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  • Title: Predicting chromosome 1p/19q codeletion by RNA expression profile: a comparison of current prediction models.
    Author: Wang ZL, Zhao Z, Wang Z, Zhang CB, Jiang T.
    Journal: Aging (Albany NY); 2019 Feb 02; 11(3):974-985. PubMed ID: 30710490.
    Abstract:
    BACKGROUND: Chromosome 1p/19q codeletion is increasingly being recognized as the crucial genetic marker for glioma patients and have been included in WHO classification of glioma in 2016. Fluorescent in situ hybridization, a widely used method in detecting 1p/19q status, has some methodological limitations which might influence the clinical management for doctors. Here, we attempted to explore an RNA sequencing computational method to detect 1p/19q status. METHODS: We included 692 samples with 1p/19q status information from TCGA cohort as training set and 222 samples with 1p/19q status information from REMBRANDT cohort as validation set. We reviewed and compared five tools: TSPairs, GSVA, PAM, Caret, smoother, with respect to their accuracy, sensitivity and specificity. RESULTS: In TCGA cohort, the GSVA method showed the highest accuracy (98.4%) in predicting 1p/19q status (sensitivity=95.5%, specificity=99.6%) and smoother method showed the second-highest accuracy (accuracy=97.8%, sensitivity=96.4%, specificity=98.3%). While in REMBRANDT cohort, smoother method exhibited the highest accuracy (98.6%) (sensitivity= 96.7%, specificity=98.9%) in 1p/19q status prediction. CONCLUSIONS: Our independent assessment of five tools revealed that smoother method was selected as the most stable and accurate method in predicting 1p/19q status. This method could be regarded as a potential alternative method for clinical practice in future.
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