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Int. J. Mol. Sci. 2010, 11(1), 370-385; doi:10.3390/ijms11010370

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

1
Human Genetics Center, University of Texas School of Public Health, Houston, TX 77030, USA
2
Department of Biology, Brigham Young University, Provo, UT 84602, USA
*
Author to whom correspondence should be addressed.
Received: 13 November 2009 / Revised: 6 January 2010 / Accepted: 17 January 2010 / Published: 25 January 2010
(This article belongs to the Special Issue Cladistic Analysis and Molecular Evolution)
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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.
Keywords: ANGPTL4; TreeSAAP; treescan; phylogenetics; association studies; selection ANGPTL4; TreeSAAP; treescan; phylogenetics; association studies; selection
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MDPI and ACS Style

Maxwell, T.J.; Bendall, M.L.; Staples, J.; Jarvis, T.; Crandall, K.A. Phylogenetics Applied to Genotype/Phenotype Association and Selection Analyses with Sequence Data from Angptl4 in Humans. Int. J. Mol. Sci. 2010, 11, 370-385.

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