Carbohydrate-dependent interaction between AMY1A/AMY2B copy number variation and APOA5 rs651821 associated with hypertriglyceridemia in Korean middle-aged adults.

Introduction: Several previous studies have reported that consumption of soft drink is associated with increased risk of hypertension (HTN) in Western societies. However, epidemiological information on such associations is very limited in Koreans. Hypothesis: We tested the hypothesis whether an increase in soft drink consumption is related to higher risk of HTN among Korean middle aged adults from Korean community based Cohort (Ansan-Ansung cohort). Methods: Data from Ansan-Ansung cohort from 2001 to 2010 in the Korean genome and epidemiology study (KoGES) were used for statistical analyses. Among the participants, we selected 5,296 subjects (2,475 men and 2,821 women, aged 39-64 yrs) who were free from presence of HTN, diabetes, cardiovascular disease and cancer at baseline and those who completely followed up for 10.4 years. Participants who completed a semi-quantitative food frequency questionnaire for dietary assessment and questionnaire for baseline health status in 2001-2002 were included in analyses. Subjects were categorized as quartile based on their soft drink consumption. Soft drink consumption was calculated as frequency per week summed up by consumption frequency of soda (such as Coke and Sprite) and other beverages (including sweet rice drink and Citrus tea). To assess the relationship between soft drink consumption and HTN, we estimated multivariable-adjusted hazard ratio (HR) and 95% confidence intervals (CIs) using cox regression analysis. In addition, stratified analysis by body mass index (BMI) was conducted. Results: During the follow-up period of 10.4 years, we ascertained 1,035 incident cases (19.5% of study population) of HTN. Total soft drink consumption showed significant association with increased risk for HTN after adjusting for potential confounders (age, sex, total energy intake, BMI, and socio-economic factors). The adjusted HR of HTN for the highest quartile of soft drink consumption was 1.24 (95% CIs: 1.02-1.51) compared to the lowest quartile. Furthermore, we found that higher consumption of soft drink was significantly associated with increased incidence of HTN in subjects with BMI ≥25 (HR: 1.54; 95% CIs: 1.15-2.01), whereas there was no significant association among subjects with BMI <25. Conclusions: In conclusion, this study suggested that soft drink consumption contributes to increased risk of HTN, being prominent in obese participants. Our results support recommendations to reduce the consumption of soft drink to prevent and control HTN, although further large prospective studies or randomized controlled trials are warranted to confirm the observed association.

For predicting phenotypes and executing precision medicine, combination analysis of single nucleotide variants (SNVs) genotyping with copy number variations (CNVs) is required. The aim of this study was to discover SNVs or common copy CNVs and examine the combined frequencies of SNVs and CNVs in pharmacogenes using the Korean genome and epidemiology study (KoGES), a consortium project. The genotypes (N = 72,299) and CNV data (N = 1000) were provided by the Korean National Institute of Health, Korea Centers for Disease Control and Prevention. The allele frequencies of SNVs, CNVs, and combined SNVs with CNVs were calculated and haplotype analysis was performed. CYP2D6 rs1065852 (c.100C>T, p.P34S) was the most common variant allele (48.23%). A total of 8454 haplotype blocks in 18 pharmacogenes were estimated. DMD ranked the highest in frequency for gene gain (64.52%), while TPMT ranked the highest in frequency for gene loss (51.80%). Copy number gain of CYP4F2 was observed in 22 subjects; 13 of those subjects were carriers with CYP4F2*3 gain. In the case of TPMT, approximately one-half of the participants (N = 308) had loss of the TPMT*1*1 diplotype. The frequencies of SNVs and CNVs in pharmacogenes were determined using the Korean cohort-based genome-wide association study.

