Normal breast expression data

[Denise O' Mahony]

Hi I am interested in performing an eQTL analysis based on expression data from METABRIC on breast cancer. I have found previous publications where a similar analysis was conducted for breast cancer samples (N=1,980), as well as matched normal samples (N=138) of European ancestry (e.g. Fachal et al. 2020 and Michailidou et al. 2017). How can I find the sampleIDs for the normal breast samples and their corresponding expression data?

Kind Regards, 

Denise O’ Mahony

PhD Candidate in Medical Genetics

Biostatistics Unit

Cyprus School of Molecular Medicine | The Cyprus Institute of Neurology & Genetics 

6 Iroon Avenue, 2371 Ayios Dometios, Nicosia, Cyprus | PO Box 23462, 1683 Nicosia, Cyprus
*: email: den...@cing.ac.cy | ü: www.cing.ac.cy

[Matthijs Pon]

Hi Denise,

Thanks for reaching out! The METABRIC study in cBioPortal unfortunately does not contain RNAseq data for the matched normals. Normal expression data does not get loaded into cBioPortal (please see the FAQ for more information on how normal RNAseq data is used in cBio). If the study contains normal RNAseq data, it should be provided in the publications (here).

I hope this helps! If you have any further questions, please hit reply all, so our continued conversation is captured by the cBioPortal google groups.

With kind regards, Matthijs Pon

Data Engineer cBioPortal

E matt...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

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