Genetic Epidemiology最新文献

{"title":"Gene-based association tests in family samples using GWAS summary statistics","authors":"Peng Wang,&nbsp;Xiao Xu,&nbsp;Ming Li,&nbsp;Xiang-Yang Lou,&nbsp;Siqi Xu,&nbsp;Baolin Wu,&nbsp;Guimin Gao,&nbsp;Ping Yin,&nbsp;Nianjun Liu","doi":"10.1002/gepi.22548","DOIUrl":"10.1002/gepi.22548","url":null,"abstract":"<p>Genome-wide association studies (GWAS) have led to rapid growth in detecting genetic variants associated with various phenotypes. Owing to a great number of publicly accessible GWAS summary statistics, and the difficulty in obtaining individual-level genotype data, many existing gene-based association tests have been adapted to require only GWAS summary statistics rather than individual-level data. However, these association tests are restricted to unrelated individuals and thus do not apply to family samples directly. Moreover, due to its flexibility and effectiveness, the linear mixed model has been increasingly utilized in GWAS to handle correlated data, such as family samples. However, it remains unknown how to perform gene-based association tests in family samples using the GWAS summary statistics estimated from the linear mixed model. In this study, we show that, when family size is negligible compared to the total sample size, the diagonal block structure of the kinship matrix makes it possible to approximate the correlation matrix of marginal <i>Z</i> scores by linkage disequilibrium matrix. Based on this result, current methods utilizing summary statistics for unrelated individuals can be directly applied to family data without any modifications. Our simulation results demonstrate that this proposed strategy controls the type 1 error rate well in various situations. Finally, we exemplify the usefulness of the proposed approach with a dental caries GWAS data set.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 3","pages":"103-113"},"PeriodicalIF":2.1,"publicationDate":"2024-02-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22548","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139691642","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}

{"title":"Mitigating type 1 error inflation and power loss in GxE PRS: Genotype–environment interaction in polygenic risk score models","authors":"Dovini Jayasinghe,&nbsp;Md. Moksedul Momin,&nbsp;Kerri Beckmann,&nbsp;Elina Hyppönen,&nbsp;Beben Benyamin,&nbsp;S. Hong Lee","doi":"10.1002/gepi.22546","DOIUrl":"10.1002/gepi.22546","url":null,"abstract":"<p>The use of polygenic risk score (PRS) models has transformed the field of genetics by enabling the prediction of complex traits and diseases based on an individual's genetic profile. However, the impact of genotype–environment interaction (GxE) on the performance and applicability of PRS models remains a crucial aspect to be explored. Currently, existing genotype–environment interaction polygenic risk score (GxE PRS) models are often inappropriately used, which can result in inflated type 1 error rates and compromised results. In this study, we propose novel GxE PRS models that jointly incorporate additive and interaction genetic effects although also including an additional quadratic term for nongenetic covariates, enhancing their robustness against model misspecification. Through extensive simulations, we demonstrate that our proposed models outperform existing models in terms of controlling type 1 error rates and enhancing statistical power. Furthermore, we apply the proposed models to real data, and report significant GxE effects. Specifically, we highlight the impact of our models on both quantitative and binary traits. For quantitative traits, we uncover the GxE modulation of genetic effects on body mass index by alcohol intake frequency. In the case of binary traits, we identify the GxE modulation of genetic effects on hypertension by waist-to-hip ratio. These findings underscore the importance of employing a robust model that effectively controls type 1 error rates, thus preventing the occurrence of spurious GxE signals. To facilitate the implementation of our approach, we have developed an innovative R software package called GxEprs, specifically designed to detect and estimate GxE effects. Overall, our study highlights the importance of accurate GxE modeling and its implications for genetic risk prediction, although providing a practical tool to support further research in this area.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 2","pages":"85-100"},"PeriodicalIF":2.1,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22546","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139671559","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}

