Genome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alternative to brute force solutions involving the use of very large cohorts, we propose the use of the Gene Set Analysis (GSA), a different analysis strategy based on testing the association of modules of functionally related genes. We show here how the Gene Set-based Analysis of Polymorphisms (GeSBAP), which is a simple implementation of the GSA strategy for the analysis of genome-wide association studies, provides a significant increase in the power testing for this type of studies. GeSBAP is freely available at http://bioinfo.cipf.es/gesbap/.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703970 | PMC |
| http://dx.doi.org/10.1093/nar/gkp481 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Epigenome-wide association study of perceived discrimination in the Multi-Ethnic Study of Atherosclerosis (MESA).
Epigenetics
December 2025
Survey Research Center, Institute for Social Research, University of Michigan, Ann Arbor, MI, USA.
Perceived discrimination, recognized as a chronic psychosocial stressor, has adverse consequences on health. DNA methylation (DNAm) may be a potential mechanism by which stressors get embedded into the human body at the molecular level and subsequently affect health outcomes. However, relatively little is known about the effects of perceived discrimination on DNAm.
View Article and Find Full Text PDFComposite microRNA-genetic risk score model links to migraine and implicates its pathogenesis.
Brain
January 2025
Department of Neurology, Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan.
The neurobiological mechanisms driving the ictal-interictal fluctuations and the chronification of migraine remain elusive. We aimed to construct a composite genetic-microRNA model that could reflect the dynamic perturbations of the disease course and inform the pathogenesis of migraine. We prospectively recruited four groups of participants, including interictal episodic migraine (i.
View Article and Find Full Text PDFIdentification of association between mitochondrial dysfunction and sarcopenia using summary-data-based Mendelian randomization and colocalization analyses.
J Gerontol A Biol Sci Med Sci
January 2025
Department of Joint Surgery, HongHui Hospital, Xi'an Jiaotong University, Xi'an, Shaanxi, China.
Background: Mitochondrial dysfunction has been demonstrated to be an important hallmark of sarcopenia, yet its specific mechanism remains obscure. In this study, mitochondrial-related genes were used as instrumental variables to proxy for mitochondrial dysfunction, and summary data for sarcopenia-related traits were used as outcomes to examine their genetic association.
Methods: A total of 1,136 mitochondrial-related genes from the human MitoCarta3.
The Role of 418 Gut Microbiota in Small Cell Lung Cancer Progression: A Mendelian Randomisation Study.
J Coll Physicians Surg Pak
January 2025
Department of Radiotherapy, Binhai County People's Hospital, Yancheng, Jiangsu, China.
Objective: To investigate the causal influence of gut microbiota on small cell lung cancer (SCLC) progression using Mendelian randomisation (MR), providing insights into the gut-lung axis in lung cancer pathology.
Study Design: Analytical study. Place and Duration of the Study: Department of Radiotherapy, Binhai County People's Hospital, Yancheng, Jiangsu, China, and Department of Paediatrics, General Hospital of Ningxia Medical University, Yinchuan, Ningxia, China, from January to May 2024.
The interplay of sex and genotype in disease associations: a comprehensive network analysis in the UK Biobank.
Hum Genomics
January 2025
Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Richards Building B304, 3700 Hamilton Walk, Philadelphia, PA, 19104, USA.
Background: Disease comorbidities and longer-term complications, arising from biologically related associations across phenotypes, can lead to increased risk of severe health outcomes. Given that many diseases exhibit sex-specific differences in their genetics, our objective was to determine whether genotype-by-sex (GxS) interactions similarly influence cross-phenotype associations. Through comparison of sex-stratified disease-disease networks (DDNs)-where nodes represent diseases and edges represent their relationships-we investigate sex differences in patterns of polygenicity and pleiotropy between diseases.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!