cBioPortal user reported error

[Elena Karydi]

https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=laml_tcga_pan_can_atlas_2018%2Cacc_tcga_pan_can_atlas_2018%2Cblca_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018%2Cbrca_tcga_pan_can_atlas_2018%2Ccesc_tcga_pan_can_atlas_2018%2Cchol_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018%2Cdlbc_tcga_pan_can_atlas_2018%2Cesca_tcga_pan_can_atlas_2018%2Cgbm_tcga_pan_can_atlas_2018%2Chnsc_tcga_pan_can_atlas_2018%2Ckich_tcga_pan_can_atlas_2018%2Ckirc_tcga_pan_can_atlas_2018%2Ckirp_tcga_pan_can_atlas_2018%2Clihc_tcga_pan_can_atlas_2018%2Cluad_tcga_pan_can_atlas_2018%2Clusc_tcga_pan_can_atlas_2018%2Cmeso_tcga_pan_can_atlas_2018%2Cov_tcga_pan_can_atlas_2018%2Cpaad_tcga_pan_can_atlas_2018%2Cpcpg_tcga_pan_can_atlas_2018%2Cprad_tcga_pan_can_atlas_2018%2Csarc_tcga_pan_can_atlas_2018%2Cskcm_tcga_pan_can_atlas_2018%2Cstad_tcga_pan_can_atlas_2018%2Ctgct_tcga_pan_can_atlas_2018%2Cthym_tcga_pan_can_atlas_2018%2Cthca_tcga_pan_can_atlas_2018%2Cucs_tcga_pan_can_atlas_2018%2Cucec_tcga_pan_can_atlas_2018%2Cuvm_tcga_pan_can_atlas_2018%2Cbrca_tcga%2Cccle_broad_2019%2Ccoad_cptac_2019%2Ccoadread_tcga%2Cgbm_cptac_2021%2Cluad_cptac_2020%2Clusc_cptac_2021%2Cmng_utoronto_2021%2Cov_tcga%2Cpaad_cptac_2021%2Cbrain_cptac_2020%2Cbrca_cptac_2020%2Cbrca_dldccc_2022&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic%2Ccna&case_set_id=all&gene_list=GMNN&geneset_list=%20&tab_index=tab_visualize&Action=Submit&comparison_groupOrder=%5B%22Unprofiled%20group%22%2C%22GMNN%22%5D&comparison_selectedGroups=%5B%22Altered%20group%22%2C%22Unaltered%20group%22%2C%22GMNN%22%5D;{"type":"ErrorBoundary","log":"TypeError: undefined is not an object (evaluating 't.cancerType.name')"}

[David Heery (staff)]

https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=prad_mich%2Cprad_su2c_2019%2Cprad_su2c_2015%2Cprad_mcspc_mskcc_2020%2Cnepc_wcm_2016%2Cprad_broad_2013%2Cprad_broad%2Cprad_cpcg_2017%2Cprad_fhcrc%2Cprad_mskcc%2Cprad_pik3r1_msk_2021%2Cprad_cdk12_mskcc_2020%2Cprad_mskcc_2014%2Cprad_p1000%2Cprad_eururol_2017%2Cprad_tcga_pub%2Cprad_tcga%2Cprad_tcga_gdc%2Cprad_tcga_pan_can_atlas_2018%2Cprad_mskcc_cheny1_organoids_2014%2Cprostate_dkfz_2018%2Cprad_msk_2019%2Cprostate_msk_2024%2Cprad_mskcc_2017%2Cprad_organoids_msk_2022%2Cprostate_pcbm_swiss_2019%2Cprad_msk_mdanderson_2023%2Cprad_msk_stopsack_2021%2Cmpcproject_broad_2021&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=KAT6A&geneset_list=%20&tab_index=tab_visualize&Action=Submit;{"type":"ErrorBoundary","log":"TypeError: Cannot read properties of undefined (reading 'name')"}

Professor David M Heery BSc PhD AFHEA

Head of Division of Biomolecular Science & Medicinal Chemistry

Gene Regulation & RNA Biology Laboratory

BioDiscovery Institute

School of Pharmacy

University of Nottingham

Nottingham NG7 2RD

United Kingdom

This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please contact the sender and delete the email and attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. Email communications with the University of Nottingham may be monitored where permitted by law.

[Prasanna Jagannathan]

Hi David,

Thanks for emailing cBioPortal team. The reason why the error happens is because the study "prostate_pcbm_swiss_2019" does not have two important columns which are not mandatory.

