scholarly journals PGG.Han: the Han Chinese genome database and analysis platform

2019 ◽  
Vol 48 (D1) ◽  
pp. D971-D976 ◽  
Author(s):  
Yang Gao ◽  
Chao Zhang ◽  
Liyun Yuan ◽  
YunChao Ling ◽  
Xiaoji Wang ◽  
...  
Keyword(s):  
Chinese Population ◽  
Association Studies ◽  
Natural Populations ◽  
Han Chinese ◽  
Genotype Imputation ◽  
Specific Reference ◽  
Single Nucleotide Variants ◽  
Genome Database ◽  
Han Chinese Population ◽  
Genome Wide

Abstract As the largest ethnic group in the world, the Han Chinese population is nonetheless underrepresented in global efforts to catalogue the genomic variability of natural populations. Here, we developed the PGG.Han, a population genome database to serve as the central repository for the genomic data of the Han Chinese Genome Initiative (Phase I). In its current version, the PGG.Han archives whole-genome sequences or high-density genome-wide single-nucleotide variants (SNVs) of 114 783 Han Chinese individuals (a.k.a. the Han100K), representing geographical sub-populations covering 33 of the 34 administrative divisions of China, as well as Singapore. The PGG.Han provides: (i) an interactive interface for visualization of the fine-scale genetic structure of the Han Chinese population; (ii) genome-wide allele frequencies of hierarchical sub-populations; (iii) ancestry inference for individual samples and controlling population stratification based on nested ancestry informative markers (AIMs) panels; (iv) population-structure-aware shared control data for genotype-phenotype association studies (e.g. GWASs) and (v) a Han-Chinese-specific reference panel for genotype imputation. Computational tools are implemented into the PGG.Han, and an online user-friendly interface is provided for data analysis and results visualization. The PGG.Han database is freely accessible via http://www.pgghan.org or https://www.hanchinesegenomes.org.

Association ofNKAPL,TSPAN18, andMPC2gene variants with schizophrenia based on new data and a meta-analysis in Han Chinese

2016 ◽  
Vol 29 (2) ◽  
pp. 87-94 ◽  
Author(s):  
Zhen Li ◽  
Tingting Shen ◽  
Ran Xin ◽  
Baoyun Liang ◽  
Juan Jiang ◽  
...  
Keyword(s):  
Chinese Population ◽  
Association Studies ◽  
Meta Analysis ◽  
Han Chinese ◽  
Genome Wide Association Studies ◽  
Han Chinese Population ◽  
Genotype Frequencies ◽  
Genome Wide ◽  
Significant Difference ◽  
High Heritability

BackgroundSchizophrenia (SZ) is suggested to be a complex polygenetic disorder with high heritability. Genome-wide association studies have found that the rs1635, rs11038167, and rs10489202 polymorphisms are associated with SZ in Han Chinese. However, results of validation studies are inconsistent. This study aimed to test the association between theNKAPLrs1635,TSPAN18rs11038167, andMPC2rs10489202 polymorphisms and SZ in a Chinese population.MethodsThis study contained 700 unrelated SZ patients (300 Zhuang and 400 Han) and 700 gender- and age-matched controls (300 Zhuang and 400 Han). The polymorphisms inTSPAN18(rs11038167),NKAPL(rs1635), andMPC2(rs10489202) were genotyped using the Sequenom MassARRAY method. Statistical analyses were performed with PLINK program and SPSS l6.0 for Windows. STATA11.1 was used for meta-analysis.ResultsNo statistically significant difference was found in different allele and genotype frequencies of rs1635, rs11038167, and rs10489202 between SZ cases and controls of Zhuang and Han ethnicities and the total samples (allp>0.05). Further meta-analysis suggested that single-nucleotide polymorphism rs10489202 was significantly associated with SZ in a Han Chinese population (pOR=0.002).ConclusionsOur case–control study failed to validate the significant association ofNKAPLrs1635,TSPAN18rs11038167, andMPC2rs10489202 polymorphisms with SZ susceptibility in the southern Zhuang or Han Chinese population. However, meta-analysis showed a significant association betweenMPC2variant rs10489202 and SZ susceptibility in Han Chinese.

scholarly journals Gender-Specific Association ofATP2B1Variants with Susceptibility to Essential Hypertension in the Han Chinese Population