{"title":"Interval estimate of causal effect in summary data based Mendelian randomization in the presence of winner's curse","authors":"Kai Wang","doi":"10.1002/gepi.22545","DOIUrl":"10.1002/gepi.22545","url":null,"abstract":"<p>This research focuses on the interval estimation of the causal effect of an exposure on an outcome using the summary data-based Mendelian randomization (SMR) method while accounting for the winner's curse caused by the selection of single nucleotide polymorphism instruments. This issue is understudied and is important as the point estimate is biased. Since Fieller's theorem and its variations are not suitable for constructing a confidence interval, we use the box method. This box method is known to be conservative and thus provides a lower bound on the coverage level. To assess the performance of the box method, we use simulation studies and compare it with the support interval we proposed earlier and the Wald interval derived from the SMR method. All three methods are applied to a study of causal genes for Alzheimer's disease. Overall, the box method presents an alternative for constructing interval estimates for a causal effect while addressing the winner's curse issue.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 2","pages":"74-84"},"PeriodicalIF":2.1,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22545","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139570440","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}

{"title":"simmrd: An open-source tool to perform simulations in Mendelian randomization","authors":"Noah Lorincz-Comi,&nbsp;Yihe Yang,&nbsp;Xiaofeng Zhu","doi":"10.1002/gepi.22544","DOIUrl":"10.1002/gepi.22544","url":null,"abstract":"<p>Mendelian randomization (MR) has become a popular tool for inferring causality of risk factors on disease. There are currently over 45 different methods available to perform MR, reflecting this extremely active research area. It would be desirable to have a standard simulation environment to objectively evaluate the existing and future methods. We present <span>simmrd</span>, an open-source software for performing simulations to evaluate the performance of MR methods in a range of scenarios encountered in practice. Researchers can directly modify the <span>simmrd</span> source code so that the research community may arrive at a widely accepted framework for researchers to evaluate the performance of different MR methods.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 2","pages":"59-73"},"PeriodicalIF":2.1,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22544","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139542107","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}

{"title":"DYNATE: Localizing rare-variant association regions via multiple testing embedded in an aggregation tree","authors":"Xuechan Li,&nbsp;John Pura,&nbsp;Andrew Allen,&nbsp;Kouros Owzar,&nbsp;Jianfeng Lu,&nbsp;Matthew Harms,&nbsp;Jichun Xie","doi":"10.1002/gepi.22542","DOIUrl":"10.1002/gepi.22542","url":null,"abstract":"<p>Rare-variants (RVs) genetic association studies enable researchers to uncover the variation in phenotypic traits left unexplained by common variation. Traditional single-variant analysis lacks power; thus, researchers have developed various methods to aggregate the effects of RVs across genomic regions to study their collective impact. Some existing methods utilize a static delineation of genomic regions, often resulting in suboptimal effect aggregation, as neutral subregions within the test region will result in an attenuation of signal. Other methods use varying windows to search for signals but often result in long regions containing many neutral RVs. To pinpoint short genomic regions enriched for disease-associated RVs, we developed a novel method, DYNamic Aggregation TEsting (DYNATE). DYNATE dynamically and hierarchically aggregates smaller genomic regions into larger ones and performs multiple testing for disease associations with a controlled weighted false discovery rate. DYNATE's main advantage lies in its strong ability to identify short genomic regions highly enriched for disease-associated RVs. Extensive numerical simulations demonstrate the superior performance of DYNATE under various scenarios compared with existing methods. We applied DYNATE to an amyotrophic lateral sclerosis study and identified a new gene, <i>EPG5</i>, harboring possibly pathogenic mutations.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 1","pages":"42-55"},"PeriodicalIF":2.1,"publicationDate":"2023-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138444394","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}

