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Recent deep learning algorithms have further improved risk classification capabilities. However, an appropriate feature selection method is required to overcome dimensionality issues in population-based genetic studies. In this Korean case–control study of nonsyndromic cleft lip with or without cleft palate (NSCL/P), we compared the predictive performance of models that were developed by using the genetic-algorithm-optimized neural networks ensemble (GANNE) technique with those models that were generated by eight conventional risk classification methods, including polygenic risk score (PRS), random forest (RF), support vector machine (SVM), extreme gradient boosting (XGBoost), and deep-learning-based artificial neural network (ANN). GANNE, which is capable of automatic input SNP selection, exhibited the highest predictive power, especially in the 10-SNP model (AUC of 88.2%), thus improving the AUC by 23% and 17% compared to PRS and ANN, respectively. Genes mapped with input SNPs that were selected by using a genetic algorithm (GA) were functionally validated for risks of developing NSCL/P in gene ontology and protein–protein interaction (PPI) network analyses. The IRF6 gene, which is most frequently selected via GA, was also a major hub gene in the PPI network. Genes such as RUNX2, MTHFR, PVRL1, TGFB3, and TBX22 significantly contributed to predicting NSCL/P risk. GANNE is an efficient disease risk classification method using a minimum optimal set of SNPs; however, further validation studies are needed to ensure the clinical utility of the model for predicting NSCL/P risk.

G protein-coupled receptor 119 (GPR119) is known to be a promising therapeutic target for type 2 diabetes. Recently, it has been reported that the GPR119 agonist increases bone mineral density in an animal model of diabetes, suggesting that GPR119 may play a key role in bone metabolism. In this study, we investigated the functional role of GPR119 in receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast formation. We found that the GPR119 expression was markedly increased in preosteoclasts and then downregulated in mature osteoclasts. Activation of GPR119 with AS1269574, a potent selective agonist for GPR119, inhibited the generation of multinuclear osteoclasts from bone marrow-derived macrophages. Confirming this observation, targeted silencing of GPR119 using short hairpin RNA abrogated the AS1269574-mediated suppressive effect on osteoclast formation. GPR119 activation attenuated the expression of c-Fos and nuclear factor of activated T cells cytoplasmic 1 (NFATc1) and blocked RANKL-stimulated phosphorylation of IκBα, c-Jun N-terminal protein kinase (JNK), and extracellular signal-regulated kinase (ERK) but not p38. In addition, GPR119 activation suppressed preosteoclast fusion by downregulating the expression of the dendritic cell-specific transmembrane (DC-STAMP), a molecule that is essential for cell-cell fusion in osteoclast formation. Furthermore, ectopic expression of DC-STAMP restored AS1269574-mediated inhibition of osteoclast fusion. Taken together, our findings demonstrate that GPR119 plays a negative role in osteoclast differentiation and fusion induced by RANKL, and therefore may represent a potential target for bone resorption-associated diseases.

Pleiotropy has important implications for understanding the genetic basis and risk assessment of osteoporosis. Our aim was to identify pleiotropic genetic variants associated with the development of osteoporosis and predict osteoporosis risk by leveraging pleiotropic variants. We evaluated the effects of 21 conventional risk factors and 185 single-nucleotide polymorphisms (SNPs) in 63 inflammation- and metabolism-related genes on osteoporosis risk in a community-based Korean cohort study of 1025 participants, the Hallym Aging Study. Ten nongenetic factors, including sex (female) and hematocrit level, and 12 SNPs across ten genes showed evidence of association with incident osteoporosis in 270 initially osteoporosis-free subjects who completed a 6-year follow up. Three gene variants, rs1801282 (PPARG-Pro12Ala, hazard ratio (HR) = 3.26, P = 0.008), rs1408282 (near EPHA7, HR = 1.87, P = 0.002), and rs2076212 (PNPLA3-Gly115Cys, HR = 2.24, P = 0.024), were associated with significant differences in survival among the three genotype groups (Pdiff = 0.042, 0.003, and 0.048, respectively). Individuals in the highest polygenic risk score tertile were 27.9 fold more likely to develop osteoporosis than those in the lowest tertile (P = 0.004). The PPARG gene in particular was a hub pleiotropic gene in the epistasis network. Our findings highlight pleiotropic modulations of metabolism- and inflammation-related genes in the development of osteoporosis and demonstrate the contribution of pleiotropic genetic variants in prediction of osteoporosis risk.

GPR84, a member of the G protein-coupled receptor family, is found predominantly in immune cells, such as macrophages, and functions as a pivotal modulator of inflammatory responses. In this study, we investigated the role of GPR84 in receptor activator of nuclear factor-κB ligand (RANKL)-induced osteoclast differentiation. Our microarray data showed that GPR84 was significantly downregulated in osteoclasts compared to in their precursors, macrophages. The overexpression of GPR84 in bone marrow-derived macrophages suppressed the formation of multinucleated osteoclasts without affecting precursor proliferation. In addition, GPR84 overexpression attenuated the induction of c-Fos and nuclear factor of activated T cells, cytoplasmic 1 (NFATc1), which are transcription factors that are critical for osteoclastogenesis. Furthermore, knockdown of GPR84 using a small hairpin RNA promoted RANKL-mediated osteoclast differentiation and gene expression of osteoclastogenic markers. Mechanistically, GPR84 overexpression blocked RANKL-stimulated phosphorylation of IκBα and three MAPKs, JNK, ERK, and p38. GPR84 also suppressed NF-κB transcriptional activity mediated by RANKL. Conversely, GPR84 knockdown enhanced RANKL-induced activation of IκBα and the three MAPKs. Collectively, our results revealed that GPR84 functions as a negative regulator of osteoclastogenesis, suggesting that it may be a potential therapeutic target for osteoclast-mediated bone-destructive diseases. This article is protected by copyright. All rights reserved

