Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue.

Author(s): Menon R, Deng M, Boehm D, Braun M, Fend F, Biskup S, Perner S

Publication: Int J Mol Sci, 2012, Vol. 13, Page 8933-42

PubMed ID: 22942743 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 using a FFPE prostate specimen instead of a snap-frozen prostate specimen on whole exome sequencing results from a single patient. DNA was extracted from three 3 mm punches per specimen using RecoverAll for FFPE specimens and PureLink from the frozen specimen.

   Summary of Findings:

   43.9, 42.5 and 51.0 million unique reads were generated using FFPE normal, FFPE tumor and frozen tumor specimens, respectively, with an average of 86 times coverage. 7707 SNVs were found in frozen tumor specimens and 6853 and 5445 SNVs were found in FFPE normal and FFPE tumor specimens, respectively. 84.9% of the identified SNVs in FFPE tumor were also found in the frozen tumor specimen. Excluding SNVs identified in the normal specimen, the FFPE tumor specimen had 864 SNVs and the frozen tumor had 2151 SNVs. The false positive rate of detecting SNVs using FFPE tissue was approximately 10% which mostly reflected an increase in transversion mutations in FFPE tissue. Small differences in copy number between FFPE and frozen tumors specimens were identified.

   Biospecimens

   • Tissue - Prostate

   Preservative Types

   • Formalin
   • Frozen

   Diagnoses:

   • Neoplastic - Normal Adjacent
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   DNA	DNA sequencing

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) Snap frozen

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