Abstracts from the 8th International Conference for Healthcare and Medical Students (ICHAMS)
(Source: BMC Proceedings)
Source: BMC Proceedings - August 13, 2019 Category: Biomedical Science Source Type: research

CISBETI 2019 - International Congress of Health, Well-Being, Technology and Innovation
(Source: BMC Proceedings)
Source: BMC Proceedings - July 24, 2019 Category: Biomedical Science Source Type: research

Abstract Book - 4 th B Chromosome Conference
(Source: BMC Proceedings)
Source: BMC Proceedings - June 17, 2019 Category: Biomedical Science Source Type: research

Proceedings of the 2017 Advancing the Science of Community Engaged Research (CEnR) Conference
ConclusionsCommunity and stakeholder engagement can directly impact research by enhancing clinical trial design, increasing relevance, and increasing recruitment, accrual and retention (Staley K.: Exploring Impact: Public 53 Involvement in NHS, Public Health and Social Care Research – INVOLVE.; 2009, Johnson et al Clin Transl Sci 8:388-54 390, 2015, Joosten et al Acad Med 90:1646-1650, 2015). The 2017 Advancing the Science of Community Engaged Research meeting,Innovative and Effective Methods of Stakeholder Engagement in Translational Research facilitated meaningful engagement of diverse stakeholder groups including ...
Source: BMC Proceedings - April 19, 2019 Category: Biomedical Science Source Type: research

Proceedings of Advancing the Science of Community Engaged Research (CEnR): Innovative and Effective Methods of Stakeholder Engagement in Translational Research: abstracts
(Source: BMC Proceedings)
Source: BMC Proceedings - April 19, 2019 Category: Biomedical Science Source Type: research

People and research: improved health systems for West Africans, by West Africans - report on special supplement
(Source: BMC Proceedings)
Source: BMC Proceedings - February 5, 2019 Category: Biomedical Science Source Type: research

Addressing challenges in children ’s mental health in disaster-affected areas in Japan and the Philippines – highlights of the training program by the National Center for Global Health and Medicine
AbstractBackground and purposeNatural disasters such as earthquakes, typhoons, floods, and volcanic eruptions frequently occur in Republic of Philippines and mental health care for children affected by these natural disasters is a major public health concern. Aiming to train health professionals on children ’s mental health, to conduct a situational analysis to identify the local needs and resources for children’s mental health, and to propose a mental health program for children that can be transferred from Japan to the Philippines, the National Center for Global Health and Medicine (NCGM) conduct ed a trainin...
Source: BMC Proceedings - December 19, 2018 Category: Biomedical Science Source Type: research

Proceedings of the 3rd BEAT-PCD Conference and 4th PCD Training School
In this report, we summarize the meeting, highlighting developments made during the meeting. (Source: BMC Proceedings)
Source: BMC Proceedings - December 18, 2018 Category: Biomedical Science Source Type: research

Abstracts from the 3rd BEAT-PCD Conference and 4th PCD Training School
(Source: BMC Proceedings)
Source: BMC Proceedings - December 18, 2018 Category: Biomedical Science Source Type: research

Cholera prevention and control in Asian countries
AbstractCholera remains a major public health problem in many countries. Poor sanitation and inappropriate clean water supply, insufficient health literacy and community mobilization, absence of national plans and cross-border collaborations are major factors impeding optimal control of cholera in endemic countries.In March 2017, a group of experts from 10 Asian cholera-prone countries that belong to the Initiative against Diarrheal and Enteric Diseases in Africa and Asia (IDEA), together with representatives from the World Health Organization, the US National Institutes of Health, International Vaccine Institute, Agence d...
Source: BMC Proceedings - December 7, 2018 Category: Biomedical Science Source Type: research

Abstracts from the 7th International Conference for Healthcare and Medical Students (ICHAMS)
(Source: BMC Proceedings)
Source: BMC Proceedings - October 29, 2018 Category: Biomedical Science Source Type: research

