NA genome assembly for some genomic mutations

[Matteo Tiberti]

Dear cBioPortal and users,

I am retrieving POLD1 mutations through the cBioPortal API and found a few mutation occurrences for which the detailed response reports ncbiBuild as NA.

Four occur in msk_impact_50k_2026_mutations and three in ucec_ccr_msk_2022_mutations. They are:

A171V chr19:50905304C>T
K648N chr19:50912430G>T
T1017R chr19:50919963C>G

The coordinates are consistent with the GRCh37/hg19 POLD1 locus.

In the official msk_impact_50k_2026 DataHub mutation file, the POLD1 rows specify NCBI_Build=GRCh37, while the API returns NA for the affected occurrences. 

In the ucec_ccr_msk_2022 mutation file, the build is blank for the affected records and appears blank throughout the POLD1 subset. 

I found these issues just working on POLD1, but I'll have to repeat the same data fetch for many other (hundreds) of genes so this is more a general problem for me.

Would it be safe to default all the entries I find as NA to having been built on GRCh37? I suspect these come before a time when hg38-defined mutations were available, but I'm not sure. Any other way around this?

Thank you in advance

_____________________________

Matteo Tiberti, PhD

Staff Scientist at the Cancer Structural Biology group
Danish Cancer Society Research Center

Strandboulevarden 49

2100, Copenhagen, Denmark

[JJ Gao]

Hi Matteo,

Thanks for reporting this to us! I did more analysis and found this issue happens to other studies too [1]. Good news is that you can default to the study reference genome version [2] (for ucec_ccr_msk_2022 it is GRCh37/hg19).

[1] https://github.com/cBioPortal/datahub/issues/2345

[2] https://www.cbioportal.org/api/studies/ucec_ccr_msk_2022

Best,

-JJ

[Matteo Tiberti]

Hi JJ,

Thank you so much for the quick response and the information! Good to know it will be fixed and that we can proceed nonetheless with the information we found in the issue.

Kind regards,

_____________________________

Matteo Tiberti, PhD

Staff Scientist at the Cancer Structural Biology group
Danish Cancer Society Research Center

Strandboulevarden 49

2100, Copenhagen, Denmark