Datasets containing post neoadjuvant therapy triple-negative breast cancer samples ?

Question

[oliver.hickman]

Does anyone know of studies or datasets that feature samples from patients following neoadjuvant therapy in breast cancer?

Specifically I am looking for profiles of tumours post-treatment that have relapsed. Most interested in triple negative samples.

Thanks

Answer 1

[Kevin Blighe]

I have data from the neoadjuvant setting in breast cancer, but most ER-positive cases, and not yet published. For triple negative breast cancer (TNBC), I found a few datasets, but most microarray-based gene expression:

• E-GEOD-43816 - Response to Neoadjuvant Chemotherapy in Triple Negative Breast tumors
• E-GEOD-45898 - Gene Expression analysis of therapeutical response in Triple Negative Breast tumors
• E-GEOD-43502 - Identification of Prognosis-Relevant Subgroups in Patients with Chemoresistant Triple Negative Breast Cancer
• E-GEOD-18864 - Tumor expression data from neoadjuvant trial of cisplatin monotherapy in triple negative breast cancer patients

There appears to also be TNBC-specific studies under the ICGC, too. If you take a look at the European Genome-phenome Archive (EGA), you'll find them, like, for example, this one: https://www.ebi.ac.uk/ega/studies/EGAS00001000092

There is also some TNBC samples in the TCGA data. You can infer TNBC status by following my methodology, here: How to download triple negative breast cancer RNA-seq fpkm data from GDC.

Kevin