Rim Kim ◽  
Hyun-Seok Jin ◽  
Yong-Bin Eom
Keyword(s):  
Chronic Kidney Disease ◽  
Kidney Disease ◽  
Association Study ◽  
Genome Wide Association Study ◽  
Rare Variants ◽  
Geographic Region ◽  
Genome Wide Association ◽  
Integrated Analysis ◽  
Indoleamine 2,3 Dioxygenase ◽  
Genome Wide

Chronic kidney disease (CKD) causes progressive damage to kidney function with increased inflammation. This process contributes to complex amino acid changes. Indoleamine 2,3-dioxygenase (IDO) has been proposed as a new biomarker of CKD in previous studies. In our research, we performed a metabolite genome-wide association study (mGWAS) to identify common and rare variants associated with IDO activity in a Korean population. In addition, single-nucleotide polymorphisms (SNPs) selected through mGWAS were further analyzed for associations with the estimated glomerular filtration rate (eGFR) and CKD. A total of seven rare variants achieved the genome-wide significance threshold (p < 1 × 10−8). Among them, four genes (TNFRSF19, LOC105377444, LOC101928535, and FSTL5) associated with IDO activity showed statistically significant associations with eGFR and CKD. Most of these rare variants appeared specifically in an Asian geographic region. Furthermore, 15 common variants associated with IDO activity were detected in this study and five novel genes (RSU1, PDGFD, SNX25, LOC107984031, and UBASH3B) associated with CKD and eGFR were identified. This study discovered several loci for IDO activity via mGWAS and provided insight into the underlying mechanisms of CKD through association analysis with CKD. To the best of our knowledge, this is the first study to suggest a genetic link between IDO activity and CKD through comparative and integrated analysis.

scholarly journals A Genome-Wide Association Study of Diabetic Kidney Disease in Subjects With Type 2 Diabetes

Diabetes ◽  
2018 ◽  
Vol 67 (7) ◽  
pp. 1414-1427 ◽  
Author(s):  
Natalie R. van Zuydam ◽  
Emma Ahlqvist ◽  
Niina Sandholm ◽  
Harshal Deshmukh ◽  
N. William Rayner ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Kidney Disease ◽  
Association Study ◽  
Diabetic Kidney Disease ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Diabetic Kidney ◽  
Genome Wide ◽  
A Genome

scholarly journals Genome-wide association study identifies the PLAG1-OXR1 region on BTA14 for carcass meat yield in cattle

2019 ◽  
Vol 51 (5) ◽  
pp. 137-144 ◽  
Author(s):  
Rui Zhang ◽  
Jian Miao ◽  
Yuxin Song ◽  
Wengang Zhang ◽  
Lingyang Xu ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Carcass Traits ◽  
Coiled Coil ◽  
Genome Wide Association ◽  
Strong Linkage Disequilibrium ◽  
Meat Yield ◽  
Fatty Acid Binding ◽  
Genome Wide ◽  
A Genome

Carcass meat yield is an important carcass trait that contributes to the production efficiency and economic benefits in beef cattle. It is therefore critical to identify quantitative trait loci associated with carcass traits to enable selection. Our previous studies have identified several causal variants within the pleomorphic adenoma gene 1 ( PLAG1) and coiled-coil-helix-coiled-coil-helix domain-containing 7 ( CHCHD7) genes on BTA14 for carcass traits in Chinese Simmental. In the current study, we carried out a genome-wide association study for carcass meat yield in 472 Wagyu cattle with Bovine HD SNP array. Our results showed that 27 single nucleotide polymorphisms (SNPs) were identified for tenderloin weight (TDW), striploin weight (SPW), chuck roll weight (CRW), bicep weight (BPW), knuckle weight (KCW), and flank steak weight (FSW) in Wagyu cattle. Of these SNPs, 10 distinct SNPs were detected within the oxidation resistance 1 ( OXR1), fatty acid binding protein 5 ( FABP5), TNF receptor superfamily member 11b ( TNFRSF11B), and zinc finger CCCH-type containing 3 ( ZC3H3) genes on BTA14. Notably, three significant SNPs, BovineHD1400016738, BovineHD1400016743, and BovineHD1400016665 within OXR1, were shown strong linkage disequilibrium (r2 > 0.8) and significantly associated with CRW ( P = 1.37 × 10−8 ~ 1.94 × 10−8). Moreover, Ingenuity Pathway Analysis showed that OXR1, FABP5, and CAP1A genes were involved in a single network and FABP5 may regulate the expression of OXR1 gene via node gene, peroxisome proliferator-activated receptor gamma ( PPARG). Overall, this study suggests that OXR1 and FABP5 are candidate genes affecting carcass traits in Wagyu and the PLAG1-OXR1 region on BTA14 as a putative susceptibility locus for carcass meat yield for both Chinese Simmental and Wagyu.

scholarly journals Integration of genome-wide association study and expression quantitative trait locus mapping for identification of endometriosis-associated genes

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ya-Ching Chou ◽  
Ming-Jer Chen ◽  
Pi-Hua Chen ◽  
Ching-Wen Chang ◽  
Mu-Hsien Yu ◽  
...  
Keyword(s):  
Association Study ◽  
Quantitative Trait ◽  
Genome Wide Association Study ◽  
Chromosome 9 ◽  
Genome Wide Association ◽  
Chromosome 1 ◽  
Eqtl Analysis ◽  
Taiwanese Population ◽  
Genome Wide ◽  
A Genome

