BACKGROUND: Until recently, genome-wide association study (GWAS)-based findings have provided a substantial genetic contribution to type 2 diabetes mellitus (T2DM) or related glycemic traits. However, identification of allelic heterogeneity and population-specific genetic variants under consideration of potential confounding factors will be very valuable for clinical applicability. To identify novel susceptibility loci for T2DM and glycemic traits, we performed a two-stage genetic association study in a Korean population. METHODS: We performed a logistic analysis for T2DM, and the first discovery GWAS was analyzed for 1,042 cases and 2,943 controls recruited from a population-based cohort (KARE, n=8,842). The second stage, de novo replication analysis, was performed in 1,216 cases and 1,352 controls selected from an independent population-based cohort (Health 2, n=8,500). A multiple linear regression analysis for glycemic traits was further performed in a total of 14,232 nondiabetic individuals consisting of 7,696 GWAS and 6,536 replication study participants. A meta-analysis was performed on the combined results using effect size and standard errors estimated for stage 1 and 2, respectively. RESULTS: A combined meta-analysis for T2DM identified two new (rs11065756 and rs2074356) loci reaching genome-wide significance in CCDC63 and C12orf51 on the 12q24 region. In addition, these variants were significantly associated with fasting plasma glucose and homeostasis model assessment of beta-cell function. Interestingly, two independent single nucleotide polymorphisms were associated with sex-specific stratification in this study. CONCLUSION: Our study showed a strong association between T2DM and glycemic traits. We further observed that two novel loci with multiple diverse effects were highly specific to males. Taken together, these findings may provide additional insights into the clinical assessment or subclassification of disease risk in a Korean population.
Blood Glucose ; Cohort Studies ; Diabetes Mellitus, Type 2* ; Fasting ; Genetic Association Studies ; Genome-Wide Association Study* ; Homeostasis ; Humans ; Linear Models ; Male ; Polymorphism, Single Nucleotide ; Population Characteristics

Adiponectin may affect bone through interactions with two known receptors, adiponectin receptors (ADIPOR) 1 and 2. We examined the association between polymorphisms of ADIPOR1 and ADIPOR2 and bone mineral density (BMD) in postmenopausal Korean women. Six polymorphisms in ADIPOR1 and four polymorphisms in ADIPOR2 were selected and genotyped in all study participants (n = 1,329). BMD at the lumbar spine and femur neck were measured using dual-energy X-ray absorptiometry. Lateral thoracolumbar (T4-L4) radiographs were obtained for vertebral fracture assessment and the occurrence of non-vertebral fractures examined using self-reported data. P values were adjusted for multiple testing using Bonferroni correction (Pcorr). ADIPOR1 rs16850799 and rs34010966 polymorphisms were significantly associated with femur neck BMD (Pcorr = 0.036 in the dominant model; Pcorr = 0.024 and Pcorr = 0.006 in the additive and dominant models, respectively). Subjects with the rare allele of each polymorphism had lower BMD, and association of rs34010966 with BMD showed a gene dosage effect. However, ADIPOR2 single nucleotide polymorphisms and haplotypes were not associated with BMD at any site. Our results suggest that ADIPOR1 polymorphisms present a useful genetic marker for BMD in postmenopausal Korean women.
Base Sequence ; Bone Density/*genetics ; Female ; Femur Neck/physiology ; Genetic Association Studies ; Genetic Markers ; Genetic Predisposition to Disease ; Genotype ; Humans ; Osteoporosis, Postmenopausal/*genetics ; Polymorphism, Single Nucleotide ; Postmenopause ; Receptors, Adiponectin/*genetics ; Republic of Korea ; Sequence Analysis, DNA