Methods for detecting methylation by SNP interaction in GAW20 simulation
AbstractTo examine whether single-nucleotide polymorphism (SNP) by methylation interactions can be detected, we analyzed GAW20 simulated triglycerides at visits 3 and 4 against baseline (visits 1 and 2) under 4 general linear models and 2 tree-based models in 200 replications of a sample of 680 individuals. Effects for SNPs, methylation cytosine-phosphate-guanine (CpG) effects, and interactions for SNP/CpG pairs were included. Causative SNPs/CpG pairs distributed on autosomal chromosomes 1 to 20 were tested to examine sensitivity. We also tested noncausative SNP/CpG pairs on chromosomes 21 and 22 to estimate the empirical ...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Using penalized regression to predict phenotype from SNP data
ConclusionsLASSO regression results in a heavy shrinkage of the regression coefficients, and also requires large sample sizes (several thousand individuals) to achieve good prediction. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Analysis of genetic and nongenetic factors influencing triglycerides-lowering drug effects based on paired observations
In this study, we assessed both genetic and nongenetic factors that influence drug responses and stratified patients into groups based on differential drug effect and sensitivity. Our methodology of investigating genetic factors and nongenetic factors is applicable to studying differential effects of other drugs, such as statins, and provides an approach to the development of personalized medicine. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Heritability and genetic associations of triglyceride and HDL-C levels using pedigree-based and empirical kinships
This study compares the use of pedigree and empirical kinships in the GAW20 data set. Two phenotypes were assessed: triglyceride levels and high-density lipoprotein cholesterol (HDL-C) levels pre- and postintervention with the cholesterol-reducing drug fenofibrate. Using SOLAR (Sequential Oligogenic Linkage Analysis Routines), pedigree-based kinships and empirically calculated kinships (using IBDLD and LDAK) were used to calculate phenotype heritability. In addition, a genome-wide association study was conducted using each kinship model for each phenotype to identify genetic variants significantly associated with phenotypi...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Evaluation of a phenotype imputation approach using GAW20 simulated data
AbstractStatistical power, which is the probability of correctly rejecting a false null hypothesis, is a limitation of genome-wide association studies (GWAS). Sample size is a major component of statistical power that can be easily affected by missingness in phenotypic data and restrain the ability to detect associated single-nucleotide polymorphisms (SNPs) with small effect sizes. Although some phenotypes are hard to collect because of cost and loss to follow-up, correlated phenotypes that are easily collected can be leveraged for association analysis. In this paper, we evaluate a phenotype imputation method that incorpor...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Family-based genome-wide association of inflammation biomarkers and fenofibrate treatment response in the GOLDN study
AbstractIn this paper we analyzed whole-genome genetic information provided by GAW20 from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study for family data. Lipid levels such as triglycerides (TGs) and high-density lipoprotein (HDL) are measured at different time points before and after administration of an anti-inflammatory drug fenofibrate. Apart from that, the data contain some covariates and whole-genome genotype information. We propose 2 novel approaches based on Henderson ’s iterative mixed model to identify associated loci corresponding to (a) inflammatory biomarkers like TGs and HDLs togethe...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

CpG-set association assessment of lipid concentration changes and DNA methylation
This study ’s goals were to investigate region-based associations between DNA methylation sites and lipid-level changes in response to the treatment with fenofibrate in the GAW20 data and to investigate whether improvements in power could be obtained by taking into account correlations between DNA methylatio n at neighboring cytosine-phosphate-guanine (CpG) sites. To this end, we applied both a recently developed block-based data-dimension-reduction approach and a region-based variance-component (VC) linear mixed model to GAW20 data. We compared analyses of unrelated individuals with familial data. The region-based V...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

