Data mining techniques for cancer detection using serum proteomic profiling

Pathological changes in an organ or tissue may be reflected in proteomic patterns in serum. It is possible that unique serum proteomic patterns could be used to discriminate cancer samples from non-cancer ones. Due to the complexity of proteomic profiling, a higher order analysis such as data mining is needed to uncover the differences in complex proteomic patterns. The objectives of this paper are (1) to briefly review the application of data mining techniques in proteomics for cancer detection/diagnosis; (2) to explore a novel analytic method with different feature selection methods; (3) to compare the results obtained on different datasets and that reported by Petricoin et al. in terms of detection performance and selected proteomic patterns.

Three serum SELDI MS data sets were used in this research to identify serum proteomic patterns that distinguish the serum of ovarian cancer cases from non-cancer controls. A support vector machine-based method is applied in this study, in which statistical testing and genetic algorithm-based methods are used for feature selection respectively. Leave-one-out cross validation with receiver operating characteristic (ROC) curve is used for evaluation and comparison of cancer detection performance.

The results showed that (1) data mining techniques can be successfully applied to ovarian cancer detection with a reasonably high performance; (2) the classification using features selected by the genetic algorithm consistently outperformed those selected by statistical testing in terms of accuracy and robustness; (3) the discriminatory features (proteomic patterns) can be very different from one selection method to another. In other words, the pattern selection and its classification efficiency are highly classifier dependent. Therefore, when using data mining techniques, the discrimination of cancer from normal does not depend solely upon the identity and origination of cancer-related proteins.