HisCoM-G×E: Hierarchical Structural Component Analysis of Gene-Based Gene-Environment Interactions.
generalized structured component analysis (GSCA)
gene–environment interactions
genome-wide association study (GWAS)
Journal
International journal of molecular sciences
ISSN: 1422-0067
Titre abrégé: Int J Mol Sci
Pays: Switzerland
ID NLM: 101092791
Informations de publication
Date de publication:
14 Sep 2020
14 Sep 2020
Historique:
received:
27
07
2020
revised:
31
08
2020
accepted:
04
09
2020
entrez:
17
9
2020
pubmed:
18
9
2020
medline:
25
2
2021
Statut:
epublish
Résumé
Gene-environment interaction (G×E) studies are one of the most important solutions for understanding the "missing heritability" problem in genome-wide association studies (GWAS). Although many statistical methods have been proposed for detecting and identifying G×E, most employ single nucleotide polymorphism (SNP)-level analysis. In this study, we propose a new statistical method, Hierarchical structural CoMponent analysis of gene-based Gene-Environment interactions (HisCoM-G×E). HisCoM-G×E is based on the hierarchical structural relationship among all SNPs within a gene, and can accommodate all possible SNP-level effects into a single latent variable, by imposing a ridge penalty, and thus more efficiently takes into account the latent interaction term of G×E. The performance of the proposed method was evaluated in simulation studies, and we applied the proposed method to investigate gene-alcohol intake interactions affecting systolic blood pressure (SBP), using samples from the Korea Associated REsource (KARE) consortium data.
Identifiants
pubmed: 32937825
pii: ijms21186724
doi: 10.3390/ijms21186724
pmc: PMC7555026
pii:
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : the Korea Health Industry Development Institute (KHIDI) funded by the Ministry of Health & Welfare
ID : HI16C2037
Organisme : the Ministry of Science, ICT and Future Planning through the National Research Foundation
ID : 2013M3A9C4078158
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