☆ 4.6 Article

mGWAS-Explorer 2.0: Causal Analysis and Interpretation of Metabolite-Phenotype Associations

METABOLITES (2023)

Related references

Note: Only part of the references are listed.

Article Genetics & Heredity

Genomic atlas of the plasma metabolome prioritizes metabolites implicated in human diseases

Yiheng Chen et al.

Summary: Through genome-wide association studies, this study identified associations between 690 metabolites and 248 loci, as well as associations between 143 metabolite ratios and 69 loci. The integration of metabolite-gene and gene expression information revealed 94 effector genes for 109 metabolites and 48 metabolite ratios. The use of Mendelian randomization identified 22 metabolites and 20 metabolite ratios with estimated causal effects on 12 traits and diseases.

NATURE GENETICS (2023)

Add to Collection

Article Biology

Phenome-wide Mendelian randomisation analysis identifies causal factors for age-related macular degeneration

Thomas H. Julian et al.

Summary: Age-related macular degeneration (AMD) is a leading cause of blindness, and this study aims to identify causal factors and potential therapeutic targets for AMD through a phenome-wide Mendelian randomisation (MR) study. The results of this study support several putative causal factors for AMD and provide avenues for future translational research.

ELIFE (2023)

Add to Collection

Article Horticulture

Meta-QTL for morphological traits and pharmaceutical alkaloids in periwinkle (Catharanthus roseus (L.) 'G. Don')

Nikwan Shariatipour et al.

Summary: This study used a meta-QTL analysis method to identify the most reliable and accurate QTL controlling morphological traits and terpenoid indole alkaloids (TIAs) in Catharanthus roseus. The results showed a reduction in confidence interval (CI) for 18 MQTLs on C. roseus chromosomes. Co-localisation analysis revealed the most common QTLs associated with vindoline and catharanthine. Six specific MQTLs were identified as the most important and reliable chromosome regions for refining genetic control of the tested traits. The consensus map provided valuable information for improving genomic and marker-assisted selection in pharmacological research.

JOURNAL OF HORTICULTURAL SCIENCE & BIOTECHNOLOGY (2023)

Add to Collection

Review Biochemistry & Molecular Biology

Understanding the assumptions underlying Mendelian randomization

Christiaan de Leeuw et al.

Summary: With the availability of large genetic data sets, Mendelian Randomization (MR) has become popular as a secondary analysis method. Using genetic variants as instrumental variables, MR can estimate causal effects between phenotypes when experimental research is not feasible. However, strong assumptions are required, and not meeting these assumptions can lead to biased results. Therefore, understanding and evaluating these assumptions is crucial when using MR.

EUROPEAN JOURNAL OF HUMAN GENETICS (2022)

Add to Collection

Article Medicine, Research & Experimental

Causal Inference with Genetic Data: Past, Present, and Future

Jean-Baptiste Pingault et al.

Summary: This article introduces the convergence of genetics and causal inference, as well as a set of methods in this field. The article also provides introductory concepts that are useful for readers unfamiliar with genetically informed methods. The authors conclude that the existing applications and foreseeable developments in this field will bring rapid rewards, not only in terms of our understanding of human disease and development, but also in tangible translational applications.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Metabolome Genome-Wide Association Study Identifies 74 Novel Genomic Regions Influencing Plasma Metabolites Levels

Pirro G. Hysi et al.

Summary: This study conducted a genome-wide association study on the levels of circulating metabolites in European subjects, identifying 202 unique genomic regions associated with 478 different metabolites. The replication study confirmed the robustness of these associations and discovered 74 novel genomic regions not previously associated with any metabolites.

METABOLITES (2022)

Add to Collection

Article Genetics & Heredity

Integrative Pathway Analysis of SNP and Metabolite Data Using a Hierarchical Structural Component Model

Taeyeong Jung et al.

Summary: This study proposes an integrative pathway analysis method for SNP and metabolite data to identify pathways associated with type 2 diabetes. The method adds biological insights into disease-related pathways by considering the genetic predispositions of metabolites.

