2026-04-29T04:10:00Zhttps://repisalud.isciii.es/rest/oai/request

oai: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

00925njm 22002777a 4500 dc 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 author 2018-03-31 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. 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 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.