Genome-Wide Association Study Reveals Four Loci for Lipid Ratios in the Korean Population and the Constitutional Subgroup

Genome-wide association studies in a large Korean cohort identify novel quantitative trait loci for 36 traits and illuminate their genetic architectures

Genome-wide association studies (GWAS) have been predominantly conducted in populations of European ancestry, limiting opportunities for biological discovery in diverse populations. We report GWAS findings from 153,950 individuals across 36 quantitative traits in the Korean Cancer Prevention Study-II (KCPS2) Biobank. We discovered 301 novel genetic loci in KCPS2, including an association between thyroid-stimulating hormone and CD36. Meta-analysis with the Korean Genome and Epidemiology Study, Biobank Japan, Taiwan Biobank, and UK Biobank identified 4,588 loci that were not significant in any contributing GWAS. We describe differences in genetic architectures across these East Asian and European samples. We also highlight East Asian specific associations, including a known pleiotropic missense variant in ALDH2, which fine-mapping identified as a likely causal variant for a diverse set of traits. Our findings provide insights into the genetic architecture of complex traits in East Asian populations and highlight how broadening the population diversity of GWAS samples can aid discovery.

Genome-wide Association Study of Susceptibility Loci for Self-Reported Atopic Dermatitis and Allergic Rhinitis in the Korean Population

BACKGROUND

Allergic diseases include atopic dermatitis (AD) and allergic rhinitis (AR), which are chronic, relapsing inflammatory disorders of the skin or mucosa that usually accompany immunoglobulin E-mediated immune responses. They are complex, multifactorial diseases with an etiology involving interactions between genetic and environmental factors.

OBJECTIVE

We performed a genome-wide association study (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with allergic diseases in the Korean population.

METHODS

A total of 8,840 samples were obtained from the Korean Association Resource Consortium dataset of the Korean Genome and Epidemiology Study Ansan-Anseong cohort. The allergic disease phenotype was determined based on self-reported physician diagnoses. After quality control, 8,823 subjects with 877,242 variants remained for the final analysis. The GWAS was performed using logistic regression analysis in an additive model adjusted for age and sex.

RESULTS

A total of 636 patients with allergic disease and 8,176 controls were analyzed. Three SNPs were associated with allergic disease at a level of genome-wide suggestive significance (p<1.0×10-5) in the Korean population: rs7275360, located in neural cell adhesion molecule 2; rs698195; and rs3750552, located in family with sequence similarity 189, member A2. These polymorphisms were on chromosomes 21q21.1, 7q31.1, and 9q21.12, respectively.

CONCLUSION

We identified 3 novel SNPs significantly associated with allergic diseases in the Korean population. Further research is required to confirm the association between these novel SNPs and allergic disease in the Korean population and in other ethnicities.

Sex-related differences in single nucleotide polymorphisms associated with dyslipidemia in a Korean population

BACKGROUND

The prevalence of dyslipidemia has increased steadily in Korea, and the incidence of dyslipidemia differs by sex. In this study, we identified single nucleotide polymorphisms (SNPs) related to dyslipidemia in Korean cohorts through genome-wide association study (GWAS) analysis.

METHODS

Genotyping was conducted to determine the genotypes of 72,298 participants and investigate genotypes for 7,079,946 SNPs. Sex, age, and BMI were set as covariates for GWAS, and significant SNPs were identified in the discovery and replication stages using logistic regression.

RESULTS

GWAS of the entire cohort revealed a total of five significant SNPs: rs117026536 (LPL), rs651821 (APOA5), rs9804646 (APOA5), rs9926440 (CETP), and rs429358 (APOE). GWAS of the male subjects revealed a total of four significant SNPs. While rs9804646 (APOA5) and rs429358 (APOE) were significant for all the subjects, rs662799 (APOA5) and rs56156922 (CETP) were significant only for the male subjects. GWAS of the female subjects revealed two significant SNPs, rs651821 (APOA5) and rs9804646 (APOA5), both of which were significant in all the subjects.

CONCLUSION

This is the first study to identify sex-related differences in genetic polymorphisms in Korean populations with dyslipidemia. Further studies considering environmental variables will be needed to elucidate these sex-related genetic differences in dyslipidemia.

Genome-wide study on 72,298 individuals in Korean biobank data for 76 traits

Genome-wide association studies (GWAS) on diverse ancestry groups are lacking, resulting in deficits of genetic discoveries and polygenic scores. We conducted GWAS for 76 phenotypes in Korean biobank data, namely the Korean Genome and Epidemiology Study (KoGES) (n = 72,298). Our analysis discovered 2,242 associated loci, including 122 novel associations, many of which were replicated in Biobank Japan (BBJ) GWAS. We also applied several up-to-date methods for genetic association tests to increase the power, discovering additional associations that are not identified in simple case-control GWAS. We evaluated genetic pleiotropy to investigate genes associated with multiple traits. Following meta-analysis of 32 phenotypes between KoGES and BBJ, we further identified 379 novel associations and demonstrated the improved predictive performance of polygenic risk scores by using the meta-analysis results. The summary statistics of 76 KoGES GWAS phenotypes are publicly available, contributing to a better comprehension of the genetic architecture of the East Asian population.