FRONTIERS IN GENETICS (2022)

Add to Collection

Article Biochemistry & Molecular Biology

Rare and common genetic determinants of metabolic individuality and their effects on human health

Praveen Surendran et al.

Summary: Garrod's concept of 'chemical individuality' contributes to understanding the molecular origins of human diseases. The genetic architecture of the human plasma metabolome was studied using high-throughput metabolomic technologies, revealing associations between genetic variants and metabolite levels.

NATURE MEDICINE (2022)

Add to Collection

Article Biochemistry & Molecular Biology

mGWAS-Explorer: Linking SNPs, Genes, Metabolites, and Diseases for Functional Insights

Le Chang et al.

Summary: A user-friendly web-based platform called mGWAS-Explorer was introduced in this study to connect SNPs, metabolites, genes, and known disease associations through powerful network visual analytics. The platform can be applied in metabolomics research to provide functional insights from genes to metabolites.

METABOLITES (2022)

Add to Collection

Article Genetics & Heredity

Integrating transcriptomics, metabolomics, and GWAS helps reveal molecular mechanisms for metabolite levels and disease risk

Xianyong Yin et al.

Summary: Integrating transcriptomics, metabolomics, and disease GWAS results provides a comprehensive understanding of molecular mechanisms and pathways from genes to diseases, highlighting the influence of genetic variants on gene expression and disease risk. Prioritizing gene-metabolite pairs through integration helps pinpoint metabolic pathways in disease pathophysiology.

AMERICAN JOURNAL OF HUMAN GENETICS (2022)

Add to Collection

Article Biochemical Research Methods

MELODI Presto: a fast and agile tool to explore semantic triples derived from biomedical literature

Benjamin Elsworth et al.

Summary: The field of literature-based discovery is rapidly developing, with triples extracted from biomedical literature proving to be useful in representing knowledge. By implementing efficient search methods and an application programming interface, it is possible to explore mechanistic knowledge from the literature quickly and conveniently.

BIOINFORMATICS (2021)

Add to Collection

Article Medicine, Research & Experimental

Causal Inference Methods to Integrate Omics and Complex Traits

Eleonora Porcu et al.

Summary: The advancement in biotechnology has greatly facilitated the collection of omics data in large sample sizes worldwide. Studies associating diseases with genetic markers have led to biologically meaningful mechanisms, but identifying disease biomarkers may be just correlates of diseases. Mendelian randomization offers a framework to integrate omics and disease-associated genetic variants to pinpoint molecular traits driving disease development.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2021)

Add to Collection

Article Genetics & Heredity

Genetic overlap and causality between blood metabolites and migraine

Hamzeh M. Tanha et al.

Summary: The study utilized genome-wide association studies (GWASs) to investigate the genetic overlap and causality between blood metabolite levels and migraine risk. Significant genetic overlap was found between migraine and 44 metabolites, with shared genetic influences identified at eight independent genomic loci across different chromosomes. The findings suggest alterations in metabolite levels in individuals with migraine, with fatty acids playing a potentially protective role against migraine and a specific lipid metabolite identified as a potential therapeutic target for migraine.

AMERICAN JOURNAL OF HUMAN GENETICS (2021)

Add to Collection

Article Chemistry, Analytical

A Practical Guide to Metabolomics Software Development

Hui-Yin Chang et al.

Summary: This article introduces important considerations for metabolomics software users and developers, and provides recommendations for establishing guidelines and best practices for developing metabolomics tools, divided into three stages: preparation, tool development, and distribution and maintenance.

ANALYTICAL CHEMISTRY (2021)

Add to Collection

Article Genetics & Heredity

A cross-platform approach identifies genetic regulators of human metabolism and health

Luca A. Lotta et al.

Summary: By conducting a cross-platform analysis of metabolites, we identified various genetic regulators associated with metabolite levels, including their impact on diseases such as type 2 diabetes and macular telangiectasia type 2.

NATURE GENETICS (2021)

Add to Collection

Article Biochemistry & Molecular Biology

The Association of IL-6, TNFα and CRP Gene Polymorphisms with Coronary Artery Disease in a Tunisian Population: A Case-Control study

Nedra Grira et al.

