how to get Cinical drug response data from broad GDAC firehose?
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4.3 years ago
Chaimaa ▴ 260

hi guys,

Could anyone guide me on how to get clinical drug response data from TCGA ?

I have access to the broad GDAC firehose website GDAC data and download a "Clinical_Pick_Tier1 (MD5)" of some cancer types ,Unfortunately, i found no informations about drugs, and if even exist are all "NA".

i am expecting to get some information like drug name or even drug id, but i have found nothing about drugs

Could anyone please guide me on how or from where i can get a clinical drug response data from TCGA

drugs • 1.4k views
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4.3 years ago

Take the data from the GDC, which is the primary host site of TCGA data. See here, as an example: C: TCGA immunotherapy treated melanoma data

Kevin

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@Kevin Blighe Hi Kevin, Thanks i have got the data, I want also to ask you if I want to find the effect of a drug on a cancer pathological stage rather than entire cancer ( for example stage1 or stage 2 or stage4), is this thing can make a sense biologically?

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That's not an easy thing to predict... Generally, though, check the genes that are expressed at each Stage of the cancer, and then determine which drugs may be suitable.

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@Kevin Blighe how to determine which drugs are suitable? based on the drug information or genes informations? how if i can take a group of drugs which have more patients ( for example cisplatin and carboplatin) and check their responce for each cancer stage. this is can also make sence or still hard to determine? im looking for such papers but didnt find yet Thanks Kevin in advance

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You need both the drug information and the gene expression information. It may be beneficial to transform your gene expression data to Z-scale, whereby, then, Z>1.96 would represented genes that are statistically significantly highly expressed.

For example, if a breast cancer tumour expresses the Her2 protein (encoded by ERBB2 gene), then it is suitable for treatment by Trastuzumab.

One place where you could look is OpenTargets: https://www.opentargets.org/

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@Kevin Blighe Thanks a lot Kevin realy Appreciate your help!

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