AbstractTo determine whether genetic predisposition to endometriosis varies depending on ethnicity and in association with expression quantitative trait loci (eQTL) in a Taiwanese population. We conducted a genome-wide association study (GWAS) and replicated it in 259 individuals with laparoscopy-confirmed stage III or IV endometriosis (cases) and 171 women without endometriosis (controls). Their genomic DNA was extracted from blood and evaluated by the GWAS of Taiwan Biobank Array. Novel genetic variants that predispose individuals to endometriosis were identified using GWAS and replication, including rs10739199 (P = 6.75 × 10−5) and rs2025392 (P = 8.01 × 10−5) at chromosome 9, rs1998998 (P = 6.5 × 10−6) at chromosome 14, and rs6576560 (P = 9.7 × 10−6) at chromosome 15. After imputation, strong signals were exhibited by rs10822312 (P = 1.80 × 10−7) at chromosome 10, rs58991632 (P = 1.92 × 10−6) and rs2273422 (P = 2.42 × 10−6) at chromosome 20, and rs12566078 (P = 2.5 × 10−6) at chromosome 1. We used the Genotype-Tissue Expression (GTEx) database to observe eQTL. Among these SNPs, the cis-eQTL rs13126673 of inturned planar cell polarity protein (INTU) showed significant association with INTU expression (P = 5.1 × 10–33). Moreover, the eQTL analysis was performed on endometriotic tissues from women with endometriosis. The expression of INTU in 78 endometriotic tissue of women with endometriosis is associated with rs13126673 genotype (P = 0.034). To our knowledge, this is the first GWAS to link endometriosis and eQTL in a Taiwanese population.

scholarly journals A genome-wide association study of the longitudinal course of executive functions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bernadette Wendel ◽  
Sergi Papiol ◽  
Till F. M. Andlauer ◽  
Jörg Zimmermann ◽  
Jens Wiltfang ◽  
...  
Keyword(s):  
Executive Functions ◽  
Association Study ◽  
Time Course ◽  
Genome Wide Association Study ◽  
Digit Span ◽  
Genome Wide Association ◽  
Effect Estimate ◽  
Strong Linkage Disequilibrium ◽  
Genome Wide ◽  
A Genome

AbstractExecutive functions are metacognitive capabilities that control and coordinate mental processes. In the transdiagnostic PsyCourse Study, comprising patients of the affective-to-psychotic spectrum and controls, we investigated the genetic basis of the time course of two core executive subfunctions: set-shifting (Trail Making Test, part B (TMT-B)) and updating (Verbal Digit Span backwards) in 1338 genotyped individuals. Time course was assessed with four measurement points, each 6 months apart. Compared to the initial assessment, executive performance improved across diagnostic groups. We performed a genome-wide association study to identify single nucleotide polymorphisms (SNPs) associated with performance change over time by testing for SNP-by-time interactions using linear mixed models. We identified nine genome-wide significant SNPs for TMT-B in strong linkage disequilibrium with each other on chromosome 5. These were associated with decreased performance on the continuous TMT-B score across time. Variant rs150547358 had the lowest P value = 7.2 × 10−10 with effect estimate beta = 1.16 (95% c.i.: 1.11, 1.22). Implementing data of the FOR2107 consortium (1795 individuals), we replicated these findings for the SNP rs150547358 (P value = 0.015), analyzing the difference of the two available measurement points two years apart. In the replication study, rs150547358 exhibited a similar effect estimate beta = 0.85 (95% c.i.: 0.74, 0.97). Our study demonstrates that longitudinally measured phenotypes have the potential to unmask novel associations, adding time as a dimension to the effects of genomics.

scholarly journals Evaluation of Candidate Nephropathy Susceptibility Genes in a Genome-Wide Association Study of African American Diabetic Kidney Disease

PLoS ONE ◽  
2014 ◽  
Vol 9 (2) ◽  
pp. e88273 ◽  
Author(s):  
Nicholette D. Palmer ◽  
Maggie C. Y. Ng ◽  
Pamela J. Hicks ◽  
Poorva Mudgal ◽  
Carl D. Langefeld ◽  
...  
Keyword(s):  
African American ◽  
Kidney Disease ◽  
Association Study ◽  
Diabetic Kidney Disease ◽  
Genome Wide Association Study ◽  
Susceptibility Genes ◽  
Genome Wide Association ◽  
Diabetic Kidney ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide Association Study of a Korean Population Identifies Genetic Susceptibility to Hypertension Based on Sex-Specific Differences

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1804
Author(s):  
Seong-Beom Cho ◽  
Jinhwa Jang
Keyword(s):  
Blood Pressure ◽  
Association Study ◽  
Genetic Susceptibility ◽  
Genetic Heterogeneity ◽  
Genome Wide Association Study ◽  
Enrichment Analysis ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome ◽  
Heterogeneity Analysis

Genome-wide association studies have expanded our understanding of the genetic variation of hypertension. Hypertension and blood pressure are influenced by sex-specific differences; therefore, genetic variants may have sex-specific effects on phenotype. To identify the genetic factors influencing the sex-specific differences concerning hypertension, we conducted a heterogeneity analysis of a genome-wide association study (GWAS) on 13,926 samples from a Korean population. Using the Illumina exome chip data of the population, we performed GWASs of the male and female population independently and applied a statistical test that identified heterogeneous effects of the variants between the two groups. To gain information about the biological implication of the genetic heterogeneity, we used gene set enrichment analysis with GWAS catalog and pathway gene sets. The heterogeneity analysis revealed that the rs11066015 of ACAD10 was a significant locus that had sex-specific genetic effects on the development of hypertension. The rs2074356 of HECTD4 also showed significant genetic heterogeneity in systolic blood pressure. The enrichment analysis showed significant results that are consistent with the pathophysiology of hypertension. These results indicate a sex-specific genetic susceptibility to hypertension that should be considered in future genetic studies of hypertension.

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