The purpose of this study was to investigate changes of rotator cuff muscles after arthroscopic rotator cuff repair by measuring the muscle atrophy (MA) of rotator cuff muscles at the preoperative, immediate postoperative, and 1-year postoperative time points.Inclusion criteria were (1) arthroscopic rotator cuff repair of a full-thickness rotator cuff tear and (2) the presence of the preoperative (approximately 1 month before surgery), immediate postoperative (approximately 3 days after surgery), and 1-year postoperative magnetic resonance imaging (MRI) undertaken at our institution. Exclusion criteria were (1) the absence of any of the 3 MRIs, (2) isolated subscapularis repair, and (3) rotator cuff repair with margin convergence only. The MA was assessed with the modified tangent sign (TS), the occupation ratio (OR), and the cross-sectional areas (CSAs) of the supraspinatus and infraspinatus. Structural integrity was evaluated using Sugaya's classification. Measurements 1 year after surgery were compared with those of the preoperative and the immediate postoperative time points according to the integrity.Seventy-seven patients were included in the study. The TS improved in 23.4% of patients and worsened in 6.5% with the preoperative baseline, while it improved in 5.2% of patients and worsened in 23.4% (P.001). The OR improved in 24.5% of patients but worsened in 3.9% with the preoperative baseline, while it improved in 13.0% and worsened in 11.7% patients (P.001). The CSAs of the supraspinatus and infraspinatus changed by 8.7% ± 24.5% and -0.3% ± 16.1% with the preoperative baseline and by -12.8% ± 20.3% and -10.5% ± 14.9% with the immediate postoperative baseline (all P.001).The results of the study showed that changes of the MA after arthroscopic rotator cuff repair were different with respect to the baselines and the integrity. Generally, the MA measured with the immediate postoperative baseline worsened, whereas that measured with the preoperative baseline improved.Level III, retrospective comparative study.

While tendon degeneration has been known to be an important cause of rotator cuff disease, few studies have objectively proven the association of tendon degeneration and rotator cuff disease. The purpose of this study was to investigate changes of tendon degeneration with respect to the stage of rotator cuff disease. A total of 48 patients were included in the study: 12 with tendinopathy, 12 with a partial-thickness tear (pRCT), 12 with a full-thickness tear (fRCT), and 12 as the control. A full-thickness supraspinatus tendon sample was harvested en bloc from the middle portion between the lateral edge and the musculotendinous junction of the tendon using a biopsy punch with a diameter of 3 mm. Harvested samples were evaluated using a semi-quantitative grading scale with 7 parameters after haematoxylin and eosin staining. There was no significant difference in age, gender, symptom duration, and Kellgren-Lawrence grade between the groups except for the global fatty degeneration index. All of the seven parameters were significantly different between the groups and could be categorized as follows: early responders (fibre structure and arrangement), gradual responder (rounding of the nuclei), after-tear responders (cellularity, vascularity, and stainability), and late responder (hyalinization). The total degeneration scores were not significantly different between the control (6.08 ± 1.16) and tendinopathy (6.67 ± 1.83) (n.s.). However, the score of pRCT group (10.42 ± 1.31) was greater than that of tendinopathy (P

Personalized risk prediction for diabetic cardiovascular disease (DCVD) is at the core of precision medicine in type 2 diabetes (T2D). We first identified three marker sets consisting of 15, 47, and 231 tagging single nucleotide polymorphisms (tSNPs) associated with DCVD using a linear mixed model in 2378 T2D patients obtained from four population-based Korean cohorts. Using the genetic variants with even modest effects on phenotypic variance, we observed improved risk stratification accuracy beyond traditional risk factors (AUC, 0.63 to 0.97). With a cutoff point of 0.21, the discrete genetic liability threshold model consisting of 231 SNPs (GLT231) correctly classified 87.7% of 2378 T2D patients as high or low risk of DCVD. For the same set of SNP markers, the GLT and polygenic risk score (PRS) models showed similar predictive performance, and we observed consistency between the GLT and PRS models in that the model based on a larger number of SNP markers showed much-improved predictability. In silico gene expression analysis, additional information was provided on the functional role of the genes identified in this study. In particular, HDAC4, CDKN2B, CELSR2, and MRAS appear to be major hubs in the functional gene network for DCVD. The proposed risk prediction approach based on the liability threshold model may help identify T2D patients at high CVD risk in East Asian populations with further external validations.

Objective To identify the contribution of TGFA gene variants to the risk of nonsyndromic cleft lip with or without palate (NS-CL±P). Design The samples were from 142 Korean NS-CL±P families and 119 control parents having nonaffected children. Minor allele frequency, heterozygosity, and χ2 test for Hardy-Weinberg equilibrium were calculated for each of 10 selected single-nucleotide polymorphisms (SNPs). Ten SNPs were used to examine the association of case-parent trios with the transmission disequilibrium test (TDT) and conditional logistic regression models (CLRMs). Both allelic and genotypic TDTs for individual SNPs and sliding windows of haplotypes consisting of two to five SNPs were tested using family- and haplotype-based association test programs. Genotypic odd ratios (GORs) were obtained from CLRMs using STATA software. The parent-of-origin effect was evaluated for 10 SNPs, and a comparison between 218 case parents and 119 control parents was performed to investigate paternal and maternal ORs. Results Family-based TDT and haplotype analysis exhibited no statistical significance, but a relatively meaningful association was shown with rs3771497 (all P < .05; two SNPs, rs3771497 and rs3755377; five SNPs, rs3771497, rs3755377, rs3771485, rs11466212, and rs3771475). G/G homozygotes at rs3771497 have a significant decreased risk of NS-CL±P (GOR = 0.30, P < .01). No SNPs showed parent-of-origin effects. However, in the comparison between case parents and control parents, a single-marker analysis of maternal line showed a significant association with NS-CL±P in rs3771497 ( P < .001, recessive model). Conclusion The association of the TGFA gene with NS-CL±P in Korean populations was not clearly found. However, the etiologic effect of the TGFA gene on NS-CL±P patients should be investigated in terms of maternal genotype influence.

