Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample preparation.
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.
Ton
C C
CC
Divisions of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA.
Vartanian
N
N
Chai
X
X
Lin
M G
MG
Yuan
X
X
Malone
K E
KE
Li
C I
CI
Dawson
A
A
Sather
C
C
Delrow
J
J
Hsu
L
L
Porter
P L
PL
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
D047628:Estrogen Receptor alpha; D012334:RNA, Neoplasm; D005557:Formaldehyde