Genomic Signatures of Intestinal Metaplasia in Six Countries with Varying Incidence of Stomach Cancer

Intestinal metaplasia (IM) is a pre-cancerous condition associated with gastric cancer (GC), a deadly malignancy with varying geographic incidence. Performing a genomic analysis of over 1,500 IM samples from six countries, we identified 46 significantly mutated genes. We observed IM driver genes associated with high-risk populations and worse prognosis (ARID1A), members of the KRAS/MAPK signalling pathway (KRAS, BRAF, MAP2K1, MAP3K1, MAP2K4, NF1), and altered mucosal immunity (PIGR).

Type: Cancer Genomics
Archiver: European Genome-Phenome Archive (EGA)

4 Datasets

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD50000001538	We perform genome-wide EM-seq of 14 patients with concurrent matched normal, dysplasia and early gastric samples from South Korea. The dataset contains cram files from 38 samples.	Illumina NovaSeq 6000	38
EGAD50000001539	We generated whole genome sequencing data from 15 pairs of IM and matched normal. The dataset contains cram files from 30 samples.	Illumina NovaSeq 6000	30
EGAD50000001540	We perform targeted DNA sequencing of intestinal metaplasia of 463 IM and paired germline samples. An additional 48 IM and paired germline samples were included as validation cohort. The dataset contains cram files from 1022 IM and paired normal samples.	Illumina NovaSeq 6000	1022
EGAD50000002010	We perform bulk RNA-seq of 10 and single cell RNAseq of 2 intestinal metaplasia samples. We also perform stereoseq spatial transcriptomic analysis of 4 gastric cancer samples. The dataset contain cram files from 10 bulk RNAseq samples, and raw fastq files from 2 single cell RNAseq and 4 stereo-seq samples.	DNBSEQ-T7 Illumina NovaSeq 6000	16