Identification of the associations between genes and quantitative traits using entropy-based kernel densityestimation

Genetic associations have been quantified using a number of statistical measures. Entropy-based mutual information may be one of the more direct ways of estimating the association, in the sense that it does not depend on the parametrization. For this purpose, both the entropy and conditional entropy of the phenotype distribution should be obtained. Quantitative traits, however, do not usually allow an exact evaluation of entropy. The estimation of entropy needs a probability density function, which can be approximated by kernel density estimation. We have investigated the proper sequence of procedures for combining the kernel density estimation and entropy estimation with a probability density function in order to calculate mutual information. Genotypes and their interactions were constructed to set the conditions for conditional entropy. Extensive simulation data created using three types of generating functions were analyzed using two different kernels as well as two types of multifactor dimensionality reduction and another probability density approximation method called m-spacing. The statistical power in terms of correct detection rates was compared. Using kernels was found to be most useful when the trait distributions were more complex than simple normal or gamma distributions. A full-scale genomic dataset was explored to identify associations using the 2-h oral glucose tolerance test results and γ-glutamyl transpeptidase levels as phenotypes. Clearly distinguishable single-nucleotide polymorphisms (SNPs) and interacting SNP pairs associated with these phenotypes were found and listed with empirical p-values.

MP-LASSO chart: a multi-level polar chart for visualizing group LASSO analysis of genomic data

Penalized regression has been widely used in genome-wide association studies for jointanalyses to find genetic associations. Among penalized regression models, the least absolute shrinkage and selection operator (Lasso) method effectively removes some coefficientsfrom the model by shrinking them to zero. To handle group structures, such as genes andpathways, several modified Lasso penalties have been proposed, including group Lasso andsparse group Lasso. Group Lasso ensures sparsity at the level of pre-defined groups, eliminating unimportant groups. Sparse group Lasso performs group selection as in group Lasso,but also performs individual selection as in Lasso. While these sparse methods are useful inhigh-dimensional genetic studies, interpreting the results with many groups and coefficients is not straightforward. Lasso's results are often expressed as trace plots of regressioncoefficients. However, few studies have explored the systematic visualization of group information. In this study, we propose a multi-level polar Lasso (MP-Lasso) chart, which caneffectively represent the results from group Lasso and sparse group Lasso analyses. An Rpackage to draw MP-Lasso charts was developed. Through a real-world genetic data application, we demonstrated that our MP-Lasso chart package effectively visualizes the resultsof Lasso, group Lasso, and sparse group Lasso.

Significant Shortening of Leukocyte Telomere Length in Korean Patients with Bipolar Disorder 1

Objective@#Telomere shortening has been seen in major psychiatric disorders, including major depressive disorder.However, only a few small studies have examined this in bipolar disorder (BD). We compared the telomere length in patients with BD1 or BD2 with that in matched healthy controls. @*Methods@#We included 215 patients with BD (128 BD1, 87 BD2) and 204 age- and sex-matched healthy controls. Relative telomere length was determined by quantitative polymerase chain reaction. The patients and controls were compared separately for age groups, sex, and BD subgroups (BD1 and BD2). @*Results@#We found significant telomere shortening in patients with BD1 (p ＜ 0.001), but not in patients with BD2.In male patients with BD1, the 30−39 year age group had significant shortening of telomere length than controls (p = 0.01). Female patients with BD1 in the 19−29-year age group had significantly shortened telomeres compared to the controls (p ＜ 0.01). @*Conclusion@#Our results suggest a significant reduction in telomere length in BD1. Telomere shortening would be a potential biomarker for BD.

