GEO series

Identifying expression and DNA methylation biomarkers for lung adenocarcinoma risk in East Asia [RNA-seq]

GSE314660 Homo sapiens (human) DNA methylation 61 samples Submitted 2026/02/04 Platform GPL24676

At a glance

DNA methylation · human · 61 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 61 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: Identifying expression and DNA methylation biomarkers for lung adenocarcinoma risk in East AsiaJournal of the National Cancer Institute · 2026

Summary (written by the submitters)

Lung adenocarcinoma (LUAD) is the most common type of lung cancer. A recent genome-wide association study (GWAS) of LUAD in East Asia reported 28 independent susceptibility variants across 25 loci and identified 2 genes whose genetically predicted expression levels are associated with LUAD risk, using an ancestry-matched lung tissue expression quantitative trait loci (eQTL) dataset.

Read the full summary ↓

It is desirable to identify additional susceptibility loci and to understand their underlying biological mechanisms. Using an expanded GWAS of LUAD in East Asia and ancestry-matched lung tissue eQTL and DNA methylation QTL datasets, we performed transcriptome-wide association studies and DNA methylome-wide association studies simultaneously and examined the association between measured expression of genes and DNA methylation of nearby CpGs (eQTM). Genes and nearby CpGs are termed CpG–gene–LUAD trios if these three associations hold simultaneously. At Bonferroni-corrected P<0.05, we identified a new susceptibility locus (6p21.31; lead SNP rs7772643), 10 LUAD-associated genes and 86 LUAD-associated CpGs. At false discovery rate q<0.05, we identified 28 LUAD-associated genes, 220 LUAD-associated CpGs, and 45 CpG–gene–LUAD trios; among them, 43 were direction-matched regarding these three associations. These show that 23 of the known 28 susceptibility variants for LUAD in East Asia are near these genes or CpGs and MARCH3, ELF5, IKZF3, GSDMB, CCDC116, and DSP are putative novel susceptibility loci. Few of them was reported in LUAD in European populations. This study substantially advances our understanding of the etiology of LUAD in East Asia and could be useful in developing translational applications.

Published in

Identifying expression and DNA methylation biomarkers for lung adenocarcinoma risk in East Asia

Chen TY, Chien LH, Jiang SS et al. · Journal of the National Cancer Institute 2026 · PMID 41581221 · doi:10.1093/jnci/djag021

This dataset

Open GSE314660 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE314660_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1392422 and SRA study SRP657250. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41581221) ↗

Study design

A cohort of 61 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run NES001 … NES061 and carry no group information.

Samples in this study

GSM9408838 NES001
GSM9408839 NES002
GSM9408840 NES003
GSM9408841 NES004
GSM9408842 NES005
GSM9408843 NES006
GSM9408844 NES007
GSM9408845 NES008
GSM9408846 NES009
GSM9408847 NES010
GSM9408848 NES011
GSM9408849 NES012
GSM9408850 NES013
GSM9408851 NES014
GSM9408852 NES015
GSM9408853 NES016
GSM9408854 NES017
GSM9408855 NES018
GSM9408856 NES019
GSM9408857 NES020
GSM9408858 NES021
GSM9408859 NES022
GSM9408860 NES023
GSM9408861 NES024
GSM9408862 NES025
GSM9408863 NES026
GSM9408864 NES027
GSM9408865 NES028
GSM9408866 NES029
GSM9408867 NES030
GSM9408868 NES031
GSM9408869 NES032
GSM9408870 NES033
GSM9408871 NES034
GSM9408872 NES035
GSM9408873 NES036
GSM9408874 NES037
GSM9408875 NES038
GSM9408876 NES039
GSM9408877 NES040

+ 21 more — browse all 61 samples with per-sample file links →

Datasets on a similar topic

GSE308103 Single-nucleus RNA-sequencing (snRNA-seq) analysis of normal lung tissues, precursor lung lesions and invasive lung adenocarcinomas 75 samples shares adenocarcinoma, rna-seq, lung
GSE320212 Identifying Senescence and Immune Biomarkers Predictive of Benefit to Combined CDK4/6 and PD-1 Blockade in Dedifferentiated Liposarcoma: Single-Cell RNA-seq of Serial Tumor Biopsies 23 samples shares identifying, biomarkers, rna-seq
GSE330179 mRNA-seq analysis of S100A16-mediated alternative splicing in lung adenocarcinoma under oxidative stress 18 samples shares adenocarcinoma, rna-seq, lung
GSE189357 Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [scRNA-seq] 9 samples shares adenocarcinoma, rna-seq, lung
GSE320469 Identifying severe COVID-19 risk variants modulating enhancer reporter activity in lung cells 7 samples shares identifying, lung, risk
GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares adenocarcinoma, rna-seq
GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares adenocarcinoma, rna-seq
GSE319666 Archetype analysis of lung adenocarcinoma premalignancy links heterogeneity in premalignant lesions to diverging features of invasive disease 177 samples shares adenocarcinoma, lung

Search all human RNA-seq datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.