Optimization of RNA extraction from FFPE tissues for expression profiling in the DASL assay

Biotechniques. 2008 Mar;44(3):417-23. doi: 10.2144/000112703.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Breast Neoplasms / genetics*
  • Breast Neoplasms / metabolism*
  • Formaldehyde
  • Gene Expression Profiling / methods*
  • Humans
  • Neoplasm Proteins / analysis*
  • Neoplasm Proteins / genetics
  • Oligonucleotide Array Sequence Analysis / methods
  • Paraffin Embedding*
  • RNA / genetics*
  • RNA / isolation & purification*
  • Specimen Handling / methods


  • Neoplasm Proteins
  • Formaldehyde
  • RNA