Oligonucleotide array outperforms SNP array on formalin-fixed paraffin-embedded clinical samples.

Author(s): Nasri S, Anjomshoaa A, Song S, Guilford P, McNoe L, Black M, Phillips V, Reeve A, Humar B

Publication: Cancer Genet Cytogenet, 2010, Vol. 198, Page 1-6

PubMed ID: 20303007 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of using DNA from FFPE instead of snap-frozen colorectal specimens on DNA integrity and copy number determination using two platforms. FFPE specimens were stored for 5 years at room temperature while frozen specimens were stored at -80 degrees C for 5 years. DNA was extracted from deparaffinized FFPE specimens and snap frozen sections using QIAamp.

   Summary of Findings:

   While high molecular weight DNA was extracted from snap-frozen specimens which allowed for amplification of Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) fragments of up to 700 bp, the FFPE specimens yielded highly degraded DNA with a maximum GAPDH amplicon size of 300-400 bp. Using the SNP array, there was 53.8-87.3% agreement in copy number between FFPE and matched frozen specimens, but a more than 98% agreement was observed using the Agilent 4x44 K oligonucleotide arrays. The discrepancies using the SNP arrays were larger for the copy number variation (CNV) probes than the SNP probes, but were still significant when CNV probes were excluded from analysis. The authors state the agreement in copy number determination was independent of DNA fragment size.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Normal

   Platform:

   Analyte	Technology Platform
   DNA	DNA microarray
   DNA	CGH
   DNA	Electrophoresis
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen
   DNA microarray Specific	Type of array	Affymetrix (SNP) 6.0 Agilent 4x44 K oligonucleotide arrays
   PCR Specific	Length of gene fragment	100 bp 200 bp 300 bp 400 bp 500 bp 600 bp 700 bp
   PCR Specific	Targeted nucleic acid	GAPDH

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