Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans

Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans

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...

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Bibliographic Details
Main Authors: Todd Jarvis, Jeffrey Staples, Matthew L. Bendall, Taylor J. Maxwell, Keith A. Crandall
Format: Article
Language:English
Published: MDPI AG 2010-01-01
Series:International Journal of Molecular Sciences
Subjects:
ANGPTL4
TreeSAAP
treescan
phylogenetics
association studies
selection
Online Access:http://www.mdpi.com/1422-0067/11/1/370/
Description
Summary: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.
ISSN:1422-0067

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