RT Journal Article
T1 Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.
A1 Chin, Suet-Feung
A1 Santonja, Angela
A1 Grzelak, Marta
A1 Ahn, Soomin
A1 Sammut, Stephen-John
A1 Clifford, Harry
A1 Rueda, Oscar M
A1 Pugh, Michelle
A1 Goldgraben, Mae A
A1 Bardwell, Helen A
A1 Cho, Eun Yoon
A1 Provenzano, Elena
A1 Rojo, Federico
A1 Alba, Emilio
A1 Caldas, Carlos
K1 Copy number (CN) and breast cancer
K1 Formalin-fixed paraffin-embedded (FFPE)
K1 Shallow whole genome sequencing (sWGS)
AB 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.
YR 2018
FD 2018-03-31
LK http://hdl.handle.net/10668/12297
UL http://hdl.handle.net/10668/12297
LA en
DS RISalud
RD Apr 20, 2025