Where can I get the genelist in Oncoscan?

Question

[mangfu100]

Hi all.

I want to use oncoscan for my research and Oncoscan is specially aimed at targeting hot spots regions for Cancer

I heard that there are several cancer related genes in oncoscan sites.

However, I cannot find the cancer genelist in oncoscan.

Does anybody know where they are?

Answer 1

[Malachi Griffith]

You can obtain a BED file of coordinates targeted by the Oncoscan assay here: http://www.affymetrix.com/estore/support/file_download.affx?onloadforward=/analysis/downloads/na33/genotyping/OncoScan.na33.r1.bed.zip

I believe you will be required to log in before you can download this file. You can intersect these coordinates with known gene/transcript annotations (e.g. using bedtools) to determine the identity of genes covered by the assay.

Or you could download the annotation file provided by Affy here: http://www.affymetrix.com/Auth/analysis/downloads/na33/genotyping/OncoScan.na33.r1.annot.csv.zip

More generally, here is a thread that covers others sources of cancer related genes: Database Of Tumor Suppressors And/Or Oncogenes

[mangfu100]

Thanks for your reply.

Here is one more question.

After clicking the site above (second address you mentioned)

http://www.affymetrix.com/Auth/analysis/downloads/na33/genotyping/OncoScan.na33.r1.annot.csv.zip

the only I can see is the affymetrix main pages and I didn't know where I should go to find annotation file. (of course , I am logged in)

Could you check one more time for me please?