Summary: This study aimed to assess the association between IL-6, TNFα, and CRP gene variants and susceptibility to coronary artery disease in a Tunisian population. A case-control study involving 204 patients and 400 age-gender matched controls revealed significant differences in physiological parameters and genotypic distribution between CAD patients and controls. The findings suggest that IL-6, TNFα, and CRP gene polymorphisms may be considered as risk factors for CAD in the Tunisian population.

BIOCHEMICAL GENETICS (2021)

Add to Collection

Article Multidisciplinary Sciences

Mapping the proteo-genomic convergence of human diseases

Maik Pietzner et al.

Summary: The study identified genetic associations for plasma proteins and established a map connecting genes, proteins, and diseases, highlighting biological convergence across diseases. This proteo-genomic map helps to understand relationships between diseases and provide biological context for emerging disorders.

SCIENCE (2021)

Add to Collection

Article Agronomy

Meta-analysis of QTLome for grain zinc and iron contents in wheat (Triticum aestivum L.)

Nikwan Shariatipour et al.

Summary: Through Meta-QTL analysis, this study integrated QTL information on iron and zinc contents from seven independent segregating populations, identifying MQTLs that play important roles in genetic control of grain zinc and iron traits. These MQTLs were predominantly distributed in the non-telomeric and sub-telomeric chromosomal regions, with narrower confidence intervals. The results revealed a high co-location of QTLs for zinc and iron contents, suggesting the potential for simultaneous improvement of both micronutrients and wheat biofortification.

EUPHYTICA (2021)

Add to Collection

Article Multidisciplinary Sciences

Mendelian randomization identifies blood metabolites previously linked to midlife cognition as causal candidates in Alzheimer's disease

Jodie Lord et al.

Summary: This study explored the causal relationship between metabolites associated with midlife cognition and AD, highlighting XL.HDL.FC, total lipids, phospholipids, and XL.HDL particle concentration as potential causal candidates. Evidence suggests that GP may also play a role in AD pathology and warrants further investigation. Understanding these relationships could inform risk reduction strategies for AD, which is believed to develop decades before symptoms appear.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

Add to Collection

Article Multidisciplinary Sciences

Genome-wide association study and Mendelian randomization analysis provide insights for improving rice yield potential

Jing Su et al.

Summary: Rice yield is mainly controlled by minor-effect loci, and selecting quantitative trait locus/gene affecting component traits can further enhance yield. Loci for GPP or TP primarily have a positive genetic effect on yield, while loci for KGW have different effects; in addition, TP has a greater impact on yield than KGW and GPP.

SCIENTIFIC REPORTS (2021)

Add to Collection

Article Genetics & Heredity

Phenome-wide investigation of the causal associations between childhood BMI and adult trait outcomes: a two-sample Mendelian randomization study

Shan-Shan Dong et al.

Summary: The study identified potential causal effects of childhood obesity on 60 adult traits, but found that the detrimental effects on disease-related traits were no longer present after accounting for adult BMI. The associations between childhood BMI and increased risks of diseases in adulthood are likely attributed to individuals remaining obese in later life.

GENOME MEDICINE (2021)

Add to Collection

Article Genetics & Heredity

Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression

Urmo Vosa et al.

Summary: Genetic variants associated with traits primarily affect complex phenotypes through regulatory mechanisms on the transcriptome. Most genes show cis-eQTL effects, while distal trans-eQTL effects have lower replication rates. However, single-cell RNA-seq data prioritize intracellular trans-eQTL effects mediated by transcription factors. Additionally, a subset of genes correlated with polygenic scores for various phenotypes may serve as potential drivers for those traits.

NATURE GENETICS (2021)

Add to Collection

Article Biotechnology & Applied Microbiology

Integration of metabolomics, genomics, and immune phenotypes reveals the causal roles of metabolites in disease

Xiaojing Chu et al.

Summary: This study systematically investigated circulating metabolites in healthy subjects, revealing significant impact of major metabolic pathways on cytokine production. Through genome-wide association analysis, genetic regulation of metabolites associated with immune phenotypes was examined, leading to the identification of a locus causally associated with Crohn's disease.

