Eun Pyo Hong

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.

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.

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.

A Novel Association between Lysyl Oxidase Gene Polymorphism and Intracranial Aneurysm in Koreans

Purpose Lysyl oxidase (LOX) controls the cross-linking and maturation of elastin and collagen fibers. In this study, we investigated the association between LOX gene polymorphisms and intracranial aneurysm (IA) formation in a homogeneous Korean population. Materials and Methods This cross-sectional study involved 80 age-sex matched patients with IA and controls. Fishers exact test was performed to analyze allelic associations between ten single nucleotide polymorphisms (SNPs) and IA, including 41 ruptured and 39 unruptured cases. Haplotype-specific associations were analyzed using the omnibus test estimating asymptotic chi-square statistics. Results Of ten SNPs, three SNPs (rs2303656, rs3900446, and rs763497) were significantly associated with IA (p<0.01). The C allele of rs3900446 was significantly related to increased IA risk with a significant threshold [odds ratio (OR)=20.15, p=4.8×10−5]. Meanwhile, the A allele of rs2303656 showed a preventive effect against IA formation (p=8.2×10−4). Seventeen of 247 haplotype structures showed a suggestive association with IA (asymptotic p<0.001). Of ten SNP haplotype combinations, the CG combination of rs3900446 and rs763497 reached Bonferroni-adjusted significant threshold in IA patients (minor haplotype frequency=0.113, asymptotic p=1.3×10−5). However, there was no association between aneurysm rupture and the LOX gene. Conclusion This preliminary study indicated that LOX gene polymorphisms, such as rs2303656, rs3900446, and rs763497, may play crucial roles in IA formation in the Korean population. Our novel findings need to be validated in a large-scale independent population.

Genetic Risk Assessment of Elastin Gene Polymorphisms with Intracranial Aneurysm in Koreans

Elastin encoded by elastin gene (ELN) is a crucial extracellular matrix protein responsible for arterial resilience. The objective of this study was to identify single nucleotide polymorphisms (SNPs) of ELN gene susceptible to intracranial aneurysm (IA) in Korean population. Two SNPs of ELN gene, rs2071307 (Gly422Ser) and rs2856728 (intron), were genotyped in 90 patients with IA and 90 age and frequency matched controls. Fisher’s exact test was conducted to evaluate allelic association with IA. Of the two SNPs in ELN gene, T allele of rs2856728 (intron) showed statistically significant association with increased development of IA (odds ratio [OR]: 2.34, 95% confidence interval [CI]: 1.44–3.81, P = 7.6 × 10−4). However, G allele of rs2071307 (Gly422Ser) had no significant association with the development of IA (OR: 1.27, 95% CI: 1.44–3.81, P = 0.607). Interestingly, the odds of having rs2856728 variant was approximately 2-fold higher in males than that in females (OR: 3.46 vs. 1.88, P < 0.05). However, none of SNPs showed difference between single and multiple IA in this study. This preliminary study implies that the rs2856728 variant in ELN gene polymorphisms might play crucial roles in the development and pathogenesis of IA in Korean population.