Learning gene networks underlying clinical phenotypes using SNP perturbation
| Autor: | Judie Howrylak, Se Young Kim, Seyoung Kim, Calvin McCarter |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2020 |
| Předmět: |
0301 basic medicine
Pulmonology Single Nucleotide Polymorphisms Gene regulatory network Gene Identification and Analysis Gene Expression Genome-wide association study Genetic Networks Machine Learning 0302 clinical medicine Medical Conditions Medicine and Health Sciences Gene Regulatory Networks Biology (General) Ecology Applied Mathematics Simulation and Modeling Genomics Phenotype Phenotypes Computational Theory and Mathematics Modeling and Simulation Physical Sciences Network Analysis Algorithms Research Article Computer and Information Sciences QH301-705.5 Quantitative Trait Loci Single-nucleotide polymorphism Computational biology Biology Research and Analysis Methods Polymorphism Single Nucleotide 03 medical and health sciences Cellular and Molecular Neuroscience Respiratory Disorders Genetics Genome-Wide Association Studies SNP Humans Molecular Biology Ecology Evolution Behavior and Systematics Genetic association Models Genetic Genome Human Biology and Life Sciences Computational Biology Human Genetics Genome Analysis Genetic architecture Asthma 030104 developmental biology Expression quantitative trait loci 030217 neurology & neurosurgery Mathematics Genome-Wide Association Study |
| Zdroj: | PLoS Computational Biology PLoS Computational Biology, Vol 16, Iss 10, p e1007940 (2020) |
| ISSN: | 1553-7358 1553-734X |
| Popis: | Availability of genome sequence, molecular, and clinical phenotype data for large patient cohorts generated by recent technological advances provides an opportunity to dissect the genetic architecture of complex diseases at system level. However, previous analyses of such data have largely focused on the co-localization of SNPs associated with clinical and expression traits, each identified from genome-wide association studies and expression quantitative trait locus mapping. Thus, their description of the molecular mechanisms behind the SNPs influencing clinical phenotypes was limited to the single gene linked to the co-localized SNP. Here we introduce PerturbNet, a statistical framework for learning gene networks that modulate the influence of genetic variants on phenotypes, using genetic variants as naturally occurring perturbation of a biological system. PerturbNet uses a probabilistic graphical model to directly model the cascade of perturbation from genetic variants to the gene network to the phenotype network along with the networks at each layer of the biological system. PerturbNet learns the entire model by solving a single optimization problem with an efficient algorithm that can analyze human genome-wide data within a few hours. PerturbNet inference procedures extract a detailed description of how the gene network modulates the genetic effects on phenotypes. Using simulated and asthma data, we demonstrate that PerturbNet improves statistical power for detecting disease-linked SNPs and identifies gene networks and network modules mediating the SNP effects on traits, providing deeper insights into the underlying molecular mechanisms. Author summary We describe PerturbNet, a statistical framework for learning a gene network that modulates the influence of genetic variants on phenotypes, using genetic variants as naturally occurring perturbation of a biological system. PerturbNet directly models the cascade of perturbation from genetic variants to the gene network to the phenotype network, thus integrating the existing computational tools for eQTL mapping, GWAS, co-localization analysis of eQTL and GWAS variants, and gene network discovery under SNP perturbation within a single statistical framework. We demonstrate that PerturbNet improves statistical power for detecting disease-linked SNPs and uncovers gene networks mediating the SNP effects on traits, with computational efficiency that allows for human data analysis within several hours. |
| Databáze: | OpenAIRE |
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