Genetic Epidemiology最新文献

筛选
英文 中文
Identifying Disease Associated Multi-Omics Network With Mixed Graphical Models Based on Markov Random Field Model 基于马尔可夫随机场模型的混合图形模型识别疾病相关多组学网络。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-15 DOI: 10.1002/gepi.22605
Jaehyun Park, Sungho Won
{"title":"Identifying Disease Associated Multi-Omics Network With Mixed Graphical Models Based on Markov Random Field Model","authors":"Jaehyun Park,&nbsp;Sungho Won","doi":"10.1002/gepi.22605","DOIUrl":"10.1002/gepi.22605","url":null,"abstract":"<div>\u0000 \u0000 <p>In this article, we proposed a new method named fused mixed graphical model (FMGM), which can infer network structures associated with dichotomous phenotypes. FMGM is based on a pairwise Markov random field model, and statistical analyses including the proposed method were conducted to find biological markers and underlying network structures of the atopic dermatitis (AD) from multiomics data of 6-month-old infants. The performance of FMGM was evaluated with simulations by using synthetic datasets of power-law networks, showing that FMGM had superior performance for identifying the differences of the networks compared to the separate inference with the previous method, causalMGM (F1-scores 0.550 vs. 0.730). Furthermore, FMGM was applied to identify multiomics profiles associated with AD, and significance association was found for the correlation between carotenoid biosynthesis and RNA degradation, suggesting the importance of metabolism related to oxidative stress and microbial RNA balance. R codes can be accessed as an R package “fusedMGM,” and an example data set and a script for analyses can be found at http://figshare.com/articles/dataset/FMGM_synthetic_data_example_zip/20509113.</p>\u0000 </div>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983309","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genetically Predicted Gene Expression Effects on Changes in Red Blood Cell and Plasma Polyunsaturated Fatty Acids 基因预测对红细胞和血浆多不饱和脂肪酸变化的影响。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-15 DOI: 10.1002/gepi.22613
Nikhil K. Khankari, Timothy Su, Qiuyin Cai, Lili Liu, Elizabeth A. Jasper, Jacklyn N. Hellwege, Harvey J. Murff, Martha J. Shrubsole, Jirong Long, Todd L. Edwards, Wei Zheng
{"title":"Genetically Predicted Gene Expression Effects on Changes in Red Blood Cell and Plasma Polyunsaturated Fatty Acids","authors":"Nikhil K. Khankari,&nbsp;Timothy Su,&nbsp;Qiuyin Cai,&nbsp;Lili Liu,&nbsp;Elizabeth A. Jasper,&nbsp;Jacklyn N. Hellwege,&nbsp;Harvey J. Murff,&nbsp;Martha J. Shrubsole,&nbsp;Jirong Long,&nbsp;Todd L. Edwards,&nbsp;Wei Zheng","doi":"10.1002/gepi.22613","DOIUrl":"10.1002/gepi.22613","url":null,"abstract":"<p>Polyunsaturated fatty acids (PUFAs) including omega-3 and omega-6 are obtained from diet and can be measured objectively in plasma or red blood cells (RBCs) membrane biomarkers, representing different dietary exposure windows. In vivo conversion of omega-3 and omega-6 PUFAs from short- to long-chain counterparts occurs via a shared metabolic pathway involving fatty acid desaturases and elongase. This analysis leveraged genome-wide association study (GWAS) summary statistics for RBC and plasma PUFAs, along with expression quantitative trait loci (eQTL) to estimate tissue-specific genetically predicted gene expression effects for delta-5 desaturase (<i>FADS1</i>), delta-6 desaturase (<i>FADS2</i>), and elongase (<i>ELOVL2</i>) on changes in RBC and plasma biomarkers. Using colocalization, we identified shared variants associated with both increased gene expression and changes in RBC PUFA levels in relevant PUFA metabolism tissues (i.e., adipose, liver, muscle, and whole blood). We observed differences in RBC versus plasma PUFA levels for genetically predicted increase in <i>FADS1</i> and <i>FADS2</i> gene expression, primarily for omega-6 PUFAs linoleic acid (LA) and arachidonic acid (AA). The colocalization analysis identified rs102275 to be significantly associated with a 0.69% increase in total RBC membrane-bound LA levels (<i>p</i> = 5.4 × 10<sup>−12</sup>). Future PUFA genetic studies examining long-term PUFA biomarkers are needed to confirm our results.