GEO series

Distinct Mutational Patterns of Infection and Non-Infection-Related Bile Duct Cancers Revealed by Exome Sequencing

GSE49656 Homo sapiens (human) DNA methylation 40 samples Submitted 2013/10/20 Platform GPL13534

At a glance

DNA methylation · human · 40 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Topic: CholangiocarcinomaThis series is part of our curated briefing on it.
Samples: 40 samples
Data you can get: A processed expression table (series matrix) and the array files, from NCBI.

Summary (written by the submitters)

The impact of different carcinogenic exposures on the specific patterns of somatic mutations in human tumors remains unclear. To clarify this issue, we profiled 209 cholangiocarcinomas (CCAs) from Asia and Europe, including 108 cases caused by liver fluke Opisthorchis viverrini (OV)-infection and 101 cases due to non-OV etiologies. Whole-exome (N = 15) and prevalence screening (N = 194) revealed recurrent somatic mutations in BAP1 and ARID1A, neither of which has been previously reported to be mutated in CCA.

Read the full summary ↓

Comparisons between intrahepatic OV and non-OV CCAs demonstrated statistically significant different mutation patterns: BAP1 and IDH1/2 were more frequently mutated in non-OV CCAs, while TP53 displayed the reciprocal pattern. Functional studies demonstrated tumor suppressive roles of BAP1 and ARID1A, establishing the role of chromatin modulators in CCA pathogenesis. These findings indicate that different causative etiologies may induce distinct somatic alterations even within the same tumor type.

This dataset

Open GSE49656 in finder → Find more human methylation datasets → Cholangiocarcinoma landscape →

Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE49656_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

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

Also filed as BioProject PRJNA214647. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24185513) ↗

Samples in this study

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+ 40 more — browse all 40 samples with per-sample file links →

More Cholangiocarcinoma datasets

GSE215448 Serum exosome miRNA expression profile in patients with cholangiocarcinoma(CCA) and common bile duct stones(CBDS) 6 samples same disease briefing · shares bile, duct
GSE284669 Therapeutic Perturbation of Liver and Bile Duct Cancer through Targeted Inhibition of FSP1 and GCS Induced Ferroptosis 6 samples same disease briefing · shares bile, duct
GSE290614 Comprehensive Molecular Profiling of Combined Hepatocellular Carcinoma and Cholangiocarcinoma reveals Distinct Notch Signaling Subgroups with Prognostic Significance 18 samples same disease briefing · shares distinct
GSE280797 Screening and molecular mechanism research on bile microRNAs associated with chemotherapy efficacy in perihilar cholangiocarcinoma 8 samples same disease briefing · shares bile
GSE319935 Defining molecular signatures of the solid/pseudopapillary and pseudoglandular patterns in so-called "solid-tubulocystic intrahepatic cholangiocarcinoma vs. NIPBL::NACC1 fusion hepatic carcinoma" 6 samples same disease briefing · shares patterns
GSE33327 Integrative Molecular Analysis of Intrahepatic Cholangiocarcinoma Reveals 2 Classes That Have Different Outcomes 283 samples same disease briefing
GSE317606 A Phase II Trial of Pembrolizumab plus Granulocyte Macrophage Colony Stimulating Factor in Advanced Biliary Cancer 180 samples same disease briefing
GSE26566 Molecular classification of human cholangiocarcinoma 169 samples same disease briefing

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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.