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To explore the application of integrated clustering methods in identifying low-grade glioma subtypes and prognostic prediction.
A comprehensive clustering algorithm (MOVICS), which pools ten clustering algorithms, was used to integrate the multi-omics data of LGG patients downloaded from TCGA to obtain cluster subtypes; prognostic factors of LGG were analyzed by multifactorial Cox regression. A random forest classification prediction model was constructed using mRNA data to evaluate the classification performance and externally validated with the CGGA dataset.
LGG patients were clustered into two subtypes, and the difference in survival between the two groups was statistically significant (χ2=54.410, P<0.001). The results of multifactorial Cox regression analysis showed that age (HR=1.053，95%CI: 1.037-1.069), cancer grade (HR=2.733，95%CI: 1.836-4.069) and cluster typing (HR=3.210，95%CI: 2.216-4.650) were all prognostic factors for LGG, and the results of Nomogram plots, calibration curves and ROC curves indicated good predictive performance of the model. The average prediction accuracy of the ten-fold cross-validated RF model was 87.81%, and the C-indexes of the training set, the internal validation set, and the two external validation sets were 0.717, 0.721, 0.574, and 0.572, and the Brier scores were 0.044, 0.066, 0.179, and 0.128, and the differences in the survival of the two external validation datasets were all statistically significance (P<0.05).
The comprehensive clustering method can effectively identify LGG subtypes, which are prognostic factors for LGG patients, and has been validated in an external dataset, CGGA, which can provide an important theoretical basis for clinical personalized treatment of LGG.
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| 科 Family | 属数 Number of genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) | 属 Genus | 种数 Number of species | 占总种数比例 Percentage of total species (%) |
|---|---|---|---|---|---|---|
| 鹅膏菌科Amanitaceae | 2 | 11 | 5.26 | 鹅膏菌属 Amanita | 10 | 4.78 |
| 小菇科 Mycenaceae | 2 | 12 | 5.74 | 丝盖伞属 Inocybe | 5 | 2.39 |
| 多孔菌科 Polyporaceae | 8 | 14 | 6.70 | 蜡蘑属 Laccaria | 5 | 2.39 |
| 红菇科 Russulaceae | 3 | 23 | 11.00 | 小皮伞属 Marasmius | 6 | 2.87 |
| 小菇属 Mycena | 11 | 5.26 | ||||
| 光柄菇属 Pluteus | 5 | 2.39 | ||||
| 红菇属 Russula | 17 | 8.13 | ||||
| 栓菌属 Trametes | 5 | 2.39 |
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