GEO series

Copy number alterations of 103 hepatocellular carcinomas with hepatitis C virus etiology

GSE9845 Homo sapiens (human) Genome variation profiling by SNP array; SNP genotyping by SNP array 197 samples Submitted 2008/06/22 Platform GPL3720

At a glance

human · 197 samples

Organism: Homo sapiens (human)
Samples: 197 samples: 86 × NY vs 62 × B vs 49 × MGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI.

Summary (written by the submitters)

To characterize the genetic alterations that instigate hepatitis C virus-induced hepatocellular carcinoma (HCC), we conducted an integrative genomic analysis of 103 HCCs. Most tumors harbored 1q gain, 8q gain or 8p loss, with occasional alterations in 13 additional chromosome arms. In addition to amplifications at 11q13 in 6 tumors, 4 tumors harbored focal gains at 6p21 incorporating VEGFA, which were confirmed in 4 of 113 HCC in an independent validation set.

Read the full summary ↓

Strikingly, this locus overlapped with copy gains in 4 of 371 lung adenocarcinomas. Overexpression of VEGFA via 6p21 gain suggested a cell-nonautonomous mechanism of oncogene activation. Hierarchical clustering of gene expression among 91 tumors identified 5 classes, including ‘Wnt-CTNNB1’, ‘proliferation’ and ‘interferon-related’ gene classes. We also discovered a novel class defined by polysomy of chromosome 7, gains of which were associated with early tumor recurrence after resection. These findings reveal key alterations in HCC pathogenesis and implicate potential therapeutic targets. Keywords: disease state analysis

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 (GSE9845_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 PRJNA105127. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 18701503) ↗

Study design

86 × NY vs 62 × B vs 49 × M

Supports a between-group comparison across 197 samples.

How we read this: 3 replicated groups read from 197 sample titles; they account for 197 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM248782 B13 B
GSM248783 B15 B
GSM248784 B17 B
GSM248785 B19 B
GSM248786 B21 B
GSM248787 B23 B
GSM248788 B25 B
GSM248789 B27 B
GSM248790 B29 B
GSM248791 B31 B
GSM248792 B33 B
GSM248793 B35 B
GSM248794 B37 B
GSM248795 B39 B
GSM248796 B41 B
GSM248797 B66 B
GSM248798 B68 B
GSM248799 B70 B
GSM248800 B72 B
GSM248801 B74 B
GSM248802 B76 B
GSM248803 B78 B
GSM248804 B80 B
GSM248805 B82 B
GSM248806 B84 B
GSM248807 B86 B
GSM248808 B88 B
GSM248809 B90 B
GSM248810 B94 B
GSM248811 B96 B
GSM248812 B98 B
GSM248813 M100 M
GSM248814 M102 M
GSM248815 M104 M
GSM248816 M106 M
GSM248817 M11 M
GSM248818 M13 M
GSM248819 M15 M
GSM248820 M17 M
GSM248821 M31 M

+ 157 more — browse all 197 samples with per-sample file links →

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