scholarly journals Use of longitudinal data in genetic studies in the genome-wide association studies era: summary of Group 14

2009 ◽  
Vol 33 (S1) ◽  
pp. S93-S98 ◽  
Author(s):  
Berit Kerner ◽  
Kari E. North ◽  
M. Daniele Fallin
Keyword(s):  
Longitudinal Data ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Group 14 ◽  
Genetic Studies ◽  
Genome Wide

scholarly journals Efficient multivariate analysis algorithms for longitudinal genome-wide association studies

2019 ◽  
Vol 35 (23) ◽  
pp. 4879-4885 ◽  
Author(s):  
Chao Ning ◽  
Dan Wang ◽  
Lei Zhou ◽  
Julong Wei ◽  
Yuanxin Liu ◽  
...  
Keyword(s):  
Longitudinal Data ◽  
Software Package ◽  
Mixed Model ◽  
Linear Mixed Model ◽  
Association Studies ◽  
Genome Wide Association ◽  
Supplementary Information ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Computational Speed

Abstract Motivation Current dynamic phenotyping system introduces time as an extra dimension to genome-wide association studies (GWAS), which helps to explore the mechanism of dynamical genetic control for complex longitudinal traits. However, existing methods for longitudinal GWAS either ignore the covariance among observations of different time points or encounter computational efficiency issues. Results We herein developed efficient genome-wide multivariate association algorithms for longitudinal data. In contrast to existing univariate linear mixed model analyses, the proposed method has improved statistic power for association detection and computational speed. In addition, the new method can analyze unbalanced longitudinal data with thousands of individuals and more than ten thousand records within a few hours. The corresponding time for balanced longitudinal data is just a few minutes. Availability and implementation A software package to implement the efficient algorithm named GMA (https://github.com/chaoning/GMA) is available freely for interested users in relevant fields. Supplementary information Supplementary data are available at Bioinformatics online.

Two-Stage Procedures for the Identification of Gene × Environment and Gene × Gene Interactions in Genome-Wide Association Studies

2016 ◽  
Author(s):  
Charles Kooperberg ◽  
James Y. Dai ◽  
Li Hsu
Keyword(s):  
Association Studies ◽  
Gene Interaction ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Two Stage ◽  
Genetic Studies ◽  
Gene Environment ◽  
Genome Wide ◽  
Sequencing Studies ◽  
Generation Sequencing

Genome-wide association studies and next generation sequencing studies offer us an unprecedented opportunity to study the genetic etiology of diseases and other traits. Over the last few years, many replicated associations between SNPs and traits have been published. It is of particular interest to identify how genes may interact with environmental factors and other genes. In this chapter, we show that a two-stage approach, where in the first stage SNPs are screened for their potential to be involved in interactions, and interactions are then tested only among SNPs that pass the screening can greatly enhance power for detecting gene-environment and gene-gene interaction in large genetic studies compared to the tests without screening.

scholarly journals Genomic and Personalized Medicine Approaches for Substance Use Disorders (SUDs) Looking at Genome-Wide Association Studies

Biomedicines ◽  
2021 ◽  
Vol 9 (12) ◽  
pp. 1799
Author(s):  
Danilo Cozzoli ◽  
Alessia Daponte ◽  
Salvatore De Fazio ◽  
Vincenza Ariano ◽  
Maria Rita Quaranta ◽  
...  
Keyword(s):  
Substance Use ◽  
Medical Treatment ◽  
Drug Addiction ◽  
Substance Use Disorder ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Negative Consequences ◽  
Genetic Studies ◽  
Genome Wide

Drug addiction, or substance use disorder (SUD), is a chronic, relapsing disorder in which compulsive drug-seeking and drug-taking behaviour persist despite serious negative consequences. Drug abuse represents a problem that deserves great attention from a social point of view, and focuses on the importance of genetic studies to help in understanding the genetic basis of addiction and its medical treatment. Despite the complexity of drug addiction disorders, and the high number of environmental variables playing a role in the onset, recurrence, and duration of the symptoms, several studies have highlighted the non-negligible role of genetics, as demonstrated by heritability and genome-wide association studies. A correlation between the relative risk of addiction to specific substances and heritability has been recently observed, suggesting that neurobiological mechanisms may be, at least in part, inherited. All these observations point towards a scenario where the core neurobiological factors of addiction, involving the reward system, impulsivity, compulsivity, stress, and anxiety response, are transmitted, and therefore, genes and mutations underlying their variation might be detected. In the last few years, the development of new and more efficient sequencing technologies has paved the way for large-scale studies in searching for genetic and epigenetic factors affecting drug addiction disorders and their treatments. These studies have been crucial to pinpoint single nucleotide polymorphisms (SNPs) in genes that affect the reaction to medical treatments. This is critically important to identify pharmacogenomic approaches for substance use disorder, such as OPRM1 SNPs and methadone required doses for maintenance treatment (MMT). Nevertheless, despite the promising results obtained by genome-wide association and pharmacogenomic studies, specific studies related to population genetics diversity are lacking, undermining the overall applicability of the preliminary findings, and thus potentially affecting the portability and the accuracy of the genetic studies. In this review, focusing on cannabis, cocaine and heroin use, we report the state-of-the-art genomics and pharmacogenomics of SUDs, and the possible future perspectives related to medical treatment response in people that ask for assistance in solving drug-related problems.

Vasculitis: Decade in Review

2018 ◽  
Vol 15 (1) ◽  
pp. 14-22 ◽  
Author(s):  
Selcan Demir ◽  
Hafize Emine Sönmez ◽  
Seza Özen
Keyword(s):  
Targeted Therapies ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genetic Studies ◽  
The Past ◽  
Genome Wide ◽  
New Perspective

Background: In the last decade, we have come to better understand and manage the vasculitides. The classification of vasculitides has been revised. Genome- wide association studies and linkage analyses have been undertaken in hope of better understanding the pathogenesis of vasculitides. Comprehensive genetic studies have highlighted new pathways that may guide us in more targeted therapies. Description of the monogenic forms of vasculitis, such as deficiency of adenosine deaminase type 2 (DADA2), Haploinsufficiency of A20 (HA20), have introduced a new perspective to vasculopathies, and introduced alternative treatments for these diseases. Conclusion: In this review, the important discoveries in pathogenesis and consensus treatment recommendations from the past decade will be summarized.

scholarly journals Genome-Wide Association Studies for Bivariate Sparse Longitudinal Data

2011 ◽  
Vol 72 (2) ◽  
pp. 110-120 ◽  
Author(s):  
Kiranmoy Das ◽  
Jiahan Li ◽  
Guifang Fu ◽  
Zhong Wang ◽  
Rongling Wu
Keyword(s):  
Longitudinal Data ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Genome Wide
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