The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.

In earlier work, we have developed and evaluated an alternative approach to the analysis of GWAS data, based on a statistic called the PPLD. More recently, motivated by a GWAS for genetic modifiers of the X-linked Mendelian disorder Duchenne Muscular Dystrophy (DMD), we adapted the PPLD for applicat...

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Autores principales:	Veronica J Vieland, Sang-Cheol Seok
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/00003499008840e299ffa0b2baec2e63
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spelling	oai:doaj.org-article:00003499008840e299ffa0b2baec2e632021-12-02T20:08:07ZThe PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.1932-620310.1371/journal.pone.0257164https://doaj.org/article/00003499008840e299ffa0b2baec2e632021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0257164https://doaj.org/toc/1932-6203In earlier work, we have developed and evaluated an alternative approach to the analysis of GWAS data, based on a statistic called the PPLD. More recently, motivated by a GWAS for genetic modifiers of the X-linked Mendelian disorder Duchenne Muscular Dystrophy (DMD), we adapted the PPLD for application to time-to-event (TE) phenotypes. Because DMD itself is relatively rare, this is a setting in which the very large sample sizes generally assembled for GWAS are simply not attainable. For this reason, statistical methods specially adapted for use in small data sets are required. Here we explore the behavior of the TE-PPLD via simulations, comparing the TE-PPLD with Cox Proportional Hazards analysis in the context of small to moderate sample sizes. Our results will help to inform our approach to the DMD study going forward, and they illustrate several respects in which the TE-PPLD, and by extension the original PPLD, offer advantages over regression-based approaches to GWAS in this context.Veronica J VielandSang-Cheol SeokPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 9, p e0257164 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Veronica J Vieland Sang-Cheol Seok The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
description	In earlier work, we have developed and evaluated an alternative approach to the analysis of GWAS data, based on a statistic called the PPLD. More recently, motivated by a GWAS for genetic modifiers of the X-linked Mendelian disorder Duchenne Muscular Dystrophy (DMD), we adapted the PPLD for application to time-to-event (TE) phenotypes. Because DMD itself is relatively rare, this is a setting in which the very large sample sizes generally assembled for GWAS are simply not attainable. For this reason, statistical methods specially adapted for use in small data sets are required. Here we explore the behavior of the TE-PPLD via simulations, comparing the TE-PPLD with Cox Proportional Hazards analysis in the context of small to moderate sample sizes. Our results will help to inform our approach to the DMD study going forward, and they illustrate several respects in which the TE-PPLD, and by extension the original PPLD, offer advantages over regression-based approaches to GWAS in this context.
format	article
author	Veronica J Vieland Sang-Cheol Seok
author_facet	Veronica J Vieland Sang-Cheol Seok
author_sort	Veronica J Vieland
title	The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
title_short	The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
title_full	The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
title_fullStr	The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
title_full_unstemmed	The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
title_sort	ppld has advantages over conventional regression methods in application to moderately sized genome-wide association studies.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/00003499008840e299ffa0b2baec2e63
work_keys_str_mv	AT veronicajvieland theppldhasadvantagesoverconventionalregressionmethodsinapplicationtomoderatelysizedgenomewideassociationstudies AT sangcheolseok theppldhasadvantagesoverconventionalregressionmethodsinapplicationtomoderatelysizedgenomewideassociationstudies AT veronicajvieland ppldhasadvantagesoverconventionalregressionmethodsinapplicationtomoderatelysizedgenomewideassociationstudies AT sangcheolseok ppldhasadvantagesoverconventionalregressionmethodsinapplicationtomoderatelysizedgenomewideassociationstudies
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The PPLD has advantages over conventional regression methods in application to moderately sized genome-wide association studies.

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