Stroke genetics informs drug discovery and risk prediction across ancestries.

Previous genome-wide association studies (GWASs) of stroke - the second leading cause of death worldwide - were conducted predominantly in populations of European ancestry1,2. Here, in cross-ancestry GWAS meta-analyses of 110,182 patients who have had a stroke (five ancestries, 33% non-European) and 1,503,898 control individuals, we identify association signals for stroke and its subtypes at 89 (61 new) independent loci: 60 in primary inverse-variance-weighted analyses and 29 in secondary meta-regression and multitrait analyses. On the basis of internal cross-ancestry validation and an independent follow-up in 89,084 additional cases of stroke (30% non-European) and 1,013,843 control individuals, 87% of the primary stroke risk loci and 60% of the secondary stroke risk loci were replicated (P < 0.05). Effect sizes were highly correlated across ancestries. Cross-ancestry fine-mapping, in silico mutagenesis analysis3, and transcriptome-wide and proteome-wide association analyses revealed putative causal genes (such as SH3PXD2A and FURIN) and variants (such as at GRK5 and NOS3). Using a three-pronged approach4, we provide genetic evidence for putative drug effects, highlighting F11, KLKB1, PROC, GP1BA, LAMC2 and VCAM1 as possible targets, with drugs already under investigation for stroke for F11 and PROC. A polygenic score integrating cross-ancestry and ancestry-specific stroke GWASs with vascular-risk factor GWASs (integrative polygenic scores) strongly predicted ischaemic stroke in populations of European, East Asian and African ancestry5. Stroke genetic risk scores were predictive of ischaemic stroke independent of clinical risk factors in 52,600 clinical-trial participants with cardiometabolic disease. Our results provide insights to inform biology, reveal potential drug targets and derive genetic risk prediction tools across ancestries.

Does coffee drinking have beneficial effects on bone health of Taiwanese adults? A longitudinal study.

BACKGROUND: Results from studies investigating the association between coffee consumption and osteoporosis or bone mineral density (BMD) have been inconsistent. This longitudinal study was performed to assess the effect of coffee drinking on bone health of Taiwanese adults. METHODS: Data were retrieved from the Li-Shin (Landseed) Hospital in Taoyuan City. In 2006, 6152 participants completed a questionnaire on coffee drinking and other lifestyle factors. In 2014, 5077 of them were followed up. Nonetheless, a total of 2395 participants with incomplete data were excluded. The final analyses included 2682 participants comprising 1195 men and 1487 women (706 premenopausal and 781 postmenopausal). T-scores were derived from the osteo-sono assessment index (OSI) which is a surrogate of BMD. Coffee drinking was categorized as "no, medium, and high" based on the number of cups that were consumed per week in both 2006 and 2014. RESULTS: In general, medium and high coffee drinking were associated with higher T-scores. However, significant results were observed only among high drinkers (ß = 0.158; P = 0.0038). Nonetheless, the test for linear trend was significant (P = 0.0046). After stratification by sex, medium and high coffee drinking were associated with higher T-scores. However, significant results were prominent only among high male drinkers (ß = 0.237; P = 0.0067) and the test for trend was significant (P = 0.0161). Based on menopausal status, coffee drinking was associated with higher T-scores. Nevertheless, significant results were found only among premenopausal women (ß = 0.233; P = 0.0355 and ß = 0.234; P = 0.0152 for medium and high coffee drinking, respectively. The test for linear trend was significant (P = 0.0108). CONCLUSION: Coffee drinking was significantly associated with higher T-scores hence, a lower risk of osteoporosis in men and premenopausal women.

Vegetarian diet and cholesterol and TAG levels by gender.

