GEO series

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

GSE49666 Homo sapiens (human) Genome variation profiling by SNP array 30 samples Submitted 2013/11/03 Platform GPL6801

At a glance

human · 30 samples

Organism: Homo sapiens (human)
Samples: 30 samples
Data you can get: A processed table (series matrix) and supplementary 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 GSE49666 in finder → Find more human datasets →

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 (GSE49666_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 ↓

Also filed as BioProject PRJNA214694. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24185513) ↗

Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 30 more — browse all 30 samples with per-sample file links →

Datasets on a similar topic

GSE274284 Multi-omics dissection of human RAG deficiency reveals distinctive patterns of immune dysregulation but a common inflammatory signature 63 samples shares distinct, patterns
GSE261834 Distinct structural and functional heterochromatin partitioning of lamin B1 and lamin B2 revealed using genome-wide Nicking Enzyme Epitope targeted DNA sequencing. 51 samples shares distinct, revealed
GSE298022 JNK activation dynamics drive distinct gene expression patterns over time mediated by mRNA stability 45 samples shares distinct, patterns
GSE291860 Achilles tendon exhibits distinct transcriptomic changes with increased mitochondrial energy production under lunar gravity 18 samples shares distinct, duct
GSE319130 Multi-omic analysis reveals molecular subtypes with distinct immunological phenotypes in SLE [RNA-Seq] 804 samples shares distinct
GSE280480 Gene expression profiling reveals two overarching types of anaplastic large cell lymphoma with distinct targetable biology: an LLMPP study 393 samples shares distinct
GSE276544 MVA-based SARS-CoV-2 vaccine candidates encoding different spike protein conformations induce distinct early transcriptional responses which may impact subsequent adaptive immunity 305 samples shares distinct
GSE62254 Molecular analysis of gastric cancer identifies discrete subtypes associated with distinct clinical characteristics and survival outcomes: the ACRG (Asian Cancer Research Group) study [gastric tumors] 300 samples shares distinct

Search all human 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.