Evaluation of extraction methods from paraffin wax embedded tissues for PCR amplification of human and viral DNA.

Author(s): Chan PK, Chan DP, To KF, Yu MY, Cheung JL, Cheng AF

Publication: J Clin Pathol, 2001, Vol. 54, Page 401-3

PubMed ID: 11328843 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare the PCR success rate of three DNA extraction methods for different amplicon lengths of beta-globin and the human papillomavirus.

   Summary of Findings:

   Successful PCR analysis of FFPE specimens was dependent on the gene analyzed, amplicon length, and the method of DNA extraction. In general, shorter amplicons (15-355 bp) resulted in higher PCR success rates than longer amplicons (450-509 bp). For beta-globin analysis, microwave heating in a digestion buffer generated the highest PCR success rate, while Qiagen spin columns were the preferred DNA extraction method for HPV analysis. The authors note that DNA extraction by the Qiagen spin column method yielded the highest predictive value of the beta-globin housekeeping gene, with 90% of beta-globin positive samples generating an appropriate HPV product.

   Biospecimens

   • Tissue - Cervix

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   DNA	PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Analyte Extraction and Purification	Analyte isolation method	Phenol/ chloroform Microwave heating Qiagen spin column
   PCR Specific	Length of gene fragment	150 bp 355 bp 450 bp
   PCR Specific	Targeted nucleic acid	Beta-globin Human papillomavirus

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