Genetic Risk Assessment of Nonsyndromic Cleft Lip with or without Cleft Palate by Linking Genetic Networks and Deep Learning Models.

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.

The Liability Threshold Model for Predicting the Risk of Cardiovascular Disease in Patients with Type 2 Diabetes: A Multi-Cohort Study of Korean Adults.

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.

Identification of pleiotropic genetic variants affecting osteoporosis risk in a Korean elderly cohort.

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.

G protein-coupled receptor 119 is involved in RANKL-induced osteoclast differentiation and fusion.

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.

Novel Genetic Variants Associated with Lumbar Spondylosis in Koreans : A Genome-Wide Association Study.

OBJECTIVE: The aim of this study was to identify the susceptibility genes responsible for lumbar spondylosis (LS) in Korean patients. METHODS: Data from 1427 subjects were made available for radiographic grading and genome wide association studies (GWAS) analysis. Lateral lumbar spine radiographs were obtained and the various degrees of degenerative change were semi-quantitatively scored. A pilot GWAS was performed using the AffymetrixGenome-Wide Human single-nucleotide polymorphisms (SNPs), 500K array. A total of 352228 SNPs were analyzed and the association between the SNPs and case-control status was analyzed by stepwise logistic regression analyses. RESULTS: The top 100 SNPs with a cutoff p-value of less than 3.7×10-4 were selected for joint space narrowing, while a cutoff p-value of 6.0×10-4 was applied to osteophytes and the Kellgren-Lawrence (K-L) osteoarthritis grade. The SNPs with the strongest effect on disc space narrowing, osteophytes, and K-L grade were serine incorporator 1 (rs155467, odds ratio [OR]=17.58, p=1.6×10-4), stromal interaction molecule 2 (STIM1, rs210781, OR=5.53, p=5×10-4), and transient receptor potential cation channel, subfamily C (rs11224760, OR=3.99, p=4.8×10-4), respectively. Leucine-rich repeat-containing G protein-coupled receptor 4 was significantly associated with both disc space narrowing and osteophytes (rs1979400, OR=2.01, p=1.1×10-4 for disc space narrowing, OR=1.79, p=3×10-4 for osteophytes), while zinc finger and BTB domain containing 7C was significantly and negatively associated with both osteophytes and a K-L grade >2 (rs12457004,OR=0.25, p=5.8×10-4 and OR=0.27, p=5.3×10-4, respectively). CONCLUSION: We identified SNPs that potentially contribute to the pathogenesis of LS. This is the first report of a GWAS in an Asian population.

G protein-coupled receptor 84 controls osteoclastogenesis through inhibition of NF-κB and MAPK signaling pathways.

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.

Changes of fatty infiltration according to the immediate postoperative time point in magnetic resonance imaging after arthroscopic rotator cuff repair.

PURPOSE: 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. METHODS: 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. RESULTS: 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 < 0.001). In the retear group, FI in the supraspinatus and infraspinatus reduced for seven and two of 20 patients, respectively, compared with the preoperative baseline; however, no patients showed a reduced FI compared with the immediate postoperative baseline. CONCLUSIONS: The results of the study showed that the changes in FI reduced, remained or progressed in accordance with the baseline and structural integrity. FI progressed when compared with the immediate postoperative baseline than with the preoperative baseline. The immediate postoperative time point would be considered as the baseline to monitor the true changes of FI after repair. LEVEL OF EVIDENCE: Retrospective comparative study, Level III.

Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia.

BACKGROUND: Acute myeloid leukemia (AML) is a biologically and clinically heterogeneous cancer of the bone marrow that is characterized by the rapid growth of abnormal myeloid cells. METHODS: We performed a mutational analysis to identify AML somatic mutations using the whole-exome sequencing data of 36 tumor-normal sample pairs from Korean patients with de novo AML. We explored the functional impact of the genes identified in the mutational analyses through an integrated Gene Ontology (GO) and pathway analysis. RESULTS: A total of 11 genes, including NEFH (p = 6.27 × 10-13 and q = 1.18 × 10-8) and TMPRSS13 (p = 1.40 × 10-10 and q = 1.32 × 10-6), also demonstrated q values less than 0.1 in 36 Korean AML patients. Five out of the 11 novel genes have previously been reported to be associated with other cancers. Two gene mutations, CEBPA (p = 5.22 × 10-5) and ATXN3 (p = 9.75 × 10-4), showed statistical significance exclusively in the M2 and M3 subtypes of the French-American-British classifications, respectively. A total of 501 genes harbored 478 missense, 22 nonsense, 93 frameshift indels, and/or three stop codon deletions and these gene mutations significantly enriched GO terms for signal transduction (GO:0007165, p = 1.77 × 10-3), plasma membrane (GO:0005886, p = 3.07 × 10-4), and scaffold protein binding (GO:0097110, p = 8.65 × 10-4). The mitogen-activated protein kinase (hsa04010, 7.67 × 10-4) was the most enriched Kyoto Encyclopedia of Genes and Genomes pathway. CONCLUSIONS: Morphological AML subtypes may in part reflect subtype specific patterns of genomic alterations. Following validation, future studies to evaluate the usefulness of these genes in genetic testing for the early diagnosis and prognostic prediction of AML patients would be worthwhile.

