Abstract:
:In genomic analysis, it is significant though challenging to identify markers associated with cancer outcomes or phenotypes. Based on the biological mechanisms of cancers and the characteristics of datasets, we propose a novel integrative interaction approach under a semiparametric model, in which genetic and environmental factors are included as the parametric and nonparametric components, respectively. The goal of this approach is to identify the genetic factors and gene-gene interactions associated with cancer outcomes, while estimating the nonlinear effects of environmental factors. The proposed approach is based on the threshold gradient-directed regularisation technique. Simulation studies indicate that the proposed approach outperforms alternative methods at identifying the main effects and interactions, and has favourable estimation and prediction accuracy. We analysed non-small-cell lung carcinoma datasets from the Cancer Genome Atlas, and the results demonstrate that the proposed approach can identify markers with important implications and that it performs favourably in terms of prediction accuracy, identification stability, and computation cost.
journal_name
Stat Methods Med Resjournal_title
Statistical methods in medical researchauthors
Li Y,Wang F,Li R,Sun Ydoi
10.1177/0962280220909969subject
Has Abstractpub_date
2020-10-01 00:00:00pages
2865-2880issue
10eissn
0962-2802issn
1477-0334journal_volume
29pub_type
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