DNA methylation profiling to predict recurrence risk in stage Ι lung adenocarcinoma: Development and validation of a nomogram to clinical management.

Journal of Cellular and Molecular Medicine
Xianxiong MaHengyu Chen

Abstract

Increasing evidence suggested DNA methylation may serve as potential prognostic biomarkers; however, few related DNA methylation signatures have been established for prediction of lung cancer prognosis. We aimed at developing DNA methylation signature to improve prognosis prediction of stage I lung adenocarcinoma (LUAD). A total of 268 stage I LUAD patients from the Cancer Genome Atlas (TCGA) database were included. These patients were separated into training and internal validation datasets. GSE39279 was used as an external validation set. A 13-DNA methylation signature was identified to be crucially relevant to the relapse-free survival (RFS) of patients with stage I LUAD by the univariate Cox proportional hazard analysis and the least absolute shrinkage and selection operator (LASSO) Cox regression analysis and multivariate Cox proportional hazard analysis in the training dataset. The Kaplan-Meier analysis indicated that the 13-DNA methylation signature could significantly distinguish the high- and low-risk patients in entire TCGA dataset, internal validation and external validation datasets. The receiver operating characteristic (ROC) analysis further verified that the 13-DNA methylation signature had a better value to pred...Continue Reading

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Citations

Apr 22, 2021·Database : the Journal of Biological Databases and Curation·Abbas KhanDong-Qing Wei
Jul 4, 2021·Seminars in Thoracic and Cardiovascular Surgery·Jing-Sheng CaiHao-Xian Yang

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Software Mentioned

R
GEOquery
R TCGAbiolinks
dmpFinder
LASSO
GSVA package
minfi
R package ‘ glmnet
wateRmelon
survivalROC

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