High triglyceride (TG) levels are known to be associated with complex diseases such as cardiovascular disease. Here, we evaluated the effect of interactions between genetic polymorphisms and environmental factors on plasma TG levels in a Korean aging cohort. Thirty-two single nucleotide polymorphism (SNP) markers located in seven genes (ADLH2, APOE, GCKR, MC4R, TCF7L2, GATA2, and HNF1A) for TG levels were genotyped in 714 older Koreans (mean age, 68 years). We performed multiple linear regression analyses for these SNP markers under three genetic models (i.e. additive, dominant, and recessive) and evaluated their associations with multiple environmental factors, including obesity, systolic blood pressure, and drinking and smoking habits. We found evidence for four SNP-smoking interactions. The CC genotype of rs1260326 (GCKR) interacted with current smoking for lower TG levels (P G×E = 0.017). TG levels were higher in smokers with the GG genotype of rs2713604 (GATA2) than in those with the GA + AA genotypes (195.6 and 145.7 mg/dL, respectively, P G×E = 0.029). The GA + AA genotypes of rs2713603 (GATA2) were associated with elevated TG levels in smokers when compared to non-smokers carrying the GG genotype (180.6 mg/dL vs. 148.3 mg/dL, P G×E = 0.046). The C allele of rs2464196 (HNF1A) interacted with current smoking for elevated TG levels (P G×E = 0.028). The gene and cigarette smoking interactions shown in this study need to be validated in a large-scale study.

Genetic risk factors for hypertension may have age or gender specificity and pleiotropic effects. This study aims to measure the risk of genetic and non-genetic factors in the occurrence of hypertension and related diseases, with consideration of potential confounding factors and age-gender stratification. A discovery set of 352,228 genotyped plus 1.8 million imputed single-nucleotide polymorphisms were analyzed for 2,886 hypertensive cases and 3,440 healthy controls obtained from two community-based cohorts in Korea, and selected gene variants were replicated in the Health Examinee cohort (665 cases and 1,285 controls). Genome-wide association analyses were conducted in 12 groups stratified by age and gender after adjusting for potential covariates under three genetic models. Age, rural area residence, body mass index, family history of hypertension, male gender, current alcohol drinking status, and current smoking status were significantly associated with hypertension (P = 4 × 10(-151) to 0.011). Five gene variants, rs11066280 (C12orf51), rs12229654 and rs3782889 (MYL2), rs2072134 (OAS3), rs2093395 (TREML2), and rs17249754 (ATP2B1), were found to be associated with hypertension mostly in men (P = 4.76 × 10(-14) to 4.46 × 10(-7) in the joint analysis); three SNPs (rs11066280, rs12229654, and rs3782889) remained significant after Bonferroni correction in an independent population. Three gene variants, rs12229654, rs17249754, and rs11066280, were significantly associated with metabolic disorders such as hyperlipidemia and diabetes (P = 0.00071 to 0.0097, respectively). Careful consideration of the potential confounding effects in future genome-wide association studies is necessary to uncover the genetic underpinnings of complex diseases.

Objective: To investigate the association between the risk of tooth agenesis and single-nucleotide polymorphisms (SNPs) of MSX1 and PAX9 genes in nonsyndromic cleft patients. Materials and Methods: The subjects were 126 Korean nonsyndromic cleft patients. Tooth agenesis type (TAT) was classified as none (0); cleft area (1); cleft area + other area (2); and other area (3) based on agenesis of the maxillary lateral incisor (MXLI) and another tooth within or outside the cleft area. TAT was further grouped into two subcategories (0 and 1) and four subcategories (0, 1, 2, and 3). Three SNPs of MSX1 and 10 SNPs of PAX9 were investigated using Fisher's exact test and logistic regression analysis. Results: Although the association between genotype distribution of PAX9-rs7142363 and TAT was significant (P < .05 in four subcategories), genotypic odds ratios (GORs) of SNPs in each TAT were not meaningful. However, for MSX1-rs12532 and PAX9-rs2073247, associations between genotypic distribution and TAT were significant (P < .01 in four subcategories and P < .05 in two subcategories; P < .01 in two subcategories, respectively). In cleft area, GORs of MXLI agenesis in genotypes GA of MSX1-rs12532 and CT of PAX9-rs2073247 were increased by 3.14-fold and 4.15-fold compared with genotype GG of MSX1-rs12532 and CC of PAX9-rs2073247, respectively (P Conclusion: Genetic disturbances of MSX1 and PAX9 genes are associated with tooth agenesis within and outside the cleft area.

High C-reactive protein (CRP) level (above 3 mg/L), an inflammatory biomarker, is a well-known risk factor for cardiovascular disease. We investigated the longitudinal effects of interaction between genetic variants of seven candidate loci (i.e., IL6R, CRP, GCKR, IL6, CYP17A1, HNF1A, and APOE) and eight non-genetic factors (i.e., body mass index (BMI), total cholesterol to high density lipoprotein cholesterol ratio (T/HDL), systolic blood pressure, diastolic blood pressure (DBP), current smoking, alcohol consumption, regular exercise, and sleeping hours) on plasma hsCRP levels in a community-based cohort composed of 1,051 elderly Korean participants with a 6-year follow up. We applied a recently developed nonparametric approach, Survival Dimensionality Reduction (SDR) to evaluate gene-environment interactions using follow up data, and compared the results to those of conventional statistical approaches, Cox proportional hazard (CPH) regression model and log-rank test. Four gene variants significantly interacted with three non-genetic factors: SNPs rs2293571 (GCKR), rs1004467 (CYP17A1) and high DBP (HR = 3.22 and 2.95, P G×E = 0.013 and 0.017, respectively); rs2464196 (HNF1A) and two non-genetic factors, regular exercise (HR = 3.78, P G×E = 0.043) and high T/HDL (HR = 4.54, P G×E = 0.042); and rs439401 (APOE) and regular exercise (HR = 3.01, P G×E = 0.049). The interaction between the rs2464196 and T/HDL was consistently observed in both CPH model and SDR model (Accuracy = 0.86, P = 0.011). Investigating the effects of gene-environment interactions on baseline plasma hsCRP concentrations will provide clues to identify the pathway involved in increasing hsCRP level and the risks of related diseases.