A deep neural network based regression model for triglyceride concentrations prediction using epigenome-wide DNA methylation profiles
ConclusionsWe demonstrated the superiority of our proposed DNN models over the SVM model for predicting triglyceride concentrations. This study also suggests that the DNN approach has advantages over other traditional machine-learning methods to model high-dimensional epigenome-wide DNAm data and other genomic data. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Homozygosity disequilibrium associated with treatment response and its methylation regulation
AbstractHomozygosity disequilibrium (HD), indicating a nonrandom pattern of sizable runs of homozygosity that deviates from a random allocation of homozygous and heterozygous genotypes in the genome, is an important phenomenon in population genomics and medical genomics. We performed the first genome-wide study investigating the roles of HD in pharmacogenomics and pharmacoepigenomics by analyzing GAW20 data. We inferred whole-genome profiles of homozygosity intensities and performed genome-wide homozygosity association analyses to identify regions of HD associated with triglyceride (TG) response to fenofibrate by using LOH...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Logistic Bayesian LASSO for detecting association combining family and case-control data
AbstractBecause of the limited information from the GAW20 samples when only case-control or trio data are considered, we propose eLBL, an extension of the Logistic Bayesian LASSO (least absolute shrinkage and selection operator) methodology so that both types of data can be analyzed jointly in the hope of obtaining an increased statistical power, especially for detecting association between rare haplotypes and complex diseases. The methodology is further extended to account for familial correlation among the case-control individuals and the trios. A 2-step analysis strategy was taken to first perform a genome-wise single s...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Data for GAW20: genome-wide DNA sequence variation and epigenome-wide DNA methylation before and after fenofibrate treatment in a family study of metabolic phenotypes
AbstractGAW20 provided participants with an opportunity to comprehensively examine genetic and epigenetic variation among related individuals in the context of drug treatment response. GAW20 used data from 188 families (N = 1105) participating in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study (clinicaltrials.gov identifier NCT00083369), which included CD4+ T-cell DNA methylation at 463,995 cytosine-phosphate-guanine (CpG) sites measured before and after a 3-week treatment with fenofibrate, single-nucleotide variation at 906,600 loci, metabolic syndrome components ascertained before and af...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment
In this study, we applied the data set adaptive W-test to measure gene–methylation interactions. Performance was evaluated by the ability to detect a given set of causal markers in the data set obtained from the GAW20. Results from simulati on data analyses showed that the W-test was able to detect most markers. The method was also applied to chromosome 11 of the experimental data set and identified clusters of genes with neuronal and retinal functions, includingMPPED2I, GUCY2E,NAV2, andZBTB16. Genes from theTRIM family were also identified; these genes are potentially related to the regulation of triglyceride levels...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Genome-wide analysis in multiple-case families: assessing the relationship between triglyceride and methylation
AbstractThe main goal of this paper is to estimate the effect of triglyceride levels on methylation of cytosine-phosphate-guanine (CpG) sites in multiple-case families. These families are selected because they have 2 or more cases of metabolic syndrome (primary phenotype). The methylations at the CpG sites are the secondary phenotypes. Ascertainment corrections are needed when there is an association between the primary and secondary phenotype. We will apply the newly developed secondary phenotype analysis for multiple-case family studies to identify CpG sites where methylations are influenced by triglyceride levels. Our s...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Methods to evaluate rare variants gene-age interaction for triglycerides
AbstractTriglycerides are an important measure of heart health. Although more than 90 genes have been found to be associated to lipids, they only explain 12 to 15% of the variance in lipid levels. Evidence suggests that age may interact with the genetic effect on lipid levels. Existing methods to detect the main effect of rare variants cannot be readily applied for testing the gene environment interaction effect of rare variants, as those methods either have unstable results or inflated Type I error rates when the main effect exists. To overcome these difficulties, we developed two statistical methods: testing of optimally...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Application of Bayesian networks to GAW20 genetic and blood lipid data
ConclusionsEven when the causal relationships between variables are known, as with the simulated data, if the relationships are not strong then it is challenging to reproduce them in a Bayesian network. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Network analysis of drug effect on triglyceride-associated DNA methylation
AbstractBackgroundDNA methylation, an epigenetic modification, can be affected by environmental factors and thus regulate gene expression levels that can lead to alterations of certain phenotypes. Network analysis has been used successfully to discover gene sets that are expressed differently across multiple disease states and suggest possible pathways of disease progression. We applied this framework to compare DNA methylation levels before and after lipid-lowering medication and to identify modules that differ topologically between the two time points, revealing the association between lipid medication and these triglyce...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Identifying fenofibrate responsive CpG sites
AbstractAs part of GAW20, we analyzed the familiality and variability of methylation to identify cytosine-phosphate-guanine (CpG) sites responsive to treatment with fenofibrate. Methylation was measured at approximately 450,000 sites in pedigree members, prior to and after 3  weeks of treatment. Initially, we aimed to identify responsive sites by analyzing the pre- and posttreatment methylation changes within individuals, but these data exhibited a confounding treatment/batch effect. We applied an alternative indirect approach by searching for CpG sites whose methylati on levels exhibit a genetic response to the drug....
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Evidence of batch effects masking treatment effect in GAW20 methylation data
AbstractUsing the real data set from GAW20, we examined changes in the distribution of DNA methylation before and after treatment. Paired analysis of differences in both mean and variance had grossly inflated type 1 error, suggesting either a very large number of changes across the entire epigenome or major non-biological issues, such as batch effects. Separate analysis of Infinium I and II probes indicated differences in the pairedt-test statistics between these two types of probes. Examination of combined principal components showed that the first and fourth principal components discriminate between the before and after ...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

