Web Resources To Find Cancer Indication Where A Given Gene Is Amplified

Question

[Fred Fleche]

I would like to know if someone is aware of a web application that would give indication or patient samples in which a given gene is found to be amplified.

For instance at the Sanger there is the CONAN tool where you can enter an HUGO gene name and it gives you all the human cancer cell lines where you gene is in a genomic region with a High Level Amplification (>7).

[Lars Juhl Jensen]

What is it that you need the tool to be able to do that CONAN doesn't? To me it sounds like you answered your own question, but I have probably misunderstood something.

[Fred Fleche]

Actually CONAN is an instance related to cancer cell lines. I am looking for the same kind of tool but applied to patient samples.

[Malachi Griffith]

This tutorial describes several cancer data portals that might be relevant to this post: Exploring cancer mutation data portals

Answer 1

[2184687-1231-83-]

Integrative Oncogenomics Cancer Browser - IntOGen is also worth a look at

Answer 2

[Mary]

I'll offer a couple of cancer resources that might have some of the information you need.

1. If you know CONAN, you probably know COSMIC too, but just for the record, here's the link to COSMIC
2. This project is just getting started (just had a second data release) but you might be able to get some hot data out. International Cancer Genome Consortium. When there, go to the bottom where it says "Access to Data, Data Coordination Center" to have a look. I love the new display by Affected Genes in the different samples.
3. Cancer Genome Workbench, CGWB. We did a Tip-of-the-Week on that recently that might also help you to understand what's there.
4. The Cancer Genome Atlas (TCGA) might help.

As always, it depends on exactly what you want. But you can have a look and see if any are useful for your research.

Answer 3

[Laurent Gautier]

There is the oncomine database (but that's not free, although there is a free limited version for academic and non-profit research).

Answer 4

[Puthier]

We have developped TBrowser. It share some features with oncomine but is free. You can search through expression or CGH data for gene clusters highly enriched in any chromosomal region (you will find numerous hits for 1q21 for instance...).

[Fred Fleche]

Could you please provide a link to the resource you are referring.

[Fred Fleche]

I put a minus 1 because it does not seem that this tool provide any gene amplification data.

[Puthier]

Use query by annotation terms (e.g 1q21). Use tab key to get completion...

Answer 5

[Sophia]

I recently found this one:

CancerResource

It comes from the Charité University Hospital Berlin and includes also information on drugs/compounds targeting each gene.

Answer 6

[Michi]

The wiki page Databases for oncogenomic research may give a further hint, altough most are already mentioned here.

Answer 7

[Larry_Parnell]

It seems to me that to accomplish your goal you would also like to know what was observed in other, presumably normal samples. To do this, you can look at the Database of Genomic Variants. For example, chromosome 7 CNV Variation_69954 is seen up to 20 instances in some samples. That same view, same link, lists the genes affected by this CNV: PMS2L2, STAG3L3, SPDYE8P. It also lists the HapMap (and other) samples that were assayed.

In order to obtain data from cancer or non-cancer patient samples, especially in large numbers, you would like to have at hand the genotype data from GWAS. Processing the GWAS SNP data with a process like MADP (media/middle absolute pair-wise difference, which involves several algorithms) will give you the CNVs plus/minus a certain degree of confidence. MADP is an Affy tool. GWAS data can be hard to come by, but some are out there - see here.

[Fred Fleche]

Thanks a lot for you input Larry.