MAIP1-Related Tumor Immune Infiltration: As a Potential Prognostic Biomarker for Esophageal Cancer

Background

Esophageal cancer (EC), a common malignant tumor of digestive tract, is also one of the most deadly cancers. Accumulating studies have shown that the initiating and progressing multiple human diseases were closely related to the expression of MAIP. However, the specific roles and mechanisms of MAIP1 in EC remain incompletely defined.

Purpose

This study aims to determine the clinical significance of MAIP1 in EC and explores its potential molecular mechanisms regulating tumor immune infiltration.

Methods

We obtained RNA-seq datasets and corresponding clinical data for EC patients from the Cancer Genome Atlas (TCGA) database via the UCSC Xena browser to extract MAIP1 expression and plot survival curves to determine their prognosis. Based on the differential expression of MAIP1, EC patients were divided into high and low group to investigate the mechanism of MAIP1 in EC. In addition, the single sample gene set enrichment analysis (ssGSEA) quantified the expression of various immune cell signature marker genes and assessed the degree of immune infiltration in EC.

Results

In the TCGA-EC cohort, the overexpression of MAIP1 was observed in tumor tissues compared to normal tissues (p = 0.0038). Overall survival analysis showed that EC patients with the overexpression of MAIP1 presented a lower overall survival and worse prognosis (p = 0.004). Enrichment analysis revealed that the differential genes (DEGs) between high and low group are involved in biological functions such as extracellular matrix and organization extracellular structure. The results of ssGSEA showed that DCs, iDCs, macrophages, mast cells, and NK cells were significantly different in MAIP1^high and MAIP1^low groups, and all showed high expression in the MAIP1^low group.

Conclusion

We proposed that MAIP1 overexpression was associated with poor prognosis and tumor immune infiltration in EC. At present, there are few MAIP1-related tumor immune infiltration studies in EC, and further investigation is needed.

GWAS in Africans identifies novel lipids loci and demonstrates heterogenous association within Africa

Serum lipids are biomarkers of cardiometabolic disease risk, and understanding genomic factors contributing to their distribution is of interest. Studies of lipids in Africans are rare, though it is expected that such studies could identify novel loci. We conducted a GWAS of 4317 Africans enrolled from Nigeria, Ghana and Kenya. We evaluated linear mixed models of high-density lipoprotein cholesterol (HDLC), low-density lipoprotein cholesterol (LDLC), total cholesterol (CHOL), triglycerides (TG) and TG/HDLC. Replication was attempted in 9542 African Americans (AA). In our main analysis, we identified 28 novel associations in Africans. Of the 18 of these that could be tested in AA, three associations replicated (GPNMB-TG, ENPP1-TG and SMARCA4-LDLC). Five additional novel loci were discovered upon meta-analysis with AA (rs138282551-TG, PGBD5-HDLC, CD80-TG/HDLC, SLC44A1-CHOL and TLL2-CHOL). Analyses considering only those with predominantly West African ancestry (Nigeria, Ghana and AA) yielded new insights: ORC5-LDLC and chr20:60973327-CHOL. Among our novel findings are some loci with known connections to lipids pathways. For instance, rs147706369 (TLL2) alters a regulatory motif for sterol regulatory element-binding proteins, a family of transcription factors that control the expression of a range of enzymes involved in cholesterol, fatty acid and TG synthesis, and rs115749422 (SMARCA4), an independent association near the known LDLR locus that is rare or absent in populations without African ancestry. These findings demonstrate the utility of conducting genomic analyses in Africans for discovering novel loci and provide some preliminary evidence for caution against treating 'African ancestry' as a monolithic category.

Low nutritional status links to the prevalence of pre-metabolic syndrome and its cluster in metabolically high-risk Korean adults: A cross-sectional study