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734643/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983307","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Multivariable MR Can Mitigate Bias in Two-Sample MR Using Covariable-Adjusted Summary Associations 使用协变量调整的汇总关联,多变量MR可以减轻双样本MR的偏差。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-15 DOI: 10.1002/gepi.22606
Joe Gilbody, Maria Carolina Borges, George Davey Smith, Eleanor Sanderson
{"title":"Multivariable MR Can Mitigate Bias in Two-Sample MR Using Covariable-Adjusted Summary Associations","authors":"Joe Gilbody,&nbsp;Maria Carolina Borges,&nbsp;George Davey Smith,&nbsp;Eleanor Sanderson","doi":"10.1002/gepi.22606","DOIUrl":"10.1002/gepi.22606","url":null,"abstract":"<p>Genome-wide association studies (GWAS) are hypothesis-free studies that estimate the association between polymorphisms across the genome with a trait of interest. To increase power and to estimate the direct effects of these single-nucleotide polymorphisms (SNPs) on a trait GWAS are often conditioned on a covariate (such as body mass index or smoking status). This adjustment can introduce bias in the estimated effect of the SNP on the trait. Two-sample Mendelian randomisation (MR) studies use summary statistics from GWAS estimate the causal effect of a risk factor (or exposure) on an outcome. Covariate adjustment in GWAS can bias the effect estimates obtained from MR studies conducted using covariate adjusted GWAS data. Multivariable MR (MVMR) is an extension of MR that includes multiple traits as exposures. Here we propose the use of MVMR to correct the bias in MR studies from covariate adjustment. We show how MVMR can recover unbiased estimates of the direct effect of the exposure of interest by including the covariate used to adjust the GWAS within the analysis. We apply this method to estimate the effect of systolic blood pressure on type-2 diabetes and the effect of waist circumference on systolic blood pressure. Our analytical and simulation results show that MVMR provides unbiased effect estimates for the exposure when either the exposure or outcome of interest has been adjusted for a covariate. Our results also highlight the parameters that determine when MR will be biased by GWAS covariate adjustment. The results from the applied analysis mirror these results, with equivalent results seen in the MVMR with and without adjusted GWAS. When GWAS results have been adjusted for a covariate, biasing MR effect estimates, direct effect estimates of an exposure on an outcome can be obtained by including that covariate as an additional exposure in an MVMR estimation. However, the estimated effect of the covariate obtained from the MVMR estimation is biased.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734645/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Transferability of Single- and Cross-Tissue Transcriptome Imputation Models Across Ancestry Groups 跨祖先群体的单组织和跨组织转录组植入模型的可转移性。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-15 DOI: 10.1002/gepi.22611
Inti Pagnuco, Stephen Eyre, Magnus Rattray, Andrew P. Morris
