Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits.
The genetic basis of complex traits involves the function of many genes with small effects as well as complex gene-gene and gene-environment interactions. As one of the major players in complex diseases, the role of gene-environment interactions has been increasingly recognized. Motivated by epidemi...
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2025-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0318103 |
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| author | Jingyi Zhang Honglang Wang Yuehua Cui |
| author_facet | Jingyi Zhang Honglang Wang Yuehua Cui |
| author_sort | Jingyi Zhang |
| collection | DOAJ |
| description | The genetic basis of complex traits involves the function of many genes with small effects as well as complex gene-gene and gene-environment interactions. As one of the major players in complex diseases, the role of gene-environment interactions has been increasingly recognized. Motivated by epidemiology studies to evaluate the joint effect of environmental mixtures, we developed a functional varying-index coefficient model (FVICM) to assess the combined effect of environmental mixtures and their interactions with genes, under a longitudinal design with quantitative traits. Built upon the previous work, we extend the FVICM model to accommodate binary longitudinal traits through the development of a generalized functional varying-index coefficient model (gFVICM). This model examines how the genetic effects on a disease trait are nonlinearly influenced by a combination of environmental factors. We derive an estimation procedure for the varying-index coefficient functions using quadratic inference functions combined with penalized splines. A hypothesis testing procedure is proposed to evaluate the significance of the nonparametric index functions. Extensive Monte Carlo simulations are conducted to evaluate the performance of the method under finite samples. The utility of the method is further demonstrated through a case study with a pain sensitivity dataset. SNPs were found to have their effects on blood pressure nonlinearly influenced by a combination of environmental factors. |
| format | Article |
| id | doaj-art-35024f8fbfb24d01a2ccc7edc10db8d6 |
| institution | Kabale University |
| issn | 1932-6203 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-35024f8fbfb24d01a2ccc7edc10db8d62025-02-05T05:32:05ZengPublic Library of Science (PLoS)PLoS ONE1932-62032025-01-01201e031810310.1371/journal.pone.0318103Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits.Jingyi ZhangHonglang WangYuehua CuiThe genetic basis of complex traits involves the function of many genes with small effects as well as complex gene-gene and gene-environment interactions. As one of the major players in complex diseases, the role of gene-environment interactions has been increasingly recognized. Motivated by epidemiology studies to evaluate the joint effect of environmental mixtures, we developed a functional varying-index coefficient model (FVICM) to assess the combined effect of environmental mixtures and their interactions with genes, under a longitudinal design with quantitative traits. Built upon the previous work, we extend the FVICM model to accommodate binary longitudinal traits through the development of a generalized functional varying-index coefficient model (gFVICM). This model examines how the genetic effects on a disease trait are nonlinearly influenced by a combination of environmental factors. We derive an estimation procedure for the varying-index coefficient functions using quadratic inference functions combined with penalized splines. A hypothesis testing procedure is proposed to evaluate the significance of the nonparametric index functions. Extensive Monte Carlo simulations are conducted to evaluate the performance of the method under finite samples. The utility of the method is further demonstrated through a case study with a pain sensitivity dataset. SNPs were found to have their effects on blood pressure nonlinearly influenced by a combination of environmental factors.https://doi.org/10.1371/journal.pone.0318103 |
| spellingShingle | Jingyi Zhang Honglang Wang Yuehua Cui Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. PLoS ONE |
| title | Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. |
| title_full | Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. |
| title_fullStr | Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. |
| title_full_unstemmed | Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. |
| title_short | Generalized functional varying-index coefficient model for dynamic synergistic gene-environment interactions with binary longitudinal traits. |
| title_sort | generalized functional varying index coefficient model for dynamic synergistic gene environment interactions with binary longitudinal traits |
| url | https://doi.org/10.1371/journal.pone.0318103 |
| work_keys_str_mv | AT jingyizhang generalizedfunctionalvaryingindexcoefficientmodelfordynamicsynergisticgeneenvironmentinteractionswithbinarylongitudinaltraits AT honglangwang generalizedfunctionalvaryingindexcoefficientmodelfordynamicsynergisticgeneenvironmentinteractionswithbinarylongitudinaltraits AT yuehuacui generalizedfunctionalvaryingindexcoefficientmodelfordynamicsynergisticgeneenvironmentinteractionswithbinarylongitudinaltraits |