GEO series

Whole Genome Sequencing Informs Therapeutic Selection for Pancreatic Cancer

GSE61502 Homo sapiens (human) Genome variation profiling by SNP array 100 samples Submitted 2015/02/27 Platform GPL8882Platform GPL16104

At a glance

human · 100 samples

Organism: Homo sapiens (human)
Topic: Pancreatic cancerThis series is part of our curated briefing on it.
Samples: 100 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

Pancreatic cancer remains one of the most lethal of malignancies and a major health burden. We performed whole genome sequencing and CNV analysis of 100 pancreatic ductal adenocarcinomas. Chromosomal rearrangements leading to gene disruption were frequent, affecting genes known to be important in pancreatic cancer (TP53, SMAD4, CDKN2A, ARID1A, ROBO2) and novel candidate drivers of pancreatic carcinogenesis (KDM6A and PREX2).

Read the full summary ↓

Patterns of structural variation classified PDAC into 4 subtypes with potential clinical utility: stable, locally rearranged, scattered and unstable. A significant proportion harboured focal amplifications, many of which contained druggable oncogenes (ERBB2, MET, FGFR1, CDK6, PIK3R3, and PIK3CA), but at low individual frequency. Genomic instability co-segregated with inactivation of DNA maintenance genes (BRCA1, BRCA2, PALB2 or RPA1), and a mutational signature of DNA damage repair deficiency. This subgroup was associated with response to platinum-based therapy and defines candidate biomarkers of therapeutic responsiveness.

This dataset

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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 (GSE61502_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 PRJNA261329. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25719666) ↗

Samples in this study

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+ 100 more — browse all 100 samples with per-sample file links →

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GSE148188 NOXA dependent induction of apoptosis in pancreatic cancer cells 49 samples same disease briefing · shares pancreatic
GSE119794 Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer 40 samples same disease briefing · shares pancreatic
GSE120127 Role of BAP1 in pancreatic cancer 38 samples same disease briefing · shares pancreatic
GSE14245 Multiple Salivary Biomarkers for Early Detection of Pancreatic Cancer 24 samples same disease briefing · shares pancreatic
GSE141017 Single cell transcriptomes of pancreatic pre-invasive lesions and cancer reveal acinar metaplastic cells’ heterogeneity 12 samples same disease briefing · shares pancreatic

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