There is increasing evidence of a biochemical link between lipid oxidation and bone metabolism. Paraoxonase 1 (PON1) prevents the oxidation of low-density lipoprotein (LDL) and metabolizes biologically active phospholipids in oxidized LDLs. Here, we performed association analyses of genetic variation in PON1 to ascertain its contribution to osteoporotic fractures (OFs) and bone mineral density (BMD). We directly sequenced the PON1 gene in 24 Korean individuals and identified 26 sequence variants. A large population of Korean postmenopausal women (n = 1,329) was then genotyped for eight selected PON1 polymorphisms. BMD at the lumbar spine and femoral neck was measured using dual-energy X-ray absorptiometry. Lateral thoracolumbar (T4-L4) radiographs were obtained for vertebral fracture assessment, and the occurrence of non-vertebral fractures (i.e., wrist, hip, forearm, humerus, rib, and pelvis) was examined using self-reported data. Multivariate analyses showed that none of the polymorphisms was associated with BMD at either site. However, +5989A>G and +26080T>C polymorphisms were significantly associated with non-vertebral and vertebral fractures, respectively, after adjustment for covariates. Specifically, the minor allele of +5989A>G exerted a highly protective effect against non-vertebral fractures (OR = 0.59, P = 0.036), whereas the minor allele of +26080T>C was associated with increased susceptibility to vertebral fractures (OR = 1.73, P = 0.020). When the risk for any OFs (i.e., vertebral or non-vertebral) was considered, the statistical significance of both polymorphisms persisted (P = 0.002-0.010). These results suggest that PON1 polymorphisms could be one of useful genetic markers for OF risk in postmenopausal women.
Aged ; Alleles ; Aryldialkylphosphatase/*genetics ; Bone Density ; Female ; Gene Frequency ; Gene Order ; Genetic Markers ; Genetic Predisposition to Disease ; Haplotypes ; Humans ; Korea/epidemiology ; Linkage Disequilibrium ; Male ; Middle Aged ; Molecular Typing ; Osteoporotic Fractures/epidemiology/*genetics ; *Polymorphism, Genetic ; *Postmenopause ; Risk Factors

No abstract available.
Microsatellite Repeats

The Epstein-Barr virus-transformed lymphoblastoid cell line (LCL) is one of the major genomic resources for human genetics and immunological studies. Use of LCLs is currently extended to pharmacogenetic studies to investigate variations in human gene expression as well as drug responses between individuals. We evaluated four common internal controls for gene expression analysis of selected hematopoietic transcriptional regulatory genes between B cells and LCLs. In this study, the expression pattern analyses showed that TBP (TATA box-binding protein) is a suitable internal control for normalization, whereas GAPDH (glyceraldehyde-3-phosphate dehydrogenase) is not a good internal control for gene expression analyses of hematopoiesis-related genes between B cells and LCLs at different subculture passages. Using the TBP normalizer, we found significant gene expression changes in selected hematopoietic transcriptional regulatory genes (downregulation of RUNX1 , RUNX3 , CBFB , TLE1, and NOTCH2; upregulation of MSC and PLAGL2) between B cells and LCLs at different passage numbers. These results suggest that these hematopoietic transcriptional regulatory genes are potential cellular targets of EBV infection, contributing to EBV-mediated B-cell transformation and LCL immortalization.
B-Lymphocytes ; Cell Line ; Epstein-Barr Virus Infections ; Gene Expression ; Genes, Regulator ; Genetics, Medical ; Humans ; Organophosphates ; Real-Time Polymerase Chain Reaction ; Up-Regulation

Osteoarthritis (OA) is the most common degenerative joint disorder in the elderly population. To identify OA-associated genetic variants and candidate genes, we conducted a genome-wide association study (GWAS). A total 3,793 samples (476 cases: wrist + knee and 3317 controls) from a community-based epidemiological study were genotyped using the Affymetrix SNP 5.0. An intronic SNP (rs4789934) in the TIMP2 (tissue inhibitor of metalloproteinase-2) showed the most significance with OA (odd ratio [OR] = 2.06, 95% confidence interval [CI] = 1.52-2.81, p = 4.01 x 10(-6)). Furthermore, a polymorphism (rs1352677) in the NKAIN2 (Na+/K+ transporting ATPase interacting 2) was suggestively associated with OA (OR = 1.43, CI = 1.22-1.66, p = 7.01 x 10(-6)). The present study provides new insights into the identification of genetic predisposing factors for OA.
Adenosine Triphosphatases ; Aged ; Epidemiologic Studies ; Genome-Wide Association Study ; Humans ; Introns ; Joints ; Knee ; Osteoarthritis ; Wrist

Obesity provokes many serious human diseases, including various cardiovascular diseases and diabetes. Body mass index (BMI) is a highly heritable trait that is broadly used to diagnose obesity. To identify genetic loci associated with obesity in Asians, we conducted a genome-wide association study (GWAS) of a population of Korean adults (n=6,742, age 40~60 years) and detected six BMI risk loci (TNR, FAM124B, RGS12, NFE2L3, MC4R and FTO) having p<1x10(-5). However, in the replication study, only melanocortin 4 receptor gene (MC4R) (rs9946888, p=4.58x10(-7)) was replicated with marginal significance (p<0.05) in the second cohort (n=5,102, age 40~60 years). This study indicates that each locus associated with BMI has very weak genetic effect.
Adult ; Asian Continental Ancestry Group ; Body Mass Index ; Cardiovascular Diseases ; Cohort Studies ; Genetic Loci ; Genome-Wide Association Study ; Humans ; Obesity ; Receptor, Melanocortin, Type 4

