Abstract
In disease screening, a biomarker combination developed by combining multiple markers tends to have a higher sensitivity than an individual marker. Parametric methods for marker combination rely on the inverse of covariance matrices, which is often a non-trivial problem for high-dimensional data generated by modern high-throughput technologies. Additionally, another common problem in disease diagnosis is the existence of limit of detection (LOD) for an instrument–that is, when a biomarker's value falls below the limit, it cannot be observed and is assigned an NA value. To handle these two challenges in combining high-dimensional biomarkers with the presence of LOD, we propose a resample-replace lasso procedure. We first impute the values below LOD and then use the graphical lasso method to estimate the means and precision matrices for the high-dimensional biomarkers. The simulation results show that our method outperforms alternative methods such as either substitute NA values with LOD values or remove observations that have NA values. A real case analysis on a protein profiling study of glioblastoma patients on their survival status indicates that the biomarker combination obtained through the proposed method is more accurate in distinguishing between two groups.
Original language | English (US) |
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Pages (from-to) | 4278-4293 |
Number of pages | 16 |
Journal | Journal of Applied Statistics |
Volume | 49 |
Issue number | 16 |
DOIs | |
State | Published - 2022 |
Keywords
- Limit of detection (LOD)
- area under the receiver operating characteristic curve (AUC)
- graphical lasso
- high-dimensional data
- imputation
- precision matrix
ASJC Scopus subject areas
- Statistics and Probability
- Statistics, Probability and Uncertainty
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A resample-replace lasso procedure for combining high-dimensional markers with limit of detection
Wang, J. (Creator), Zhao, Y. (Creator), Tang, L. L. (Creator), Mueller, C. (Creator) & Li, Q. (Creator), Taylor & Francis, 2021
DOI: 10.6084/m9.figshare.16661105.v1, https://tandf.figshare.com/articles/journal_contribution/A_resample-replace_lasso_procedure_for_combining_high-dimensional_markers_with_limit_of_detection/16661105/1
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