{"title":"Transferability of Single- and Cross-Tissue Transcriptome Imputation Models Across Ancestry Groups","authors":"Inti Pagnuco,&nbsp;Stephen Eyre,&nbsp;Magnus Rattray,&nbsp;Andrew P. Morris","doi":"10.1002/gepi.22611","DOIUrl":"10.1002/gepi.22611","url":null,"abstract":"<p>Transcriptome-wide association studies (TWAS) investigate the links between genetically regulated gene expression and complex traits. TWAS involves imputing gene expression using expression quantitative trait loci (eQTL) as predictors and testing the association between the imputed expression and the trait. The effectiveness of TWAS depends on the accuracy of these imputation models, which require genotype and gene expression data from the same samples. However, publicly accessible resources, such as the Genotype Tissue Expression (GTEx) Project, are biased toward individuals of European ancestry, potentially reducing prediction accuracy into other ancestry groups. This study explored eQTL transferability across ancestry groups by comparing two imputation models: PrediXcan (tissue-specific) and UTMOST (cross-tissue). Both models were trained on tissues from the GTEx Project using European ancestry individuals and then tested on data sets of European ancestry and African American individuals. Results showed that both models performed best when the training and testing data sets were from the same ancestry group, with the cross-tissue approach generally outperforming the tissue-specific approach. This study underscores that eQTL detection is influenced by ancestry and tissue context. Developing ancestry-specific reference panels across tissues can improve prediction accuracy, enhancing TWAS analysis and our understanding of the biological processes contributing to complex traits.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11734644/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
General Kernel Machine Methods for Multi-Omics Integration and Genome-Wide Association Testing With Related Individuals 多组学整合和相关个体全基因组关联检测的通用核机方法。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-15 DOI: 10.1002/gepi.22610
Amarise Little, Ni Zhao, Anna Mikhaylova, Angela Zhang, Wodan Ling, Florian Thibord, Andrew D. Johnson, Laura M. Raffield, Joanne E. Curran, John Blangero, Jeffrey R. O'Connell, Huichun Xu, Jerome I. Rotter, Stephen S. Rich, Kenneth M. Rice, Ming-Huei Chen, Alexander Reiner, Charles Kooperberg, Thao Vu, Lifang Hou, Myriam Fornage, Ruth J.F. Loos, Eimear Kenny, Rasika Mathias, Lewis Becker, Albert V. Smith, Eric Boerwinkle, Bing Yu, Timothy Thornton, Michael C. Wu
{"title":"General Kernel Machine Methods for Multi-Omics Integration and Genome-Wide Association Testing With Related Individuals","authors":"Amarise Little,&nbsp;Ni Zhao,&nbsp;Anna Mikhaylova,&nbsp;Angela Zhang,&nbsp;Wodan Ling,&nbsp;Florian Thibord,&nbsp;Andrew D. Johnson,&nbsp;Laura M. Raffield,&nbsp;Joanne E. Curran,&nbsp;John Blangero,&nbsp;Jeffrey R. O'Connell,&nbsp;Huichun Xu,&nbsp;Jerome I. Rotter,&nbsp;Stephen S. Rich,&nbsp;Kenneth M. Rice,&nbsp;Ming-Huei Chen,&nbsp;Alexander Reiner,&nbsp;Charles Kooperberg,&nbsp;Thao Vu,&nbsp;Lifang Hou,&nbsp;Myriam Fornage,&nbsp;Ruth J.F. Loos,&nbsp;Eimear Kenny,&nbsp;Rasika Mathias,&nbsp;Lewis Becker,&nbsp;Albert V. Smith,&nbsp;Eric Boerwinkle,&nbsp;Bing Yu,&nbsp;Timothy Thornton,&nbsp;Michael C. Wu","doi":"10.1002/gepi.22610","DOIUrl":"10.1002/gepi.22610","url":null,"abstract":"<div>\u0000 \u0000 <p>Integrating multi-omics data may help researchers understand the genetic underpinnings of complex traits and diseases. However, the best ways to integrate multi-omics data and use them to address pressing scientific questions remain a challenge. One important and topical problem is how to assess the aggregate effect of multiple genomic data types (e.g. genotypes and gene expression levels) on a phenotype, particularly while accommodating routine issues, such as having related subjects' data in analyses. In this paper, we extend an existing composite kernel machine regression model to integrate two multi-omics data types, while accommodating for general correlation structures amongst outcomes. Due to the kernel machine regression framework, our methods allow for the integration of high-dimensional omics data with small, nonlinear, and interactive effects, and accommodation of general study designs. Here, we