{"title":"Bias and mean squared error in Mendelian randomization with invalid instrumental variables","authors":"Lu Deng,&nbsp;Sheng Fu,&nbsp;Kai Yu","doi":"10.1002/gepi.22541","DOIUrl":"10.1002/gepi.22541","url":null,"abstract":"<p>Mendelian randomization (MR) is a statistical method that utilizes genetic variants as instrumental variables (IVs) to investigate causal relationships between risk factors and outcomes. Although MR has gained popularity in recent years due to its ability to analyze summary statistics from genome-wide association studies (GWAS), it requires a substantial number of single nucleotide polymorphisms (SNPs) as IVs to ensure sufficient power for detecting causal effects. Unfortunately, the complex genetic heritability of many traits can lead to the use of invalid IVs that affect both the risk factor and the outcome directly or through an unobserved confounder. This can result in biased and imprecise estimates, as reflected by a larger mean squared error (MSE). In this study, we focus on the widely used two-stage least squares (2SLS) method and derive formulas for its bias and MSE when estimating causal effects using invalid IVs. Using those formulas, we identify conditions under which the 2SLS estimate is unbiased and reveal how the independent or correlated pleiotropic effects influence the accuracy and precision of the 2SLS estimate. We validate these formulas through extensive simulation studies and demonstrate the application of those formulas in an MR study to evaluate the causal effect of the waist-to-hip ratio on various sleeping patterns. Our results can aid in designing future MR studies and serve as benchmarks for assessing more sophisticated MR methods.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 1","pages":"27-41"},"PeriodicalIF":2.1,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136397137","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}

{"title":"Limitation of permutation-based differential correlation analysis","authors":"Hoseung Song,&nbsp;Michael C. Wu","doi":"10.1002/gepi.22540","DOIUrl":"10.1002/gepi.22540","url":null,"abstract":"<p>The comparison of biological systems, through the analysis of molecular changes under different conditions, has played a crucial role in the progress of modern biological science. Specifically, differential correlation analysis (DCA) has been employed to determine whether relationships between genomic features differ across conditions or outcomes. Because ascertaining the null distribution of test statistics to capture variations in correlation is challenging, several DCA methods utilize permutation which can loosen parametric (e.g., normality) assumptions. However, permutation is often problematic for DCA due to violating the assumption that samples are exchangeable under the null. Here, we examine the limitations of permutation-based DCA and investigate instances where the permutation-based DCA exhibits poor performance. Experimental results show that the permutation-based DCA often fails to control the type I error under the null hypothesis of equal correlation structures.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"47 8","pages":"637-641"},"PeriodicalIF":2.1,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72014121","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}

{"title":"Correction to “Abstracts”","authors":"","doi":"10.1002/gepi.22543","DOIUrl":"10.1002/gepi.22543","url":null,"abstract":"<p>(2023), Abstracts. Genetic Epidemiology, 47: 520–581. https://doi.org/10.1002/gepi.22539</p><p>In the originally published Abstracts, there were authors missing for “Two-sample Mendelian Randomization Study of Circulating Metabolites and Prostate Cancer Risk in Hispanic Populations” (abstract 49). The correct authors and affiliations appear below and have been updated on the online version of the abstracts.</p><p>Harriett Fuller¹, Rebecca Rohde², Heather Highland², Jiayi Shen³, Bing Yu⁴, Eric Boerwinkle⁴, Megan Grove⁴, Kari E. North², David V. Conti³, Christopher A. Haiman³, Kristin Young², Burcu F. Darst¹</p><p>¹Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA</p><p>²Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA</p><p>³Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, California, USA</p><p>⁴School of Public Health, The University of Texas Health Science Center at Houston, Houston, Texas, USA</p><p>We apologize for this error.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"47 8","pages":"642"},"PeriodicalIF":2.1,"publicationDate":"2023-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22543","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135241247","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}