Although the role of adiponectin and leptin in the etiology of metabolic syndrome (MetS) has been explored in various populations, limited knowledge is available on the prospective association of adiponectin and leptin with the risk of MetS development. The present study aimed to evaluate the associations of adiponectin, leptin, and the leptin-adiponectin (LA) ratio with the future risk of MetS in middle-aged and older Korean adults. Using a prospective, population-based Ansan-Ansung cohort of the Korean Genome and Epidemiology Study (KoGES), 2691 Korean adults (1317 men and 1374 women) were included in the present study. Serum adiponectin and leptin concentrations were measured using commonly available enzyme-linked immunosorbent assay kits. Multivariable Cox proportional hazard models were used to investigate the relationships of the different adiponectin and leptin concentrations and LA ratio with the incident MetS. During a mean follow-up of 6.75 years, a total of 359 (27.26%) men and 385 (28.02%) women were identified as developing new-onset MetS. After controlling for covariates, higher adiponectin levels were associated with lower incidence of MetS (hazard ratio (HR) for third vs. first tertile: 0.53, 95% confidence interval (CI): 0.40–0.70 for men and HR: 0.54, 95% CI: 0.42–0.71 for women), while higher leptin levels (HR for third vs. first tertile: 2.88, 95% CI: 2.01–4.13 for men and HR: 1.55, 95% CI: 1.13–2.13 for women) and LA ratio (HR for third vs. first tertile: 3.07, 95% CI: 2.13–4.44 for men and HR: 1.94, 95% CI: 1.41–2.66 for women) were associated with an increased incidence of MetS. Among men, in the fully adjusted models an increase by one standard deviation (SD) in adiponectin levels was associated with a 10% decrease in MetS risk (HR per SD: 0.90, 95% CI: 0.85–0.95) while leptin and LA ratio was associated with a 5% (HR per SD: 1.05, 95% CI: 1.01–1.08) and 40% (HR per SD: 1.40, 95% CI: 1.22–1.62) increase in MetS risk, respectively. Among women, a significant association with MetS risk was observed only in adiponectin levels (HR per SD: 0.91, 95% CI: 0.88–0.95). We found that higher adiponectin level was associated with a lower risk of MetS, while higher leptin level and LA ratio were associated with elevated MetS incidence, irrespective of body mass index at baseline in both Korean men and women. Adiponectin and leptin levels and LA ratio could play a role as a useful biomarker in the prediction of future MetS development among middle-aged and older Koreans.

BackgroundThe association between dietary cholesterol and metabolic diseases remains controversial. However, the majority of studies focus on egg intake, and there is a limitation in the availability of prospective cohort studies. Our study examined the association between dietary cholesterol and the incidence risk of metabolic syndrome (MetS) in middle aged adults using large prospective cohort study in Republic of Korea.MethodsThe Health Examinees cohort from the Korean Genome and Epidemiology Study was used from baseline to follow-up. Dietary cholesterol intake was assessed by the validated semi-quantitative food frequency questionnaire. Participants were classified as quintile groups according to adjusted dietary cholesterol for total energy intake. MetS was defined as more than 3 of the 5 components of MetS. Hazard ratio (HR) and 95% confidence intervals (CI) for MetS were evaluated by multivariable cox regression analyses.ResultsOf the total 40,578 participants, metabolic syndrome developed in 4,172 (10.28%) individuals during an average follow-up period of approximately 4.76 years. Dietary cholesterol did not exhibit a significant association with the risk of MetS after adjusting for potential confounding factors, but a trend was observed indicating an increased risk with higher intake (p for trend = 0.044). Among the components of MetS, the incidence risk of high waist circumference (HR: 1.164, 95% CI: 1.049–1.290), high blood pressure (HR: 1.188, 95% CI: 1.075–1.313), high serum triglyceride (HR: 1.132, 95% CI: 1.044–1.227) and high fasting blood glucose (HR: 1.217, 95% CI: 1.132–1.308) in the group that consumed the highest dietary cholesterol intake was increased compared with the group that consumed the lowest dietary cholesterol intake. Dose-response relationship suggested a positive linear association between dietary cholesterol intake and the risk of high waist circumference (p-linearity = 0.004), blood pressure (p-linearity = 0.012), and triglycerides (p-linearity = 0.005).ConclusionThis study suggests a positive association between dietary cholesterol intake and the risk of MetS and its components (abdominal obesity, hypertension, hypertriglyceridemia, and hyperglycemia) in middle-aged Korean adults.