An efficient analytic approach in genome-wide identification of methylation quantitative trait loci response to fenofibrate treatment
ConclusionsBy using a novel analytic approach, we efficiently identified thousands ofcis re-meQTLs that provide a unique resource for further characterizing functional roles and gene targets of the SNPs that are most responsive to fenofibrate treatment. Our efficient analytic approach can be extended to large response quantitative trait locus studies with large sample sizes and multiple time points data. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Assessment of fenofibrate-methylation interactions on triglycerides using longitudinal family data
AbstractBackgroundTriglyceride (TG) concentrations decrease in response to fenofibrate treatment, and also are associated with DNA methylation. But how interactions between fenofibrate response and DNA methylation affect TGs remains unclear.MethodsIn the present study, we identified and compared differential methylation sites associated with TG concentrations in individuals before and after fenofibrate treatment. We then estimated interactions between fenofibrate treatment and methylation to identify differential methylation effects associated with fenofibrate treatment on TG concentrations using the entire longitudinal fa...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Methods for detecting methylation by SNP interaction in GAW20 simulation
AbstractTo examine whether single-nucleotide polymorphism (SNP) by methylation interactions can be detected, we analyzed GAW20 simulated triglycerides at visits 3 and 4 against baseline (visits 1 and 2) under 4 general linear models and 2 tree-based models in 200 replications of a sample of 680 individuals. Effects for SNPs, methylation cytosine-phosphate-guanine (CpG) effects, and interactions for SNP/CpG pairs were included. Causative SNPs/CpG pairs distributed on autosomal chromosomes 1 to 20 were tested to examine sensitivity. We also tested noncausative SNP/CpG pairs on chromosomes 21 and 22 to estimate the empirical ...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Using penalized regression to predict phenotype from SNP data
ConclusionsLASSO regression results in a heavy shrinkage of the regression coefficients, and also requires large sample sizes (several thousand individuals) to achieve good prediction. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Analysis of genetic and nongenetic factors influencing triglycerides-lowering drug effects based on paired observations
In this study, we assessed both genetic and nongenetic factors that influence drug responses and stratified patients into groups based on differential drug effect and sensitivity. Our methodology of investigating genetic factors and nongenetic factors is applicable to studying differential effects of other drugs, such as statins, and provides an approach to the development of personalized medicine. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Heritability and genetic associations of triglyceride and HDL-C levels using pedigree-based and empirical kinships
This study compares the use of pedigree and empirical kinships in the GAW20 data set. Two phenotypes were assessed: triglyceride levels and high-density lipoprotein cholesterol (HDL-C) levels pre- and postintervention with the cholesterol-reducing drug fenofibrate. Using SOLAR (Sequential Oligogenic Linkage Analysis Routines), pedigree-based kinships and empirically calculated kinships (using IBDLD and LDAK) were used to calculate phenotype heritability. In addition, a genome-wide association study was conducted using each kinship model for each phenotype to identify genetic variants significantly associated with phenotypi...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Evaluation of a phenotype imputation approach using GAW20 simulated data
AbstractStatistical power, which is the probability of correctly rejecting a false null hypothesis, is a limitation of genome-wide association studies (GWAS). Sample size is a major component of statistical power that can be easily affected by missingness in phenotypic data and restrain the ability to detect associated single-nucleotide polymorphisms (SNPs) with small effect sizes. Although some phenotypes are hard to collect because of cost and loss to follow-up, correlated phenotypes that are easily collected can be leveraged for association analysis. In this paper, we evaluate a phenotype imputation method that incorpor...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Family-based genome-wide association of inflammation biomarkers and fenofibrate treatment response in the GOLDN study
AbstractIn this paper we analyzed whole-genome genetic information provided by GAW20 from the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study for family data. Lipid levels such as triglycerides (TGs) and high-density lipoprotein (HDL) are measured at different time points before and after administration of an anti-inflammatory drug fenofibrate. Apart from that, the data contain some covariates and whole-genome genotype information. We propose 2 novel approaches based on Henderson ’s iterative mixed model to identify associated loci corresponding to (a) inflammatory biomarkers like TGs and HDLs togethe...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