GENOME BIOLOGY (2021)

Add to Collection

Article Biochemical Research Methods

EpiGraphDB: a database and data mining platform for health data science

Yi Liu et al.

Summary: The study developed EpiGraphDB, a graph database and analytical platform for human population health data science. Three case studies demonstrated the practical value of the platform, including addressing mis-inference, identifying new drug targets, and integrating evidence from different sources.

BIOINFORMATICS (2021)

Add to Collection

Article Biochemistry & Molecular Biology

QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes

Zhanye Zheng et al.

NUCLEIC ACIDS RESEARCH (2020)

Add to Collection

Review Genetics & Heredity

A Multi-Omics Perspective of Quantitative Trait Loci in Precision Medicine

Youqiong Ye et al.

TRENDS IN GENETICS (2020)

Add to Collection

Article Genetics & Heredity

Phenome-wide Mendelian randomization mapping the influence of the plasma proteome on complex diseases

Jie Zheng et al.

NATURE GENETICS (2020)

Add to Collection

Article Multidisciplinary Sciences

Assessing the causal association of glycine with risk of cardio-metabolic diseases

Laura B. L. Wittemans et al.

NATURE COMMUNICATIONS (2019)

Add to Collection

Review Genetics & Heredity

Benefits and limitations of genome-wide association studies

Vivian Tam et al.

NATURE REVIEWS GENETICS (2019)

Add to Collection

Review Clinical Neurology

Gene-environment interaction and Mendelian randomisation

P. Kolber et al.

REVUE NEUROLOGIQUE (2019)

Add to Collection

Article Neurosciences

High ethanol sensitive glycine receptors regulate firing in D1 medium spiny neurons in the nucleus accumbens

S. Gallegos et al.

NEUROPHARMACOLOGY (2019)

Add to Collection

Review Genetics & Heredity

The Post-GWAS Era: From Association to Function

Michael D. Gallagher et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2018)

Add to Collection

Article Genetics & Heredity

Detection of widespread horizontal pleiotropy in causal relationships inferred from Mendelian randomization between complex traits and diseases

Marie Verbanck et al.

NATURE GENETICS (2018)

Add to Collection

Review Genetics & Heredity

Using genetic data to strengthen causal inference in observational research

Jean-Baptiste Pingault et al.

NATURE REVIEWS GENETICS (2018)

Add to Collection

Article Medicine, General & Internal

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

Neil M. Davies et al.

BMJ-BRITISH MEDICAL JOURNAL (2018)

Add to Collection

Article Medicine, General & Internal

Reading Mendelian randomisation studies: a guide, glossary, and checklist for clinicians

Neil M. Davies et al.

BMJ-BRITISH MEDICAL JOURNAL (2018)

Add to Collection

Article Biology

The MR-Base platform supports systematic causal inference across the human phenome

Gibran Hemani et al.

ELIFE (2018)

Add to Collection

Review Multidisciplinary Sciences

Arachidonic acid: Physiological roles and potential health benefits - A review

Hatem Tallima et al.

JOURNAL OF ADVANCED RESEARCH (2018)

Add to Collection

Article Medicine, Research & Experimental

Interleukin-1beta may act on hepatocytes to boost plasma homocysteine - The increased cardiovascular risk associated with elevated homocysteine may be mediated by this cytokine

Mark F. McCarty et al.

MEDICAL HYPOTHESES (2017)

Add to Collection

Article Genetics & Heredity

Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites

Tao Long et al.

NATURE GENETICS (2017)

Add to Collection

Article Genetics & Heredity

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

Katrina M. de lange et al.

NATURE GENETICS (2017)

Add to Collection

Article Mathematical & Computational Biology

A framework for the investigation of pleiotropy in two-sample summary data Mendelian randomization

Jack Bowden et al.

STATISTICS IN MEDICINE (2017)

Add to Collection

Review Genetics & Heredity

10 Years of GWAS Discovery: Biology, Function, and Translation

Peter M. Visscher et al.

