KRAS mut/WT patient ID disconnect between portal/paper

[Ali Livernois]

Hello,

I hope I’m using the correct contact point - Would you please redirect me if not?

I struggling to figure out why the KRAS mutation frequency in TCGA-PDAC is reported differently between cbioportal  and the publication linked to that dataset. 

The publication reports a KRAS mutation frequency of 93% (140/150 PDAC samples) while the portal reports a KRAS mutation frequency of only 69.3%  (105/153 PAAD samples with subtype ductal). The same patient IDs are shown to have a KRAS mutation in the paper but are wild type on cbioportal.

I would very much appreciate any assistance or insight you could provide on this disconnect.

Publication: Cancer Genome Atlas Research Network. Electronic address: andrew_...@dfci.harvard.edu; Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PMID: 28810144; PMCID: PMC5964983.

Many thanks,

Alexandra

	Alexandra Livernois, Ph.D. (she / her) Senior Scientist, Bioinformatics, Translational Research ali.li...@zymeworks.com 114 East 4th Avenue, Suite 800 | Vancouver, BC | V5T 1G4

 

 

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[Benjamin Gross]

Hi Alexandra,

I’ve forwarded your question to our data curation team.  Someone should follow up with you over the next couple of days.

Thank you for your patience.

-Benjamin

On Mar 18, 2026, at 2:22 PM, 'Ali Livernois' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com> wrote:

Hello,

I hope I’m using the correct contact point - Would you please redirect me if not?

I struggling to figure out why the KRAS mutation frequency in TCGA-PDAC is reported differently between cbioportal  and the publication linked to that dataset. 

The publication reports a KRAS mutation frequency of 93% (140/150 PDAC samples) while the portal reports a KRAS mutation frequency of only 69.3%  (105/153 PAAD samples with subtype ductal). The same patient IDs are shown to have a KRAS mutation in the paper but are wild type on cbioportal.

I would very much appreciate any assistance or insight you could provide on this disconnect.

Publication: Cancer Genome Atlas Research Network. Electronic address: andrew_...@dfci.harvard.edu; Cancer Genome Atlas Research Network. Integrated Genomic Characterization of Pancreatic Ductal Adenocarcinoma. Cancer Cell. 2017 Aug 14;32(2):185-203.e13. doi: 10.1016/j.ccell.2017.07.007. PMID: 28810144; PMCID: PMC5964983.

Many thanks,

Alexandra

Alexandra Livernois, Ph.D. (she / her) Senior Scientist, Bioinformatics, Translational Research ali.li...@zymeworks.com 114 East 4th Avenue, Suite 800 | Vancouver, BC | V5T 1G4

 

 

Notice of Confidentiality: The information transmitted is intended only for the person or entity to which it is addressed and may contain confidential and/or privileged material. Any review, re-transmission, dissemination or other use of or taking of any action in reliance upon this information by persons or entities other than the intended recipient is prohibited. If you received this in error please contact the sender immediately by return electronic transmission and then immediately delete this transmission including all attachments without copying, distributing or disclosing the same.

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[Ali Livernois]

Thank you very much, Benjamin!

Best,

Alexandra

From: Benjamin Gross <benjami...@gmail.com>
Date: Wednesday, March 18, 2026 at 3:44 PM
To: Ali Livernois <ali.li...@zymeworks.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] KRAS mut/WT patient ID disconnect between portal/paper

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[Ramya Madupuri]

Hi Alexandra,

Thanks for reaching out! The discrepancy is because the dataset on cBioPortal (PAAD TCGA PanCancer Atlas) is not the same as the one used in the paper (PMID: 28810144).

The PanCancer Atlas dataset is a later, reprocessed version of TCGA using standardized pipelines across cancer types, so mutation calls can differ from the original publication. We do not currently host the exact dataset from the paper in the portal, and to match their numbers more closely, you’d need to use the original mutation calls from that study.

Hope this helps! Let us know if you have any questions.

Best,

Ramya

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/CO6PR18MB39245749D71D640CEC2DD706F94CA%40CO6PR18MB3924.namprd18.prod.outlook.com.

[Ali Livernois]

Hi Ramya,

Thank you very much for this information, much appreciated.

Best,

Alexandra 

From: Ramya Madupuri <ramyama...@gmail.com>
Date: Monday, March 23, 2026 at 8:19 AM
To: Ali Livernois <ali.li...@zymeworks.com>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>, Benjamin Gross <benjami...@gmail.com>
Subject: Re: [cbioportal] KRAS mut/WT patient ID disconnect between portal/paper

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