Solute carrier family 35 member F3 (SLC35F3) mediates intracellular thiamine transport, which is crucial for carbohydrate metabolism as thiamine is required for key pathways such as glycolysis and the tricarboxylic acid cycle. This study aimed to investigate the impact of the interaction between SLC35F3 and dietary carbohydrate intake on the incidence of metabolic syndrome (MetS). The study included 3923 Korean adults over 40 years of age from the Korean Genome and Epidemiology Study. The association between dietary carbohydrate intake, SLC35F3 rs10910387 genotypes, and MetS incidence was studied using multivariable Cox proportional hazard models. Over an average of 8.5 years of follow-ups, we documented 1471 MetS cases. MetS incidence was 1.88 times greater in men with the TT genotype and the highest carbohydrate intake than in those with the CC genotype and lowest carbohydrate intake (Hazard Ratio (HR) 1.88, 95% confidence interval (CI) 1.03–3.41). MetS incidence were 2.22 and 2.53 times higher in women with the TT genotype and carbohydrate intake tertile 2 and 3, respectively, than those with the CC genotype and carbohydrate intake tertile 1 (HR 2.22, 95% CI 1.12–4.42; HR 2.53, 95% CI 1.38–4.61). In summary, we report a novel interaction between SLC35F3 rs10910387 genotypes and dietary carbohydrate intake on MetS in Koreans.

Addressing dietary factors to lower blood pressure can be a crucial strategy at the population level to mitigate the risk of hypertension. In a prior investigation, a tailored food score was used as a dietary index relevant to hypertension among Korean adults. This current study aims to assess the association between the overall quality of the diet, taking into account more precise food components, and evaluate the risk of developing hypertension. This prospective cohort study included 5,342 adults aged 40-70 without hypertension who participated in the Korean Genome and Epidemiology Study (KoGES) from 2001 to 2016. The improved Recommended Food Score for Hypertension (iRFSH) is a modified version of the Recommended Food Score to assess the consumption of foods recommended in the Dietary Approaches to Stop Hypertension (DASH) diet for Korean foods. A higher score reflects greater consumption of recommended foods, indicative of higher dietary quality. The maximum total score is 65. High blood pressure, which includes both hypertension and prehypertension, was analyzed using Cox proportional hazard regression models to examine its prospective relationship with iRFSH. Among 2,478 males and 2,864 females with 10.8 mean years of follow-up, a higher score of iRFSH was associated with a lower risk of hypertension in the highest quintile compared to the lowest quintile [total: hazard ratio (HR): 0.79; 95% confidence interval (CI): 0.72, 0.87; female: HR: 0.71; 95% CI: 0.62, 0.83]. Higher iRFSH is associated with a lower incidence of hypertension. Our results suggest that the iRFSH may be a potential tool for assessing dietary quality and dietary patterns and predicting the risk of hypertension in Korean adults.

Dietary carbohydrate quality and quantity in relation to the incidence of type 2 diabetes: A prospective cohort study of middle-aged and older Korean adults.

This cohort study examined the association between total and individual dairy products and the risk of developing the metabolic syndrome (MetS) and its components in Korean adults from the Korean Genome and Epidemiology Study. We prospectively analysed 5510 participants aged 40-69 years without the MetS at baseline during a 10-year follow-up period. Dairy consumption was assessed with a semi-quantitative FFQ at baseline and after 4 years. The MetS was defined according to the criteria by the National Cholesterol Education Program Adult Treatment Panel III. The Cox's proportional hazard model was used to examine the association between consumption of total dairy products, milk and yogurt in servings per week and the risk of incident MetS or individual components. A total of 2103 subjects developed the MetS (38·2 %) during an average follow-up of 67·4 months (range 17-104 months). Frequent dairy consumption (>7 servings of total dairy and milk/week, ≥4 servings of yogurt/week) was associated with a reduced risk of incident MetS and its components. In the multivariable adjusted model, hazard ratios for the MetS were 0·51 (95 % CI 0·43, 0·61) for total dairy products, 0·50 (95 % CI 0·38, 0·66) for milk and 0·67 (95 % CI 0·57, 0·78) for yogurt in frequent consumers compared with non-consumers. An inverse association between milk/yogurt and low HDL-cholesterol was shown only in women. In conclusion, high consumption of individual dairy products including milk and yogurt as well as total dairy were associated with a reduced risk of incident MetS and individual components in Korean adults.

