Screening and verification of long noncoding RNA promoter methylation sites in hepatocellular carcinoma

Cancer Cell International
Zhuo LinHongwei Sun

Abstract

Long noncoding ribonucleic acid (lncRNA) promoter methylation is closely related to the occurrence and development of hepatocellular carcinoma (HCC). Thus, we aim to screen and verify the lncRNA promoter methylation sites associated with overall survival (OS), vascular invasion, pathological grade, and clinical stage in HCC. Methylation-related data including clinical characteristic, transcriptome, methylation, and messenger RNA (mRNA) expression were taken from the Cancer Genome Atlas (TCGA) database. The OS, vascular invasion, pathological grade, and clinical stage-related lncRNA promoter methylation models were developed by the least absolute shrinkage and selection operator (LASSO) algorithm based on the lncRNA promoter methylation sites screened via R software. The Kaplan-Meier analysis, the area under the receiver operating characteristic (ROC) curve (AUC), the calibration curve (C-index) were performed to evaluate the performance of these models. Finally, the methylation-specific polymerase chain reaction (MS-PCR) was performed to verify the accuracy of these models based on 146 HCC tissues from our hospital. A total of 10 methylation sites were included in the OS-related lncRNA promoter methylation model that could effe...Continue Reading

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Citations

Sep 7, 2020·World Journal of Surgical Oncology·Wan-Ping GuoWei Ma
Jan 26, 2021·OncoTargets and Therapy·Miao DaShuwen Han

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Methods Mentioned

BETA
chip
PCR

Software Mentioned

MedCalc
R
SurvivalROC
- Logistic
pheatmap
LASSO
COX

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