Significant Shortening of Leukocyte Telomere Length in Korean Patients with Bipolar Disorder 1

Objective@#Telomere shortening has been seen in major psychiatric disorders, including major depressive disorder.However, only a few small studies have examined this in bipolar disorder (BD). We compared the telomere length in patients with BD1 or BD2 with that in matched healthy controls. @*Methods@#We included 215 patients with BD (128 BD1, 87 BD2) and 204 age- and sex-matched healthy controls. Relative telomere length was determined by quantitative polymerase chain reaction. The patients and controls were compared separately for age groups, sex, and BD subgroups (BD1 and BD2). @*Results@#We found significant telomere shortening in patients with BD1 (p ＜ 0.001), but not in patients with BD2.In male patients with BD1, the 30−39 year age group had significant shortening of telomere length than controls (p = 0.01). Female patients with BD1 in the 19−29-year age group had significantly shortened telomeres compared to the controls (p ＜ 0.01). @*Conclusion@#Our results suggest a significant reduction in telomere length in BD1. Telomere shortening would be a potential biomarker for BD.

Electroporation of AsCpf1/RNP at the Zygote Stage is an Efficient Genome Editing Method to Generate Knock-Out Mice Deficient in Leukemia Inhibitory Factor

METHODS@#The efficiency of electroporation-based delivery of AsCpf1/mRNA and AsCpf1/RNP to target exon 3 of leukemia inhibitory factor (Lif) into mouse zygotes was evaluated. Embryos that developed to the two-cell stage after zygote electroporation were transferred into the oviducts of surrogate mothers to produce AsCpf1-mediated LIF KO mice. The genome editing efficiency of blastocysts and pups was tested using the T7E1 assay and/or DNA sequencing. Congenital abnormalities and reproductive phenotypes in LIF KO mice produced by electroporation with AsCpf1/RNP were examined. @*RESULTS@#Survival and two-cell development of electroporated zygotes were comparable between the AsCpf1/mRNA and AsCpf1/RNP groups, whereas genome editing efficiency was relatively higher in the AsCpf1/RNP group (13.3% vs 18.1% at blastocyst and 33.3% vs 45.5% at offspring), respectively. Two mouse lines with a frameshift mutation in exon 3 of the Lif gene were established from the AsCpf1/RNP group. All congenital abnormalities of LIF KO mice produced by AsCpf1/RNP electroporation were observed. AsCpf1-mediated LIF KO mice showed postnatal growth retardation and implantation failure, both of which are major phenotypes of LIF KO mice generated by conventional gene targeting. @*CONCLUSION@#Electroporation of AsCpf1/RNP at the zygote stage is an efficient genome editing method to produce KO mice.

Electroporation of AsCpf1/RNP at the Zygote Stage is an Efficient Genome Editing Method to Generate Knock-Out Mice Deficient in Leukemia Inhibitory Factor

METHODS@#The efficiency of electroporation-based delivery of AsCpf1/mRNA and AsCpf1/RNP to target exon 3 of leukemia inhibitory factor (Lif) into mouse zygotes was evaluated. Embryos that developed to the two-cell stage after zygote electroporation were transferred into the oviducts of surrogate mothers to produce AsCpf1-mediated LIF KO mice. The genome editing efficiency of blastocysts and pups was tested using the T7E1 assay and/or DNA sequencing. Congenital abnormalities and reproductive phenotypes in LIF KO mice produced by electroporation with AsCpf1/RNP were examined. @*RESULTS@#Survival and two-cell development of electroporated zygotes were comparable between the AsCpf1/mRNA and AsCpf1/RNP groups, whereas genome editing efficiency was relatively higher in the AsCpf1/RNP group (13.3% vs 18.1% at blastocyst and 33.3% vs 45.5% at offspring), respectively. Two mouse lines with a frameshift mutation in exon 3 of the Lif gene were established from the AsCpf1/RNP group. All congenital abnormalities of LIF KO mice produced by AsCpf1/RNP electroporation were observed. AsCpf1-mediated LIF KO mice showed postnatal growth retardation and implantation failure, both of which are major phenotypes of LIF KO mice generated by conventional gene targeting. @*CONCLUSION@#Electroporation of AsCpf1/RNP at the zygote stage is an efficient genome editing method to produce KO mice.