CANCER_TYPE: Cancer Type
CANCER_TYPE_DETAILED: Cancer Type Detailed, a sub-type of the specified CANCER_TYPE

However, these columns are mandatory for the "Cancer Types Summary" tab to function.

If you remove this study from the study list, the page will work as expected.

Please reply only to "cbiop...@googlegroups.com" <cbiop...@googlegroups.com>

thanks

Jag

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[David Heery (staff)]

Excellent - thank you so much

David

Sent from Outlook for iOS

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From: Prasanna Jagannathan <jagn...@gmail.com>
Sent: Monday, November 24, 2025 4:38:07 PM
To: David Heery (staff) <david...@nottingham.ac.uk>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] cBioPortal user reported error

 

You don't often get email from jagn...@gmail.com. Learn why this is important

[Prasanna Jagannathan]

Hi Elena

Thanks for contact us. We are looking into the issue and will reach out to you soon.

Please reply only to cbiop...@googlegroups.com

thanks

Jag

On Mon, 24 Nov 2025 at 08:12, Elena Karydi <karyd...@gmail.com> wrote:

https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=laml_tcga_pan_can_atlas_2018%2Cacc_tcga_pan_can_atlas_2018%2Cblca_tcga_pan_can_atlas_2018%2Clgg_tcga_pan_can_atlas_2018%2Cbrca_tcga_pan_can_atlas_2018%2Ccesc_tcga_pan_can_atlas_2018%2Cchol_tcga_pan_can_atlas_2018%2Ccoadread_tcga_pan_can_atlas_2018%2Cdlbc_tcga_pan_can_atlas_2018%2Cesca_tcga_pan_can_atlas_2018%2Cgbm_tcga_pan_can_atlas_2018%2Chnsc_tcga_pan_can_atlas_2018%2Ckich_tcga_pan_can_atlas_2018%2Ckirc_tcga_pan_can_atlas_2018%2Ckirp_tcga_pan_can_atlas_2018%2Clihc_tcga_pan_can_atlas_2018%2Cluad_tcga_pan_can_atlas_2018%2Clusc_tcga_pan_can_atlas_2018%2Cmeso_tcga_pan_can_atlas_2018%2Cov_tcga_pan_can_atlas_2018%2Cpaad_tcga_pan_can_atlas_2018%2Cpcpg_tcga_pan_can_atlas_2018%2Cprad_tcga_pan_can_atlas_2018%2Csarc_tcga_pan_can_atlas_2018%2Cskcm_tcga_pan_can_atlas_2018%2Cstad_tcga_pan_can_atlas_2018%2Ctgct_tcga_pan_can_atlas_2018%2Cthym_tcga_pan_can_atlas_2018%2Cthca_tcga_pan_can_atlas_2018%2Cucs_tcga_pan_can_atlas_2018%2Cucec_tcga_pan_can_atlas_2018%2Cuvm_tcga_pan_can_atlas_2018%2Cbrca_tcga%2Cccle_broad_2019%2Ccoad_cptac_2019%2Ccoadread_tcga%2Cgbm_cptac_2021%2Cluad_cptac_2020%2Clusc_cptac_2021%2Cmng_utoronto_2021%2Cov_tcga%2Cpaad_cptac_2021%2Cbrain_cptac_2020%2Cbrca_cptac_2020%2Cbrca_dldccc_2022&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Cgistic%2Ccna&case_set_id=all&gene_list=GMNN&geneset_list=%20&tab_index=tab_visualize&Action=Submit&comparison_groupOrder=%5B%22Unprofiled%20group%22%2C%22GMNN%22%5D&comparison_selectedGroups=%5B%22Altered%20group%22%2C%22Unaltered%20group%22%2C%22GMNN%22%5D;{"type":"ErrorBoundary","log":"TypeError: undefined is not an object (evaluating 't.cancerType.name')"}

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[Guckin, Danielle]

https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=chol_icgc_2017%2Cchol_msk_2018%2Cchol_nccs_2013%2Cchol_nus_2012%2Cchol_tcga%2Cchol_tcga_gdc%2Cchol_tcga_pan_can_atlas_2018%2Cgbc_mskcc_2022%2Cgbc_msk_2018%2Cgbc_shanghai_2014%2Cchol_jhu_2013%2Cihch_mskcc_2020%2Cihch_msk_2021%2Cihch_ismms_2015%2Cihch_smmu_2014%2Cbiliary_tract_summit_2022&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=AKT2&geneset_list=%20&tab_index=tab_visualize&Action=Submit;{"type":"ErrorBoundary","log":"TypeError: Cannot read properties of undefined (reading 'name')"}

Hi, I keep receiving the error above when performing the following steps:

• Select tumor type (for example, biliary tract)
• Select all listed studies matching filter
• Query by Gene
• Enter Gene (for example, AKT2)
• Select Cancer Types Summary 

Please let me know if there is anything I can do. 

