Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay.
Formalin-fixed paraffin-embedded (FFPE) breast tumor tissues are readily available and represent a largely untapped, vast resource for molecular profiling of clinical samples with long-term follow-up data. We have optimized the conditions and parameters that result in the preparation of total RNA that is of the necessary quality for use in the DASL (cDNA-mediated annealing, selection, extension, and ligation) assay in which expression of 502 genes are analyzed simultaneously using as little as 100 ng of input RNA.
Abramovitz
Mark
M
VM Institute of Research, Montreal, Quebec, Canada.
Ordanic-Kodani
Maja
M
Wang
Yuefang
Y
Li
Zhenhong
Z
Catzavelos
Charles
C
Bouzyk
Mark
M
Sledge
George W
GW
Moreno
Carlos S
CS
Leyland-Jones
Brian
B
D001943:Breast Neoplasms / Q000235:genetics* / Q000378:metabolism*; D005557:Formaldehyde; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D009363:Neoplasm Proteins / Q000032:analysis* / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D016612:Paraffin Embedding; D012313:RNA / Q000235:genetics* / Q000302:isolation & purification*; D013048:Specimen Handling / Q000379:methods
D009363:Neoplasm Proteins; D005557:Formaldehyde; D012313:RNA