Fatty infiltration (FI) is known to be an irreversible change which continues degeneration after rotator cuff repair. Previous studies evaluated postoperative changes in FI using a preoperative baseline. This study aimed to investigate the changes in FI using an immediate postoperative baseline. We hypothesized that FI was progressed more when measured relative to an immediate postoperative baseline than to a preoperative baseline. From 2008 to 2010, 77 patients who met the following criteria were included in this study: arthroscopic rotator cuff repair of a full-thickness rotator cuff tear and presence of preoperative (approximately 1 month before surgery), immediate postoperative (approximately 3 days after surgery), and 1-year postoperative (at least 9 months to 1 year after surgery) magnetic resonance imaging (MRI) undertaken. The exclusion criteria were: absence of any of the three MRIs, isolated subscapularis repair, and rotator cuff repair with margin convergence only. The MRIs were examined to assess the Goutallier grade of the rotator cuff muscles for the assessment of FI. Structural integrity was evaluated using the Sugaya classification. Measurements 1 year after surgery were compared with those at the preoperative and immediate postoperative time points according to the integrity. In the total and retear group, FI in the supraspinatus and infraspinatus 1 year after surgery did not change significantly relative to the preoperative baseline (all n.s.), but progressed compared to the immediate postoperative baseline (all p

Objective: To test the null hypothesis that there is no significant difference in the initial growth pattern among three cleft types before alveolar bone graft (ABG) according to cleft type (unilateral cleft lip and alveolus [UCLA], unilateral cleft lip and palate [UCLP], and cleft palate [CP]). Materials and Methods: Samples consisted of the UCLA group, the UCLP group, and the CP group. Individuals were treated with the identical surgical technique by the same surgeon and had no history of orthodontic/orthopedic treatment. Lateral cephalograms taken 1 month before ABG were analyzed using 29 variables. One-way analysis of variance (ANOVA) testing and bivariate and logistic regression analyses were performed. Results: An increasing tendency for Class III relationships in the order of UCLA, UCLP, and CP was noted (ANB, AB-to-facial plane angle, AB-to-mandibular plane angle; P , .001, respectively). UCLP and CP groups demonstrated more posterior positioning of the maxilla (SNA, A-to-N-perp; P , .001, respectively) and a hyperdivergent pattern (gonial angle, SN-GoMe angle, FMA; P , .001, respectively) compared with the UCLA group. Because no differences in palatal plane angle and SN-to-occlusal plane angle were noted among the three groups, the hyperdivergent pattern in the UCLP and CP groups might be due to an innate growth pattern and eventual adaptation of the mandible to maxillary growth. UCLP and CP groups showed more Class III relationships (ANB: P , .05, P , .001, respectively) and a more hyperdivergent pattern (FMA: P , .05, P , .01, respectively) than the UCLA group. Conclusion: When the degree of cleft involvement increases from the primary palate to the secondary palate, the predominance of the Class III relationship and the hyperdivergent pattern increases also. (Angle Orthod 2011;81:1103–1110.)

Adiponectin is associated with obesity and insulin resistance. To date, there has been no genome-wide association study (GWAS) of adiponectin levels in Asians. Here we present a GWAS of a cohort of Korean volunteers. A total of 4,001 subjects were genotyped by using a genome-wide marker panel in a two-stage design (979 subjects initially and 3,022 in a second stage). Another 2,304 subjects were used for follow-up replication studies with selected markers. In the discovery phase, the top SNP associated with mean log adiponectin was rs3865188 in CDH13 on chromosome 16 (p = 1.69 × 10(-15) in the initial sample, p = 6.58 × 10(-39) in the second genome-wide sample, and p = 2.12 × 10(-32) in the replication sample). The meta-analysis p value for rs3865188 in all 6,305 individuals was 2.82 × 10(-83). The association of rs3865188 with high-molecular-weight adiponectin (p = 7.36 × 10(-58)) was even stronger in the third sample. A reporter assay that evaluated the effects of a CDH13 promoter SNP in complete linkage disequilibrium with rs3865188 revealed that the major allele increased expression 2.2-fold. This study clearly shows that genetic variants in CDH13 influence adiponectin levels in Korean adults.

Hypertension is the most prevalent disease worldwide and is itself a risk factor for cerebral, cardiac, and renal diseases. The inconsistency of candidate genes suggested by previous genomewide association studies (GWASs) may be due to not only differences in study design and genetic or environmental background but also the difference in the power of analysis between continuous traits and discrete traits. We analyzed 352,228 single nucleotide polymorphisms (SNPs) in 8842 unrelated Koreans obtained from Ansan and Ansung cohorts. We performed a series of GWA analyses using three different phenotype models; young hypertensive cases (278 subjects) versus elderly normotensive controls (680 subjects); the upper 25% (2211 hypertensive cases) versus the lower 25% of the SBP distribution (2211 hypotensive controls); and finally SBP and DBP as continuous traits (8842 subjects). The numbers of young hypertensive cases and elderly normotensive controls were not large enough to achieve genomewide significance. The model comparing the upper 25% subjects to the lower 25% of subjects showed a power that was approximate to that of QTL analysis. Two neighboring SNPs of the ATP2B1 gene, rs17249754 (SBP, p=; DBP, p=) and rs7136259 (SBP, p=; DBP, p=), were associated with both SBP and DBP. Interestingly, a SNP of the RPL6 gene, rs11066280, revealed a significant genomewide association with SBP in men only (p=), and four SNPs located near the MAN2A1 gene showed a strong association with DBP only in elderly men aged 60-70 years (e.g., rs6421827, p=). However, we did not observe any gene variant attaining genomewide significance consistently in the three phenotype models except for the ATP2B1 gene variants. In general, the association signal with blood pressure was stronger in women than in men. Genes identified in GWASs are expected to open the way for prevention, early diagnosis, and personalized treatment of hypertension.

