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Testing for homogeneity of gametic disequilibrium across strata

BACKGROUND: Assessing the non-random associations of alleles at different loci, or gametic disequilibrium, can provide clues about aspects of population histories and mating behavior and can be useful in locating disease genes. For gametic data which are available from several strata with different...

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Autores principales: Yin, Xiaolin, Ma, Wenqing, Tang, Manlai, Guo, Jianhua
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2007
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2245972/
https://www.ncbi.nlm.nih.gov/pubmed/18096053
http://dx.doi.org/10.1186/1471-2156-8-85
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author Yin, Xiaolin
Ma, Wenqing
Tang, Manlai
Guo, Jianhua
author_facet Yin, Xiaolin
Ma, Wenqing
Tang, Manlai
Guo, Jianhua
author_sort Yin, Xiaolin
collection PubMed
description BACKGROUND: Assessing the non-random associations of alleles at different loci, or gametic disequilibrium, can provide clues about aspects of population histories and mating behavior and can be useful in locating disease genes. For gametic data which are available from several strata with different allele probabilities, it is necessary to verify that the strata are homogeneous in terms of gametic disequilibrium. RESULTS: Using the likelihood score theory generalized to nuisance parameters we derive a score test for homogeneity of gametic disequilibrium across several independent populations. Simulation results demonstrate that the empirical type I error rates of our score homogeneity test perform satisfactorily in the sense that they are close to the pre-chosen 0.05 nominal level. The associated power and sample size formulae are derived. We illustrate our test with a data set from a study of the cystic fibrosis transmembrane conductance regulator gene. CONCLUSION: We propose a large-sample homogeneity test on gametic disequilibrium across several independent populations based on the likelihood score theory generalized to nuisance parameters. Our simulation results show that our test is more reliable than the traditional test based on the Fisher's test of homogeneity among correlation coefficients.
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spelling pubmed-22459722008-02-20 Testing for homogeneity of gametic disequilibrium across strata Yin, Xiaolin Ma, Wenqing Tang, Manlai Guo, Jianhua BMC Genet Methodology Article BACKGROUND: Assessing the non-random associations of alleles at different loci, or gametic disequilibrium, can provide clues about aspects of population histories and mating behavior and can be useful in locating disease genes. For gametic data which are available from several strata with different allele probabilities, it is necessary to verify that the strata are homogeneous in terms of gametic disequilibrium. RESULTS: Using the likelihood score theory generalized to nuisance parameters we derive a score test for homogeneity of gametic disequilibrium across several independent populations. Simulation results demonstrate that the empirical type I error rates of our score homogeneity test perform satisfactorily in the sense that they are close to the pre-chosen 0.05 nominal level. The associated power and sample size formulae are derived. We illustrate our test with a data set from a study of the cystic fibrosis transmembrane conductance regulator gene. CONCLUSION: We propose a large-sample homogeneity test on gametic disequilibrium across several independent populations based on the likelihood score theory generalized to nuisance parameters. Our simulation results show that our test is more reliable than the traditional test based on the Fisher's test of homogeneity among correlation coefficients. BioMed Central 2007-12-20 /pmc/articles/PMC2245972/ /pubmed/18096053 http://dx.doi.org/10.1186/1471-2156-8-85 Text en Copyright © 2007 Yin et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Yin, Xiaolin
Ma, Wenqing
Tang, Manlai
Guo, Jianhua
Testing for homogeneity of gametic disequilibrium across strata
title Testing for homogeneity of gametic disequilibrium across strata
title_full Testing for homogeneity of gametic disequilibrium across strata
title_fullStr Testing for homogeneity of gametic disequilibrium across strata
title_full_unstemmed Testing for homogeneity of gametic disequilibrium across strata
title_short Testing for homogeneity of gametic disequilibrium across strata
title_sort testing for homogeneity of gametic disequilibrium across strata
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2245972/
https://www.ncbi.nlm.nih.gov/pubmed/18096053
http://dx.doi.org/10.1186/1471-2156-8-85
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