Lead: USC – University of Santiago de Compostela
WP leader: Angel Carracedo
WP3 will be responsible for DNA extraction and somatic sequencing of ~10,000 tumour samples (mostly formalin-fixed paraffin-embedded), with sufficient coverage and power to deal with tumour heterogeneity. A targeted sequencing panel will be developed using information from large-scale tumour profiling studies (e.g. METABRIC and ICGC/TCGA). The main aim of the panel will be to characterise recurrent mutations and Copy Number Aberrations (CNAs) that identify aetiologically or clinically relevant subtypes. Subtypes will be defined by e.g. sets of genes, function of variants, and unsupervised hierarchical clustering.
- To evaluate online data sources for somatic mutations in breast cancer and develop a panel for sequencing.
- To perform DNA extractions and targeted sequencing of key breast cancer genes in ~10,000 tumours and paired germline DNA.
- To perform bioinformatics analyses to call somatic variants.