Investigation of gene-gene interactions of clock genes for chronotype in a healthy Korean population

Chronotype is an important moderator of psychiatric illnesses, which seems to be controlled in some part by genetic factors. Clock genes are the most relevant genes for chronotype. In addition to the roles of individual genes, gene-gene interactions of clock genes substantially contribute to chronotype. We investigated genetic associations and gene-gene interactions of the clock genes BHLHB2, CLOCK, CSNK1E, NR1D1, PER1, PER2, PER3, and TIMELESS for chronotype in 1293 healthy Korean individuals. Regression analysis was conducted to find associations between single nucleotide polymorphism (SNP) and chronotype. For gene-gene interaction analyses, the quantitative multifactor dimensionality reduction (QMDR) method, a nonparametric model-free method for quantitative phenotypes, were performed. No individual SNP or haplotype showed a significant association with chronotype by both regression analysis and single-locus model of QMDR. QMDR analysis identified NR1D1 rs2314339 and TIMELESS rs4630333 as the best SNP pairs among two-locus interaction models associated with chronotype (cross-validation consistency [CVC] = 8/10, p = 0.041). For the three-locus interaction model, the SNP combination of NR1D1 rs2314339, TIMELESS rs4630333, and PER3 rs228669 showed the best results (CVC = 4/10, p < 0.001). However, because the mean differences between genotype combinations were minor, the clinical roles of clock gene interactions are unlikely to be critical.

Investigation of gene-gene interactions of clock genes for chronotype in a healthy Korean population

Chronotype is an important moderator of psychiatric illnesses, which seems to be controlled in some part by genetic factors. Clock genes are the most relevant genes for chronotype. In addition to the roles of individual genes, gene-gene interactions of clock genes substantially contribute to chronotype. We investigated genetic associations and gene-gene interactions of the clock genes BHLHB2, CLOCK, CSNK1E, NR1D1, PER1, PER2, PER3, and TIMELESS for chronotype in 1293 healthy Korean individuals. Regression analysis was conducted to find associations between single nucleotide polymorphism (SNP) and chronotype. For gene-gene interaction analyses, the quantitative multifactor dimensionality reduction (QMDR) method, a nonparametric model-free method for quantitative phenotypes, were performed. No individual SNP or haplotype showed a significant association with chronotype by both regression analysis and single-locus model of QMDR. QMDR analysis identified NR1D1 rs2314339 and TIMELESS rs4630333 as the best SNP pairs among two-locus interaction models associated with chronotype (cross-validation consistency [CVC] = 8/10, p = 0.041). For the three-locus interaction model, the SNP combination of NR1D1 rs2314339, TIMELESS rs4630333, and PER3 rs228669 showed the best results (CVC = 4/10, p < 0.001). However, because the mean differences between genotype combinations were minor, the clinical roles of clock gene interactions are unlikely to be critical.

Effects of Academic Relationships on Academic Burnout in Health Professions Students / 의학교육논단

There are several dimensions of academic burnout experienced by medical and health science college students. The purpose of this study was to examine the effects of academic relationships on academic burnout. Data was collected from 476 Eulji University students using an online survey over 4 days in April of 2018. Of the 264 respondents, 111 studied medicine (42.0%), 105 studied nursing (39.8%), and 48 studied clinical pathology (18.1%). The questionnaire was composed of the following sections: demographics (four questions), general life characteristics (seven questions), academic enthusiasm (eight questions), academic relationships (15 questions), and academic burnout sub-dimensions (partially revised Maslach Burnout Inventory-Student Survey Scale) (11 questions). T-tests and one-way analysis of variance were performed to illustrate the differences among the three departments. The effects of academic relationships and academic enthusiasm on academic burnout were analyzed using linear regression. Comparing the three departments, academic burnout was not found to be statistically significant (p=0.296). However, medical students' academic enthusiasm was significantly lower (p<0.001) and academic relationships were significantly higher (p<0.001) than nursing and clinical pathology students. The difference in academic burnout among the three departments was not significant. However, medical students have stronger academic relationships, while nursing and clinical pathology students were more focused on academics. Relationships and academic enthusiasm contribute to reducing academic burnout. Therefore, strategies need to be developed to deal with academic burnout considering relationship factors.

