Changes in the METABRIC database

[Stefano Confalonieri]

Good evening
Our group has worked on the METABRIC database for several years, since
its release.
In 2019 the database was incorporated in the cbioportal, but with less
samples , 1904 on Illumina v3 microarray, and less genes then the
original DB 35.655 probeset vs 24.368 gene/transcript.
Now in November 2022, but I noticed it only three days ago, the METABRIC
DB changed again, and now there are the original 1980 samples, and even
less genes (20.602 instead of 24.368 of the 1904 samples dataset).
I also noticed that several genes changed their level of expression and
that also the follow up for some patient has been updated.

Since I worked for three years on the 1904 samples dataset, for several
project in my lab, I would like to know, if possible, why and how you
changed the dataset.
And most important, if I should reanalyze all my data on this new
dataset (1980 samples, 20.602 genes) because it is the final and stable
version?

Thank you very much for any info you can give to me.

All the best
Stefano


--
Dr. Stefano Confalonieri
Senior Staff Scientist
Department of Experimental Oncology
European Institute of Oncology
Via Adamello 16, 20139 Milano, Italy
Phone: +39 02 94372755
Mail: stefano.co...@ieo.it

[5x1000]<http://www.ieo.it/it/SCIENCE-IN-SOCIETY/Le-nostre-iniziative/5-per-mille/>

[Tali Mazor]

Hi Stefano - Thanks for reaching out about this. We are looking into this and will get back to you.

-Tali

--
You received this message because you are subscribed to the Google Groups "cBioPortal for Cancer Genomics Discussion Group" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cbioportal+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/13f28a1d-3fa1-99af-1e5b-648ce3a13a74%40ieo.it.

[Stefano Confalonieri]

Hi Tali, good evening
any news?

thank you very much

Stefano

-- 
Dr. Stefano Confalonieri
Department of Experimental Oncology
European Institute of Oncology
Via Adamello 16, 20139 Milano, Italy
Phone: +39 02 94372755
Mail: stefano.co...@ieo.it

[Ritika Kundra]

Hello Dr. Stefano,

The reason for the data update was due to new samples and profiles sent to us by the author of the study itself:
https://groups.google.com/g/cbioportal/c/ffy4mqGIh8E/m/Fslt9TOrAQAJ

We can contact them and check if your old analysis can still be used. From the portal side, we can add a log of changes to the study folder (https://github.com/cBioPortal/datahub/tree/master/public/brca_metabric), so in case you do use the older dataset, you can refer the that dated freeze.

Thanks,

Ritika

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/e4fda243-f358-b31e-716f-32f6bee10d85%40ieo.it.