Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.

An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa"...

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Autores principales:	Han-Ming Liu, Jin-Ping Zheng, Dan Yang, Zhao-Fa Liu, Zi Li, Zhen-Zhen Hu, Ze-Nan Li
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/27d90c29bd1c4d0e9604bc505262e397
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spelling	oai:doaj.org-article:27d90c29bd1c4d0e9604bc505262e3972021-12-02T20:06:42ZRecessive/dominant model: Alternative choice in case-control-based genome-wide association studies.1932-620310.1371/journal.pone.0254947https://doaj.org/article/27d90c29bd1c4d0e9604bc505262e3972021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0254947https://doaj.org/toc/1932-6203An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa" to the phenotype is different from "AA" and "aa". From the perspective of biological phenomena, the coding is reasonable since the phenotypes of lives are not "black and white". A case-control based study, however, has only two phenotypes, case and control, which means that the phenotypes are "black and white". It suggests that a recessive/dominant model may be an alternative to the additive model. In order to investigate whether the alternative is feasible, we conducted comparative experiments on several models used in those studies through chi-square test and logistic regression. Our simulation experiments demonstrate that a recessive model is better than the additive model. The area under the curve of the former has increased by 5% compared with the latter, the discrimination of identifying risk single nucleotide polymorphisms has been improved by 61%, and the precision has also reached 1.10 times that of the latter. Furthermore, the real data experiments show that the precision and area under the curve of the former are 16% and 20% higher than the latter respectively, and the area under the curve of dominant model of the former is 13% higher than the latter. The results indicate a recessive/dominant model may be an alternative to the additive model and suggest a new route for case-control-based studies.Han-Ming LiuJin-Ping ZhengDan YangZhao-Fa LiuZi LiZhen-Zhen HuZe-Nan LiPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0254947 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Han-Ming Liu Jin-Ping Zheng Dan Yang Zhao-Fa Liu Zi Li Zhen-Zhen Hu Ze-Nan Li Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.
description	An additive genetic model is usually employed in case-control-based genome-wide association studies. The model usually encodes "AA", "Aa" and "aa" ("a" represents the minor allele) as three different numbers, implying the contribution of genotype "Aa" to the phenotype is different from "AA" and "aa". From the perspective of biological phenomena, the coding is reasonable since the phenotypes of lives are not "black and white". A case-control based study, however, has only two phenotypes, case and control, which means that the phenotypes are "black and white". It suggests that a recessive/dominant model may be an alternative to the additive model. In order to investigate whether the alternative is feasible, we conducted comparative experiments on several models used in those studies through chi-square test and logistic regression. Our simulation experiments demonstrate that a recessive model is better than the additive model. The area under the curve of the former has increased by 5% compared with the latter, the discrimination of identifying risk single nucleotide polymorphisms has been improved by 61%, and the precision has also reached 1.10 times that of the latter. Furthermore, the real data experiments show that the precision and area under the curve of the former are 16% and 20% higher than the latter respectively, and the area under the curve of dominant model of the former is 13% higher than the latter. The results indicate a recessive/dominant model may be an alternative to the additive model and suggest a new route for case-control-based studies.
format	article
author	Han-Ming Liu Jin-Ping Zheng Dan Yang Zhao-Fa Liu Zi Li Zhen-Zhen Hu Ze-Nan Li
author_facet	Han-Ming Liu Jin-Ping Zheng Dan Yang Zhao-Fa Liu Zi Li Zhen-Zhen Hu Ze-Nan Li
author_sort	Han-Ming Liu
title	Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.
title_short	Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.
title_full	Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.
title_fullStr	Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.
title_full_unstemmed	Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.
title_sort	recessive/dominant model: alternative choice in case-control-based genome-wide association studies.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/27d90c29bd1c4d0e9604bc505262e397
work_keys_str_mv	AT hanmingliu recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies AT jinpingzheng recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies AT danyang recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies AT zhaofaliu recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies AT zili recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies AT zhenzhenhu recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies AT zenanli recessivedominantmodelalternativechoiceincasecontrolbasedgenomewideassociationstudies
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Recessive/dominant model: Alternative choice in case-control-based genome-wide association studies.

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