title: Adapting simultaneous analysis phylogenomic techniques to study complex disease gene relationships.
abstract: The characterization of complex diseases remains a great challenge for biomedical researchers due to the myriad interactions of genetic and environmental factors. Network medicine approaches strive to accommodate these factors holistically. Phylogenomic techniques that can leverage available genomic data may provide an evolutionary perspective that may elucidate knowledge for gene networks of complex diseases and provide another source of information for network medicine approaches. Here, an automated method is presented that leverages publicly available genomic data and phylogenomic techniques, resulting in a gene network. The potential of approach is demonstrated based on a case study of nine genes associated with Alzheimer Disease, a complex neurodegenerative syndrome. The developed technique, which is incorporated into an update to a previously described Perl script called "ASAP," was implemented through a suite of Ruby scripts entitled "ASAP2," first compiles a list of sequence-similarity based orthologues using PSI-BLAST and a recursive NCBI BLAST+ search strategy, then constructs maximum parsimony phylogenetic trees for each set of nucleotide and protein sequences, and calculates phylogenetic metrics (Incongruence Length Difference between orthologue sets, partitioned Bremer support values, combined branch scores, and Robinson-Foulds distance) to provide an empirical assessment of evolutionary conservation within a given genetic network. In addition to the individual phylogenetic metrics, ASAP2 provides results in a way that can be used to generate a gene network that represents evolutionary similarity based on topological similarity (the Robinson-Foulds distance). The results of this study demonstrate the potential for using phylogenomic approaches that enable the study of multiple genes simultaneously to provide insights about potential gene relationships that can be studied within a network medicine framework that may not have been apparent using traditional, single-gene methods. Furthermore, the results provide an initial integrated evolutionary history of an Alzheimer Disease gene network and identify potentially important co-evolutionary clustering that may warrant further investigation.
authors.affiliation: Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA.
authors.forename: Joseph D
authors.initials: JD
authors.lastname: Romano
authors.affiliation: Department of Medicine, Endocrinology Unit, University of Vermont, Burlington, VT 05405, USA.
authors.forename: William G
authors.initials: WG
authors.lastname: Tharp
authors.affiliation: Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT 05405, USA; Center for Clinical and Translational Science, University of Vermont, Burlington, VT 05405, USA; Department of Computer Science, University of Vermont, Burlington, VT 05405, USA. Electronic address: neil.sarkar@uvm.edu.
authors.forename: Indra Neil
authors.initials: IN
authors.lastname: Sarkar
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D056726:Genetic Association Studies / Q000379:methods*; D020022:Genetic Predisposition to Disease / Q000235:genetics*; D006801:Humans; D008322:Mammals / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D011506:Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D011506:Proteins
keywords: Alzheimer Disease; Bioinformatics; Comparative genomics; Phylogenetics; Simultaneous analysis