{"title":"Haplotype reconstruction for genetically complex regions with ambiguous genotype calls: Illustration by the KIR gene region","authors":"Lars L. J. van der Burg,&nbsp;Liesbeth C. de Wreede,&nbsp;Henning Baldauf,&nbsp;Jürgen Sauter,&nbsp;Johannes Schetelig,&nbsp;Hein Putter,&nbsp;Stefan Böhringer","doi":"10.1002/gepi.22538","DOIUrl":"10.1002/gepi.22538","url":null,"abstract":"<p>Advances in DNA sequencing technologies have enabled genotyping of complex genetic regions exhibiting copy number variation and high allelic diversity, yet it is impossible to derive exact genotypes in all cases, often resulting in ambiguous genotype calls, that is, partially missing data. An example of such a gene region is the killer-cell immunoglobulin-like receptor (<i>KIR</i>) genes. These genes are of special interest in the context of allogeneic hematopoietic stem cell transplantation. For such complex gene regions, current haplotype reconstruction methods are not feasible as they cannot cope with the complexity of the data. We present an expectation–maximization (EM)-algorithm to estimate haplotype frequencies (HTFs) which deals with the missing data components, and takes into account linkage disequilibrium (LD) between genes. To cope with the exponential increase in the number of haplotypes as genes are added, we add three components to a standard EM-algorithm implementation. First, reconstruction is performed iteratively, adding one gene at a time. Second, after each step, haplotypes with frequencies below a threshold are collapsed in a rare haplotype group. Third, the HTF of the rare haplotype group is profiled in subsequent iterations to improve estimates. A simulation study evaluates the effect of combining information of multiple genes on the estimates of these frequencies. We show that estimated HTFs are approximately unbiased. Our simulation study shows that the EM-algorithm is able to combine information from multiple genes when LD is high, whereas increased ambiguity levels increase bias. Linear regression models based on this EM, show that a large number of haplotypes can be problematic for unbiased effect size estimation and that models need to be sparse. In a real data analysis of <i>KIR</i> genotypes, we compare HTFs to those obtained in an independent study. Our new EM-algorithm-based method is the first to account for the full genetic architecture of complex gene regions, such as the <i>KIR</i> gene region. This algorithm can handle the numerous observed ambiguities, and allows for the collapsing of haplotypes to perform implicit dimension reduction. Combining information from multiple genes improves haplotype reconstruction.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"48 1","pages":"3-26"},"PeriodicalIF":2.1,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/gepi.22538","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41198906","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}

{"title":"Data-adaptive and pathway-based tests for association studies between somatic mutations and germline variations in human cancers","authors":"Zhongyuan Chen,&nbsp;Han Liang,&nbsp;Peng Wei","doi":"10.1002/gepi.22537","DOIUrl":"10.1002/gepi.22537","url":null,"abstract":"<p>Cancer is a disease driven by a combination of inherited genetic variants and somatic mutations. Recently available large-scale sequencing data of cancer genomes have provided an unprecedented opportunity to study the interactions between them. However, previous studies on this topic have been limited by simple, low statistical power tests such as Fisher's exact test. In this paper, we design data-adaptive and pathway-based tests based on the score statistic for association studies between somatic mutations and germline variations. Previous research has shown that two single-nucleotide polymorphism (SNP)-set-based association tests, adaptive sum of powered score (aSPU) and data-adaptive pathway-based (aSPUpath) tests, increase the power in genome-wide association studies (GWASs) with a single disease trait in a case–control study. We extend aSPU and aSPUpath to multi-traits, that is, somatic mutations of multiple genes in a cohort study, allowing extensive information aggregation at both SNP and gene levels. <math>\u0000 <semantics>\u0000 <mrow>\u0000 <mi>p</mi>\u0000 </mrow>\u0000 <annotation> $p$</annotation>\u0000 </semantics></math>-values from different parameters assuming varying genetic architecture are combined to yield data-adaptive tests for somatic mutations and germline variations. Extensive simulations show that, in comparison with some commonly used methods, our data-adaptive somatic mutations/germline variations tests can be applied to multiple germline SNPs/genes/pathways, and generally have much higher statistical powers while maintaining the appropriate type I error. The proposed tests are applied to a large-scale real-world International Cancer Genome Consortium whole genome sequencing data set of 2583 subjects, detecting more significant and biologically relevant associations compared with the other existing methods on both gene and pathway levels. Our study has systematically identified the associations between various germline variations and somatic mutations across different cancer types, which potentially provides valuable utility for cancer risk prediction, prognosis, and therapeutics.</p>","PeriodicalId":12710,"journal":{"name":"Genetic Epidemiology","volume":"47 8","pages":"617-636"},"PeriodicalIF":2.1,"publicationDate":"2023-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41198905","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}