Omics feature selection with the extended SIS R package: identification of a body mass index epigenetic multimarker in the Strong Heart Study.
Am J Epidemiol
; 193(7): 1010-1018, 2024 07 08.
Article
in En
| MEDLINE
| ID: mdl-38375692
ABSTRACT
The statistical analysis of omics data poses a great computational challenge given their ultra-high-dimensional nature and frequent between-features correlation. In this work, we extended the iterative sure independence screening (ISIS) algorithm by pairing ISIS with elastic-net (Enet) and 2 versions of adaptive elastic-net (adaptive elastic-net (AEnet) and multistep adaptive elastic-net (MSAEnet)) to efficiently improve feature selection and effect estimation in omics research. We subsequently used genome-wide human blood DNA methylation data from American Indian participants in the Strong Heart Study (n = 2235 participants; measured in 1989-1991) to compare the performance (predictive accuracy, coefficient estimation, and computational efficiency) of ISIS-paired regularization methods with that of a bayesian shrinkage and traditional linear regression to identify an epigenomic multimarker of body mass index (BMI). ISIS-AEnet outperformed the other methods in prediction. In biological pathway enrichment analysis of genes annotated to BMI-related differentially methylated positions, ISIS-AEnet captured most of the enriched pathways in common for at least 2 of all the evaluated methods. ISIS-AEnet can favor biological discovery because it identifies the most robust biological pathways while achieving an optimal balance between bias and efficient feature selection. In the extended SIS R package, we also implemented ISIS paired with Cox and logistic regression for time-to-event and binary endpoints, respectively, and a bootstrap approach for the estimation of regression coefficients.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Algorithms
/
Body Mass Index
/
DNA Methylation
/
Epigenomics
Limits:
Aged
/
Female
/
Humans
/
Male
/
Middle aged
Language:
En
Journal:
Am J Epidemiol
Year:
2024
Document type:
Article
Country of publication:
United States