title: Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay.
abstract: 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 (cDNA-mediated Annealing, Selection, extension, and Ligation) 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.
authors.affiliation: The Queensland Institute of Medical Research, Brisbane, Australia.
authors.forename: Nic
authors.initials: N
authors.lastname: Waddell
authors.forename: Sibylle
authors.initials: S
authors.lastname: Cocciardi
authors.forename: Julie
authors.initials: J
authors.lastname: Johnson
authors.forename: Sue
authors.initials: S
authors.lastname: Healey
authors.forename: Anna
authors.initials: A
authors.lastname: Marsh
authors.forename: Joan
authors.initials: J
authors.lastname: Riley
authors.forename: Leonard
authors.initials: L
authors.lastname: da Silva
authors.forename: Ana Cristina
authors.initials: AC
authors.lastname: Vargas
authors.forename: Lynne
authors.initials: L
authors.lastname: Reid
authors.forename: Peter T
authors.initials: PT
authors.lastname: Simpson
authors.forename: Sunil R
authors.initials: SR
authors.lastname: Lakhani
authors.forename: Georgia
authors.initials: G
authors.lastname: Chenevix-Trench
mesh_terms: D064007:Ataxia Telangiectasia Mutated Proteins; D001943:Breast Neoplasms / Q000235:genetics*; D018797:Cell Cycle Proteins / Q000235:genetics; D015925:Cryopreservation; D004268:DNA-Binding Proteins / Q000235:genetics; D005260:Female; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods*; D019398:Genes, BRCA1; D024522:Genes, BRCA2; D016678:Genome; D006801:Humans; D009386:Neoplastic Syndromes, Hereditary / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D017346:Protein Serine-Threonine Kinases / Q000235:genetics; D012334:RNA, Neoplasm / Q000032:analysis; D015203:Reproducibility of Results; D012189:Retrospective Studies; D025521:Tumor Suppressor Proteins / Q000235:genetics
chemical_list: D018797:Cell Cycle Proteins; D004268:DNA-Binding Proteins; D012334:RNA, Neoplasm; D025521:Tumor Suppressor Proteins; D005557:Formaldehyde; C576324:ATM protein, human; D064007:Ataxia Telangiectasia Mutated Proteins; D017346:Protein Serine-Threonine Kinases