Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.

For most complex traits, results from genome-wide association studies show that the proportion of the phenotypic variance attributable to the additive effects of individual SNPs, that is, the heritability explained by the SNPs, is substantially less than the estimate of heritability obtained by stan...

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Autores principales:	Sven Stringer, Eske M Derks, René S Kahn, William G Hill, Naomi R Wray
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/84345986f3824d699195f01655d997ab
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spelling	oai:doaj.org-article:84345986f3824d699195f01655d997ab2021-11-18T09:02:05ZAssumptions and properties of limiting pathway models for analysis of epistasis in complex traits.1932-620310.1371/journal.pone.0068913https://doaj.org/article/84345986f3824d699195f01655d997ab2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23935903/?tool=EBIhttps://doaj.org/toc/1932-6203For most complex traits, results from genome-wide association studies show that the proportion of the phenotypic variance attributable to the additive effects of individual SNPs, that is, the heritability explained by the SNPs, is substantially less than the estimate of heritability obtained by standard methods using correlations between relatives. This difference has been called the "missing heritability". One explanation is that heritability estimates from family (including twin) studies are biased upwards. Zuk et al. revisited overestimation of narrow sense heritability from twin studies as a result of confounding with non-additive genetic variance. They propose a limiting pathway (LP) model that generates significant epistatic variation and its simple parametrization provides a convenient way to explore implications of epistasis. They conclude that over-estimation of narrow sense heritability from family data ('phantom heritability') may explain an important proportion of missing heritability. We show that for highly heritable quantitative traits large phantom heritability estimates from twin studies are possible only if a large contribution of common environment is assumed. The LP model is underpinned by strong assumptions that are unlikely to hold, including that all contributing pathways have the same mean and variance and are uncorrelated. Here, we relax the assumptions that underlie the LP model to be more biologically plausible. Together with theoretical, empirical, and pragmatic arguments we conclude that in outbred populations the contribution of additive genetic variance is likely to be much more important than the contribution of non-additive variance.Sven StringerEske M DerksRené S KahnWilliam G HillNaomi R WrayPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 7, p e68913 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Sven Stringer Eske M Derks René S Kahn William G Hill Naomi R Wray Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
description	For most complex traits, results from genome-wide association studies show that the proportion of the phenotypic variance attributable to the additive effects of individual SNPs, that is, the heritability explained by the SNPs, is substantially less than the estimate of heritability obtained by standard methods using correlations between relatives. This difference has been called the "missing heritability". One explanation is that heritability estimates from family (including twin) studies are biased upwards. Zuk et al. revisited overestimation of narrow sense heritability from twin studies as a result of confounding with non-additive genetic variance. They propose a limiting pathway (LP) model that generates significant epistatic variation and its simple parametrization provides a convenient way to explore implications of epistasis. They conclude that over-estimation of narrow sense heritability from family data ('phantom heritability') may explain an important proportion of missing heritability. We show that for highly heritable quantitative traits large phantom heritability estimates from twin studies are possible only if a large contribution of common environment is assumed. The LP model is underpinned by strong assumptions that are unlikely to hold, including that all contributing pathways have the same mean and variance and are uncorrelated. Here, we relax the assumptions that underlie the LP model to be more biologically plausible. Together with theoretical, empirical, and pragmatic arguments we conclude that in outbred populations the contribution of additive genetic variance is likely to be much more important than the contribution of non-additive variance.
format	article
author	Sven Stringer Eske M Derks René S Kahn William G Hill Naomi R Wray
author_facet	Sven Stringer Eske M Derks René S Kahn William G Hill Naomi R Wray
author_sort	Sven Stringer
title	Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
title_short	Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
title_full	Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
title_fullStr	Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
title_full_unstemmed	Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
title_sort	assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/84345986f3824d699195f01655d997ab
work_keys_str_mv	AT svenstringer assumptionsandpropertiesoflimitingpathwaymodelsforanalysisofepistasisincomplextraits AT eskemderks assumptionsandpropertiesoflimitingpathwaymodelsforanalysisofepistasisincomplextraits AT reneskahn assumptionsandpropertiesoflimitingpathwaymodelsforanalysisofepistasisincomplextraits AT williamghill assumptionsandpropertiesoflimitingpathwaymodelsforanalysisofepistasisincomplextraits AT naomirwray assumptionsandpropertiesoflimitingpathwaymodelsforanalysisofepistasisincomplextraits
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Assumptions and properties of limiting pathway models for analysis of epistasis in complex traits.

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