Association study of newly identified age-related macular degeneration susceptible loci SOD2, MBP, and C8orf42 in Han Chinese population.
Ontology highlight
ABSTRACT:
SUBMITTER: Kan M
PROVIDER: S-EPMC3986977 | biostudies-literature | 2014
REPOSITORIES: biostudies-literature
Publications
Association study of newly identified age-related macular degeneration susceptible loci SOD2, MBP, and C8orf42 in Han Chinese population.
Kan Mengyuan M Liu Fatao F Weng Xiaoling X Ye Junyi J Wang Ting T Xu Mingqing M He Lin L Liu Yun Y
Diagnostic pathology 20140325
A recent genome-wide association study has reported three newly identified susceptible loci (rs2842992 near the gene SOD2, rs1789110 near the gene MBP and rs722782 near the gene C8orf42) to be associated with the geographic atrophy subtype of age-related macular degeneration in European-descent population. We investigated the correlation between these variants and advanced age-related macular degeneration for the first time in a Han Chinese cohort; however, no evidence supports these previously ...[more]
Similar Datasets
Project description:BackgroundRecent genome-wide association studies (GWAS) have mapped several novel loci influencing blood lipid levels in Caucasians. We sought to explore whether the genetic variants at newly identified lipid-associated loci were associated with CHD susceptibility in a Chinese Han population.Methodology/principal findingsWe conducted a two-stage case-control study in a Chinese Han population. The first-stage, consisting of 1,376 CHD cases and 1,376 sex and age- frequency matched controls, examined 5 novel lipid-associated single-nucleotide polymorphisms (SNPs) identified from GWAS among Caucasians in relation to CHD risk in Chinese. We then validated significant SNPs in the second-stage, consisting of 1,269 cases and 2,745 controls. We also tested associations between SNPs within the five novel loci and blood lipid levels in 4,121 controls. We identified two novel SNPs (rs599839 in CELSR2-PSRC1-SORT1 and rs16996148 in NCAN-CILP2) that were significantly associated with reduced CHD risk in Chinese (odds ratios (95% confidence intervals) in the dominant model 0.76 (0.61-0.90; P = 0.001), 0.67 (0.57-0.77; P = 3.4×10(-8)), respectively). Multiple linear regression analyses using dominant model showed that rs599839 was significantly associated with decreased LDL levels (P = 0.022) and rs16996148 was significantly associated with increased LDL and HDL levels (P = 2.9×10(-4) and 0.001, respectively).Conclusions/significanceWe identified two novel SNPs (rs599839 and rs16996148) at newly identified lipid-associated loci that were significantly associated with CHD susceptibility in a Chinese Han population.
| S-EPMC3215720 | biostudies-literature
Project description:Facial shape differences are one of the most significant phenotypes in humans. It is affected largely by skull shape. However, research into the genetic basis of the craniofacial morphology has rarely been reported. The present study aimed to identify genetic variants influencing craniofacial morphology in northern Han Chinese through whole-exome sequencing (WES). Phenotypic data of the volunteers' faces and skulls were obtained through three-dimensional CT scan of the skull. A total of 48 phenotypes (35 facial and 13 cranial phenotypes) were used for the bioinformatics analysis. Four genetic loci were identified affecting the craniofacial shapes. The four candidate genes are RGPD3, IGSF3, SLC28A3, and USP40. Four single-nucleotide polymorphism (SNP) site mutations in RGPD3, IGSF3, and USP40 were significantly associated with the skull shape (p < 1×10-6), and three SNP site mutations in RGPD3, IGSF3, and SLC28A3 were significantly associated with the facial shape (p < 1×10-6). The rs62152530 site mutation in the RGPD3 gene may be closely associated with the nasal length, ear length, and alar width. The rs647711 site mutation in the IGSF3 gene may be closely associated with the nasal length, mandibular width, and width between the mental foramina. The rs10868138 site mutation in the SLC28A3 gene may be associated with the nasal length, alar width, width between tragus, and width between the mental foramina. The rs1048603 and rs838543 site mutations in the USP40 gene may be closely associated with the pyriform aperture width. Our findings provide useful genetic information for the determination of face morphology.
