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Exploring case–control genetic association tests using phase diagrams

Paper ID Volume ID Publish Year Pages File Format Full-Text
15361 1407 2008 9 PDF Available
Title
Exploring case–control genetic association tests using phase diagrams
Abstract

BackgroundsBy a new concept called “phase diagram”, we compare two commonly used genotype-based tests for case–control genetic analysis, one is a Cochran-Armitage trend test (CAT test at x=0.5x=0.5, or CAT0.5) and another (called MAX2) is the maximization of two Chi-square test results: one from the two-by-two genotype count table that combines the baseline homozygotes and heterozygotes, and another from the table that combines heterozygotes with risk homozygotes. CAT0.5 is more suitable for multiplicative disease models and MAX2 is better for dominant/recessive models.MethodsWe define the CAT0.5-MAX2 phase diagram on the disease model space such that regions where MAX2 is more powerful than CAT0.5 are separated from regions where the CAT0.5 is more powerful, and the task is to choose the appropriate parameterization to make the separation possible.ResultsWe find that using the difference of allele frequencies (δpδp) and the difference of Hardy–Weinberg disequilibrium coefficients (δϵδϵ) can separate the two phases well, and the phase boundaries are determined by the angle tan⁡−1(δp/δϵ)tan⁡−1(δp/δϵ), which is an improvement over the disease model selection using δϵδϵ only.ConclusionsWe argue that phase diagrams similar to the one for CAT0.5-MAX2 have graphical appeals in understanding power performance of various tests, clarifying simulation schemes, summarizing case–control datasets, and guessing the possible mode of inheritance.

Keywords
Genetic association; Hardy–Weinberg disequilibrium; Phase diagram; Cochran-Armitage trend test; MAX2 test
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Publisher
Database: Elsevier - ScienceDirect
Journal: Computational Biology and Chemistry - Volume 32, Issue 6, December 2008, Pages 391–399
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us