A Predictive Factor of the Quality of Microarray Comparative Genomic Hybridization Analysis for Formalin-fixed Paraffin-embedded Archival Tissue.

Author(s): Nakao K, Oikawa M, Arai J, Mussazhanova Z, Kondo H, Shichijo K, Nakashima M, Hayashi T, Yoshiura K, Hatachi T, Nagayasu T

Publication: Diagn Mol Pathol, 2013, Vol. 22, Page 174-80

PubMed ID: 23846445 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 formalin fixation, storage duration and WGA on DNA yield and DNA quality and the effects of WGA on aCGH profiles in FFPE breast, lung and thyroid tumors. Regions with >70% tumor tissue were macrodissected from 10-20 10 uM sections and deparaffinized in xylene. Following digestion with proteinase K, DNA was extracted using QIAamp DNA mini kit.

   Summary of Findings:

   Lower A at 260 to 230, less dsDNA and less labeling were observed with DNA extracted from FFPE specimens than the frozen counterparts, but the A260/A280 ratio was similar in frozen and FFPE specimens. For the two breast tumors with both frozen and FFPE specimens available, the aCGH profiles were similar between FFPE and frozen specimens. Of the 11 specimens showing HER-2 amplification by FISH, 8 showed amplification by aCGH using FFPE specimens, and the sensitivity, specificity and accuracy of aCGH for HER-2 status was 81.8%, 94.1%, and 89.3%, respectively. The DLRSpread was modestly correlated with the storage time of the FFPE specimen (r=0.551, p<0.0001) and negatively correlated with dSDNA ratio and degree of labeling (r=-0.796 and r=-0.481, respectively; p<0.001). Use of WGA did not improve aCGH results for FFPE specimens. The dsDNA yield, as determined by fluoremetry, was an indicator of aCGH performance.

   Biospecimens

   • Tissue - Breast
   • Tissue - Thyroid Gland
   • Tissue - Lung

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Carcinoma
   • Neoplastic

   Platform:

   Analyte	Technology Platform
   DNA	Array CGH
   DNA	Fluorometry
   DNA	FISH
   DNA	Spectrophotometry
   DNA	Whole genome amplification
   Morphology	H-and-E microscopy

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Storage duration	1-43 years
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Frozen
   Whole genome amplification Specific	Nucleic acid amplification	Amplified Unamplified
   FISH Specific	Targeted nucleic acid	HER-2
   Array CGH Specific	Technology platform	FISH

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