AMERICAN JOURNAL OF HUMAN GENETICS (2017)

Add to Collection

Article Physiology

Glycine enhances muscle protein mass associated with maintaining Akt-mTOR-FOXO1 signaling and suppressing TLR4 and NOD2 signaling in piglets challenged with LPS

Yulan Liu et al.

AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY (2016)

Add to Collection

Article Genetics & Heredity

Consistent Estimation in Mendelian Randomization with Some Invalid Instruments Using a Weighted Median Estimator

Jack Bowden et al.

GENETIC EPIDEMIOLOGY (2016)

Add to Collection

Review Cell Biology

Metabolomics: beyond biomarkers and towards mechanisms

Caroline H. Johnson et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2016)

Add to Collection

Article Toxicology

Inhibition of homocysteine-induced endoplasmic reticulum stress and endothelial cell damage by L-serine and glycine

Woo-Cheol Sim et al.

TOXICOLOGY IN VITRO (2016)

Add to Collection

Article Oncology

The associations between serum biomarkers and stenosis of the coronary arteries

Lei Feng et al.

ONCOTARGET (2016)

Add to Collection

Article Public, Environmental & Occupational Health

Using published data in Mendelian randomization: a blueprint for efficient identification of causal risk factors

Stephen Burgess et al.

EUROPEAN JOURNAL OF EPIDEMIOLOGY (2015)

Add to Collection

Review Biochemistry & Molecular Biology

Genetics of human metabolism: an update

Gabi Kastenmueller et al.

HUMAN MOLECULAR GENETICS (2015)

Add to Collection

Article Public, Environmental & Occupational Health

Mendelian randomization with invalid instruments: effect estimation and bias detection through Egger regression

Jack Bowden et al.

INTERNATIONAL JOURNAL OF EPIDEMIOLOGY (2015)

Add to Collection

Article Multidisciplinary Sciences

A global reference for human genetic variation

David M. Altshuler et al.

NATURE (2015)

Add to Collection

Review Nutrition & Dietetics

Role of homocysteine in the development of cardiovascular disease

Paul Ganguly et al.

NUTRITION JOURNAL (2015)

Add to Collection

Article Genetics & Heredity

An atlas of genetic influences on human blood metabolites

So-Youn Shin et al.

NATURE GENETICS (2014)

Add to Collection

Review Cardiac & Cardiovascular Systems

Alcohol and the heart: To abstain or not to abstain?

Rajesh Movva et al.

INTERNATIONAL JOURNAL OF CARDIOLOGY (2013)

Add to Collection

Article Cardiac & Cardiovascular Systems

Secretory Phospholipase A2-IIA and Cardiovascular Disease

Michael V. Holmes et al.

JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY (2013)

Add to Collection

Review Genetics & Heredity

Meta-analysis methods for genome-wide association studies and beyond

Evangelos Evangelou et al.

NATURE REVIEWS GENETICS (2013)

Add to Collection

Article Biochemical Research Methods

SemMedDB: a PubMed-scale repository of biomedical semantic predications

Halil Kilicoglu et al.

BIOINFORMATICS (2012)

Add to Collection

Article Cardiac & Cardiovascular Systems

Effect of Long-Term Exposure to Lower Low-Density Lipoprotein Cholesterol Beginning Early in Life on the Risk of Coronary Heart Disease A Mendelian Randomization Analysis

Brian A. Ference et al.

JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY (2012)

Add to Collection

Article Genetics & Heredity

Genetics Meets Metabolomics: A Genome-Wide Association Study of Metabolite Profiles in Human Serum

Christian Gieger et al.

PLOS GENETICS (2008)

Add to Collection

Article Nutrition & Dietetics

Peripheral blood mononuclear cell fatty acid composition and inflammatory mediator production in adult Crohn's disease

TM Trebble et al.

CLINICAL NUTRITION (2004)

Add to Collection

Article Public, Environmental & Occupational Health

'Mendelian randomization': can genetic epidemiology contribute to understanding environmental determinants of disease?

GD Smith et al.

INTERNATIONAL JOURNAL OF EPIDEMIOLOGY (2003)

Add to Collection

© Peeref 2019-2024. All rights reserved.