| S-EPMC6554238 | biostudies-literature
Project description:Recent investigations demonstrated that genetic factors might play an important role in sporadic Parkinson's disease (sPD). To clarify the specific loci susceptibility to sPD, we analyze the relationship between 30 candidate single nucleotide polymorphisms (SNPs) and sPD in the population of Han ancestry from Chinese mainland (HACM) by using genome-wide association study, sequenom massARRAY, DNA sequence, and biological information analysis. Results showed that the subjects carrying the T allele of rs863108 and rs28499371 exhibited a decreased risk for sPD. The subjects carrying the T allele of rs80315856 exhibited an increased risk for sPD. The A/T genotype of rs863108 and the C/T genotype of rs28499371 were a potential increased risk for sPD, and the G/T genotype of rs80315856 and T/T genotype of rs2270568 were a potential decreased risk for sPD. The minor allele frequency (MAF) of rs80315856 and rs2270568 was higher in sPD. The T allele of rs80315856 and rs2270568 might be a risk locus for sPD. Our data suggested that the alteration of these SNPs might play some roles through changing/affecting LINC01524/LOC105372666, DMRT2/SMARCA2, PLEKHN1, and FLJ23172/FNDC3B genes in the pathogenesis of sPD.
| S-EPMC7835639 | biostudies-literature
Project description:Forty-nine susceptible loci have been reported to be significantly associated with vitiligo by genome-wide association studies (GWASs) in European-derived whites. To date, some of these reported susceptibility loci have not yet been validated in the Chinese Han population. The purpose of this study was to examine whether the 16 reported susceptible loci in European-derived whites were associated with vitiligo in the Chinese Han population. Imputation was performed using our previous GWAS dataset by IMPUTE v2.2.2. The 16 imputed top single-nucleotide polymorphisms (SNPs) with suggestive signals, together with the reported SNPs, were genotyped in a total of 2581 patients and 2579 controls by the Sequenom MassARRAY system. PLINK 2.0 software was used to perform association analysis. The dbSNP database, HaploReg, and eQTL data were adopted to annotate the biological function of the SNPs. Finally, four SNPs from three loci were significantly associated with vitiligo, including rs3747517 (P = 1.29 × 10-3, OR = 0.87) in 2q24.2, rs4807000 (P = 7.78 × 10-24, OR = 0.66) and rs6510827 (P = 3.65 × 10-5, OR = 1.19) in 19p13.3, and rs4822024 (P = 6.37 × 10-10, OR = 0.67) in 22q13.2. According to the dbSNP database, rs3747517 is a missense variant of IFIH1, rs4807000 and rs6510827 are located in TICAM1, and rs4822024 is located 6 kb upstream of TEF. Further bioinformatics analysis by HaploReg and eQTL found that rs4807000, rs6510827, and rs4822024 are involved in regulating gene expression. Our study revealed the strong association of 2q24.2 (rs3747517), 19p13.3 (rs4807000, rs6510827), and 22q13.2 (rs4822024) with the risk of vitiligo in the Chinese Han population, which implicates common factors for vitiligo across different ethnicities, and helps expand the understanding of the genetic basis of this disease.
| S-EPMC7744663 | biostudies-literature
Project description:PurposeSingle nucleotide polymorphisms (SNPs) in the complement component 1 inhibitor (SERPING1) gene have been shown to be significantly associated with age-related macular degeneration (AMD) in Caucasian populations. A replication study of an association between these SNPs and AMD in a Chinese population is reported in this study.MethodsSix SNPs, including rs2511990, rs1005510, rs11546660, rs2511989, rs2511988, and rs4926 in SERPING1 were genotyped in a Han Chinese subject group using the SNaPshot method of ABI. This subject group was composed of 194 patients with choroidal neovascularization (CNV or wet) AMD, 78 patients with soft drusen, and 285 matched controls. P values of the SNPs were calculated using an additive model. Haplotype frequencies between cases and controls were compared by chi2 analysis. The haplotype analysis was performed using Haploview 4.0.ResultsNone of the six SNPs showed significant association with AMD. None of the major haplotypes were observed to be significantly associated with AMD or choroidal neovascularization AMD (CNV) after a stringent Bonferroni correction.ConclusionsWe demonstrate that SNPs in SERPING1 are not significantly associated with AMD in the mainland Han Chinese population.
