High quality and quantity Genome-wide germline genotypes from FFPE normal tissue.

Author(s): Cannon-Albright LA, Cooper KG, Georgelas A, Bernard PS

Publication: BMC Res Notes, 2011, Vol. 4, Page 159

PubMed ID: 21615924 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 long term storage of paraffin blocks on DNA yield, purity, and integrity, and on genome-wide SNP analysis. For 2 specimens, SNP analysis using DNA from formalin-fixed prostate tissue was compared to SNP analysis using DNA from whole blood obtained from the same patient.

   Summary of Findings:

   Only 4 of 5 archived prostate cancer specimens had enough normal adjacent tissue for DNA extraction. The specimen that did not contain sufficient tissue had been stored for the longest time (41 y). DNA yield and purity, as assessed by spectrophotometry, were good from the 4 archived specimens, but the authors state that DNA integrity was questionable. Genotyping call rates for the formlain-fixed archived specimens ranged from 0.873 to 0.989. Genotyping calls were concordant between DNA from blood and from the archived tissue specimens 99.98% and 99.3% of the time for the two cases analyzed.

   Biospecimens

   • Tissue - Prostate
   • Bodily Fluid - Blood

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Normal Adjacent

   Platform:

   Analyte	Technology Platform
   DNA	Spectrophotometry
   DNA	Electrophoresis
   DNA	SNP assay

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Storage duration	18 y 20 y 25 y 26 y 41 y
   Biospecimen Acquisition	Biospecimen location	Prostate Blood

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