PT  - JOURNAL ARTICLE
AU  - Suet Feung Chin
AU  - Angela Santoja
AU  - Marta Grzelak
AU  - Soomin Ahn
AU  - Stephen-John Sammut
AU  - Harry Clifford
AU  - Oscar M. Rueda
AU  - Michelle Pugh
AU  - Mae A. Goldgraben
AU  - Helen A. Bardwell
AU  - Eun Yoon Cho
AU  - Elena Provenzano
AU  - Federico Rojo
AU  - Emilio Alba
AU  - Carlos Caldas
TI  - Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers
AID  - 10.1101/231480
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 231480
4099  - http://biorxiv.org/content/early/2017/12/08/231480.short
4100  - http://biorxiv.org/content/early/2017/12/08/231480.full
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.