2026-04-29T04:10:25Zhttps://repisalud.isciii.es/rest/oai/requestoai:repisalud.isciii.es:20.500.12105/175842024-09-21T21:28:19Zcom_20.500.12105_15322com_20.500.12105_2051col_20.500.12105_16927col_20.500.12105_16977
Repisalud
author
Chin, Suet-Feung
author
Santonja, Angela
author
Grzelak, Marta
author
Ahn, Soomin
author
Sammut, Stephen-John
author
Clifford, Harry
author
Rueda, Oscar M
author
Pugh, Michelle
author
Goldgraben, Mae A
author
Bardwell, Helen A
author
Cho, Eun Yoon
author
Provenzano, Elena
author
Rojo, Federico
author
Alba, Emilio
author
Caldas, Carlos
2024-02-08T14:41:10Z
2024-02-08T14:41:10Z
2018-03-31
http://hdl.handle.net/10668/12297
http://hdl.handle.net/20.500.12105/17584
29608913
10.1016/j.yexmp.2018.03.006
1096-0945
Experimental and molecular pathology
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.
eng
Copy number (CN) and breast cancer
Formalin-fixed paraffin-embedded (FFPE)
Shallow whole genome sequencing (sWGS)
Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.
research article