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)
• ISSN: 0014-4800; 1096-0945
• DOI: 10.1016/j.yexmp.2018.03.006

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 due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling.