Genetics and population analysis: Estimating and testing high-dimensional mediation effects in epigenetic studies

Haixiang Zhang; Yinan Zheng; Zhou Zhang; Tao Gao; Brian Joyce; Grace Yoon; Wei Zhang; Joel Schwartz; Allan Just; Elena Colicino; Pantel Vokonas; Lihui Zhao; Jinchi Lv; Andrea Baccarelli; Lifang Hou; Lei Liu

doi:10.1093/bioinformatics/btw351

Genetics and population analysis: Estimating and testing high-dimensional mediation effects in epigenetic studies

Haixiang Zhang, Yinan Zheng, Zhou Zhang, Tao Gao, Brian Joyce, Grace Yoon, Wei Zhang, Joel Schwartz, Allan Just, Elena Colicino, Pantel Vokonas, Lihui Zhao, Jinchi Lv, Andrea Baccarelli, Lifang Hou, Lei Liu

Research output: Contribution to journal › Article › peer-review

111 Scopus citations

Abstract

Motivation: High-dimensional DNA methylation markers may mediate pathways linking environmental exposures with health outcomes. However, there is a lack of analytical methods to identify significant mediators for high-dimensional mediation analysis. Results: Based on sure independent screening and minimax concave penalty techniques, we use a joint significance test for mediation effect. We demonstrate its practical performance using Monte Carlo simulation studies and apply this method to investigate the extent to which DNA methylation markers mediate the causal pathway from smoking to reduced lung function in the Normative Aging Study. We identify 2 CpGs with significant mediation effects.

Original language	English
Pages (from-to)	3150-3154
Number of pages	5
Journal	Bioinformatics
Volume	32
Issue number	20
DOIs	https://doi.org/10.1093/bioinformatics/btw351
State	Published - Oct 15 2016

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Zhang, H., Zheng, Y., Zhang, Z., Gao, T., Joyce, B., Yoon, G., Zhang, W., Schwartz, J., Just, A., Colicino, E., Vokonas, P., Zhao, L., Lv, J., Baccarelli, A., Hou, L., & Liu, L. (2016). Genetics and population analysis: Estimating and testing high-dimensional mediation effects in epigenetic studies. Bioinformatics, 32(20), 3150-3154. https://doi.org/10.1093/bioinformatics/btw351

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abstract = "Motivation: High-dimensional DNA methylation markers may mediate pathways linking environmental exposures with health outcomes. However, there is a lack of analytical methods to identify significant mediators for high-dimensional mediation analysis. Results: Based on sure independent screening and minimax concave penalty techniques, we use a joint significance test for mediation effect. We demonstrate its practical performance using Monte Carlo simulation studies and apply this method to investigate the extent to which DNA methylation markers mediate the causal pathway from smoking to reduced lung function in the Normative Aging Study. We identify 2 CpGs with significant mediation effects.",

author = "Haixiang Zhang and Yinan Zheng and Zhou Zhang and Tao Gao and Brian Joyce and Grace Yoon and Wei Zhang and Joel Schwartz and Allan Just and Elena Colicino and Pantel Vokonas and Lihui Zhao and Jinchi Lv and Andrea Baccarelli and Lifang Hou and Lei Liu",

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Zhang, H, Zheng, Y, Zhang, Z, Gao, T, Joyce, B, Yoon, G, Zhang, W, Schwartz, J, Just, A, Colicino, E, Vokonas, P, Zhao, L, Lv, J, Baccarelli, A, Hou, L & Liu, L 2016, 'Genetics and population analysis: Estimating and testing high-dimensional mediation effects in epigenetic studies', Bioinformatics, vol. 32, no. 20, pp. 3150-3154. https://doi.org/10.1093/bioinformatics/btw351

TY - JOUR

T1 - Genetics and population analysis

T2 - Estimating and testing high-dimensional mediation effects in epigenetic studies

AU - Zhang, Haixiang

AU - Zheng, Yinan

AU - Zhang, Zhou

AU - Gao, Tao

AU - Joyce, Brian

AU - Yoon, Grace

AU - Zhang, Wei

AU - Schwartz, Joel

AU - Just, Allan

AU - Colicino, Elena

AU - Vokonas, Pantel

AU - Zhao, Lihui

AU - Lv, Jinchi

AU - Baccarelli, Andrea

AU - Hou, Lifang

AU - Liu, Lei

PY - 2016/10/15

Y1 - 2016/10/15

N2 - Motivation: High-dimensional DNA methylation markers may mediate pathways linking environmental exposures with health outcomes. However, there is a lack of analytical methods to identify significant mediators for high-dimensional mediation analysis. Results: Based on sure independent screening and minimax concave penalty techniques, we use a joint significance test for mediation effect. We demonstrate its practical performance using Monte Carlo simulation studies and apply this method to investigate the extent to which DNA methylation markers mediate the causal pathway from smoking to reduced lung function in the Normative Aging Study. We identify 2 CpGs with significant mediation effects.

AB - Motivation: High-dimensional DNA methylation markers may mediate pathways linking environmental exposures with health outcomes. However, there is a lack of analytical methods to identify significant mediators for high-dimensional mediation analysis. Results: Based on sure independent screening and minimax concave penalty techniques, we use a joint significance test for mediation effect. We demonstrate its practical performance using Monte Carlo simulation studies and apply this method to investigate the extent to which DNA methylation markers mediate the causal pathway from smoking to reduced lung function in the Normative Aging Study. We identify 2 CpGs with significant mediation effects.

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DO - 10.1093/bioinformatics/btw351

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AN - SCOPUS:84995414933

SN - 1367-4803

VL - 32

SP - 3150

EP - 3154

JO - Bioinformatics

JF - Bioinformatics

IS - 20

ER -

Genetics and population analysis: Estimating and testing high-dimensional mediation effects in epigenetic studies

Abstract

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