title: Phylogenetics applied to genotype/phenotype association and selection analyses with sequence data from angptl4 in humans.
abstract: Genotype/phenotype association analyses (Treescan) with plasma lipid levels and functional site prediction methods (TreeSAAP and PolyPhen) were performed using sequence data for ANGPTL4 from 3,551 patients in the Dallas Heart Study. Biological assays of rare variants in phenotypic tails and results from a Treescan analysis were used as "known" variants to assess the site prediction abilities of PolyPhen and TreeSAAP. The E40K variant in European Americans and the R278Q variant in African Americans were significantly associated with multiple lipid phenotypes. Combining TreeSAAP and PolyPhen performed well to predict "known" functional variants while reducing noise from false positives.
authors.affiliation: Human Genetics Center, University of Texas School of Public Health, Houston, 77030, USA. Taylor.J.Maxwell@uth.tmc.edu <Taylor.J.Maxwell@uth.tmc.edu>
authors.forename: Taylor J
authors.initials: TJ
authors.lastname: Maxwell
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Bendall
authors.forename: Jeffrey
authors.initials: J
authors.lastname: Staples
authors.forename: Todd
authors.initials: T
authors.lastname: Jarvis
authors.forename: Keith A
authors.initials: KA
authors.lastname: Crandall
mesh_terms: D000075803:Angiopoietin-Like Protein 4; D042682:Angiopoietins / Q000235:genetics* / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods; D056726:Genetic Association Studies; D014644:Genetic Variation; D005838:Genotype; D006239:Haplotypes; D006801:Humans; D016366:Open Reading Frames; D010641:Phenotype; D010802:Phylogeny; D012641:Selection, Genetic
chemical_list: C474772:ANGPTL4 protein, human; D000075803:Angiopoietin-Like Protein 4; D042682:Angiopoietins