Random DNA fragmentation allows detection of single-copy, single-exon alterations of copy number by oligonucleotide array CGH in clinical FFPE samples.
Author(s): Hostetter G, Kim SY, Savage S, Gooden GC, Barrett M, Zhang J, Alla L, Watanabe A, Einspahr J, Prasad A, Nickoloff BJ, Carpten J, Trent J, Alberts D, Bittner M
Publication: Nucleic Acids Res, 2010, Vol. 38, Page e9
PubMed ID: 19875416 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of using FFPE instead of frozen colorectal tumor specimens on detection of copy number changes by array hybridization. The reliability of determining copy number changes using FFPE specimens was investigated using skin squamous cell carcinoma specimens. Three to ten 12 um sections were deparaffinized with xylene, digested with proteinase K for 72 h at 58 degrees C, and DNA was extracted with phenol-chloroform extraction with phase-lock gel centrifugation tubes followed by chromatography with DNeasy Tissue Kit. FFPE blocks were stored up to 10 years prior to DNA extraction.
Summary of Findings:
DNA fragments extracted from FFPE specimens included high molecular weight DNA. Concordance between copy number changes detected using FFPE and frozen colorectal specimens was generally high, but some differences were found, and the FFPE specimens had a higher signal to noise ratio than the frozen specimens. Using FFPE skin squamous cell carcinoma specimens, the authors identified a novel deletion and showed that comparative genomic hybridization (CGH) is highly reliable using FFPE specimens.
Biospecimens
Preservative Types
- Formalin
- Frozen
Diagnoses:
- Neoplastic - Carcinoma
Platform:
Analyte Technology Platform DNA Array CGH Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Preservation Type of fixation/preservation Formalin (buffered)
Frozen