Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers

• Published in: Experimental and molecular pathology Vol. 104; no. 3; pp. 161 - 169
• Main Authors: Chin, Suet-Feung, Santonja, Angela, Grzelak, Marta, Ahn, Soomin, Sammut, Stephen-John, Clifford, Harry, Rueda, Oscar M., Pugh, Michelle, Goldgraben, Mae A., Bardwell, Helen A., Cho, Eun Yoon, Provenzano, Elena, Rojo, Federico, Alba, Emilio, Caldas, Carlos
• Format: Journal Article
• Language: English
• Published: Netherlands Elsevier Inc 01.06.2018; Elsevier
• Subjects: Biomarkers, Tumor - genetics; Breast Neoplasms - genetics; Breast Neoplasms - pathology; Case-Control Studies; Copy number (CN) and breast cancer; DNA - analysis; DNA - genetics; DNA Copy Number Variations; Female; Formaldehyde - chemistry; Formalin-fixed paraffin-embedded (FFPE); Gene Expression Profiling; Genomics; High-Throughput Nucleotide Sequencing - methods; Humans; Neoplasm Invasiveness; Paraffin Embedding - methods; Sequence Analysis, DNA; Shallow whole genome sequencing (sWGS); Tissue Fixation - methods; Whole Genome Sequencing - methods; Copy number (CN) and breast cancer; Shallow whole genome sequencing (sWGS); Formalin-fixed paraffin-embedded (FFPE)

Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised...