Graphical Modeling of Biological Pathways in Genome-wide Association Studies

Author(s):  
Min Chen ◽  
Judy Cho ◽  
Hongyu Zhao
2017 ◽  
Vol 12 ◽  
pp. 117727191769581 ◽  
Author(s):  
Chindo Hicks ◽  
Ritika Ramani ◽  
Oliver Sartor ◽  
Ritu Bhalla ◽  
Lucio Miele ◽  
...  

High-throughput genotyping has enabled discovery of genetic variants associated with an increased risk of developing prostate cancer using genome-wide association studies (GWAS). The goal of this study was to associate GWAS information of patients with primary organ–confined and metastatic prostate cancer using gene expression data and to identify molecular networks and biological pathways enriched for genetic susceptibility variants involved in the 2 disease states. The analysis revealed gene signatures for the 2 disease states and a gene signature distinguishing the 2 patient groups. In addition, the analysis revealed molecular networks and biological pathways enriched for genetic susceptibility variants. The discovered pathways include the androgen, apoptosis, and insulinlike growth factor signaling pathways. This analysis established putative functional bridges between GWAS discoveries and the biological pathways involved in primary organ–confined and metastatic prostate cancer.


2018 ◽  
Vol 103 (9) ◽  
pp. 3155-3168 ◽  
Author(s):  
Michael H Guo ◽  
Joel N Hirschhorn ◽  
Andrew Dauber

Abstract Context In the last decade, genome-wide association studies (GWASs) have catalyzed our understanding of the genetics of height and have identified hundreds of regions of the genome associated with adult height and other height-related body measurements. Evidence Acquisition GWASs related to height were identified via PubMed search and a review of the GWAS catalog. Evidence Synthesis The GWAS results demonstrate that height is highly polygenic: that is, many thousands of genetic variants distributed across the genome each contribute to an individual’s height. These height-associated regions of the genome are enriched for genes in known biological pathways involved in growth, such as fibroblast growth factor signaling, as well as for genes expressed in relevant tissues, such as the growth plate. GWASs can also uncover previously unappreciated biological pathways, such as theSTC2/PAPPA/IGFBP4 pathway. The genes implicated by GWASs are often the same genes that are the genetic causes of Mendelian growth disorders or skeletal dysplasias, and GWAS results can provide complementary information about these disorders. Conclusions Here, we review the rationale behind GWASs and what we have learned from GWASs for height, including how it has enhanced our understanding of the underlying biology of human growth. We also highlight the implications of GWASs in terms of prediction of adult height and our understanding of Mendelian growth disorders.


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