Thanks,

Dani

[Aaron L]

Will have a look.  Thanks for the report Danielle.

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[Prasanna Jagannathan]

Hi Danielle

Thanks for emailing us.

Before viewing the CancerTypeSummary page,  in the studyview page, plz unselect patients who have NA for CancerType as shown in the image below.

This will allow the CancerTypeSummary page to load.

Please reply only to "cbiop...@googlegroups.com" <cbiop...@googlegroups.com>

thanks

Jag

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[Mahesh Chandrasekharan]

https://www.cbioportal.org/results/cancerTypesSummary?cancer_study_list=msk_ch_2020%2Cpan_origimed_2020%2Cmsk_met_2021%2Cmsk_chord_2024%2Cmsk_impact_2017%2Cmixed_allen_2018%2Cmetastatic_solid_tumors_mich_2017%2Cpancan_pcawg_2020%2Csummit_2018%2Ctmb_mskcc_2018%2Cntrk_msk_2019&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna%2Cgistic&case_set_id=all&gene_list=VRK1%250AVRK2%250ASTAG1%250ASTAG2%250ABANF1%250ABANF2&geneset_list=%20&tab_index=tab_visualize&Action=Submit;{"type":"ErrorBoundary","log":"TypeError: Cannot read properties of undefined (reading 'name')"}

Please help!

Thanks 

Mahesh

Mahesh B. Chandrasekharan, PhD

Assistant Professor of Radiation Oncology

Investigator, Huntsman Cancer Institute

Adjunct Assistant Professor of Hematology & Hematological Malignancies

University of Utah School of Medicine

2000 Circle of Hope Room 3715

Huntsman Cancer Institute

Salt Lake City, UT 84112-5540

Phone: 801-213-4220

Administrative Assistant: Katie Kvam (801-585-3599)

Lab site: https://uofuhealth.utah.edu/huntsman/labs/chandrasekharan

 

[Prasanna Jagannathan]

Hi Mahesh,

Thanks for emailing cBioPortal group.

Before viewing the CancerTypeSummary page,  in the studyview page, plz unselect patients who have NA for CancerType as shown in the image below.

This will allow the CancerTypeSummary page to load.

Please reply only to "cbiop...@googlegroups.com" <cbiop...@googlegroups.com>

thanks

Jag

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[Aaron L]

Yes, I can see the exact problem in the code.  Will have it fixed by EOD.   For now you can use the trick Jag proposes.

--Aaron

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[Prasanna Jagannathan]

Hi Danielle

Please follow the below steps.

Instead of "Query by Gene", click on "Explore Selected Studies" button. Then add the chart for Cancer Type if it is not already there. Then  the various "Cancer Type" values in table format will be available. Select all except NA.

On the top right of the screen, enter the Gene list and then click the Query button.

thanks

Jag

On Tue, 25 Nov 2025 at 14:31, Guckin, Danielle <guc...@upmc.edu> wrote:

Hi, 

I don't see that as an option (the website looks different for me). I am selecting a specific tumor type (bowel), with all the associated studies. Then querying a specific gene, in which the Cancer Types Summary tab is the only tab that does not work anymore. See screenshots below. 

Thanks,

Danielle

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From: Prasanna Jagannathan <jagn...@gmail.com>
Sent: Tuesday, November 25, 2025 10:53 AM
To: Guckin, Danielle <guc...@upmc.edu>

Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] cBioPortal user reported error

[Aaron L]

Should be fixed now.

To view this discussion visit https://groups.google.com/d/msgid/cbioportal/CALPp9F%2BFd6jvgxG3RZmUHFVchj0%3DK5aeg5yDhfwFcDXjb4tpkQ%40mail.gmail.com.

[Guckin, Danielle]

Hi, 

I don't see that as an option (the website looks different for me). I am selecting a specific tumor type (bowel), with all the associated studies. Then querying a specific gene, in which the Cancer Types Summary tab is the only tab that does not work anymore. See screenshots below. 

Thanks,

Danielle

---

From: Prasanna Jagannathan <jagn...@gmail.com>
Sent: Tuesday, November 25, 2025 10:53 AM
To: Guckin, Danielle <guc...@upmc.edu>
Cc: cbiop...@googlegroups.com <cbiop...@googlegroups.com>
Subject: Re: [cbioportal] cBioPortal user reported error