Effects of an Experience-focused Prenatal Program on Stress, Anxiety, Childbirth Confidence, and Maternal-Fetal Attachment on Women in Their First Pregnancy

PURPOSE: To evaluate the effectiveness of an experience-focused prenatal program on stress, anxiety, childbirth confidence, and maternal-fetal attachment for women in their first pregnancy. METHODS: The participants were 57 pregnant women at 32 weeks or more of a first pregnancy who agreed to participate in this study. The data were analyzed with descriptive statistics, t-test, χ2 test, and Fisher's exact test using the SPSS 21.0 program. RESULTS: The experimental group showed significant differences in stress, anxiety, childbirth confidence, and maternal-fetal attachment from the control group. CONCLUSION: The four-week experience-focused prenatal program can be used for women in their first pregnancy to reduce their stress and anxiety and to increase their childbirth confidence and maternal- fetal attachment.

Multi-block Analysis of Genomic Data Using Generalized Canonical Correlation Analysis

Recently, there have been many studies in medicine related to genetic analysis. Many genetic studies have been performed to find genes associated with complex diseases. To find out how genes are related to disease, we need to understand not only the simple relationship of genotypes but also the way they are related to phenotype. Multi-block data, which is a summation form of variable sets, is used for enhancing the analysis of the relationships of different blocks. By identifying relationships through a multi-block data form, we can understand the association between the blocks in comprehending the correlation between them. Several statistical analysis methods have been developed to understand the relationship between multi-block data. In this paper, we will use generalized canonical correlation methodology to analyze multi-block data from the Korean Association Resource project, which has a combination of single nucleotide polymorphism blocks, phenotype blocks, and disease blocks.

Polymorphism in the Promoter Region of SEMA5A Is Associated with Sociality Traits in Korean Subjects with Autism Spectrum Disorders

In this study, we evaluated the association between autism spectrum disorders (ASDs) and 10 single-nucleotide polymorphisms (SNPs) in the 5' region of the semaphorin 5A gene (SEMA5A) for 250 Korean trios including children with ASDs. Family-based association testing and haplotype analysis revealed a statistically significant association between rs194085 and multiple sociality traits with Korean ASDs in the dominant model (p < 0.001, corrected p=0.035). This indicates that genetic variations in the 5' region of SEMA5A play a role in the genetic predisposition to sociality traits in Korean ASDs.

Genetic Association Analysis of Fasting and 1- and 2-Hour Glucose Tolerance Test Data Using a Generalized Index of Dissimilarity Measure for the Korean Population

Glucose tolerance tests have been devised to determine the speed of blood glucose clearance. Diabetes is often tested with the standard oral glucose tolerance test (OGTT), along with fasting glucose level. However, no single test may be sufficient for the diagnosis, and the World Health Organization (WHO)/International Diabetes Federation (IDF) has suggested composite criteria. Accordingly, a single multi-class trait was constructed with three of the fasting phenotypes and 1- and 2-hour OGTT phenotypes from the Korean Association Resource (KARE) project, and the genetic association was investigated. All of the 18 possible combinations made out of the 3 sets of classification for the individual phenotypes were taken into our analysis. These were possible due to a method that was recently developed by us for estimating genomic associations using a generalized index of dissimilarity. Eight single-nucleotide polymorphisms (SNPs) that were found to have the strongest main effect are reported with the corresponding genes. Four of them conform to previous reports, located in the CDKAL1 gene, while the other 4 SNPs are new findings. Two-order interacting SNP pairs of are also presented. One pair (rs2328549 and rs6486740) has a prominent association, where the two single-nucleotide polymorphism locations are CDKAL1 and GLT1D1. The latter has not been found to have a strong main effect. New findings may result from the proper construction and analysis of a composite trait.

