Programatically downloading mutation data in tsv format

[RAINFORD, Jethro (CAMBRIDGE UNIVERSITY HOSPITALS NHS FOUNDATION TRUST)]

Hi,

When viewing mutations for a gene and filtering to driver mutations, it is possible to download the table data in tsv format. We have a need to get the data from this table for a variety of genes which is not ideal to do manually (ideally 200+ genes). I have seen there is an API spec available but I am not sure if any of the endpoints give the data from this table (or a superset of this data that may then be filtered down). Are you able to provide any advice on how we could query this?

Example URL: https://genie.cbioportal.org/results/mutations?cancer_study_list=genie_public&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna&case_set_id=genie_public_cnaseq&gene_list=AKT1&geneset_list=%20&tab_index=tab_visualize&Action=Submit

Thanks in advance for your help!

Best wishes,

Jethro

Jethro Rainford | Principal Clinical Bioinformatician | Cambridge Genomics Laboratory 

Working pattern: Monday – Friday 9:00 - 17:30

 

East Genomics

Box 143 | Level 6 | Addenbrooke’s Treatment Centre | Cambridge University Hospital NHS Foundation Trust | Hills Road | Cambridge |CB2 0QQ

Tel: (01223) 348866 | https://www.eastgenomics.nhs.uk

 

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[Benjamin Gross]

Hi Jethro,

If you register with the AACR Project GENIE Public project on synapse, you should be able to download the entire mutation file.  You can find more information at the link below.

Best,

-Benjamin

On Aug 8, 2025, at 11:56 AM, 'RAINFORD, Jethro (CAMBRIDGE UNIVERSITY HOSPITALS NHS FOUNDATION TRUST)' via cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com> wrote:

Hi,

When viewing mutations for a gene and filtering to driver mutations, it is possible to download the table data in tsv format. We have a need to get the data from this table for a variety of genes which is not ideal to do manually (ideally 200+ genes). I have seen there is an API spec available but I am not sure if any of the endpoints give the data from this table (or a superset of this data that may then be filtered down). Are you able to provide any advice on how we could query this?

Example URL: https://genie.cbioportal.org/results/mutations?cancer_study_list=genie_public&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&profileFilter=mutations%2Cstructural_variants%2Ccna&case_set_id=genie_public_cnaseq&gene_list=AKT1&geneset_list=%20&tab_index=tab_visualize&Action=Submit

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Thanks in advance for your help!

Best wishes,

Jethro

Jethro Rainford | Principal Clinical Bioinformatician | Cambridge Genomics Laboratory 

Working pattern: Monday – Friday 9:00 - 17:30

 

East Genomics

Box 143 | Level 6 | Addenbrooke’s Treatment Centre | Cambridge University Hospital NHS Foundation Trust | Hills Road | Cambridge |CB2 0QQ

Tel: (01223) 348866 | https://www.eastgenomics.nhs.uk

 

Cambridge University Hospitals NHS Foundation Trust is part of the National Institute for Health Research – Cambridge Biomedical Research Centre and a member of Cambridge University Health Partners.

 This email is confidential, see https://www.cuh.nhs.uk/patient-privacy/email-disclaimer/

************************************************************************************** ******************************

This message may contain confidential information. If you are not the intended recipient please:
i) inform the sender that you have received the message in error before deleting it; and
ii) do not disclose, copy or distribute information in this e-mail or take any action in relation to its content (to do so is strictly prohibited and may be unlawful).
Thank you for your co-operation.

NHS.net Connect is the secure email, collaboration and directory service available for all NHS staff in England. NHS.netConnect is approved for exchanging patient data and other sensitive information with NHS.net Connect and other accredited email services.

For more information and to find out how you can switch visit Joining NHS.net Connect – NHS.net Connect Support

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