Tooth loss has been suggested as a potential risk factor for stroke. We conducted a prospective cohort study of stroke in Korea on hypertension, diabetes, smoking, and tooth loss to characterize their independent effects and interactions. The overall risk of stroke and the risk of different subtypes of stroke were evaluated in relation to tooth loss using Cox proportional hazards models among 867,256 Korean men and women, aged 30-95 years, who received health insurance from the National Health Insurance Corporation and were medically evaluated between 1992 and 1995, with tooth loss measured. The overall prevalence of having at least one tooth removed among the people in the study was 29.8% (31.9% for men and 22.3% for women). During a 14-year follow-up, 28,258 strokes with 5105 fatal strokes occurred. For men and women, tooth loss was associated with total stroke and stroke subtypes. In a multivariable model adjusting for selected covariates, a graded association between higher tooth loss and higher risk of total stroke was observed in men [> or =7 lost teeth versus 0 (hazard ratio (HR)=1.3; 95% confidence interval (CI), 1.2-1.4)] and in women (HR=1.2; 95% CI, 1.0-1.3). The HRs for ischemic and hemorrhagic stroke were also similar in men and women. There was evidence of interaction of hemorrhagic stroke risk with hypertension and tooth loss. Tooth loss is independently associated with increased risk of stroke and hypertension does interact antagonistically, particularly for hemorrhagic stroke.

Background and purpose The objective of this study was to develop the stroke risk prediction model among Korean population with high risk of stroke. Methods The data in this prospective cohort study came from 47,233 stroke events occurring over 13 years among 1,223,740 Koreans, aged 30–84 years, who were insured by the National Health Insurance Corporation (NHIC) and take a biennial medical examination from 1992 to 1995. The Cox proportional Hazard Model was used to develop the Korean Stroke Risk Prediction (KSRP) model for each sex. Also, the split-half method was applied for developing a model with the first half and for testing with the rest. Results The average 10-year risk for stroke was 3.52% for men and 3.66% for women. In general, actual stroke event rates were similar to the event rates predicted by the KSRP model. The discrimination using the KSRP model in the Korean cohort was high: the area under the receiver operating characteristic curve was 0.8165 [95% confidence interval (CI), 0.7993–0.8337] for men and 0.8095 (0.7875–0.8315) for women. A graded association between predicted stroke risk and actual stroke event was observed in men [highest versus lowest deciles of the predicted risk (hazard ratio (HR) 63.17; 95% confidence interval (CI), 52.30–76.31)] and in women (HR, 120.34; 95% CI, 85.31–169.77). Conclusions The KSRP model could be used to predict the risk of stroke and would provide a useful guide to identify the groups at high risk for stroke among Korean.

Objective: Obesity is known to be associated with diverse disease outcomes; however, the effect of body weight on the occurrence of stroke remains controversial and has not been studied sufficiently, particularly among Asian populations and among women. The purpose of this study was to investigate the effect of BMI on the risk of stroke among Korean women. Methods and Procedures: The overall risk of stroke and the risk of different subtypes of stroke were evaluated in relation to BMI using Cox's proportional hazard models among 439,582 Korean women, aged 30–95 years, in a 13-year prospective cohort study with enrollment from 1992–1995. Stratified analyses were performed for age groups and cigarette smoking status. Results: The average BMI was 23.2 kg/m2 at baseline. The overall risk of stroke was the lowest in the group with a BMI

Isolated oral clefts, including cleft lip with/without cleft palate (CL/P) and cleft palate (CP), have a complex and heterogeneous etiology. Case-parent trios from three populations were used to study genes spanning chromosome 2, where single nucleotide polymorphic (SNP) markers were analyzed individually and as haplotypes. Case-parent trios from three populations (74 from Maryland, 64 from Singapore and 95 from Taiwan) were genotyped for 962 SNPs in 104 genes on chromosome 2, including two well-recognized candidate genes: TGFA and SATB2. Individual SNPs and haplotypes (in sliding windows of 2-5 SNPs) were used to test for linkage and disequilibrium separately in CL/P and CP trios. A novel candidate gene (ZNF533) showed consistent evidence of linkage and disequilibrium in all three populations for both CL/P and CP. SNPs in key regions of ZNF533 showed considerable variability in estimated genotypic odds ratios and their significance, suggesting allelic heterogeneity. Haplotype frequencies for regions of ZNF533 were estimated and used to partition genetic variance into among-and within-population components. Wright's fixation index, a measure of genetic diversity, showed little difference between Singapore and Taiwan compared with Maryland. The tensin-1 gene (TNS1) also showed evidence of linkage and disequilibrium among both CL/P and CP trios in all three populations, albeit at a lower level of significance. Additional genes (VAX2, GLI2, ZHFX1B on 2p; WNT6-WNT10A and COL4A3-COL4A4 on 2q) showed consistent evidence of linkage and disequilibrium only among CL/P trios in all three populations, and TGFA showed significant evidence in two of three populations.

High-throughput genotyping systems promise to be an efficient means of identifying susceptibility genes involved in the etiology of non-Mendelian disorders. Adequate amounts of high-quality DNA are essential, however, for large-scale genotyping studies (1). The supply of genomic DNA is frequently limited, and the quality of DNA obtained from oral buccal swabs or Guthrie cards has not been thoroughly evaluated for high-throughput single-nucleotide polymorphism (SNP) genotyping (2)(3). Whole-genome amplification (WGA) technologies offer the opportunity to expand DNA from depleted biological samples. The first generation of WGA strategies (i.e., PCR-based methods) (4)(5), however, was limited by substantial amplification bias and incomplete coverage of genetic markers (6)(7). Recently, new strategies for WGA, such as multiple displacement amplification (MDA) or OmniPlex® WGA technology (Rubicon Genomics) have been developed. MDA is an isothermal amplification with the bacteriophage φ29 DNA polymerase (6)(8), whereas OmniPlex uses in vitro libraries with fragmented DNA (∼1.5 kb) to amplify the entire genome by PCR (9). To apply WGA technology to BeadArray™ genotyping (Illumina), the utility of MDA and/or OmniPlex on DNA samples derived from lymphoblast cells has been evaluated (9)(10). In this study, we determined the genotyping success rate and reliability of 2 MDA variants (8)(11) and OmniPlex with and without 7-deaza-dGTP, using buccal swabs, whole blood, dried blood spots, and sheared genomic DNA on 1260- and 1228-SNP BeadArray panels. The 7-deaza-dGTP nucleotide analog was included in an attempt to ensure amplification of GC-rich DNA. After Institutional Review Board approval and informed consent were obtained, DNA samples were collected from participants in a study of oral clefts (12). Genomic DNA samples were prepared from peripheral blood by protein precipitation (13). Buccal cells were obtained by rubbing the inside of cheeks with a brush (Medical Packaging), and DNA …

Summary The genetic bases underlying the range and severity of phenotypes in Mendelian disorders is poorly understood; however, improvements in this area have the potential to facilitate analysis of oligogenic disorders. The nail dysplasia observed in Nail Patella Syndrome (NPS) was selected as a quantifiable variable within a Mendelian disorder, for which data could be readily obtained, to allow investigation of the genetic basis of variation. Analysis of SNP haplotypes across the LMX1B gene demonstrated association between the haplotype of the mutant allele and the variability in the nail score (p = 0.024). These results are in contrast to those obtained previously, which supported a modifying role for the wild-type allele. Since there is no evidence that particular mutations, or classes of mutation, are associated with the variation (p > 0.5), further work is required to identify the elements associated with the LMX1B gene that mediate phenotypic severity.

