Tissue preparation for gene expression profiling of colorectal carcinoma: three alternatives to laser microdissection with preamplification.

Author(s): Croner RS, Guenther K, Foertsch T, Siebenhaar R, Brueckl WM, Stremmel C, Hlubek F, Hohenberger W, Reingruber B

Publication: J Lab Clin Med, 2004, Vol. 143, Page 344-51

PubMed ID: 15192650 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to evaluate three methods of colorectal tumor cell enrichment, as alternatives to laser-capture microdissection, with regard to RNA yield, quality, expression, and cost and time requirements. Of note, analysis was conducted using case-matched specimens from a single case.

   Summary of Findings:

   Cryotomy after manual microdissection and tumor cell isolation using Ber-EP4 antibodies and Dynabeads generated an equivalent amount of RNA, although the latter method required more time (60 versus 90 min) and money ($41 versus $82). While microscopically assisted manual dissection generated a third of the RNA generated by the other methods investigated, the cost was the lowest reported ($23) while it was the most time intensive (120 min). While correlations among microarrays for cell enrichment methods were variable (91-97%), detectable expression for 4 of the 5 genes examined were observed for all enrichment methods; APC expression alone was noted as marginal in Dynabead mediated isolation.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   DNA microarray Specific	Targeted nucleic acid	K-ras APC Transforming growth factor-beta p53 Smad 2
   Biospecimen Aliquots and Components	Cell capture method	Cryotomy Dynabead cell isolation Microscopic manual dissection

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