1. Comparison of the Metastasis Predictive Potential of mRNA and Long Non-Coding RNA Profiling in Systemically Untreated Breast Cancer
- Author
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Thi T. N. Do, Kristina Pilekær Sørensen, Qihua Tan, Ines Block, Martin Jakob Larsen, Mark Burton, Mads Thomassen, Martin Bak, Torben A Kruse, and Søren Cold
- Subjects
Oncology ,Cancer Research ,medicine.medical_specialty ,Machine learning methods ,mRNA ,Biology ,Article ,Metastasis ,lymph node negative ,Breast cancer ,Internal medicine ,Gene expression ,medicine ,MRNA ,Prognostic predictors ,RC254-282 ,Low-risk breast cancer ,Messenger RNA ,long non-coding RNA ,Lymph node negative ,prognostic predictors ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,systemically untreated patients ,medicine.disease ,Lncrna expression ,Primary tumor ,Long non-coding RNA ,Systemically untreated patients ,low-risk breast cancer ,machine learning methods - Abstract
Several gene expression signatures based on mRNAs and a few based on long non-coding RNAs (lncRNAs) have been developed to provide prognostic information beyond clinical evaluation in breast cancer (BC). However, the comparison of such signatures for predicting recurrence is very scarce. Therefore, we compared the prognostic utility of mRNAs and lncRNAs in low-risk BC patients using two different classification strategies. Frozen primary tumor samples from 160 lymph node negative and systemically untreated BC patients were included, 80 developed recurrence—i.e., regional or distant metastasis while 80 remained recurrence-free (mean follow-up of 20.9 years). Patients were pairwise matched for clinicopathological characteristics. Classification based on differential mRNA or lncRNA expression using seven individual machine learning methods and a voting scheme classified patients into risk-subgroups. Classification by the seven methods with a fixed sensitivity of ≥90% resulted in specificities ranging from 16–40% for mRNA and 38–58% for lncRNA, and after voting, specificities of 38% and 60% respectively. Classifier performance based on an alternative classification approach of balanced accuracy optimization also provided higher specificities for lncRNA than mRNA at comparable sensitivities. Thus, our results suggested that classification followed by voting improved prognostic power using lncRNAs compared to mRNAs regardless of classification strategy.
- Published
- 2021