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Gene expression profiling of formalin‐fixed, paraffin‐embedded familial breast tumours using the whole genome‐DASL assay
Author(s) -
Waddell Nic,
Cocciardi Sibylle,
Johnson Julie,
Healey Sue,
Marsh Anna,
Riley Joan,
Silva Leonard da,
Vargas Ana Cristina,
Reid Lynne,
Simpson Peter T,
Lakhani Sunil R,
ChenevixTrench Georgia
Publication year - 2010
Publication title -
the journal of pathology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.964
H-Index - 184
eISSN - 1096-9896
pISSN - 0022-3417
DOI - 10.1002/path.2728
Subject(s) - transcriptome , genome , rna , gene expression profiling , pathology , breast tumours , biology , breast cancer , microbiology and biotechnology , cancer research , gene , gene expression , medicine , cancer , genetics
Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin‐fixed, paraffin‐embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumour banks. Once samples are fixed in formalin, the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study, we have evaluated the ability of the whole genome DASL (c D NA‐mediated A nnealing, S election, extension, and L igation) assay from Illumina to perform transcriptomic analysis of archived breast tumour tissue in formalin‐fixed, paraffin‐embedded (FFPE) blocks. We profiled 76 familial breast tumours from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non‐ BRCA1/2 families. We found that replicate samples correlated well with each other ( r 2 = 0.9–0.98). In 12/15 cases, the matched formalin‐fixed and frozen samples predicted the same tumour molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterization of many diseases. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.