Comparison of the DNA Extraction Methods for Polymerase Chain Reaction Amplification from Formalin-Fixed (original) (raw)
Author(s): Sato Y, Sugie R, Tsuchiya B, Kameya T, Natori M, Mukai K
Publication: Diagn Mol Pathol, 2001, Vol. 10, Page 265
PubMed ID: 11763318PubMed Review Paper? No
Purpose of Paper
To assess the quantity and quality of DNA extracted from formalin fixed paraffin embedded tissues (FFPE), and its applicability for PCR analysis using six different extraction methods.
Conclusion of Paper
Optimal results for all analyses were obtained with a nonorganic DNA extraction method: deparaffinization by microwave irradiation, and proteinase K digestion at 48 degrees C overnight.
Study Purpose
Comparative analysis of DNA yield and size distribution using six different DNA extraction methods for FFPE tissue.
Summary of Findings:
DNA extraction methods using nonorganic solutions yielded a greater quantity of DNA , 1.5-fold greater, than more traditional phenol-chloroform methods. The lowest DNA yield was observed with microwave irradiation, protein digestion, and phenol-chloroform purification. Further, the size distribution of DNA extracted using nonorganic methods was shifted, with a greater abundance of shorter molecules than observed with organic solution extraction methods.
2. ###### Study Purpose
To assess the applicability of DNA extracted from FFPE tissue by different methods for PCR analysis of different size amplicons of the beta-globin gene.
Summary of Findings:
PCR amplification of the largest product (989 bp) was unsuccessful, with the exception of the microwave irradiation/ nonorganic DNA extraction method, while amplification levels of shorter products (110 and 268 bp) were comparable among extraction techniques. Amplification of the 536 bp product was extraction method dependent, with the microwave irradiation/ nonorganic DNA extraction method yielding the most product.
3. ###### Study Purpose
To determine the applicability of DNA extracted from FFPE tissue using microwave irradiation and nonorganic DNA isolation for the PCR-single strand confirmation polymorphism (SSCP) assay of the beta-catenin gene.
Summary of Findings:
PCR-SSCP analysis of exon 3 of the beta-catenin gene was successful in all six cases examined, with no alterations observed. Results were confirmed by direct sequencing.
Biospecimens
- [ Tissue - Stomach](/brd/analyte-browse/result?cat=location&location=Stomach&type=Cells/Tissue "Browse by analytes where the Biospecimen Location is "Stomach" and the Biospecimen Type is Tissue")
Preservative Types
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
- Neoplastic - Lymphoma
Platform:
| Analyte | Technology Platform |
|---|---|
| DNA | DNA sequencing |
| DNA | PCR |
Pre-analytical Factors:
| Classification | Pre-analytical Factor | Value(s) |
|---|---|---|
| [PCR Specific](/brd/pre-analytical-factor-browse/pcr "Browse by Pre-analytical Factors classified as "PCR"") | [Targeted nucleic acid](/brd/pre-analytical-factor-browse/result?category=PCR&type=s&exp%5Ffactor=Targeted nucleic acid "Browse "Targeted nucleic acid"") | beta-catenin |
You Recently Viewed
News and Announcements
- New Articles on the GTEx Project are Now FREELY Available!
- Just Published!
- April 24, 2024: Biobanking for Precision Medicine Seminar