focus on scientific questions that aim to assess the association between a functional grouping (such as a gene or a pathway) and a quantitative trait of interest. We use a kernel machine regression to integrate the two multi-omics data types, as they may relate to the trait, and perform a global test of association. We demonstrate the advantage of this approach over single data type association tests via simulation. Finally, we apply this method to a large, multi-ethnic data set to investigate how predicted gene expression and rare genetic variation may be related to two platelet traits.</p>\u0000 </div>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142983296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Refinement of a Published Gene-Physical Activity Interaction Impacting HDL-Cholesterol: Role of Sex and Lipoprotein Subfractions 已发表的基因-身体活动相互作用影响高密度脂蛋白胆固醇的改进:性别和脂蛋白亚组分的作用。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-07 DOI: 10.1002/gepi.22607
Kenneth E. Westerman, Tuomas O. Kilpeläinen, Magdalena Sevilla-Gonzalez, Margery A. Connelly, Alexis C. Wood, Michael Y. Tsai, Kent D. Taylor, Stephen S. Rich, Jerome I. Rotter, James D. Otvos, Amy R. Bentley, Samia Mora, Hugues Aschard, D. C. Rao, Charles Gu, Daniel I. Chasman, Alisa K. Manning, The CHARGE Gene-Lifestyle Interactions Working Group
{"title":"Refinement of a Published Gene-Physical Activity Interaction Impacting HDL-Cholesterol: Role of Sex and Lipoprotein Subfractions","authors":"Kenneth E. Westerman,&nbsp;Tuomas O. Kilpeläinen,&nbsp;Magdalena Sevilla-Gonzalez,&nbsp;Margery A. Connelly,&nbsp;Alexis C. Wood,&nbsp;Michael Y. Tsai,&nbsp;Kent D. Taylor,&nbsp;Stephen S. Rich,&nbsp;Jerome I. Rotter,&nbsp;James D. Otvos,&nbsp;Amy R. Bentley,&nbsp;Samia Mora,&nbsp;Hugues Aschard,&nbsp;D. C. Rao,&nbsp;Charles Gu,&nbsp;Daniel I. Chasman,&nbsp;Alisa K. Manning,&nbsp;The CHARGE Gene-Lifestyle Interactions Working Group","doi":"10.1002/gepi.22607","DOIUrl":"10.1002/gepi.22607","url":null,"abstract":"<div>\u0000 \u0000 <p>Large-scale gene–environment interaction (GxE) discovery efforts often involve analytical compromises for the sake of data harmonization and statistical power. Refinement of exposures, covariates, outcomes, and population subsets may be helpful to establish often-elusive replication and evaluate potential clinical utility. Here, we used additional datasets, an expanded set of statistical models, and interrogation of lipoprotein metabolism via nuclear magnetic resonance (NMR)-based lipoprotein subfractions to refine a previously discovered GxE modifying the relationship between physical activity (PA) and HDL-cholesterol (HDL-C). We explored this GxE in the Women's Genome Health Study (WGHS; <i>N</i> = 23,294; the strongest cohort-specific signal in the original meta-analysis), the UK Biobank (UKB; <i>N</i> = 281,380), and the Multi-Ethnic Study of Atherosclerosis (MESA; <i>N</i> = 4587), using self-reported PA (MET-min/wk) and genotypes at rs295849 (nearest gene: <i>LHX1</i>). As originally reported, minor allele carriers of rs295849 in WGHS had a stronger positive association between PA and HDL-C (<i>p</i><sub>int</sub> = 0.002). When testing available NMR metabolites to refine the HDL-C outcome, we found a stronger interaction effect on medium-sized HDL particle concentrations (M-HDL-P; <i>p</i><sub>int</sub> = 1.0 × 10<sup>−4</sup>) than HDL-C. Meta-regression revealed a systematically larger interaction effect in cohorts from the original meta-analysis with a greater fraction of women (<i>p</i> = 0.018). In the UKB, GxE effects were stronger in women and using M-HDL-P as the outcome. In MESA, the primary interaction for HDL-C showed nominal significance (<i>p</i><sub>int</sub> = 0.013), but without clear sex differences and with a greater magnitude for large HDL-P. Our work provides additional insights into a known gene-PA interaction while illustrating the importance of phenotype and model refinement toward understanding and replicating GxEs.</p>\u0000 </div>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142978271","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Bayesian Effect Size Ranking to Prioritise Genetic Risk Variants in Common Diseases for Follow-Up Studies 常见疾病遗传风险变异的贝叶斯效应大小排序用于后续研究。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-03 DOI: 10.1002/gepi.22608