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Jin Xu ◽  
Hai-xia Qian ◽  
Su-pei Hu ◽  
Li-ya Liu ◽  
Mi Zhou ◽  
...  
Keyword(s):  
Essential Hypertension ◽  
Chinese Population ◽  
Propensity Score Analysis ◽  
Association Studies ◽  
Han Chinese ◽  
Minor Effect ◽  
Strong Linkage Disequilibrium ◽  
Genome Wide Association Studies ◽  
Han Chinese Population ◽  
Genome Wide

Previous genome-wide association studies (GWASs) found that severalATP2B1variants are associated with essential hypertension (EHT). But the “genome-wide significant”ATP2B1SNPs (rs2681472, rs2681492, rs17249754, and rs1105378) are in strong linkage disequilibrium (LD) and are located in the same LD block in Chinese populations. We asked whether there are other SNPs within theATP2B1gene associated with susceptibility to EHT in the Han Chinese population. Therefore, we performed a case-control study to investigate the association of seven tagSNPs within theATP2B1gene and EHT in the Han Chinese population, and we then analyzed the interaction among different SNPs and nongenetic risk factors for EHT. A total of 902 essential hypertensive cases and 902 normotensive controls were involved in the study. All 7 tagSNPs within theATP2B1gene were retrieved from HapMap, and genotyping was performed using the Tm-shift genotyping method. Chi-squared test, logistic regression, and propensity score analysis showed that rs17249754 was associated with EHT, particularly in females. The MDR analysis demonstrated that the interaction of rs2070759, rs17249754, TC, TG, and BMI increased the susceptibility to hypertension. Crossover analysis and stratified analysis indicated that BMI has a major effect on the development of hypertension, whileATP2B1variants have a minor effect.

scholarly journals Genome-wide association study of morbid obesity in Han Chinese

BMC Genetics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Kuang-Mao Chiang ◽  
Heng-Cheng Chang ◽  
Hsin-Chou Yang ◽  
Chien-Hsiun Chen ◽  
Hsin-Hung Chen ◽  
...  
Keyword(s):  
Morbid Obesity ◽  
Chinese Population ◽  
Association Studies ◽  
Han Chinese ◽  
Genome Wide Association ◽  
Joint Analysis ◽  
Genome Wide Association Studies ◽  
Han Chinese Population ◽  
Second Stage ◽  
Genome Wide

Abstract Background As obesity is becoming pandemic, morbid obesity (MO), an extreme type of obesity, is an emerging issue worldwide. It is imperative to understand the factors responsible for huge weight gain in certain populations in the modern society. Very few genome-wide association studies (GWAS) have been conducted on MO patients. This study is the first MO-GWAS study in the Han-Chinese population in Asia. Methods We conducted a two-stage GWAS with 1110 MO bariatric patients (body mass index [BMI] ≥ 35 kg/m2) from Min-Sheng General Hospital, Taiwan. The first stage involved 575 patients, and 1729 sex- and age-matched controls from the Taiwan Han Chinese Cell and Genome Bank. In the second stage, another 535 patients from the same hospital were genotyped for 52 single nucleotide polymorphisms (SNPs) discovered in the first stage, and 9145 matched controls from Taiwan Biobank were matched for confirmation analysis. Results The results of the joint analysis for the second stage revealed six top ranking SNPs, including rs8050136 (p-value = 7.80 × 10− 10), rs9939609 (p-value = 1.32 × 10− 9), rs1421085 (p-value = 1.54 × 10− 8), rs9941349 (p-value = 9.05 × 10− 8), rs1121980 (p-value = 7.27 × 10− 7), and rs9937354 (p-value = 6.65 × 10− 7), which were all located in FTO gene. Significant associations were also observed between MO and RBFOX1, RP11-638 L3.1, TMTC1, CBLN4, CSMD3, and ERBB4, respectively, using the Bonferroni correction criteria for 52 SNPs (p < 9.6 × 10− 4). Conclusion The most significantly associated locus of MO in the Han-Chinese population was the well-known FTO gene. These SNPs located in intron 1, may include the leptin receptor modulator. Other significant loci, showing weak associations with MO, also suggested the potential mechanism underlying the disorders with eating behaviors or brain/neural development.