OBJECTIVE: The present study assessed the effects of vegetarian and omnivorous diets on HDL-cholesterol (HDL-C), LDL-cholesterol (LDL-C), TAG and the ratio of HDL-C to total cholesterol (TC) by gender. DESIGN: HDL-C, LDL-C, TAG and HDL-C:TC were compared among three diet groups (vegan, ovo-lacto vegetarian and omnivorous). Multivariate linear regression analysis was performed to examine factors significantly and independently associated with vegetarian status and to estimate the ß value of lipid profiles for the diet groups. Settings A cross-sectional study. Data were obtained from the Taiwanese Survey on the Prevalence of Hyperglycemia, Hyperlipidemia and Hypertension (TwSHHH). SUBJECTS: The study comprised included 3257 men and 3551 women. RESULTS: After adjusting for confounders, vegan and ovo-lacto vegetarian diets lowered LDL-C levels (ß=-10.98, P=0.005 and ß=-7.12, P=0.025, respectively) in men compared with omnivorous diet. There was a significant association between HDL-C and vegan diet (ß=-6.53, P=0.004). In females, the ß values of HDL-C, TAG and HDL-C:TC were -5.72 (P<0.0001), 16.51 (P=0.011) and -0.02 (P=0.012) for vegan diet, and -4.86 (P=0.002), 15.09 (P=0.008) and -0.01 (P=0.026) for ovo-lacto vegetarian diet, when compared with omnivorous diet. CONCLUSIONS: Vegan diet was associated with lower HDL-C concentrations in both males and females. Because the ovo-lacto vegetarian diet was effective in lowering LDL-C, it may be more appropriate for males.

Identification of an novel genetic variant associated with osteoporosis: insights from the Taiwan Biobank Study.

Purpose: The purpose of this study was to identify new independent significant SNPs associated with osteoporosis using data from the Taiwan Biobank (TWBB). Material and Methods: The dataset was divided into discovery (60%) and replication (40%) subsets. Following data quality control, genome-wide association study (GWAS) analysis was performed, adjusting for sex, age, and the top 5 principal components, employing the Scalable and Accurate Implementation of the Generalized mixed model approach. This was followed by a meta-analysis of TWBB1 and TWBB2. The Functional Mapping and Annotation (FUMA) platform was used to identify osteoporosis-associated loci. Manhattan and quantile-quantile plots were generated using the FUMA platform to visualize the results. Independent significant SNPs were selected based on genome-wide significance (P < 5 × 10-8) and independence from each other (r2 < 0.6) within a 1 Mb window. Positional, eQTL(expression quantitative trait locus), and Chromatin interaction mapping were used to map SNPs to genes. Results: A total of 29 084 individuals (3154 osteoporosis cases and 25 930 controls) were used for GWAS analysis (TWBB1 data), and 18 918 individuals (1917 cases and 17 001 controls) were utilized for replication studies (TWBB2 data). We identified a new independent significant SNP for osteoporosis in TWBB1, with the lead SNP rs76140829 (minor allele frequency = 0.055, P-value = 1.15 × 10-08). Replication of the association was performed in TWBB2, yielding a P-value of 6.56 × 10-3. The meta-analysis of TWBB1 and TWBB2 data demonstrated a highly significant association for SNP rs76140829 (P-value = 7.52 × 10-10). In the positional mapping of rs76140829, 6 genes (HABP2, RP11-481H12.1, RNU7-165P, RP11-139 K1.2, RP11-57H14.3, and RP11-214 N15.5) were identified through chromatin interaction mapping in mesenchymal stem cells. Conclusions: Our GWAS analysis using the Taiwan Biobank dataset unveils rs76140829 in the VTI1A gene as a key risk variant associated with osteoporosis. This finding expands our understanding of the genetic basis of osteoporosis and highlights the potential regulatory role of this SNP in mesenchymal stem cells.

Changes in High-Density Lipoprotein Cholesterol Levels in Relation to Coffee Consumption Among Taiwanese Adults.

PURPOSE: High-density lipoprotein cholesterol (HDL-C) is essential for cardiometabolic health. Coffee consumption influences the body's ability to regulate serum lipid profile. Although there is extensive information on coffee and cholesterol, not much is known whether changes in HDL-C concentrations are affected by coffee with or without flavoring substances. MATERIALS AND METHODS: Using historical data collected from 1272 participants in Li-Shin (Landseed) International Hospital in Northern Taiwan, we examined the relationship between HDL-C and consumption of plain black coffee with and without additives. Data on coffee consumption between 2006 and 2019 were collected based on self-reported questionnaires while HDL-C measurements were obtained from the electronic medical records of the hospital. t-test, chi-square test and multivariate linear regression analysis were used for analysis. RESULTS: In our primary analysis, we found that coffee consumption of ≥5 cups per week was positively associated with HDL-C (ß = 1.9586, p=0.0442) compared with the lowest level (<1 cup/week) of consumption. We found in a separate model that higher (≥5 cups/week) or lower (1-4 cups/week) consumption of plain black coffee without additives was associated with higher HDL-C. The corresponding ß values were 4.0674 (p = 0.0007) and 4.1253 (p = 0.0008), respectively. However, HDL-C levels were not affected by coffee with additives. CONCLUSION: We found that consumption of black coffee without additives was associated with higher concentrations of HDL-C among Taiwanese adults over the age of 30. However, HDL-C levels did not change significantly among individuals who consumed black coffee with additives.