Daniel J. M. Crouch, Jamie R. J. Inshaw, Catherine C. Robertson, Esther Ng, Jia-Yuan Zhang, Wei-Min Chen, Suna Onengut-Gumuscu, Antony J. Cutler, Carlo Sidore, Francesco Cucca, Flemming Pociot, Patrick Concannon, Stephen S. Rich, John A. Todd
{"title":"Bayesian Effect Size Ranking to Prioritise Genetic Risk Variants in Common Diseases for Follow-Up Studies","authors":"Daniel J. M. Crouch,&nbsp;Jamie R. J. Inshaw,&nbsp;Catherine C. Robertson,&nbsp;Esther Ng,&nbsp;Jia-Yuan Zhang,&nbsp;Wei-Min Chen,&nbsp;Suna Onengut-Gumuscu,&nbsp;Antony J. Cutler,&nbsp;Carlo Sidore,&nbsp;Francesco Cucca,&nbsp;Flemming Pociot,&nbsp;Patrick Concannon,&nbsp;Stephen S. Rich,&nbsp;John A. Todd","doi":"10.1002/gepi.22608","DOIUrl":"10.1002/gepi.22608","url":null,"abstract":"<p>Biological datasets often consist of thousands or millions of variables, e.g. genetic variants or biomarkers, and when sample sizes are large it is common to find many associated with an outcome of interest, for example, disease risk in a GWAS, at high levels of statistical significance, but with very small effects. The False Discovery Rate (FDR) is used to identify effects of interest based on ranking variables according to their statistical significance. Here, we develop a complementary measure to the FDR, the priorityFDR, that ranks variables by a combination of effect size and significance, allowing further prioritisation among a set of variables that pass a significance or FDR threshold. Applying to the largest GWAS of type 1 diabetes to date (15,573 cases and 158,408 controls), we identified 26 independent genetic associations, including two newly-reported loci, with qualitatively lower priorityFDRs than the remaining 175 signals. We detected putatively causal type 1 diabetes risk genes using Mendelian Randomisation, and found that these were located disproportionately close to low priorityFDR signals (<i>p</i> = 0.005), as were genes in the IL-2 pathway (<i>p</i> = 0.003). Selecting variables on both effect size and significance can lead to improved prioritisation for mechanistic follow-up studies from genetic and other large biological datasets.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11696485/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142921509","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Using Family History Data to Improve the Power of Association Studies: Application to Cancer in UK Biobank 使用家族史数据提高关联研究的能力:在英国生物银行的癌症应用。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2025-01-03 DOI: 10.1002/gepi.22609
Naomi Wilcox, Jonathan P. Tyrer, Joe Dennis, Xin Yang, John R. B. Perry, Eugene J. Gardner, Douglas F. Easton
{"title":"Using Family History Data to Improve the Power of Association Studies: Application to Cancer in UK Biobank","authors":"Naomi Wilcox,&nbsp;Jonathan P. Tyrer,&nbsp;Joe Dennis,&nbsp;Xin Yang,&nbsp;John R. B. Perry,&nbsp;Eugene J. Gardner,&nbsp;Douglas F. Easton","doi":"10.1002/gepi.22609","DOIUrl":"10.1002/gepi.22609","url":null,"abstract":"<p>In large cohort studies the number of unaffected individuals outnumbers the number of affected individuals, and the power can be low to detect associations for outcomes with low prevalence. We consider how including recorded family history in regression models increases the power to detect associations between genetic variants and disease risk. We show theoretically and using Monte-Carlo simulations that including a family history of the disease, with a weighting of 0.5 compared with true cases, increases the power to detect associations. This is a powerful approach for detecting variants with moderate effects, but for larger effect sizes a weighting of &gt; 0.5 can be more powerful. We illustrate this both for common variants and for exome sequencing data for over 400,000 individuals in UK Biobank to evaluate the association between the burden of protein-truncating variants in genes and risk for four cancer types.