A Novel Approach for Reliable Microarray Analysis of Microdissected Tumor Cells From Formalin-Fixed and Paraffin-Embedded Colorectal Cancer Resection Specimens

J Mol Med (Berl). 2009 Feb;87(2):211-24. doi: 10.1007/s00109-008-0419-y. Epub 2008 Dec 6.


We present a novel approach for microarray analysis of RNA derived from microdissected cells of routinely formalin-fixed and paraffin-embedded (FFPE) cancer resection specimens. Subsequent to RNA sample preparation and hybridization to standard GeneChips (Affymetrix), RNA samples yielded 36.43 +/- 9.60% (FFPE), 49.90 +/- 4.43% (fresh-frozen), and 53.9% (cell line) present calls. Quality control parameters and Q-RT-PCR validation demonstrated reliability of results. Microarray datasets of FFPE samples were informative and comparable to those of fresh-frozen samples. A systematic measurement difference of differentially processed tissues was eliminated by a correction step for comparative unsupervised data analysis of fresh-frozen and FFPE samples. Within FFPE samples, unsupervised clustering analyses clearly distinguished between normal and malignant tissues as well as to further separate tumor samples according to histological World Health Organization (WHO) subtypes. In summary, our approach represents a major step towards integration of microarrays into retrospective studies and enables further investigation of the relevance of microarray analysis for clinico-pathological diagnostics.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Aged, 80 and over
  • Aurora Kinases
  • Cluster Analysis
  • Colon / metabolism
  • Colorectal Neoplasms / genetics*
  • Colorectal Neoplasms / metabolism
  • Colorectal Neoplasms / pathology
  • Female
  • Formaldehyde
  • Frozen Sections
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Neoplastic*
  • HCT116 Cells
  • Humans
  • Immunohistochemistry
  • Male
  • Microdissection
  • Oligonucleotide Array Sequence Analysis / methods*
  • Paraffin Embedding
  • Protein-Serine-Threonine Kinases / genetics
  • Protein-Serine-Threonine Kinases / metabolism
  • Rectum / metabolism
  • Reproducibility of Results
  • Reverse Transcriptase Polymerase Chain Reaction / methods
  • Tissue Fixation


  • Formaldehyde
  • Aurora Kinases
  • Protein-Serine-Threonine Kinases