Serotonin receptor 3B polymorphisms are associated with type 2 diabetes: The Korean Genome and Epidemiology Study

This cross‐sectional study investigated the interaction between the genetic risk score (GRS) and abnormal high‐density lipoprotein (HDL) cholesterol lipid levels, which are modified by low‐carbohydrate diets (LCDs) and their effects on the prevalence of hypo‐HDL‐cholesterolemia (hypo‐HDL‐C) in Korean adults. Baseline data were obtained from the Ansan and Ansung study of the Korean Genome and Epidemiology Study (KoGES), conducted from 2001 to 2002, that targeted 8,314 Korean adults aged 40–69 years, including old men (47.6%) and women (52.4%), and whole genomic single nucleotide polymorphism (SNP) genotyping was performed. We identified 18 SNPs significantly associated with hypo‐HDL‐C in the proximity of several genes, including LPL, APOA5, LIPC, and CETP, and calculated the GRS. The low‐carbohydrate diet score (LCDS) was calculated on the basis of energy intake information from food frequency questionnaires. Furthermore, we performed multivariable‐adjusted logistic modeling to examine the odds ratio (OR) for hypo‐HDL‐C across tertiles of LCDS and GRS, adjusted for several covariates. Among participants in the highest GRS tertile, those in the highest tertile of the LCDS had a significantly lower risk of hypo‐HDL‐C (OR: 0.759, 95% CI (confidence interval): 0.625–0.923) than those in the lowest tertile of the LCDS. In the joint effect model, the group with the lowest GRS and highest LCDS was found to have the lowest risk of hypo‐HDL‐C prevalence. This study suggests that individuals with a high genetic risk for low HDL concentrations may have a beneficial effect on a lower intake of carbohydrates.

Genome-wide Transcriptome Profiling Reveals the Functional Impact of Rare De Novo and Recurrent CNVs in Autism Spectrum Disorders

IntroductionHypo-high-density lipoprotein cholesterolemia (hypo-HDL-C) contributes to the development of cardiovascular diseases. The hypothesis that the polygenic variants associated with hypo-HDL-C interact with lifestyle factors was examined in 58,701 middle-aged Korean adults who participated in the Korean Genome and Epidemiology Study (KoGES).MethodsParticipants were categorized into the Low-HDL (case; n = 16,980) and Normal-HDL (n = 41,721) groups. The participants in the Low-HDL group were selected using the guideline-based cutoffs for hypo-HDL-C (<40 mg/dL for men and < 50 mg/dL for women) and included those taking medication for dyslipidemia. The genes associated with hypo-HDL-C were determined through a genome-wide association study (GWAS) in a city hospital-based cohort, and the results were validated in the Ansan/Anung study. The genetic variants for the single nucleotide polymorphism (SNP)-SNP interaction were selected using a generalized multifactor dimensionality reduction analysis, and the polygenic risk score (PRS) generated was evaluated for interaction with lifestyle parameters.ResultsThe participants with hypo-HDL-C showed a 1.45 and 1.36-fold higher association with myocardial infarction and stroke, respectively. The High-PRS with four SNPs, namely ZPR1_rs3741297, CETP_rs708272, BUD13_rs180327, and ALDH1A2_rs588136, and that with the 11q23.3 haplotype were positively associated with hypo-HDL-C by about 3 times, which was a 2.4-fold higher association than the PRS of 24 SNP with p < 5×10−8. The risk alleles of CETP_rs708272 and ALDH1A2_rs588136 were linked to increased expression in the heart and decreased in the brain, respectively. The selected SNPs were linked to the reverse cholesterol transport pathway, triglyceride-rich lipoprotein particle remodeling pathway, cholesterol storage, and macrophage-derived foam cell differentiation regulation. The PRS of the 4-SNP model interacted with energy intake and smoking status, while that of the haplotype interacted with a glycemic index of the diet, sulfur microbial diet, and smoking status.DiscussionAdults with a genetic risk for hypo-HDL-C need to modulate their diet and smoking status to reduce their risk.

