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Synthesis-View: visualization and interpretation of SNP association results for multi-cohort, multi-phenotype data and meta-analysis

Sarah A Pendergrass, Scott M Dudek, Dana C Crawford, Marylyn D Ritchie
2010 BioData Mining  
As a result, we have created "Synthesis-View" software for the visualization of genotype-phenotype association data in multiple cohorts.  ...  New approaches for visualizing resultant data are necessary in order to fully interpret results and obtain a broad view of the trends between DNA variation and phenotypes, as well as provide information  ...  Acknowledgements We would like to acknowledge the following individuals for their suggestions and ideas in designing Synthesis-View: Matthew Thomas Oetjens, Janina Jeff, Logan Dumitrescu, Fredrick Schumacher  ... 
doi:10.1186/1756-0381-3-10 pmid:21162740 pmcid:PMC3012023 fatcat:k4hq6alrmrearhghrahrnb7hya

Phenome-Wide Association Studies: Embracing Complexity for Discovery

Sarah A. Pendergrass, Anurag Verma, Anna Okula, Molly A. Hall, Dana C. Crawford, Marylyn D. Ritchie
2015 Human Heredity  
Here, we describe how incorporating greater complexity into analyses through the use of additional phenotypic data and widespread deployment of phenome-wide association studies may provide new insights  ...  The genome-wide association study (GWAS) approach has well-developed methods and relatively straight-forward methodologies; however, the bigger picture of the impact of genetic architecture on phenotypic  ...  Visually exploring PheWAS results is extremely useful for identifying trends in the data, and there are several software packages that provide a way to plot PheWAS results: Synthesis-View [124, 125]  ... 
doi:10.1159/000381851 pmid:26201697 fatcat:eoc265qmjfamxknwjz3rlbr3gy

Epistatic Gene-Based Interaction Analyses for Glaucoma in eMERGE and NEIGHBOR Consortium

Shefali Setia Verma, Jessica N. Cooke Bailey, Anastasia Lucas, Yuki Bradford, James G. Linneman, Michael A. Hauser, Louis R. Pasquale, Peggy L. Peissig, Murray H. Brilliant, Catherine A. McCarty, Jonathan L. Haines, Janey L. Wiggs (+4 others)
2016 PLoS Genetics  
EMR data in detecting non-spurious and relevant associations; this analysis was aimed at confirming already known associations with glaucoma and validating the EMR derived glaucoma phenotype.  ...  We then performed an interaction analysis for variants found to be marginally associated with glaucoma (SNPs with main effect p-value <0.01) and observed interesting findings in the electronic MEdical  ...  Acknowledgments eMERGE II contributors Contributed reagents/materials/analysis tools: SSV JNCB. Wrote the paper: SSV JNCB MDR JLH JLW.  ... 
doi:10.1371/journal.pgen.1006186 pmid:27623284 pmcid:PMC5021356 fatcat:esgudypfffbqhg5nol33lipdmq