Amplification of whole tumor genomes and gene-by-gene mapping of genomic aberrations from limited sources of fresh-frozen and paraffin-embedded DNA.

Author(s): Bredel M, Bredel C, Juric D, Kim Y, Vogel H, Harsh GR, Recht LD, Pollack JR, Sikic BI

Publication: J Mol Diagn, 2005, Vol. 7, Page 171-82

PubMed ID: 15858140 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare whole genome amplification of DNA from fresh-frozen and FFPE glioblastomas by microarray analysis.

   Summary of Findings:

   Amplification of less than one nanogram of genomic DNA from either fresh frozen or FFPE tissue generated micrograms of amplified product. Both FFPE and fresh-frozen specimens generated similar amounts and sizes of amplified product. Amplification resulted in over and underrepresentation of genomic regions in both specimen types, but the changes were more notable in FFPE than frozen specimens. The regional amplification efficiency was highly reproducible and was dependent on GC content. Because of the consistency of the regional variance in amplification efficiency, the effect of amplification could be corrected for by using an amplified reference DNA from blood specimens.

   Biospecimens

   • Tissue - Brain

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Other

   Platform:

   Analyte	Technology Platform
   DNA	Spectrophotometry
   DNA	Electrophoresis
   DNA	DNA microarray

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Frozen Formalin (buffered)
   Storage	Storage duration	2-3 years
   Storage	Storage temperature	Room temperature -80 degrees C
   Preaquisition	Diagnosis/ patient condition	Glioblastoma

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