Abstract TP134: Genome Wide Association Studies in Han Chinese Populations Identify Novel Susceptibility Loci for Specific Ischemic Stroke Subtypes

Stroke ◽  
2016 ◽  
Vol 47 (suppl_1) ◽  
Author(s):  
Tai-Ming Ko ◽  
Tsong-Hai Lee Lee ◽  
Chien-Hsiun Chen ◽  
Yuan-Tsong Chen ◽  
Jer-Yuarn Wu
Keyword(s):  
Ischemic Stroke ◽  
Chinese Population ◽  
Genetic Factors ◽  
Han Chinese ◽  
Genome Wide Association ◽  
Papillary Thyroid ◽  
Susceptibility Loci ◽  
Han Chinese Population ◽  
Chinese Populations ◽  
Genome Wide

Introduction: Although family history studies in ischemic stroke support that genetic factors may be involved in the pathogenesis of two major subtypes of ischemia stroke: large-artery atherosclerosis (LAA) and small-vessel occlusion (SVO), it is still unclear which particular genetic factors contribute to LAA or SVO. Hypothesis: Because the etiology of ischemic stroke is heterogeneous, we hypothesize that genetic factors may vary by etiologic subtypes or ethnicities. Thus, we aim to identify genetic factors that contribute to LAA or SVO based on two independent Han Chinese populations. Methods: Novel genetic variants that predispose individuals to LAA and SVO were identified by genome-wide association study comprising of 824 individuals (including 444 LAA cases and 380 SVO cases) and 1,727 controls in a Han Chinese population residing in Taiwan. The LAA study was replicated in an independent Han Chinese population comprising of an additional 319 LAA cases and 1,802 controls. Results: In LAA cases, from two independent populations, we identified five single-nucleotide polymorphisms (SNPs), including SNP-1 (P = 3.10 х 10–8), SNP-2 (P = 4.00 х 10–9), SNP-3 (P = 3.57 х 10–8), SNP-4 (P = 1.76 х 10–8), and SNP-5 (P = 2.92 х 10–8), at one novel locus on chromosome 14q13.3 within PTCSC3 (encoding papillary thyroid carcinoma susceptibility candidate 3). In SVO cases, from the discovery stage, we identified two novel candidate susceptibility loci on chromosome 3p25.3 (SNP-6, P = 3.24 х 10–5) and chromosome 14 q31.1 (SNP-7, P = 2.58 х 10–4). Conclusions: For LAA, the newly identified SNPs within PTCSC3 gene were found to have genome-wide statistical significance (P < 5 х 10–8) and were shown to be located in a risk locus correlated with papillary thyroid carcinoma. Moreover, the genetic association between PTCSC3 gene and SVO was not identified, which suggested that PTCSC3 is a specific susceptibility locus for LAA. For SVO, we identified two novel candidate genetic loci which were valuable for replication by an independent population with SVO. In conclusion, our findings provide insights into the genetic basis of LAA and SVO, which may be applicable in the study of the pathogenesis of ischemic stroke and in the development of alternative therapeutic interventions.

scholarly journals Genetic Structure of the Han Chinese Population Revealed by Genome-wide SNP Variation

2009 ◽  
Vol 85 (6) ◽  
pp. 775-785 ◽  
Author(s):  
Jieming Chen ◽  
Houfeng Zheng ◽  
Jin-Xin Bei ◽  
Liangdan Sun ◽  
Wei-hua Jia ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Chinese Population ◽  
Han Chinese ◽  
Han Chinese Population ◽  
Genome Wide

scholarly journals East Asian Genome-wide association study derived loci in relation to type 2 diabetes in the Han Chinese population

2019 ◽  
Author(s):  
Sijia Zhang ◽  
Esma Jamaspishvili ◽  
Huixin Tong ◽  
Yongjie Chen ◽  
Zhongyu Zhou ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Chinese Population ◽  
Genome Wide Association Study ◽  
Meta Analysis ◽  
East Asian ◽  
Repetitive Sequences ◽  
Han Chinese ◽  
Han Chinese Population ◽  
Genome Wide

