Analysis of changes in DNA sequence copy number by comparative genomic hybridization in archival paraffin-embedded tumor samples.

Author(s): Isola J, DeVries S, Chu L, Ghazvini S, Waldman F

Publication: Am J Pathol, 1994, Vol. 145, Page 1301-8

PubMed ID: 7992835 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine if the length of formalin fixation (4-72 h) affects the quantity and quality of extracted DNA.

   Summary of Findings:

   DNA yield and quality were inversely proportional to the length of formalin fixation. The shortest fixation time examined (4 h) yielded DNA of approximately 20 kb at the greatest abundance. DNA extracted from specimens fixed for 72 h resulted in 15% of the yield obtained from specimens fixed for 4 h.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   DNA	Electrophoresis
   DNA	Fluorometry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Time in fixative	4 h 24 h 72 h

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2. Study Purpose

   The purpose of this study was to develop a modified CGH protocol that permits analysis of FFPE specimens.

   Summary of Findings:

   The authors observed optimal yield of high molecular weight DNA (10-30% efficiency) and success (80-90% of FFPE specimens) with 72 h of proteinase K digestion, use of 20 to 30 5 um paraffin sections, and fluorescein- and Texas Red-labeled probes.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   DNA	CGH

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Aliquots and Components	Aliquot size/volume	20-30, 5 um paraffin sections 1-3, 5 um paraffin sections
   Analyte Extraction and Purification	Analyte isolation method	1 mol/L sodium isothiocyanate 3 mg/ml proteinase K (unspecified duration) 0.3 mg/ml proteinase K (72 h)
   CGH Specific	Detection method	Fluorescein and Texas Red Biotin and Avidin FITC Digoxygenin and Rhodamin
   Biospecimen Preservation	Time in fixative	> 12 h

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3. Study Purpose

   The purpose of this study was to validate the use of the modified CGH protocol in autopsy and FFPE specimens, as well as to compare DNA sequence copy number changes among FFPE and case matched fresh frozen specimens.

   Summary of Findings:

   Using the modified DNA extraction and CGH detection methods, CGH analysis was successful using a single autopsy specimen as well as a 30 year old archival paraffin tissue block. Independent CGH analysis of FFPE and case matched fresh frozen specimens resulted in a high (95%) concordance rate. Differences in copy number among frozen and FFPE specimens were verified or believed to be a result of normal cell contamination in frozen specimens.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma
   • Autopsy

   Platform:

   Analyte	Technology Platform
   DNA	CGH

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen

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