Risk prediction of pulmonary tuberculosis using genetic and conventional risk factors in adult Korean population.

A complex interplay among host, pathogen, and environmental factors is believed to contribute to the risk of developing pulmonary tuberculosis (PTB). The lack of replication of published genome-wide association study (GWAS) findings limits the clinical utility of reported single nucleotide polymorphisms (SNPs). We conducted a GWAS using 467 PTB cases and 1,313 healthy controls obtained from two community-based cohorts in Korea. We evaluated the performance of PTB risk models based on different combinations of genetic and nongenetic factors and validated the results in an independent Korean population comprised of 179 PTB cases and 500 healthy controls. We demonstrated the polygenic nature of PTB and nongenetic factors such as age, sex, and body mass index (BMI) were strongly associated with PTB risk. None of the SNPs achieved genome-wide significance; instead, we were able to replicate the associations between PTB and ten SNPs near or in the genes, CDCA7, GBE1, GADL1, SPATA16, C6orf118, KIAA1432, DMRT2, CTR9, CCDC67, and CDH13, which may play roles in the immune and inflammatory pathways. Among the replicated SNPs, an intergenic SNP, rs9365798, located downstream of the C6orf118 gene showed the most significant association under the dominant model (OR = 1.59, 95% CI 1.32-1.92, P = 2.1×10-6). The performance of a risk model combining the effects of ten replicated SNPs and six nongenetic factors (i.e., age, sex, BMI, cigarette smoking, systolic blood pressure, and hemoglobin) were validated in the replication set (AUC = 0.80, 95% CI 0.76-0.84). The strategy of combining genetic and nongenetic risk factors ultimately resulted in better risk prediction for PTB in the adult Korean population.

Degree of tendon degeneration and stage of rotator cuff disease.

PURPOSE: 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. METHODS: 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. RESULTS: 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 < 0.001), and so was the score of fRCT (12.33 ± 1.15) than that of pRCT (p = 0.009). CONCLUSION: This study showed that the degeneration of supraspinatus tendon increases as the stage of rotator cuff disease progresses from tendinopathy to pRCT, and then to fRCT. The degree of degeneration of tendinopathy was not different from that of normal but aged tendons, and significant tendon degeneration began from the stage of pRCT. The clinical relevance of the study is that strategies and goals of the treatment for rotator cuff disease should be specific to its stage, in order to prevent disease progression for tendinopathy and pRCT, as well to restore the structural integrity for fRCT. LEVEL OF EVIDENCE: Diagnostic, Level I.

Changes of Muscle Atrophy According to the Immediate Postoperative Time Point in Magnetic Resonance Imaging After Arthroscopic Rotator Cuff Repair.

PURPOSE: 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. METHODS: 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. RESULTS: 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). CONCLUSIONS: 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 OF EVIDENCE: Level III, retrospective comparative study.

Genetic effect of transforming growth factor alpha gene variants on the risk of nonsyndromic cleft lip with or without palate in korean populations.

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 χ(2) 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.

Genetic risk assessment for cardiovascular disease with seven genes associated with plasma C-reactive protein concentrations in Asian populations.

Plasma C-reactive protein (CRP) level is a predictor of cardiovascular risk. We performed a meta-analysis on the effect of 12 single-nucleotide polymorphisms (SNPs) within 8 candidate loci in 36 752 Asians. In addition, we created weighted genetic risk scores (wGRSs) to evaluate the combined effects of genetic variants, which were suggested in the meta-analysis, for predicting the risks of elevated CRP levels as well as increased risks of hypertension and cardiovascular disease (CVD) in 748 Koreans. Nine SNPs located in seven genes, CRP, IL6R, GCKR, IL6, CYP17A1, HNF1A and APOE, were significantly associated with circulating CRP levels in this meta-analysis. Two SNPs, rs7310409 (HNF1A, P=3.4 × 10(-23)) and rs7553007 (CRP, P=3.4 × 10(-17)), had the most significant effects on CRP levels; and two SNPs, rs2097677 (IL6) and rs1004467 (CYP17A1) have never been found in the previous European meta-analysis. In Koreans, the subjects in the highest wGRS group had an ∼2.5-fold higher mean CRP level compared with those in the lowest wGRS group (P=2.1 × 10(-5)). We observed significant increases in the risks of hypertension (odds ratio=2.18, P=0.006) and CVD (odds ratio=9.59, P=3.2 × 10(-6)) among the subjects in the highest wGRS group. The wGRS models specific to Koreans may warrant further validation to be used as a proxy for the risk of CVD in Asians.