Oral clefts, one of the most common forms of birth defects, are considered to be of complex etiology, including both genetic and environmental causes. To date, however, no particular genetic cause has been confirmed for isolated, nonsyndromic oral clefts. Previous case-control and family-based association studies reported an association between an intronic CA repeat of the MSX1 gene and risk for oral clefts. In this study, we identify eight single-nucleotide polymorphisms (SNPs) in the MSX1 gene, and present genotype results for these SNPs in a set of 206 oral cleft cases and their parents. We performed single-marker and haplotype-based transmission disequilibrium tests (TDTs), and tested for evidence of interaction between MSX1 haplotypes and exposure to maternal smoking in the first trimester, using a case-only approach. The haplotype TDT analyses further implicate this gene, or region, in controlling the risk for oral clefts, particularly for cleft palate. In addition, case-only haplotype analyses suggest an interaction between variation in the MSX1 gene and exposure to maternal smoking. This study encourages further focus on the MSX1 gene region to ultimately determine specific variants predisposing to oral clefts.

Normal-karyotype acute myeloid leukemia (NK-AML) is a highly malignant and cytogenetically heterogeneous hematologic cancer. We searched for somatic mutations from 10 pairs of tumor and normal cells by using a highly efficient and reliable analysis workflow for whole-exome sequencing data and performed association tests between the NK-AML and somatic mutations. We identified 21 nonsynonymous single nucleotide variants (SNVs) located in a coding region of 18 genes. Among them, the SNVs of three leukemia-related genes (MUC4, CNTNAP2, and GNAS) reported in previous studies were replicated in this study. We conducted stepwise genetic risk score (GRS) models composed of the NK-AML susceptible variants and evaluated the prediction accuracy of each GRS model by computing the area under the receiver operating characteristic curve (AUC). The GRS model that was composed of five SNVs (rs75156964, rs56213454, rs6604516, rs10888338, and rs2443878) showed 100% prediction accuracy, and the combined effect of the three reported genes was validated in the current study (AUC, 0.98; 95% confidence interval, 0.92 to 1.00). Further study with large sample sizes is warranted to validate the combined effect of these somatic point mutations, and the discovery of novel markers may provide an opportunity to develop novel diagnostic and therapeutic targets for NK-AML.

The purpose of this study was to investigate the contribution of PAX9 gene to the risk of nonsyndromic cleft lip with or without cleft palate (NS-CL/P). The samples consisted of 142 Korean NS-CL/P families (90 males and 52 females; 9 cleft lip, 26 cleft lip and alveolus, and 107 cleft lip and palate; 76 trios and 66 dyads). A total of 10 single-nucleotide polymorphisms (SNPs) were tested for association with Korean CL/P case-parent trios using transmission disequilibrium test (TDT) and conditional logistic regression models. The minor allele frequency, heterozygosity, and a χ test for Hardy-Weinberg equilibrium at each SNP were computed between parents. Pairwise linkage disequilibrium was computed as both D' and r2 for all SNPs. Both allelic and genotypic TDTs were performed for individual SNPs using family-based association test program. Sliding windows of haplotypes consisting of 2 to 8 SNPs were tested using haplotype-based association test program. Genotypic odd ratios were obtained from conditional logistic regression models using STATA software. The family-based TDT using individual SNPs and 2- to 8-SNP haplotypes of the gene indicated a significant association at rs17104928 (P = 0.014). The haplotype analysis revealed that the association was most significant for the haplotype consisting of 3 SNPs (rs2073247, rs17104928, and rs17176643; P = 0.007). G/A heterozygote at rs17104928 had a significantly increased association with NS-CL/P (genotypic odd ratio, 2.88; 95% confidence interval, 1.42-5.84; P = 0.0014, dominant model). The high-risk SNP and genotype may provide a better understanding of the etiologic role of PAX9 gene in NS-CL/P and potential options for genetic counseling.

OBJECTIVE: To test the null hypothesis that there is no significant difference in the initial growth pattern among three cleft types before alveolar bone graft (ABG) according to cleft type (unilateral cleft lip and alveolus [UCLA], unilateral cleft lip and palate [UCLP], and cleft palate [CP]). MATERIALS AND METHODS: Samples consisted of the UCLA group, the UCLP group, and the CP group. Individuals were treated with the identical surgical technique by the same surgeon and had no history of orthodontic/orthopedic treatment. Lateral cephalograms taken 1 month before ABG were analyzed using 29 variables. One-way analysis of variance (ANOVA) testing and bivariate and logistic regression analyses were performed. RESULTS: An increasing tendency for Class III relationships in the order of UCLA, UCLP, and CP was noted (ANB, AB-to-facial plane angle, AB-to-mandibular plane angle; P < .001, respectively). UCLP and CP groups demonstrated more posterior positioning of the maxilla (SNA, A-to-N-perp; P < .001, respectively) and a hyperdivergent pattern (gonial angle, SN-GoMe angle, FMA; P < .001, respectively) compared with the UCLA group. Because no differences in palatal plane angle and SN-to-occlusal plane angle were noted among the three groups, the hyperdivergent pattern in the UCLP and CP groups might be due to an innate growth pattern and eventual adaptation of the mandible to maxillary growth. UCLP and CP groups showed more Class III relationships (ANB: P < .05, P < .001, respectively) and a more hyperdivergent pattern (FMA: P < .05, P < .01, respectively) than the UCLA group. CONCLUSION: When the degree of cleft involvement increases from the primary palate to the secondary palate, the predominance of the Class III relationship and the hyperdivergent pattern increases also.

