Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study

Author:

Zhao Zhongming,Guo An-Yuan,van den Oord Edwin JCG,Aliev Fazil,Jia Peilin,Edenberg Howard J,Riley Brien P,Dick Danielle M,Bettinger Jill C,Davies Andrew G,Grotewiel Michael S,Schuckit Marc A,Agrawal Arpana,Kramer John,Nurnberger John I,Kendler Kenneth S,Webb Bradley T,Miles Michael F

Abstract

Abstract Background A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. Results In this study, we performed a unique multi-species evidence-based data integration using three microarray experiments in mice or humans that generated an initial alcohol dependence (AD) related genes list, human linkage and association results, and gene sets implicated in C. elegans and Drosophila. We then used permutation and false discovery rate (FDR) analyses on the genome-wide association studies (GWAS) dataset from the Collaborative Study on the Genetics of Alcoholism (COGA) to evaluate the ranking results and weighting matrices. We found one weighting score matrix could increase FDR based q-values for a list of 47 genes with a score greater than 2. Our follow up functional enrichment tests revealed these genes were primarily involved in brain responses to ethanol and neural adaptations occurring with alcoholism. Conclusions These results, along with our experimental validation of specific genes in mice, C. elegans and Drosophila, suggest that a cross-species evidence-based approach is useful to identify candidate genes contributing to alcoholism.

Publisher

Springer Science and Business Media LLC

Subject

Genetics,Biotechnology

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