| S-EPMC2803124 | biostudies-literature
Project description:A large proportion of pulmonary embolism (PE) heritability remains unexplained, particularly among the East Asian (EAS) population. Our study aims to expand the genetic architecture of PE and reveal more genetic determinants in Han Chinese. We conducted the first genome-wide association study (GWAS) of PE in Han Chinese, then performed the GWAS meta-analysis based on the discovery and replication stages. To validate the effect of the risk allele, qPCR and Western blotting experiments were used to investigate possible changes in gene expression. Mendelian randomization (MR) analysis was employed to implicate pathogenic mechanisms, and a polygenic risk score (PRS) for PE risk prediction was generated. After meta-analysis of the discovery dataset (622 cases, 8853 controls) and replication dataset (646 cases, 8810 controls), GWAS identified 3 independent loci associated with PE, including the reported loci FGG rs2066865 (p-value = 3.81 × 10-14), ABO rs582094 (p-value = 1.16 × 10-10) and newly reported locus FABP2 rs1799883 (p-value = 7.59 × 10-17). Previously reported 10 variants were successfully replicated in our cohort. Functional experiments confirmed that FABP2-A163G(rs1799883) promoted the transcription and protein expression of FABP2. Meanwhile, MR analysis revealed that high LDL-C and TC levels were associated with an increased risk of PE. Individuals with the top 10% of PRS had over a fivefold increased risk for PE compared to the general population. We identified FABP2, related to the transport of long-chain fatty acids, contributing to the risk of PE and provided more evidence for the essential role of metabolic pathways in PE development.
| S-EPMC10116678 | biostudies-literature
Project description:PurposeA nonsynonymous coding variant in the manganese superoxide dismutase (SOD2) gene (V16A, rs4880) has been implicated in neovascular age-related macular degeneration (AMD). However, the findings have been inconsistent. Two studies in Japanese populations reported an opposite direction of association of the same allele at the V16A variant, whereas one study in a Northern Irish population found no effect of the variant on the risk of developing neovascular AMD. To address these apparently contradictory reports, we validated the association in a Japanese population.MethodsIn a Japanese population, we genotyped the V16A variant in 116 neovascular AMD patients, 140 polypoidal choroidal vasculopathy (PCV) patients, and 189 control participants. This association was also tested in a population of PCV participants to avoid variable findings across studies due to underlying sample heterogeneity and because disease phenotype was not well described in previous studies. We analyzed a tagging single nucleotide polymorphism (SNP) in addition to the V16A variant to capture all common SOD2 variations verified by the HapMap project. Genotyping was conducted using TaqMan technology. Associations were tested using single-SNP and haplotype analyses as well as a meta-analysis of the published literature. Population stratification was also evaluated in our study population.ResultsWe found no detectable association of the V16A variant or any other common SOD2 variation with either neovascular AMD or PCV, as demonstrated by both single-SNP and haplotype analyses. Population structure analyses precluded stratification artifacts in our study cohort. A meta-analysis of the association between the V16A variant and neovascular AMD also failed to detect a significant association.ConclusionsWe found no evidence to support the role of any common SOD2 variations including the V16A variant in the susceptibility to neovascular AMD or PCV. Our study highlights the importance and difficulty in replicating genetic association studies of complex human diseases.