An Icelandic study showed a significant positive association between phosphodiesterase 4D (PDE4D) gene variants and stroke. However, subsequent studies reported conflicting results, possibly due to small sample sizes and the heterogeneity of the studies.We performed a meta-analysis on 6 SNPs of the PDE4D gene to investigate the association between this gene and ischemic stroke by integrating the results of previous studies, comprising 11,834 cases and 15,233 controls. A pooled genotypic odds ratio (OR) for each SNP was determined under 3 genetic models (i.e. dominant, recessive, and codominant) using both fixed- and random-effects models with consideration for heterogeneity and publication bias across studies.Among the SNPs included in this study, SNP56 (rs702553) showed the most significant association with ischemic stroke in a meta-analysis comprised of 7 homogenous studies. The overall OR of the TT genotype compared to the AA genotype was 1.29 (95% CI 1.03-1.61; p = 0.022). For SNP83 (rs966221), a protective effect of the ancestral allele T was observed only in Asian populations (ORTT 0.79, 95% CI 0.69-0.90; p = 0.0005). This meta-analysis revealed a significant association of PDE4D gene variants with the risk of ischemic stroke, and further investigations are warranted to evaluate possible ethnic-specific effects.

Isolated cleft lip with or without cleft palate (CL/P) is among the most common human birth defects, with a prevalence of 1 in 700 live births. The paired box (PAX) genes have been suggested as candidate genes for CL/P based largely on mouse models; however, few human studies have focused on this gene family. This study tests for association between markers in four PAX genes and CL/P using a case-parent trio design considering parent-of-origin effects. Trios from four populations (76 from Maryland, 146 from Taiwan, 35 from Singapore, and 40 from Korea) were genotyped for 34 single nucleotide polymorphisms (SNPs) in the PAX3, PAX6, PAX7, and PAX9 genes. We performed the transmission disequilibrium test (TDT) on individual SNPs. Parent-of-origin effects were assessed using the transmission asymmetry test (TAT) and the parent-of-origin likelihood ratio test (PO-LRT). TDT analysis showed one SNP (rs766325) in PAX7 yielding evidence of linkage and association when parent-of-origin was not considered, with an OR(transmission)=1.62 (P=0.003), and five SNPs in PAX6 (including two pairs in near perfect linkage disequilibrium). TAT analysis of all trios revealed two SNPs in PAX7 and four SNPs in PAX3 showing significant excess maternal transmission. For these six SNPs, the maternal OR(transmission) ranged between 1.74 and 2.40, and PO-LRT was also significant (P-values=0.035–0.012). When this analysis was limited to trios with male cases, SNPs in PAX7 showed higher maternal OR(transmission) and greater significance. PAX genes may influence the risk of CL/P through maternal effects, possibly imprinting, which seems to be stronger among male cases.

Recently, a number of different approaches have been used to examine variation in gene expression and to identify genes whose level of transcript differed greatly among unrelated individuals. Previous studies have commonly focused on identifying determinants that regulate gene expressions by targeting individual genes. However, it is difficult to detect true differences in the level of gene expression among genotypes from noise due to issues such as multiple testing and limited sample size. To increase the statistical power for detecting this difference, we consider a 'gene set' approach by focusing on subtle but coordinated changes in gene expression across multiple genes rather than individual genes. We defined a 'gene set' as a set of genes in the same biological pathway and focused on identifying common regulators based on an assumption that the genes within the same pathway are controlled by common regulators. We applied the gene set approach to the expression data of mRNA in Centre d'Etude du Polymorphisme Humain lymphoblast cells to identify regulators controlling the genes in a biological pathway. Our gene set approach successfully identified potent regulators controlling gene expression in an inflammatory response pathway.

Nonsyndromic cleft lip with or without cleft palate (CL/P) is one of the most common birth defects with the birth prevalence being highest in Asian (2/1000 live births), intermediate in European (1/1000 live births), and lowest in African populations (0.4/1000 live births). CL/P is a complex disease with both genetic and environmental risk factors.1 Mutations in the interferon regulatory factor 6 gene (IRF6) located on chromosome 1q32.3-q41 are responsible for a majority of van der Woude syndrome (VWS) cases. VWS is an autosomal dominant syndrome that includes an oral cleft and pits on the lower lip in approximately 85% of cases. Fifteen percent of VWS cases have an isolated cleft with no lip pits and are clinically indistinguishable from nonsyndromic CL/P.2 The GATA124F08 marker located 1Mb from IRF6 has shown a significant heterogeneity LOD (1.15) with α = 0.45,3 and an anonymous marker (D1S205) in IRF6 has yielded significant evidence of linkage and linkage disequilibrium (LD) in 106 nonsyndromic CL/P trios.4 Recently, strong evidence of overtransmission of the G allele at the IRF6 c.820G>A marker (rs2235371) was found in CL/P case-parent trios from Asia and South America,5 and a significantly higher frequency of the GG genotype was observed among 192 Thai CL/P cases compared with controls (odds ratio = 1.67).6 This variant creates a valine→isoleucine substitution at amino acid 274 (p.V274I) in the protein-binding domain [the Smad-interferon regulatory factor binding domain (SMIR)] of IRF6, but the A allele is rare in white populations. Analysis of seven other single nucleotide polymorphisms (SNPs) in and around IRF6 has shown several distinct haplotypes demonstrating altered transmission in Io-wan and Danish trios.5 Confirmatory studies using Italian, European-American, and Belgian CL/P families, respectively, have strengthened the evidence that IRF6 is important in the etiology of nonsyndromic oral clefts.7–9 Risk of CL/P associated with particular variants in IRF6 may differ among ethnic groups, however. Here, we evaluated 13 SNPs in and around IRF6 to test for association with nonsyndromic CL/P in 77 European-American (including five incomplete trios), 146 (three incomplete trios) and 34 (11 incomplete trios) Han Chinese trios from Taiwan and Singapore, respectively, plus 40 (two incomplete trios) Korean CL/P trios. Expression of IRF6 in human craniofacial structures was also determined using publicly available data.