Neuropsychological and Behavioral Profiles in Attention-Deficit Hyperactivity Disorder Children of Parents with a History of Mood Disorders: A Pilot Study

OBJECTIVE: We aimed to investigate the neurocognitive and behavioral endophenotypes of premorbid mood disorder. We compared intelligence, neuropsychological functioning, and behavioral problems among three groups: 1) a high-risk group [attention-deficit hyperactivity disorder (ADHD) children of parents with a history of a mood disorder], 2) a low-risk group (ADHD children of parents without a history of a mood disorder), and 3) normal comparison subjects. METHODS: We used the Korean Educational Development Institute Wechsler Intelligence Scale for Children-Revised (KEDI-WISC-R), the Stroop Color Word Interference Test (Stroop), the Wisconsin Card Sorting Test (WCST), and the Rey-Osterrieth Complex Figure Test (RCFT) as neurocognitive measures, and we used the Child Behavior Checklist (CBCL) as a behavioral measure. Performance on these neuropsychological tests and score on the CBCL of 18 high-risk children were compared to those of 20 low-risk children and 24 healthy children. We also assessed the children's current mood state and familial functioning to control for the confounding effects of these variables. RESULTS: Compared to low-risk and healthy children, high-risk children were impaired on the Picture Completion and Stroop Word subtest and showed higher scores on the CBCL subscales representing internalizing symptoms. These significant group differences persisted even after adjustment for the children's current mood state and familial functioning. CONCLUSION: Neuropsychological deficits in the offspring of parents with a mood disorder may be associated with the current mood state rather than with innate characteristics, while their internalizing symptoms may partially stem from innate characteristics that are endophenotypes of a premorbid mood disorder.

Polymorphisms of BDNF Gene and Autism Spectrum Disorders: Family Based Association Study with Korean Trios

OBJECTIVE: Autism spectrum disorders (ASDs) are a group of early childhood-onset neurodevelopmental disorders characterized by deficits in social interaction and language skills, and repetitive behaviors. Brain-derived neurotrophic factor (BDNF) plays a critical role in the differentiation of normal neuronal cells during embryonic and postnatal neuronal development through its neurotrophic effects. METHODS: In this study, we performed a family-based association test (FBAT) between single nucleotide polymorphisms (SNPs; rs6265, rs11030101, rs7103411, and rs7103873) or haplotypes in the BDNF gene and affection status or several quantitative traits characterized by ADI-R with151 Korean trios, including a child diagnosed as ASDs. RESULTS: While no significant association was found between SNPs or haplotypes and the ASDs disease status, a quantitative transmission disequilibrium test (QTDT) by using quantitative traits identified associations of the SNPs (rs6265 and rs11030101) with a domain score for "Restricted, Repetitive and Stereotyped patterns of behavior" (C domain), especially at the subdomain scores for "encompassing preoccupation or circumscribed pattern of interest" (C1) (rs6265A allele, dominant model, p-value=0.019; rs11030101 A allele, additive model, p-value=0.015) and "preoccupations with part of objects or non-functional elements of material" (C4) (rs11030101 A allele, additive model, p-value=0.015) within the ADI-R diagnostic algorithm. In addition, significant associations were also identified between the haplotypes and these quantitative traits (C1, p-value=0.016; C4, p-value=0.012). CONCLUSION: We conclude that BDNF gene polymorphisms have a possible role in the pathogenesis of ASDs.

The costs of hepatitis A infections in South Korea / 한국역학회지

OBJECTIVES: The incidence of hepatitis A infections among young adults has recently increased in South Korea. Although universal vaccination has often been suggested to mitigate the problem, its rationale has not been well-understood. Estimating the societal costs of hepatitis A infections might support the development of intervention strategies. METHODS: We classified hepatitis A infections into eight clinical pathways and estimated the number of occurrences and cost per case for each clinical pathway using claim data from National Health Insurance and several national surveys as well as assumptions based on previous studies. To determine the total costs of a hepatitis A infection, both direct and indirect costs were estimated. Indirect costs were estimated using the human-capital approach. All costs are adjusted to the year 2008. RESULTS: There were 30,240 identified cases of hepatitis A infections in 2008 for a total cost of 80,873 million won (2.7 million won per case). Direct and indirect costs constituted 56.2% and 43.8% of the total costs, respectively. People aged 20-39 accounted for 71.3% of total cases and 74.6% of total costs. Medical costs per capita were the lowest in the 0-4 age group and highest in the 20-29 age group. CONCLUSIONS: This study could provide evidence for development of cost-effective interventions to control hepatitis A infections. But the true costs including uncaptured and intangible costs of hepatitis A infections might be higher than our results indicate.