This study aimed to identify the association between the risk of hyper-LDL cholesterolemia (hyper-LDLC) and fatty acid consumption patterns (FACPs) using the data from the Korean Genome and Epidemiology Study (KoGES) prospective cohort. A total of 6542 middle-aged Korean adults were included in the analysis. Four FACPs were identified through principal component analysis of the reported intakes of 34 fatty acids (FAs): “long-chain FA pattern”; “short & medium-chain saturated fatty acid (SFA) pattern”; “n-3 polyunsaturated fatty acid (PUFA) pattern”; and “long-chain SFA pattern”. The “long-chain SFA pattern” lowered the risk of hyper-LDLC (relative risk (RR), 0.82; 95% confidence interval (CI), 0.72–0.94; p for trend, 0.004) and the “short & medium-chain SFA pattern” increased the risk of hyper-LDLC (RR, 1.17; 95% CI, 1.03–1.32; p for trend = 0.004). In sex-stratified analyses, the associations of the “long-chain SFA pattern” (RR, 0.73; 95% CI, 0.58–0.93; p for trend = 0.007) and the “short & medium-chain SFA pattern” (RR, 1.34; 95% CI, 1.07–1.69; p for trend = 0.003) with the hyper-LDLC risk were observed only in men, but not in women. These results suggest that FACPs with a high intake of long-chain SFA or a low intake of short and medium-chain SFA may protect Korean adults from hyper-LDLC.

The relationship between the variants of bitter taste receptor gene TAS2R4, dietary intake, and incidence of type 2 diabetes mellitus (T2DM) remains unclear. Hence, we aimed to examine the association of TAS2R4 rs2233998 variants with T2DM incidence in middle-aged and older Korean adults to understand if their association was modulated by dietary intake. Data of the Ansan-Ansung cohort from the Korean Genome and Epidemiology Study were used in this study. A total of 4552 Korean adults aged 40-69 years with no history of T2DM or cancer at baseline were followed-up for 16 years. Dietary intake was assessed using a 103-item food frequency questionnaire, and new T2DM cases were defined based on the World Health Organization and International Diabetes Federation criteria. Multivariate Cox proportional hazards models were used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for T2DM incidence. During the mean follow-up period of 11.97 years, 1082 (23.77%) new T2DM cases were identified. Women carrying the TT genotype of TAS2R4 rs2233998 exhibited 1.48 times higher incidence of T2DM (HR: 1.48; 95 CI: 1.13-1.93) than those carrying the CC genotype. TAS2R4 rs2233998 variants were positively associated with the incidence of T2DM among Korean women with high intakes of carbohydrates or sugars and low intakes of fruits or vegetables. TT carrier women in the highest tertile of carbohydrate or sugar intake exhibited an increased incidence of T2DM (HR: 2.08, 95% CI: 1.33-3.27 for carbohydrates; HR: 2.31, 95% CI: 1.53-3.51 for sugars) than CC carrier women. Women carrying the TT genotype in the lowest tertile exhibited an increased incidence of T2DM (HR: 1.55, 95% CI: 1.02-2.37 for vegetables; HR: 1.62, 95% CI: 1.06-2.48 for fruits) than women carrying the CC genotype in the highest tertile of vegetable or fruit consumption. However, no association was observed between TAS2R4 rs2233998 variants and dietary intake with T2DM incidence in Korean men. Our findings suggest that variants of TAS2R4 rs2233998 are associated with T2DM incidence, and their associations are strengthened by excessive intake of carbohydrates or sugars and inadequate intake of fruits or vegetables. Diet encompassing optimal intake of carbohydrates or sugars and high intake of fruits or vegetables may minimize the risk of developing T2DM.

