TARGET_GDC AML dataset

[Tim Somervaille]

Hi,

 

I wonder if you are able to assist? Does cBioPortal have a separate “data_clinical_sample.txt” file with event-free survival or properly censored OS data for the TARGET_GDC AML dataset? Or do you know who I could approach to get that? Am keen to do a full Kaplan-Meier analysis for a couple of factors, but the information within the current data_clinical_sample.txt does not include censoring of surviving patients.

 

Thanks so much, Tim

 

Tim Somervaille PhD FRCP FRCPath

Senior Group Leader @ Cancer Research UK Manchester Institute

Professor of Haematological Oncology @ The University of Manchester

Honorary Consultant in Haematology @ The Christie NHS Foundation Trust

[Gaofei Zhao]

Hi Tim,

Thank you for reaching out regarding the TARGET_GDC AML dataset.

It looks like the information you are looking for is located in the "data_clinical_patient.txt" file, rather than the "data_clinical_sample.txt" file. This file contains the survival-related data, including event-free survival and censored OS data.

You can find the file for this dataset here

For more details on how these columns are defined, I would recommend checking our documentation here

Please let us know if you have any other questions!

Best,

Gaofei

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[Tim Somervaille]

Gaofei,

 

Thank you so much for your response. Sorry, but my original message was perhaps confusing.

 

I was indeed referring to and looking at the “data_clinical_patient” file.

 

In the file (which I have attached) in Column K the overall survival status is shown (alive or dead) but in Column L (Overall Survival in months) values are only shown for dead patients and not live patients.

 

In cell L2 is states that “If alive, the number of months the patient has survived since initial diagnosis, otherwise the number of months the patient survived before death.”

 

So what is missing from this sheet in Column L are values for “If alive, the number of months the patient has survived since initial diagnosis”.

 

Without these it is not possible to use the data to generate a Kaplan Meier curve.

 

Any suggestions you could give to indicate how to get hold of these data would be much appreciated.

 

Best wishes and thanks,

 

Tim Somervaille

 

 

 

From: Gaofei Zhao <zhaoga...@gmail.com>
Sent: 04 March 2026 22:00
To: Tim Somervaille <tim.som...@cruk.manchester.ac.uk>
Cc: cbiop...@googlegroups.com
Subject: Re: [cbioportal] TARGET_GDC AML dataset

 

Hi Tim, Thank you for reaching out regarding the TARGET_GDC AML dataset. It looks like the information you are looking for is located in the "data_clinical_patient. txt" file, rather than the "data_clinical_sample. txt" file. 

Hi Tim,

 

Thank you for reaching out regarding the TARGET_GDC AML dataset.

 

It looks like the information you are looking for is located in the "data_clinical_patient.txt" file, rather than the "data_clinical_sample.txt" file. This file contains the survival-related data, including event-free survival and censored OS data.

 

You can find the file for this dataset here [github.com]

For more details on how these columns are defined, I would recommend checking our documentation here [docs.cbioportal.org]

 

Please let us know if you have any other questions!

 

Best,

Gaofei

 

On Tue, Mar 3, 2026 at 8:12 AM Tim Somervaille <tim.som...@cruk.manchester.ac.uk> wrote:

Hi,

 

I wonder if you are able to assist? Does cBioPortal have a separate “data_clinical_sample.txt” file with event-free survival or properly censored OS data for the TARGET_GDC AML dataset? Or do you know who I could approach to get that? Am keen to do a full Kaplan-Meier analysis for a couple of factors, but the information within the current data_clinical_sample.txt does not include censoring of surviving patients.

 

Thanks so much, Tim

 

Tim Somervaille PhD FRCP FRCPath

Senior Group Leader @ Cancer Research UK Manchester Institute

Professor of Haematological Oncology @ The University of Manchester

Honorary Consultant in Haematology @ The Christie NHS Foundation Trust

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[Tim Somervaille]

Hi Gaofei,

 

Sorry to pester you, but I wonder whether you had had a chance to look at this?

 

Thanks so much,

 

Tim