PMID- 19617290
OWN - NLM
STAT- MEDLINE
DCOM- 20090916
LR  - 20191210
IS  - 1530-8561 (Electronic)
IS  - 0009-9147 (Linking)
VI  - 55
IP  - 9
DP  - 2009 Sep
TI  - RNA extraction from archival formalin-fixed paraffin-embedded tissue: a 
      comparison of manual, semiautomated, and fully automated purification methods.
PG  - 1719-27
LID - 10.1373/clinchem.2008.122572 [doi]
AB  - BACKGROUND: Formalin-fixed paraffin-embedded (FFPE) tumor material represents a 
      valuable resource for the analysis of RNA-based biomarkers, both in research 
      laboratories and in routine clinical testing. A robust and automated 
      RNA-extraction method with a high sample throughput is required. METHODS: We 
      evaluated extraction performance for 4 silica-based RNA-extraction protocols: (a) 
      a fully automated, bead-based RNA-isolation procedure; (b) its manual 
      counterpart; (c) a semiautomated bead-based extraction system; and (d) a manual 
      column-based extraction kit. RNA from 360 sections (90 sections per extraction 
      method) of 30 FFPE tumor blocks up to 20 years of age was purified and analyzed 
      by quantitative reverse-transcription PCR for ESR1 (estrogen receptor 1), PGR 
      (progesterone receptor), ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene 
      homolog 2, neuro/glioblastoma derived oncogene homolog (avian)], and RPL37A 
      (ribosomal protein L37a). RESULTS: The semiautomated protocol gave the best 
      yield. The 3 bead-based methods showed good across-method correlations in both 
      yield and relative mRNA amounts (r = 0.86-0.95 and 0.98, respectively). In 
      contrast, correlations between any of the bead-based methods and the manual 
      column-based method were worse (r = 0.77-0.95 and 0.96, respectively). The fully 
      automated method showed the lowest variation from section to section (root mean 
      square error, 0.32-0.35 Cq, where Cq is the quantification cycle) and required 
      the least hands-on time (1 h). CONCLUSIONS: The fully automated RNA-purification 
      method showed the best reproducibility in gene expression analyses of neighboring 
      sections of tissue blocks between 3 and 20 years of age and required the least 
      overall and hands-on times. This method appears well suited for high-throughput 
      RNA analyses in both routine clinical testing and translational research studies 
      with archived FFPE material.
FAU - Bohmann, Kerstin
AU  - Bohmann K
AD  - Siemens Healthcare Diagnostics Products, Molecular Research Germany, Cologne, 
      Germany.
FAU - Hennig, Guido
AU  - Hennig G
FAU - Rogel, Uwe
AU  - Rogel U
FAU - Poremba, Christopher
AU  - Poremba C
FAU - Mueller, Berit Maria
AU  - Mueller BM
FAU - Fritz, Peter
AU  - Fritz P
FAU - Stoerkel, Stephan
AU  - Stoerkel S
FAU - Schaefer, Karl-L
AU  - Schaefer KL
LA  - eng
PT  - Comparative Study
PT  - Evaluation Study
PT  - Journal Article
DEP - 20090717
PL  - England
TA  - Clin Chem
JT  - Clinical chemistry
JID - 9421549
RN  - 0 (Biomarkers, Tumor)
RN  - 1HG84L3525 (Formaldehyde)
RN  - 63231-63-0 (RNA)
SB  - IM
MH  - *Automation
MH  - Biomarkers, Tumor/analysis/genetics
MH  - Breast Neoplasms/chemistry/genetics
MH  - Formaldehyde
MH  - Gene Expression
MH  - *Genetic Techniques
MH  - Humans
MH  - Paraffin Embedding
MH  - RNA/*isolation & purification
MH  - Reproducibility of Results
MH  - Time Factors
MH  - Tissue Fixation
EDAT- 2009/07/21 09:00
MHDA- 2009/09/17 06:00
CRDT- 2009/07/21 09:00
PHST- 2009/07/21 09:00 [entrez]
PHST- 2009/07/21 09:00 [pubmed]
PHST- 2009/09/17 06:00 [medline]
AID - clinchem.2008.122572 [pii]
AID - 10.1373/clinchem.2008.122572 [doi]
PST - ppublish
SO  - Clin Chem. 2009 Sep;55(9):1719-27. doi: 10.1373/clinchem.2008.122572. Epub 2009 
      Jul 17.