Physical Activity Might Reduce the Adverse Impacts of the FTO Gene Variant rs3751812 on the Body Mass Index of Adults in Taiwan.

The fat mass and obesity-associated (FTO) gene is a significant genetic contributor to polygenic obesity. We investigated whether physical activity (PA) modulates the effect of FTO rs3751812 on body mass index (BMI) among Taiwanese adults. Analytic samples included 10,853 Taiwan biobank participants. Association of the single-nucleotide polymorphism (SNP) with BMI was assessed using linear regression models. Physical activity was defined as any kind of exercise lasting 30 min each session, at least three times a week. Participants with heterozygous (TG) and homozygous (TT) genotypes had higher BMI compared to those with wild-type (GG) genotypes. The ß value was 0.381(p < 0.0001) for TG individuals and 0.684 (p = 0.0204) for TT individuals. There was a significant dose-response effect among carriers of different risk alleles (p trend <0.0001). Active individuals had lower BMI than their inactive counterparts (ß = -0.389, p < 0.0001). Among the active individuals, significant associations were found only with the TG genotype (ß = 0.360, p = 0.0032). Inactive individuals with TG and TT genotypes had increased levels of BMI compared to those with GG genotypes: Their ß values were 0.381 (p = 0.0021) and 0.950 (p = 0.0188), respectively. There was an interaction between the three genotypes, physical inactivity, and BMI (p trend = 0.0002). Our data indicated that increased BMI owing to genetic susceptibility by FTO rs3751812 may be reduced by physical activity.

SOX2 promoter hypermethylation in non-smoking Taiwanese adults residing in air pollution areas.

BACKGROUND: Both SOX2 promoter methylation and air pollution have been associated with lung cancer risk. However, little has been done to assess SOX2 promoter methylation in individuals living in air pollution areas. The aim of this study was to investigate SOX2 promoter methylation in non-smoking Taiwanese adults living in areas with different levels of air pollution especially particulate matter with diameter < 2.5 µm (PM2.5). METHODS: A total of 1142 individuals aged 30-70 years were recruited. Data on SOX2 methylation, residence, age, and exposure to second-hand smoke (SHS) among others were extracted from the Taiwan Biobank dataset (2008-2015). After excluding former and current smokers, alongside those with incomplete information, a total of 461 non-smokers comprising 176 men and 285 women were included in the study. Participants' residences were grouped under northern and central/southern areas because air pollution (PM2.5) is lower in northern compared to central and southern areas. RESULTS: The methylation levels in men (0.16310 ± 0.01230) and women (0.15740 ± 0.01240) were significantly different (P < .0001). In both sexes, the SOX2 promoter region was shown to be significantly hypermethylated in central and southern areas compared with the northern areas. The regression coefficient (ß) was 0.00331 (P = 0.0257) in men and 0.00514 (P < .0001) in women. CONCLUSION: SOX2 was significantly hypermethylated in both men and women residing in central and southern areas. The consistency in the results for both sexes shows that SOX2 promoter methylation could serve as a potential biomarker for industrial air pollution exposure. Moreover, it might reflect predisposition to cancer. Hence, healthy non-smokers at precancerous stages who have not been clinically diagnosed could be identified.

Methylation at cg05575921 of a smoking-related gene (AHRR) in non-smoking Taiwanese adults residing in areas with different PM2.5 concentrations.