Diet plays a crucial role as a modifiable risk factor related to the development of metabolic syndrome (MetS) and its cluster. Constitution type of traditional Korean medicine has shown accuracy to predict the risk for MetS. We attempted to examine the association between nutritional status, pre-MetS, and its cluster in Korean adults by their constitution type.Participants aged 30 to 55 years who had no cancer or cardiovascular diseases (CVDs) were assigned to join in the present study. Pre-MetS was defined as ≥2 of the following factors: abdominal obesity; elevated triglycerides (TG); reduced high-density lipoprotein cholesterol (HDL-C); elevated blood pressure (BP); and elevated fasting plasma glucose (FPG). Constitution type was categorized into Tae-Eumin (TE) or non-TE. Dietary assessment of the subjects were surveyed using a short-form of the food frequency questionnaire (FFQ) and the nutrition quotient (NQ), which uses 4 factors, namely, balance, diversity, moderation, and dietary behavior.A total of 986 subjects were evaluated by constitution type with MetS status. Of these subjects, 48.6% had pre-MetS, 89.5% were obese and had the highest waist circumference (WC) in Pre-MetS TE. BP, FPG, TG were higher, while HDL-C was lower, than normal TE or non-TE both in Pre-MetS TE and non-TE. The prevalence of pre-MetS was positively associated with lower status of dietary behavior (odds ratio [ORs]: 2.153, 95% confidence interval [CI]: 1.179-3.931) while negatively related to higher vegetables and fruits intakes (ORs: 0.594, 95% CI: 0.359-0.983) in TE. Lower status of NQ had about 2 times higher risk of Pre-MetS (ORs: 1.855, 95% CI: 1.018-3.380) and abdominal obesity (ORs: 2.035, 95% CI: 1.097-3.775) in TE compared with higher status of NQ after controlling for covariates.Poor diet was a key contributor to the development of Pre-MetS and abdominal obesity in Korean adults with TE. Customized nutrition care and integrated medicinal approaches are strongly suggested to conduct optimal preventive care for people who are vulnerable to health risk.

Genetic and Environmental Overlaps Among Sasang Constitution Types: A Multivariate Twin Study

According to the Sasang theory, humans can be categorized into one of the four Sasang constitution (SC) types. The four SC types are Tae-Yang (TY), Tae-Eum (TE), So-Yang (SY), and So-Eum (SE), which are determined mainly on the basis of anthropometric characteristics, personality, and the balance of the physiological functions of the major organ systems. There is a growing recognition in the complementary and alternative medicine area that SC types have the potential to be a useful scientific tool for the prevention, diagnosis, and treatment of diseases (Cooper, Evidence Based Complementary and Alternative Medicine, Vol. 6 (Suppl. 1), 2009, pp. 1–3). The main purposes of the present study are to estimate genetic and environmental influences on SC types, and to explore genetic and environmental correlations that affect phenotypic associations among the SC types. In total, 1,742 (365 monozygotic male, 173 dizygotic male, 675 monozygotic female, 271 dizygotic female, and 258 opposite-sex dizygotic) twins (mean age = 19.1 ± 3.1 year) completed a Sasang questionnaire. Univariate and multivariate model-fitting analyses were performed. Total (additive and non-additive) genetic influences were 71% for males and 81% for females in TE, 70% for males and 71% for females in SE, and 47% for both sexes in SY. Non-additive genetic effects were substantial, and shared environmental influences were negligible in most SC types. Multivariate model-fitting analysis revealed that non-additive genetic and individual-specific environmental correlations between TE and SE were -0.92 (95% CI [-0.89, -0.93]) and -0.62 (95% CI [-0.57, -0.68]), respectively. The corresponding estimates were -0.55 (95% CI [-0.48, -0.61]) and -0.44 (95% CI [-0.37, -0.51]) between TE and SY and 0.19 (95% CI [0.09, 0.29]) and -0.40 (95% CI [-0.32, -0.47]) between SE and SY. These results suggest that the phenotypic associations among SC types may be mediated by pleiotropic mechanism of genes.

Prediction of cholesterol ratios within a Korean population

Cholesterol ratios (total cholesterol (TC)/high-density lipoprotein cholesterol (HDL-c) and triglyceride (TG)/HDL-c) have been suggested as better indicators to predict various clinical features such as insulin resistance and heart disease. Therefore, we aimed to build a single nucleotide polymorphism (SNP) set to predict constitutional lipid metabolism. The genotype data of 7795 samples were obtained from the Korea Association Resource. Among the total of 7795 samples, 7016 subjects were used to perform 10-fold cross-validation. We selected the SNPs that showed significance constantly throughout all 10 cross-validation sets; another 779 samples were used as the final validation set. After performing the 10-fold cross-validation, the six SNPs (rs4420638 (APOC1), rs12421652 (BUD13), rs17411126 (LPL), rs6589566 (ZPR1), rs16940212 (LOC101928635) and rs10852765 (ABCA8)) were finally selected for predicting cholesterol ratios. The weighted genetic risk scores (wGRS) were calculated based on the regression slopes of the six selected SNPs. Our results showed upward trends of wGRS for both the TC/HDL-c and TG/HDL-c ratios within the 10-fold cross-validation. Similarly, the wGRS of the six SNPs also showed upward trends in analyses using the SNP selection set and final validation set. The selected six SNPs can be used to explain both the TC/HDL-c and TG/HDL-c ratios. Our results may be useful for the prospective predictions of cholesterol-related diseases.