Meta-analysis of GWAS in East Asian populations had established 10 loci that were associated with type 2 diabetes. Eight of them were with genome-wide significance and two with a border line association. Since these data have not been studied in an independent Han Chinese population, we aimed to investigate the association of these susceptibility loci with type 2 diabetes in an independent Han Chinese population. We executed a case-control study in 2 000 Chinese by the SNPscan method. Firstly, the repetitive sequences of 10 loci were assessed. Next, we investigated the association of 8 SNPs out of 10 with type 2 diabetes and constructed the GRS of those 8 SNPs. Finally, the relationship of the 8 loci and diabetes-related traits was analyzed. Based on the fact, that highly repetitive sequences were detected in 2 SNPs, we investigated the remaining 8 SNPs. With the exception of four SNPs (CMIP rs16955379, PEPD rs3786897, PSMD6 rs831571, ZFAND3 rs9470794), the other SNPs had the same direction of effect (odds ratio [OR]>1.0) as in the original reports, especially GLIS3 rs7041847 and KCNK16 rs1535500 were significantly associated with type 2 diabetes (rs1535500: p=0.005, OR=1.224, 95% CI 1.062–1.409; rs7041847: p=0.035, OR=1.118, 95% CI 1.070–1.388). The GRS constructed from the 8 SNPs was significantly associated with type 2 diabetes in the Chinese population (p=0.004, OR=1.065, 95% CI: 1.021–1.111). Among the participants with 24≤BMI<28 kg/m2 the 8 SNPs were significantly associated with type 2 diabetes (p=0.040, OR=1.079, 95% CI: 1.003–1.160). In quantitative trait analyses, WWOX rs17797882 was associated with decreased HOMA-β and increased level of TG and HDL-Ch, while PEPD rs3786897 and MAEA rs6815464 were associated with decreased fasting plasma glucose, and KCNK16 rs1535500 has shown a significant association with increased T-Ch and PSMD6 rs831571 had a significant association with decreased HDL-Ch. In Conclusion, with high probability the 8 loci identified in the East Asian GWAS meta-analysis are associated with type 2 diabetes in the Han Chinese population.

scholarly journals Genome-wide Association study of facial morphology identifies novel genetic loci in Han Chinese

2019 ◽  
Author(s):  
Yin Huang ◽  
Dan Li ◽  
Lu Qiao ◽  
Yu Liu ◽  
Qianqian Peng ◽  
...  
Keyword(s):  
Chinese Population ◽  
Genetic Regulation ◽  
Han Chinese ◽  
Facial Features ◽  
Facial Morphology ◽  
Human Face ◽  
Genetic Loci ◽  
Han Chinese Population ◽  
Genome Wide ◽  
Different Populations

AbstractHuman face is a heritable surface with many complex sensory organs. In recent years, many genetic loci associated with facial features have been reported in different populations, yet there is a lack for the Han Chinese population. We report a genome-wide association analysis of 3D normal human faces in 2659 Han Chinese with two groups of phenotypes, the partial and whole face phenotypes and the distance and angle phenotypes. We found significant signals in five genomic regions with traits related to nose or eyes, including rs970797 in 2q31.1 near HOXD1 and MTX2, rs16897517 in 8q22.2 at intron of VPS13B, rs9995821 in 4q31.3 near DCHS2 and SFRP2, rs12636297 in 3q23 near PISRT1, and rs12948076 in 17q24.3 near SOX9 and CASC17. We visualized changes in facial morphology by comparing the volume of local areas and observed that these nose-related loci were associated with different features of the nose, including nose prominence, nasion height, and nostril shape, suggesting that the nose underlies precise genetic regulation. These results provide a more comprehensive understanding of the relationship between genetic loci and human facial morphology.Author SummaryHuman face as a combination of delicate sensory organs has a strong genetic component, as evidenced by the identical appearance in twins and shared facial features in close relatives. Although facial genetics have been studied in different populations, our knowledge between genetic markers with facial features is still limited. In this paper, we found genetic variants associated with nose and eyes through a large-scale high-resolution 3D facial genetic study on the Han Chinese population. We observed that these nose-related loci were associated with different features of the nose, including nose prominence, nasion height, and nostril shape, which suggests the nose underlies precise genetic regulation. Intriguingly, we noted that genes (DCHS2 and SFRP2) related to one of these loci are differentially expressed in human and chimp cranial neural crest cells, which plays a crucial role in the early formation of facial morphology. The ongoing genetic studies of facial morphology will improve our understanding of human craniofacial development, and provide potential evolution evidence of human facial features.

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