| S-EPMC2742636 | biostudies-literature
Project description:Schizophrenia (SCZ) is a highly heritable psychiatric disorder that affects approximately 1% of population around the world. However, early relevant studies did not reach clear conclusions of the genetic mechanisms of SCZ, suggesting that additional susceptibility loci that exert significant influence on SCZ are yet to be revealed. So, in order to identify novel susceptibility genes that account for the genetic risk of SCZ, we performed a systematic family-based study using whole exome sequencing (WES) in 65 Han Chinese families. The analysis of 51 SCZ trios with both unaffected parents identified 22 exonic and 1 splice-site de novo mutations (DNMs) on a total of 23 genes, and showed that 12 genes carried rare protein-altering compound heterozygous mutations in more than one trio. In addition, we identified 26 exonic or splice-site single nucleotide polymorphisms (SNPs) on 18 genes with nominal significance (P < 5 × 10-4) using a transmission disequilibrium test (TDT) in all the families. Moreover, TDT result confirmed a SCZ susceptibility locus on 3p21.1, encompassing the multigenetic region NEK4-ITIH1-ITIH3-ITIH4. Through several different strategies to predict the potential pathogenic genes in silico, we revealed 4 previous discovered susceptibility genes (TSNARE1, PBRM1, STAB1 and OLIG2) and 4 novel susceptibility loci (PSEN1, TLR5, MGAT5B and SSPO) in Han Chinese SCZ patients. In summary, we identified a list of putative candidate genes for SCZ using a family-based WES approach, thus improving our understanding of the pathology of SCZ and providing critical clues to future functional validation.
| S-EPMC7026419 | biostudies-literature
Project description:The study was designed to reveal the relationship of toll-like receptor 4 (TLR4, rs1927914 and rs1927907) polymorphisms with risk of age-related macular degeneration (AMD), as well as the adjustment of this association by some environmental and lifestyle factors in Chinese Han population.TLR4 polymorphisms were genotyped by polymerase chain reaction-restricted fragment length polymorphisms and direct sequencing method in 138 AMD patients and 146 healthy controls. Genotype distribution in the control group was checked with Hardy-Weinberg equilibrium. Association of TLR4 polymorphisms and AMD risk was evaluated by χ test and adjusted by age and sex, smoking and drinking. Odds ratio (OR) with 95% confidence interval (95% CI) was used to represent the association strength. Logistic regressive analysis was used to calculate the adjusted OR values.CC genotype of rs1927914 had significantly lower frequency in AMD patients (P = .010), indicated a negative association with AMD risk (crude: OR = 0.358, 95% CI = 0.162-0.791; adjusted: OR = 0.355, 95% CI = 0.160-0.789). C allele of rs1927914 might decrease the susceptibility of AMD (crude: OR = 0.698, 95% CI = 0.497-0.982; adjusted: OR = 0.698, 95% CI = 0.495-0.984). No significant association has been discovered between TLR4 rs1927907 polymorphism and AMD susceptibility. Strong linkage disequilibrium existed between rs1927914 and rs1927907 polymorphisms. C-C haplotype was negatively associated with AMD risk (OR = 0.242, 95% CI = 0.121-0.485; OR = 0.242, 95% CI = 0.120-0.488).CC genotype and C allele of rs1927914 were significantly associated with the decreased AMD susceptibility.
| S-EPMC6531106 | biostudies-literature
Project description:PurposeWe have previously documented that neovascular age-related macular degeneration (nAMD) and polypoidal choroidal vasculopathy (PCV) have multiple different clinical and genetic characteristics. In this study, we investigated the association of rs42524 in the alpha-2 type I collagen (COL1A2) gene, which has been identified as a risk variant for intracranial aneurysm, with nAMD and PCV in a Han Chinese population.MethodsThe study prospectively recruited 195 patients with PCV, 136 patients with nAMD, and 181 control individuals. We genotyped the rs42524 polymorphism of COL1A2 using the Multiplex SNaPshot System and direct DNA sequencing. Genotype and allele frequencies were evaluated with PLINK software.ResultsThe rs42524 polymorphism was modestly significantly associated with nAMD [minor allele: G, p(allelic)=0.04253, odds ratio=0.5285 (95% confidence interval: 0.2832-0.9866)], but not with PCV [minor allele: G, p(allelic)=0.4164, odds ratio=1.2110 (95% confidence interval: 0.7631-1.9210)]. The pvalues for the additive model were significant for nAMD but not for the dominant or recessive models. None of the models for PCV were statistically significant. The size of our sample cohort resulted in a post hoc power of more than 80% to detect associations of rs42524 with nAMD and PCV.ConclusionsThe rs42524 polymorphism is a risk allele for nAMD in a Han Chinese population. rs42524 in COL1A2 confers different levels of susceptibility to nAMD and PCV.
| S-EPMC3398488 | biostudies-literature