Genotyping of DNA samples isolated from formalin-fixed paraffin-embedded tissues using preamplification.

Author(s): Baak-Pablo R, Dezentje V, Guchelaar HJ, van der Straaten T

Publication: J Mol Diagn, 2010, Vol. 12, Page 746-9

PubMed ID: 20847277 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to compare genotypes and call rates from FFPE breast carcinomas and fresh blood specimens and to determine the effect of preamplification of FFPE specimens.

   Summary of Findings:

   In non-preamplified FFPE specimens, 312.5 pg of DNA was necessary for genotype determination, but after preamplification of DNA from FFPE specimens, genotype could be established from as little as 9.8 pg of DNA. After preamplification of FFPE specimens, a call rate of 84-100% was achieved using TaqMan assays. In 8 patients, there was 100% concordance of genotype and copy number variation as determined from fresh blood and preamplified FFPE specimens. In contrast, 4 of 22 genotypes were not concordant when results from non-preamplified FFPE specimens were compared to those from fresh blood specimens.

   Biospecimens

   • Tissue - Breast
   • Bodily Fluid - Blood

   Preservative Types

   • Formalin
   • None (Fresh)

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   DNA	SNP assay

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Acquisition	Biospecimen location	Blood Breast
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) None (fresh)
   Biospecimen Acquisition	Anticoagulant	EDTA
   SNP assay Specific	Nucleic acid amplification	Preamplified FFPE specimen Not amplified FFPE specimen Not amplified fresh blood specimen

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