Genomic instability, the hallmark of cancer, presents with a variety of mutation types, most commonly single nucleotide variations (SNVs) and copy number variations (CNVs), which traditionally have required different methods for identification. It has proven challenging to simultaneously achieve sufficient breadth to detect CNVs and depth to detect SNVs on samples of limited input amount. The objective of this study was to validate a new methodology for detection of SNVs and CNVs in a single assay. We used a massively multiplex PCR/NGS approach combining an SNV panel covering 585 point mutation hotspots in breast cancer (Cosmic) and a CNV panel targeting 28,000 SNPs designed to detect copy number at chromosomes 1, 2, 13, 18, 21, and X, and focal regions 4p16, 5p15, 7q11, 15q, 17p, 22q11, and 22q13. We applied these panels to breast cancer cell lines and fresh frozen (FF) breast tumor samples; the presence of CNVs in circulating cell-free tumor DNA (ctDNA) in the plasma of breast cancer patients was also investigated. The CNV assay methodology was validated using genomic DNA isolated from 96 human samples with known karyotype; sensitivity to single region deletions or duplications was 100% (71/71) and specificity was 100% for normal regions in the same samples. Single-molecule sensitivity for the detection of CNVs was established by analyzing isolated single cells. Performance of the mutation assay was demonstrated with the analysis of 5 matched tumor and normal cell lines, with 24 out of 27 SNVs known to be present in these cell lines detected. The 3 undetected SNVs were determined to be a result of assay design failure. Also, multiple somatic CNVs (median: 13) were detected in all 5 tumor cell lines. Analysis of the normal cell lines found no cancer related SNVs or CNVs. In 32 FF tumor samples, 78.1% (25/32) had SNVs detected; of samples with SNVs, 88% (22/25) had SNVs in TP53 or PIK3CA. Of the same 32 FF breast tumor samples, 96.9% (31/32) showed full or partial CNVs in at least 1 and up to 15 regions; of the 31 samples with detected CNVs, 93.5% had a CNV of either 1q or 17p, two of the three most prevalent breast cancer CNVs (the 16q region was not represented in this panel). Overall, a combination of SNV and CNV testing allowed identification of genetic changes in 100% of the breast tumor samples, a significant improvement in diagnostic yield than using SNV detection alone. Of the 12 breast cancer patients with matched tumor tissue and plasma samples, 83.3% (10/12) had CNVs detected in tissue. The CNVs present in each primary tumor sample were identified in corresponding plasma ctDNA samples (1 stage IIa, 7 stage IIb, and 2 stage III). The ctDNA fractions in these samples ranged from 0.58 to 4.33%; detection required as few as 86 heterozygous SNPs per CNV. Analysis of ctDNA for cancer-associated mutations may allow earlier, safer and more accurate profiling and monitoring of breast cancer. Thus, this targeted PCR approach offers the promise of an assay able to detect both cancer-associated SNVs and CNVs in the same sample with good sensitivity and specificity, and improved detection rates compared to assays that only detect SNVs. Citation Format: Robert J Pelham, Bernhard G Zimmermann, Eser Kirkizlar, Ryan K Swenerton, Bin Hoang, Onur Sakarya, Joshua E Babiarz, Nicholas Wayham, Tudor Constantin, Styrmir Sigurjonsson, Matthew Rabinowitz, Matthew Hill. Detection of single nucleotide variations and copy number variations in breast cancer tissue and ctDNA samples using single-nucleotide polymorphism-targeted massively multiplexed PCR [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P4-02-03.