Prospective Breast Cancer Biobanking Project

A. Early detection of systemic relapses in breast cancer.

WP 1. Analysis of primary tumor.

Analysis of primary tumor and metastases (Pathology group). In this work package both DNA and RNA from the primary tumors of 125 high-risk (Luminal-B) patients will be analyzed by next-generation sequencing (NGS). Furthermore, the investigators will also analyze DNA and RNA from the available metastatic lesions (currently material available for 3/8) that have appeared, and will appear during the study period.

MiRNA and mRNA will be profiled using PureLink™ miRNA Isolation Kit (Invitrogen), Dynabeads mRNA direct micro kit (Ambion),) and Ion total RNA-seq kit V2 (Life Technologies) on our Ion Proton NGS instrument. Bioinformatic analyses of paired mRNA and microRNA expression profiles will be used to reveal differentially expressed microRNAs between patients with and without recurrences under treatment. These data will be linked to our previous studies and used to identify target candidates for microRNA analysis in exosomes and TEPs.

In addition, NGS will also be performed on DNA from the primary tumors and metastases to verify DNA mutations especially in ER and other known oncogenes, including those examined in WP3. The DNA sequencing will be performed using the Oncomine Comprehensive Assay. This is an amplicon based approach analyzing hotspot SNVs, indels, and CNVs. These analyses will provide us with a biological understanding and background knowledge for each of the individual tumor, and these datasets can also be compared to the recently published data.