Crown-Rump Length Measured in the Early First Trimester as a Predictor of Low Birth Weight

The aim of this study is to assess the association between crown-rump length (CRL) measured before the 10th gestational week and birth weight. Results from 316 transvaginal ultrasonography scans at the 46th, 53rd, 60th, 67th, and 74th days of pregnancy were compared in low birth weight (LBW) versus normal birth weight groups. A positive correlation between CRL and birth weight was observed when CRL was measured at days 60, 67, and 74. CRL measured on the 67th day of pregnancy was significantly smaller in the LBW group than in the normal birth weight group. A cut-off value of CRL=26.5 mm measured at day 67 has the highest power to predict LBW.

Association of the Catechol-o-Methyltransferase Gene Polymorphisms with Korean Autism Spectrum Disorders

This study evaluated the family-based genetic association between autism spectrum disorders (ASDs) and 5 single-nucleotide polymorphisms (SNPs) in the catechol-o-methyltransferase gene (COMT), which was found among 151 Korean ASDs family trios (dominant model Z = 2.598, P = 0.009, P(FDR) = 0.045). We found a statistically significant allele transmission or association in terms of the rs6269 SNP in the ASDs trios. Moreover, in the haplotype analysis, the haplotypes with rs6269 demonstrated significant evidence of an association with ASDs (additive model rs6269-rs4818-rs4680-rs769224 haplotype P = 0.004, P(FDR) = 0.040). Thus, an association may exist between the variants of the COMT gene and the occurrence of ASDs in Koreans.

Genome-Wide Association Scan of Korean Autism Spectrum Disorders with Language Delay: A Preliminary Study

OBJECTIVE: Communication problems are a prevalent symptom of autism spectrum disorders (ASDs), which have a genetic background. Although several genome-wide studies on ASD have suggested a number of candidate genes, few studies have reported the association or linkage of specific endophenotypes to ASDs. METHODS: Forty-two Korean ASD patients who showed a language delay were enrolled in this study with their parents. We performed a genome-wide scan by using the Affymetrix SNP Array 5.0 platform to identify candidate genes responsible for language delay in ASDs. RESULTS: We detected candidate single-nucleotide polymorphisms (SNPs) in chromosome 11, rs11212733 (p-value=9.76x10(-6)) and rs7125479 (p-value=1.48x10(-4)), as a marker of language delay in ASD using the transmission disequilibrium test and multifactor dimensionality reduction test. CONCLUSION: Although our results suggest that several SNPs are associated with language delay in ASD, rs11212733 we were not able to observe any significant results after correction of multiple comparisons. This may imply that more samples may be required to identify genes associated with language delay in ASD.

External cross-validation of bioelectrical impedance analysis for the assessment of body composition in Korean adults

Bioelectrical impedance analysis (BIA) models must be validated against a reference method in a representative population sample before they can be accepted as accurate and applicable. The purpose of this study was to compare the eight-electrode BIA method with DEXA as a reference method in the assessment of body composition in Korean adults and to investigate the predictive accuracy and applicability of the eight-electrode BIA model. A total of 174 apparently healthy adults participated. The study was designed as a cross-sectional study. FM, %fat, and FFM were estimated by an eight-electrode BIA model and were measured by DEXA. Correlations between BIA_%fat and DEXA_%fat were 0.956 for men and 0.960 for women with a total error of 2.1%fat in men and 2.3%fat in women. The mean difference between BIA_%fat and DEXA_%fat was small but significant (P < 0.05), which resulted in an overestimation of 1.2 +/- 2.2%fat (95% CI: -3.2-6.2%fat) in men and an underestimation of -2.0 +/- 2.4%fat (95% CI: -2.3-7.1%fat) in women. In the Bland-Altman analysis, the %fat of 86.3% of men was accurately estimated and the %fat of 66.0% of women was accurately estimated to within 3.5%fat. The BIA had good agreement for prediction of %fat in Korean adults. However, the eight-electrode BIA had small, but systemic, errors of %fat in the predictive accuracy for individual estimation. The total errors led to an overestimation of %fat in lean men and an underestimation of %fat in obese women.