The importance of family history of type 2 diabetes (FHD) as a risk factor for atherosclerotic cardiovascular disease (ASCVD) remains controversial. A report of diabetes in parents and siblings was used to establish FHD in a cohort of 1,005,230 Koreans aged 30-95 years insured by the National Health Insurance Corporation who had a biennial medical evaluation during 1992-1995. ASCVD morbidity and mortality from 1993 to 2005 were examined in relation to FHD and other ASCVD risk factors. The risk of ischemic heart disease (IHD) increased significantly (19%) in men with FHD but not in women. A strong interaction was observed between FHD and personal history of diabetes for the occurrence of ASCVD; men with both diabetes and FHD were at significantly increased risk of developing IHD, cerebrovascular disease and ASCVD with hazard ratios (HR) of 2.28, 2.07, and 2.12, respectively, compared to those who had neither FHD nor type 2 diabetes. Corresponding risks were 2.64, 2.03, and 2.10 in women, respectively. This study demonstrates that risk of ASCVD is increased among those with diabetes and a family history of diabetes; suggesting that genetic factors associated with occurrence of familial diabetes may increase risk of ASCVD beyond the risk among people without FHD.

Evaluations of screening or diagnostic tests sometimes incorporate measures of overall accuracy, diagnostic accuracy, or test efficiency. These terms refer to a single summary measurement calculated from 2 x 2 contingency tables that is the overall probability that a patient will be correctly classified by a screening or diagnostic test. We assessed the value of overall accuracy in studies of test validity, a topic that has not received adequate emphasis in the clinical literature.Guided by previous reports, we summarize the issues concerning the use of overall accuracy. To document its use in contemporary studies, a search was performed for test evaluation studies published in the clinical literature from 2000 to 2002 in which overall accuracy derived from a 2 x 2 contingency table was reported.Overall accuracy is the weighted average of a test's sensitivity and specificity, where sensitivity is weighted by prevalence and specificity is weighted by the complement of prevalence. Overall accuracy becomes particularly problematic as a measure of validity as 1) the difference between sensitivity and specificity increases and/or 2) the prevalence deviates away from 50%. Both situations lead to an increasing deviation between overall accuracy and either sensitivity or specificity. A summary of results from published studies (N = 25) illustrated that the prevalence-dependent nature of overall accuracy has potentially negative consequences that can lead to a distorted impression of the validity of a screening or diagnostic test.Despite the intuitive appeal of overall accuracy as a single measure of test validity, its dependence on prevalence renders it inferior to the careful and balanced consideration of sensitivity and specificity.

A hospital-based, case-control study was conducted to measure risk factors for hemorrhagic fever with renal syndrome in Korean soldiers. Between October 1989 and January 1992, 196 cases and 295 controls were admitted into the study. Information was collected on behavioral and environmental variables, and the data were analyzed by multiple logistic regression. The strongest risk factors were seeing Apodemus in the area (odds ratio [OR] = 4.9), living in a primitive dwelling such as a lean-to (OR = 3.9), and being exposed to dust (OR = 3.7). The most protective factors were living in barracks (OR = 0.3-0.5) and self-reported use of any insecticide or insect repellent (OR = 0.5).

The purpose of this study was to investigate the contribution of MSX1 gene to the risk of nonsyndromic cleft lip with or without cleft palate (NS-CL ± P) in the Korean population. The samples consisted of 142 NS-CL ± P families (9 with cleft lip, 26 with cleft lip and alveolus, and 107 with cleft lip and palate; 76 trios and 66 dyads). Three single nucleotide polymorphisms (SNPs: rs3821949, rs12532, and rs4464513) were tested for association with NS-CL ± P case-parent trios using transmission disequilibrium test (TDT) and conditional logistic regression models (CLRMs). Minor allele frequency, heterozygosity, χ(2) test for Hardy-Weinberg equilibrium, and pairwise linkage disequilibrium (LD) at each SNP were computed. The family- and haplotype-based association test programs were used to perform allelic and genotypic TDTs for individual SNPs and to fabricate sliding windows of haplotypes. Genotypic odds ratios (GORs) were obtained from CLRMs using R software. Although the family-based TDT indicated a meaningful association for rs3821949 (P = 0.028), the haplotype analysis did not reveal any significant association with rs3821949, rs12532, or rs4464513. The A allele at rs3821949 had a significant increased risk of NS-CL ± P (GOR, 1.64; 95% confidence interval,1.03-2.63; P = 0.038, additive model). A positive association is suggested between MSX1 rs3821949 and NS-CL ± P in the Korean population.

OBJECTIVES This study aimed to measure the association between the adiponectin, C1Q and collagen domain-containing (ADIPOQ) gene variants and obesity in Koreans. METHODS Three single nucleotide polymorphisms located in the ADIPOQ gene were genotyped in a population-based cross-sectional study of 986 healthy Koreans. Three different case-control groups (i.e. G1, G2, and G3) were defined according to body mass index (BMI) and serum adiponectin levels. Allelic and genotypic associations of this gene with obesity were measured using multivariate logistic regression analyses in each group. RESULTS The G allele of -11377C>G, a polymorphism located in the promoter region of the ADIPOQ gene (odds ratio (OR), 1.48; 95% confidence interval, 1.13-1.94) and most haplotypes including this allele significantly increased the risk for obesity. However, the OR decreased from 3.98 (G1 group) to 2.90 (G2 group) and 2.30 (G3 group) when a less strict definition of obesity was used. Most haplotypes, including this allele, significantly increased the risk of obesity. The statistical evidence from the GG genotype of -11377C>G (OR, 3.98) and the GT/GT diplotype composed of -11377G>C and +45T>G (OR, 5.20) confirmed the contribution of the G allele toward a predisposition for obesity. CONCLUSION These results suggest the contribution of the ADIPOQ gene toward susceptibility to obesity in healthy Koreans. The high-risk genotypes and haplotypes identified here may provide more information for identifying individuals who are at risk of obesity.