title: Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation.
abstract: Archived formalin-fixed, paraffin embedded (FFPE) tissues constitute a vast, well-annotated, but underexploited resource for the molecular study of cancer progression, largely because degradation, chemical modification, and cross-linking, render FFPE RNA a suboptimal substrate for conventional analytical methods. We report here a modified protocol for RNA extraction from FFPE tissues which maximized the success rate (with 100% of samples) in the expression profiling of a set of 60 breast cancer samples on the WG-DASL platform; yielding data of sufficient quality such that in hierarchical clustering (a) 12/12 (100%) replicates correctly identified their respective counterparts, with a high self-correlation (r = 0.979), and (b) the overall sample set grouped with high specificity into ER+ (38/40; 95%) and ER- (18/20; 90%) subtypes. These results indicate that a large fraction of decade-old FFPE samples, of diverse institutional origins and processing histories, can yield RNA suitable for gene expression profiling experiments.
authors.affiliation: Divisions of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA.
authors.forename: C C
authors.initials: CC
authors.lastname: Ton
authors.forename: N
authors.initials: N
authors.lastname: Vartanian
authors.forename: X
authors.initials: X
authors.lastname: Chai
authors.forename: M G
authors.initials: MG
authors.lastname: Lin
authors.forename: X
authors.initials: X
authors.lastname: Yuan
authors.forename: K E
authors.initials: KE
authors.lastname: Malone
authors.forename: C I
authors.initials: CI
authors.lastname: Li
authors.forename: A
authors.initials: A
authors.lastname: Dawson
authors.forename: C
authors.initials: C
authors.lastname: Sather
authors.forename: J
authors.initials: J
authors.lastname: Delrow
authors.forename: L
authors.initials: L
authors.lastname: Hsu
authors.forename: P L
authors.initials: PL
authors.lastname: Porter
mesh_terms: D001940:Breast / Q000473:pathology; D001943:Breast Neoplasms / Q000378:metabolism* / Q000473:pathology*; D016000:Cluster Analysis; D015331:Cohort Studies; D047628:Estrogen Receptor alpha / Q000096:biosynthesis; D005260:Female; D005557:Formaldehyde / Q000494:pharmacology; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D007150:Immunohistochemistry / Q000379:methods; D016612:Paraffin Embedding / Q000379:methods; D012334:RNA, Neoplasm / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D047628:Estrogen Receptor alpha; D012334:RNA, Neoplasm; D005557:Formaldehyde