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Research Paper|Volume 11, Issue 3|pp 974—985

Predicting chromosome 1p/19q codeletion by RNA expression profile: a comparison of current prediction models

Zhi-liang Wang1, Zheng Zhao1, Zheng Wang2, Chuan-bao Zhang2, Tao Jiang1,2,3,4
  • 1Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
  • 2Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
  • 3China National Clinical Research Center for Neurological Diseases, Beijing, China
  • 4Center of Brain Tumor, Beijing Institute for Brain Disorders, Beijing, China
Received: October 20, 2018Accepted: January 24, 2019Published: February 2, 2019
https://doi.org/10.18632/aging.101795

Copyright: © 2019 Wang et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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.