RT Journal Article
SR Electronic
T1 Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 231480
DO 10.1101/231480
A1 Suet Feung Chin
A1 Angela Santoja
A1 Marta Grzelak
A1 Soomin Ahn
A1 Stephen-John Sammut
A1 Harry Clifford
A1 Oscar M. Rueda
A1 Michelle Pugh
A1 Mae A. Goldgraben
A1 Helen A. Bardwell
A1 Eun Yoon Cho
A1 Elena Provenzano
A1 Federico Rojo
A1 Emilio Alba
A1 Carlos Caldas
YR 2017
UL http://biorxiv.org/content/early/2017/12/08/231480.abstract
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 3.8ng 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.