Investigation of Parental Transmission of RUNX2 Single Nucleotide Polymorphism and Its Association With Nonsyndromic Cleft Lip With or Without Palate.

OBJECTIVE: To investigate the association and parental transmission of RUNX2 single nucleotide polymorphisms (SNPs) with risk of nonsyndromic cleft lip with or without cleft palate (NS-CL±P). DESIGN: Four RUNX2 SNPs in 142 Korean NS-CL±P families (nine cleft lip, 26 cleft lip and alveolus, and 107 cleft lip and palate; 76 trios and 66 dyads) were genotyped. The minor allele frequency, heterozygosity, and chi-square test for Hardy-Weinberg equilibrium at each SNP were computed between parents. Pairwise linkage disequilibrium was computed as D' and r(2) for all SNPs. Both allelic and genotypic transmission disequilibrium tests (TDTs) were performed for individual SNPs using a family-based association test program. Sliding windows of haplotypes consisting of two to four SNPs were tested using a haplotype-based association test program. Genotypic odds ratios (GORs) were calculated from conditional logistic regression models. Parent-of-origin effects were assessed using transmission asymmetry test and parent-of-origin likelihood ratio test. RESULTS: The family-based TDT showed significant evidence of linkage and association at rs1934328 (P = .001). In the haplotype analysis, two, three, and four haplotypes containing rs1934328 revealed significant associations (P = .0017, P = .0022, and P = .0020, respectively). The genotypes A/T and T/T at rs1934328 were significantly associated with NS-CL±P compared with the genotype A/A (GOR = 2.75, 95% confidence interval [CI] = 1.39-5.45, P =0.0019 in the dominant model; GOR = 5.38, 95% CI = 1.34-21.68, P = .0046 in the additive model). However, no parent-of origin effect was observed. CONCLUSION: These findings suggest possible involvement of RUNX2-rs194328 in the etiology of NS-CL±P in Korean cleft-parent trios without excess parental transmission.

Male-specific genetic effect on hypertension and metabolic disorders.

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.

Associations between the risk of tooth agenesis and single-nucleotide polymorphisms of MSX1 and PAX9 genes in nonsyndromic cleft patients.

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 <. 01; P < .05). In cleft area + other area, the GOR of agenesis of MXLI and another tooth in genotype AA of MSX1-rs12532 was increased by fivefold compared with genotype GG (P < .05). CONCLUSION: Genetic disturbances of MSX1 and PAX9 genes are associated with tooth agenesis within and outside the cleft area.

Genetic risk prediction for normal-karyotype acute myeloid leukemia using whole-exome sequencing.

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.

Association between MSX1 SNPs and nonsyndromic cleft lip with or without cleft palate in the Korean population.

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.

Sample size and statistical power calculation in genetic association studies.

A sample size with sufficient statistical power is critical to the success of genetic association studies to detect causal genes of human complex diseases. Genome-wide association studies require much larger sample sizes to achieve an adequate statistical power. We estimated the statistical power with increasing numbers of markers analyzed and compared the sample sizes that were required in case-control studies and case-parent studies. We computed the effective sample size and statistical power using Genetic Power Calculator. An analysis using a larger number of markers requires a larger sample size. Testing a single-nucleotide polymorphism (SNP) marker requires 248 cases, while testing 500,000 SNPs and 1 million markers requires 1,206 cases and 1,255 cases, respectively, under the assumption of an odds ratio of 2, 5% disease prevalence, 5% minor allele frequency, complete linkage disequilibrium (LD), 1:1 case/control ratio, and a 5% error rate in an allelic test. Under a dominant model, a smaller sample size is required to achieve 80% power than other genetic models. We found that a much lower sample size was required with a strong effect size, common SNP, and increased LD. In addition, studying a common disease in a case-control study of a 1:4 case-control ratio is one way to achieve higher statistical power. We also found that case-parent studies require more samples than case-control studies. Although we have not covered all plausible cases in study design, the estimates of sample size and statistical power computed under various assumptions in this study may be useful to determine the sample size in designing a population-based genetic association study.

Association between PAX9 single-nucleotide polymorphisms and nonsyndromic cleft lip with or without cleft palate.

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.