CpG-set association assessment of lipid concentration changes and DNA methylation
This study ’s goals were to investigate region-based associations between DNA methylation sites and lipid-level changes in response to the treatment with fenofibrate in the GAW20 data and to investigate whether improvements in power could be obtained by taking into account correlations between DNA methylatio n at neighboring cytosine-phosphate-guanine (CpG) sites. To this end, we applied both a recently developed block-based data-dimension-reduction approach and a region-based variance-component (VC) linear mixed model to GAW20 data. We compared analyses of unrelated individuals with familial data. The region-based V...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

A deep neural network based regression model for triglyceride concentrations prediction using epigenome-wide DNA methylation profiles
ConclusionsWe demonstrated the superiority of our proposed DNN models over the SVM model for predicting triglyceride concentrations. This study also suggests that the DNN approach has advantages over other traditional machine-learning methods to model high-dimensional epigenome-wide DNAm data and other genomic data. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Homozygosity disequilibrium associated with treatment response and its methylation regulation
AbstractHomozygosity disequilibrium (HD), indicating a nonrandom pattern of sizable runs of homozygosity that deviates from a random allocation of homozygous and heterozygous genotypes in the genome, is an important phenomenon in population genomics and medical genomics. We performed the first genome-wide study investigating the roles of HD in pharmacogenomics and pharmacoepigenomics by analyzing GAW20 data. We inferred whole-genome profiles of homozygosity intensities and performed genome-wide homozygosity association analyses to identify regions of HD associated with triglyceride (TG) response to fenofibrate by using LOH...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Logistic Bayesian LASSO for detecting association combining family and case-control data
AbstractBecause of the limited information from the GAW20 samples when only case-control or trio data are considered, we propose eLBL, an extension of the Logistic Bayesian LASSO (least absolute shrinkage and selection operator) methodology so that both types of data can be analyzed jointly in the hope of obtaining an increased statistical power, especially for detecting association between rare haplotypes and complex diseases. The methodology is further extended to account for familial correlation among the case-control individuals and the trios. A 2-step analysis strategy was taken to first perform a genome-wise single s...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Data for GAW20: genome-wide DNA sequence variation and epigenome-wide DNA methylation before and after fenofibrate treatment in a family study of metabolic phenotypes
AbstractGAW20 provided participants with an opportunity to comprehensively examine genetic and epigenetic variation among related individuals in the context of drug treatment response. GAW20 used data from 188 families (N = 1105) participating in the Genetics of Lipid Lowering Drugs and Diet Network (GOLDN) study (clinicaltrials.gov identifier NCT00083369), which included CD4+ T-cell DNA methylation at 463,995 cytosine-phosphate-guanine (CpG) sites measured before and after a 3-week treatment with fenofibrate, single-nucleotide variation at 906,600 loci, metabolic syndrome components ascertained before and af...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Gene-methylation epistatic analyses via the W-test identifies enriched signals of neuronal genes in patients undergoing lipid-control treatment
In this study, we applied the data set adaptive W-test to measure gene–methylation interactions. Performance was evaluated by the ability to detect a given set of causal markers in the data set obtained from the GAW20. Results from simulati on data analyses showed that the W-test was able to detect most markers. The method was also applied to chromosome 11 of the experimental data set and identified clusters of genes with neuronal and retinal functions, includingMPPED2I, GUCY2E,NAV2, andZBTB16. Genes from theTRIM family were also identified; these genes are potentially related to the regulation of triglyceride levels...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Genome-wide analysis in multiple-case families: assessing the relationship between triglyceride and methylation
