Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA.

Author(s): Little SE, Vuononvirta R, Reis-Filho JS, Natrajan R, Iravani M, Fenwick K, Mackay A, Ashworth A, Pritchard-Jones K, Jones C

Publication: Genomics, 2006, Vol. 87, Page 298

PubMed ID: 16271290 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   Comparative analysis of WGA by DOP and GenomePlex using FFPE and frozen specimens.

   Summary of Findings:

   WGA using fresh tissue, compared to FFPE specimens, produced more reliable results with a greater amplification efficiency for both methods analyzed, although GenomePlex yielded more product that DOP. For FFPE specimens, GenomePlex amplification resulted in shorter products (800 bp vs 1 kb) and reduced amplification efficiency compared to DOP. Further, in FFPE specimens, DOP amplification was more consistent across samples compared to GenomePlex (85 vs 58%).

   Biospecimens

   • Tissue - Kidney

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Other

   Platform:

   Analyte	Technology Platform
   DNA	Array CGH
   DNA	Electrophoresis
   DNA	Spectrophotometry

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
   Array CGH Specific	Nucleic acid amplification	GenomePlex DOP

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2. Study Purpose

   To compare aCGH reproducibility after WGA by GenomePlex and DOP.

   Summary of Findings:

   aCGH analyses after GenomePlex WGA were highly reproducible in both frozen and FFPE specimens, while aCGH results with DOP amplification were largely variable across and within a case for FFPE specimens.

   Biospecimens

   • Tissue - Kidney

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Other

   Platform:

   Analyte	Technology Platform
   DNA	Array CGH

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
   Array CGH Specific	Nucleic acid amplification	GenomePlex DOP

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3. Study Purpose

   To assess the degree of artifactual amplification generated by WGA using GenomePlex and DOP and detected by aCGH.

   Summary of Findings:

   Artifactual amplification was determined by assessment of chromosome location. Biased amplification of specific gene loci (chromosome 1p, 16p, and 19) were prevalent in DOP but not GenomePlex amplified FFPE samples.

   Biospecimens

   • Tissue - Kidney

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Other

   Platform:

   Analyte	Technology Platform
   DNA	Array CGH

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   null Specific	Nucleic acid amplification	Genomeplex DOP

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4. Study Purpose

   To determine whether the concentration of template DNA impacts GenomPlex amplification efficiency of FFPE specimens.

   Summary of Findings:

   GenomePlex amplification efficiency was not affected by alterations in the concentration of DNA template.

   Biospecimens

   • Tissue - Kidney

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Other

   Platform:

   Analyte	Technology Platform
   DNA	Array CGH

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Array CGH Specific	Template/input amount	5 ng 10 ng 50 ng

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