Conventional biomarker discovery focuses mostly on the identification of single markers and thus often has limited success in disease diagnosis and prognosis. This study proposes a method to identify an optimized protein biomarker panel based on MS studies for predicting the risk of major adverse cardiac events (MACE) in patients. Since the simplicity and concision requirement for the development of immunoassays can only tolerate the complexity of the prediction model with a very few selected discriminative biomarkers, established optimization methods, such as conventional genetic algorithm (GA), thus fails in the high-dimensional space. In this paper, we present a novel variant of GA that embeds the recursive local floating enhancement technique to discover a panel of protein biomarkers with far better prognostic value for prediction of MACE than existing methods, including the one approved recently by FDA (Food and Drug Administration). The new pragmatic method applies the constraints of MACE relevance and biomarker redundancy to shrink the local searching space in order to avoid heavy computation penalty resulted from the local floating optimization. The proposed method is compared with standard GA and other variable selection approaches based on the MACE prediction experiments. Two powerful classification techniques, partial least squares logistic regression (PLS-LR) and support vector machine classifier (SVMC), are deployed as the MACE predictors owing to their ability in dealing with small scale and binary response data. New preprocessing algorithms, such as low-level signal processing, duplicated spectra elimination, and outliner patient's samples removal, are also included in the proposed method. The experimental results show that an optimized panel of seven selected biomarkers can provide more than 77.1% MACE prediction accuracy using SVMC. The experimental results empirically demonstrate that the new GA algorithm with local floating enhancement (GA-LFE) can achieve the better MACE prediction performance comparing with the existing techniques. The method has been applied to SELDI/MALDI MS datasets to discover an optimized panel of protein biomarkers to distinguish disease from control.
- Biomarker panel
- Genetic algorithm
- Major adverse cardiac events (MACE)
- Mass spectrometry
- Recursive local floating search
ASJC Scopus subject areas
- Molecular Biology