AbstractThe main goal of this paper is to estimate the effect of triglyceride levels on methylation of cytosine-phosphate-guanine (CpG) sites in multiple-case families. These families are selected because they have 2 or more cases of metabolic syndrome (primary phenotype). The methylations at the CpG sites are the secondary phenotypes. Ascertainment corrections are needed when there is an association between the primary and secondary phenotype. We will apply the newly developed secondary phenotype analysis for multiple-case family studies to identify CpG sites where methylations are influenced by triglyceride levels. Our s...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Methods to evaluate rare variants gene-age interaction for triglycerides
AbstractTriglycerides are an important measure of heart health. Although more than 90 genes have been found to be associated to lipids, they only explain 12 to 15% of the variance in lipid levels. Evidence suggests that age may interact with the genetic effect on lipid levels. Existing methods to detect the main effect of rare variants cannot be readily applied for testing the gene environment interaction effect of rare variants, as those methods either have unstable results or inflated Type I error rates when the main effect exists. To overcome these difficulties, we developed two statistical methods: testing of optimally...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Application of Bayesian networks to GAW20 genetic and blood lipid data
ConclusionsEven when the causal relationships between variables are known, as with the simulated data, if the relationships are not strong then it is challenging to reproduce them in a Bayesian network. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Network analysis of drug effect on triglyceride-associated DNA methylation
AbstractBackgroundDNA methylation, an epigenetic modification, can be affected by environmental factors and thus regulate gene expression levels that can lead to alterations of certain phenotypes. Network analysis has been used successfully to discover gene sets that are expressed differently across multiple disease states and suggest possible pathways of disease progression. We applied this framework to compare DNA methylation levels before and after lipid-lowering medication and to identify modules that differ topologically between the two time points, revealing the association between lipid medication and these triglyce...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Identifying fenofibrate responsive CpG sites
AbstractAs part of GAW20, we analyzed the familiality and variability of methylation to identify cytosine-phosphate-guanine (CpG) sites responsive to treatment with fenofibrate. Methylation was measured at approximately 450,000 sites in pedigree members, prior to and after 3  weeks of treatment. Initially, we aimed to identify responsive sites by analyzing the pre- and posttreatment methylation changes within individuals, but these data exhibited a confounding treatment/batch effect. We applied an alternative indirect approach by searching for CpG sites whose methylati on levels exhibit a genetic response to the drug....
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

Evidence of batch effects masking treatment effect in GAW20 methylation data
AbstractUsing the real data set from GAW20, we examined changes in the distribution of DNA methylation before and after treatment. Paired analysis of differences in both mean and variance had grossly inflated type 1 error, suggesting either a very large number of changes across the entire epigenome or major non-biological issues, such as batch effects. Separate analysis of Infinium I and II probes indicated differences in the pairedt-test statistics between these two types of probes. Examination of combined principal components showed that the first and fourth principal components discriminate between the before and after ...
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research

An efficient analytic approach in genome-wide identification of methylation quantitative trait loci response to fenofibrate treatment
ConclusionsBy using a novel analytic approach, we efficiently identified thousands ofcis re-meQTLs that provide a unique resource for further characterizing functional roles and gene targets of the SNPs that are most responsive to fenofibrate treatment. Our efficient analytic approach can be extended to large response quantitative trait locus studies with large sample sizes and multiple time points data. (Source: BMC Proceedings)
Source: BMC Proceedings - September 17, 2018 Category: Biomedical Science Source Type: research