作者
Pauline Robbe, Niko Popitsch, Samantha JL Knight, Pavlos Antoniou, Jennifer Becq, Miao He, Alexander Kanapin, Anastasia Samsonova, Dimitrios V Vavoulis, Mark T Ross, Zoya Kingsbury, Maite Cabes, Sara DC Ramos, Suzanne Page, Helene Dreau, Kate Ridout, Louise J Jones, Alice Tuff-Lacey, Shirley Henderson, Joanne Mason, Francesca M Buffa, Clare Verrill, David Maldonado-Perez, Ioannis Roxanis, Elena Collantes, Lisa Browning, Sunanda Dhar, Stephen Damato, Susan Davies, Mark Caulfield, David R Bentley, Jenny C Taylor, Clare Turnbull, Anna Schuh
发表日期
2018/10
期刊
Genetics in Medicine
卷号
20
期号
10
页码范围
1196-1205
出版商
Nature Publishing Group
简介
Purpose
Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS.
Methods
We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples.
Results
We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA …
学术搜索中的文章
P Robbe, N Popitsch, SJL Knight, P Antoniou, J Becq… - Genetics in Medicine, 2018