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2025-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22609","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142921513","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Additional article of this Special Issue was previously published in another issue of Genetic Epidemiology. That is: 本特刊的其他文章曾在另一期《遗传流行病学》上发表过。即
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2024-11-25 DOI: 10.1002/gepi.22604
{"title":"Additional article of this Special Issue was previously published in another issue of Genetic Epidemiology. That is:","authors":"","doi":"10.1002/gepi.22604","DOIUrl":"https://doi.org/10.1002/gepi.22604","url":null,"abstract":"<p>Gorfine, M., Qu, C.,Peters, U., &amp; Hsu, L. (2024). Unveiling challenges in Mendelian randomization for gene-environment interaction. Genetic Epidemiology, 48, 164–189. https://doi.org/10.1002/gepi.22552</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 8","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142714718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A Novel One-Sample Mendelian Randomization Approach for Count-Type Outcomes That Is Robust to Correlated and Uncorrelated Pleiotropic Effects 针对计数型结果的新型单样本孟德尔随机化方法,对相关和不相关的多向效应具有鲁棒性。
IF 1.7 4区 医学
Genetic Epidemiology Pub Date : 2024-11-05 DOI: 10.1002/gepi.22602
Janaka S. S. Liyanage, Jane S. Hankins, Jeremie H. Estepp, Deokumar Srivastava, Sara R. Rashkin, Clifford Takemoto, Yun Li, Yuehua Cui, Motomi Mori, Mitchell J. Weiss, Guolian Kang
{"title":"A Novel One-Sample Mendelian Randomization Approach for Count-Type Outcomes That Is Robust to Correlated and Uncorrelated Pleiotropic Effects","authors":"Janaka S. S. Liyanage,&nbsp;Jane S. Hankins,&nbsp;Jeremie H. Estepp,&nbsp;Deokumar Srivastava,&nbsp;Sara R. Rashkin,&nbsp;Clifford Takemoto,&nbsp;Yun Li,&nbsp;Yuehua Cui,&nbsp;Motomi Mori,&nbsp;Mitchell J. Weiss,&nbsp;Guolian Kang","doi":"10.1002/gepi.22602","DOIUrl":"10.1002/gepi.22602","url":null,"abstract":"<div>\u0000 \u0000 <p>We propose two novel one-sample Mendelian randomization (MR) approaches to causal inference from count-type health outcomes, tailored to both equidispersion and overdispersion conditions. Selecting valid single-nucleotide polymorphisms (SNPs) as instrumental variables (IVs) poses a key challenge for MR approaches, as it requires meeting the necessary IV assumptions. To bolster the proposed approaches by addressing violations of IV assumptions, we incorporate a process for removing invalid SNPs that violate the assumptions. In simulations, our proposed approaches demonstrate robustness to the violations, delivering valid estimates, and interpretable type-I errors and statistical power. This increases the practical applicability of the models. We applied the proposed approaches to evaluate the causal effect of fetal hemoglobin (HbF) on the vaso-occlusive crisis and acute chest syndrome (ACS) events in patients with sickle cell disease (SCD) and revealed the causal relation between HbF and ACS events in these patients. We also developed a user-friendly Shiny web application to facilitate researchers' exploration of causal relations.</p>\u0000 </div>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"49 1","pages":""},"PeriodicalIF":1.7,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142582841","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信