BACKGROUND: DNA methylation is associated with cancer, metabolic, neurological, and autoimmune disorders. Hypomethylation of aryl hydrocarbon receptor repressor (AHRR) especially at cg05575921 is associated with smoking and lung cancer. Studies on the association between AHRR methylation at cg05575921 and sources of polycyclic aromatic hydrocarbon (PAH) other than smoking are limited. The aim of our study was to assess the pattern of blood DNA methylation at cg05575921 in non-smoking Taiwanese adults living in areas with different PM2.5 levels. METHODS: Data on blood DNA methylation, smoking, and residence were retrieved from the Taiwan Biobank dataset (2008-2015). Current and former smokers, as well as individuals with incomplete information were excluded from the current study. The final analysis included 708 participants (279 men and 429 women) aged 30-70 years. PM2.5 levels have been shown to increase as one moves from the northern through central towards southern Taiwan. Based on this trend, the study areas were categorized into northern, north-central, central, and southern regions. RESULTS: Living in PM2.5 areas was associated with lower methylation levels: compared with the northern area (reference area), living in north-central, central, and southern areas was associated with lower methylation levels at cg05575921. However, only methylation levels in those living in central and southern areas were significant (ß = - 0.01003, P = 0.009 and ß = - 0.01480, P < 0.001, respectively. Even though methylation levels in those living in the north-central area were not statistically significant, the test for linear trend was significant (P < 0.001). When PM2.5 was included in the regression model, a unit increase in PM2.5 was associated with 0.00115 (P < 0.001) lower cg05575921 methylation levels. CONCLUSION: Living in PM2.5 areas was inversely associated with blood AHRR methylation levels at cg05575921. The methylation levels were lowest in participants residing in southern followed by central and north-central areas. Moreover, when PM2.5 was included in the regression model, it was inversely associated with methylation levels at cg05575921. Blood methylation at cg05575921 (AHRR) in non-smokers might indicate different exposures to PM2.5 and lung cancer which is a PM2.5-related disease.

HDL and associated factors stratified by sex and menopausal status: results from a community-based survey in Taiwan.

AIM: To investigate factors, especially modifiable factors associated with high-density lipoprotein (HDL) in Taiwanese based on sex and menopausal status. MATERIALS AND METHODS: Participants comprised 2022 men and 2392 women (1267 menopausal and 1125 non-menopausal) aged ≥30 years who resided in Pingzhen district, Taoyuan from 2006-2011. Their data, obtained through questionnaires and measurements were retrieved from the Li-Shin Hospital. RESULTS: Higher HDL was associated with total cholesterol, underweight, and alcohol drinking in both men and women. It was also associated with education, blood group B, and marital status in men as well as with age in women. Moreover, it was associated with total cholesterol, underweight, and age in both menopausal and non-menopausal women. Furthermore, it was associated with marital status in non-menopausal women and alcohol drinking in menopausal women. Lower HDL was associated with triglycerides, low-density lipoprotein (LDL), overweight, obesity, waist-hip ratio (WHR), uric acid, and smoking in both men and women and with coffee drinking in only women. It was also associated with uric acid, triglycerides, LDL, overweight, obesity, WHR, and body fat in both menopausal and non-menopausal women. Moreover, it was associated with coffee drinking in menopausal women. CONCLUSION: Modifiable factors associated with HDL differ according to sex and menopausal status. Sex and menopausal status should be considered when implementing lifestyle changes to raise HDL. For example, both men and women should maintain a normal weight as well as quit smoking.

Fast-searching algorithm for vector quantization using projection and triangular inequality.

In this paper, a new and fast-searching algorithm for vector quantization is presented. Two inequalities, one used for terminating the searching process and the other used to delete impossible codewords, are presented to reduce the distortion computations. Our algorithm makes use of a vector's features (mean value, edge strength, and texture strength) to reject many unlikely codewords that cannot be rejected by other available approaches. Experimental results show that our algorithm is superior to other algorithms in terms of computing time and the number of distortion calculations. Compared with available approaches, our method can reduce the computing time and the number of distortion computations significantly. Compared with the best method of reducing distortion computation, our algorithm can further reduce the number of distortion calculations by 29% to 58.4%. Compared with the best encoding algorithm for vector quantization, our approach also further reduces the computing time by 8% to 47.7%.