Osteoporotic fracture (OF), along with bone mineral density (BMD), is an important diagnostic parameter and a clinical predictive risk factor in the assessment of osteoporosis in the elderly population. However, a genomewide association study (GWAS) on OF has not yet been clarified sufficiently. To identify OF-associated genetic variants and candidate genes, we conducted a GWAS in a population-based cohort (Korean Association Resource [KARE], n=1,427 [case: 288 and control: 1139]) and performed a de novo replication study in hospital-based individuals (Asan and Catholic Medical Center [ACMC], n=1,082 [case: 272 and control: 810]). In a combined meta-analysis, a newly identified genetic locus in an intergenic region at 10p11.2 (near genes FZD8 and ANKRD30A ) showed the most significant association (odd ratio [OR] = 2.00, 95% confidence interval [CI] = 1.47~2.74, p=1.27x10(-5)) in the same direction. We provide the first evidence for a common genetic variant influencing OF and genetic information for further investigation in bone metabolism.
Aged ; Bone Density ; Cohort Studies ; DNA, Intergenic ; Genetic Loci ; Genome-Wide Association Study ; Humans ; Osteoporosis ; Osteoporotic Fractures ; Risk Factors

A-kinase-anchoring proteins (AKAPs) are scaffold proteins which compartmentalize protein kinase A (PKA, cAMP-dependent protein kinase) and other enzymes to specific subcellular sites. The spatiotemporal control of these enzymes by AKAPs is important for cellular function like cell growth and development etc. Hence, it is important to understand the basic function of AKAPs and their functional domains. However, diverse names, function, cellular localizations and many members of AKAPs increase difficulties when researchers search appropriate AKAPs for their experimental purpose. Nevertheless, there was no previous AKAPs-related database regardless of their important cellular functions and difficulty of finding appropriate AKAPs. So, we developed AKAPs database (AKAPDB), which contains their sequence information, functions and other information derived from prediction programs and other databases. Therefore, we propose that AKAPDB can be an important tool to researchers in the related fields. AKAPDB is available via the internet at http://plaza3.snu.ac.kr/akapdb/
Cyclic AMP-Dependent Protein Kinases ; Growth and Development ; Internet ; Proteins

There has been no genome-wide association study (GWAS) for macronutrient intake as a quantitative trait. To explore genetic loci associated with total calorie and macronutrient intake, genome-wide association data of autosomal single nucleotide polymorphisms (SNPs) from Korean adults were analyzed. We conducted a GWAS in 3,690 men and women aged 40 to 60 years from an urban population-based cohort. At the baseline examination (June 18, 2001 through January 29, 2003), DNA samples of the study subjects were collected and analyzed for genotyping. The information of average daily consumption of total calorie, carbohydrate, protein, and fat was obtained from a semi-quantitative food frequency questionnaire and transformed by natural logarithm for analyses after adjustment of calorie intake. Using multivariate linear regression analysis adjusted for age, sex, and height, we tested for 352,021 SNPs and found weak associations, which do not reach genome-wide association significance, with calorie and macronutrient intake. However, a number of SNPs were found to have potential associations with macronutrient intake; in particular, signals in SORBS1 and those in PRKCB1 were likely associated with carbohydrate and fat intake, respectively. We observed an inverse association between the minor allele of the SNPs in these genes and the amount of consumption of carbohydrate or fat. Our GWAS identified loci and minor alleles weakly associated with macronutrient intake. Because SORBS1 and PRKCB1 are reportedly associated with the metabolism of glucose and lipid as well as with obesity-related diseases, further investigations on biological and functional roles of polymorphism of these genes in the relation to macronutrient intake are warranted.
Adult ; Aged ; Alleles ; Cohort Studies ; DNA ; Female ; Genetic Loci ; Genome-Wide Association Study ; Glucose ; Humans ; Linear Models ; Lipid A ; Male ; Polymorphism, Single Nucleotide ; Surveys and Questionnaires