Applicability of a System for fully automated nucleic acid extraction from formalin-fixed paraffin-embedded sections for routine KRAS mutation testing.
Author(s): Lehmann A, Schewe C, Hennig G, Denkert C, Weichert W, Budczies J, Dietel M
Publication: Diagn Mol Pathol, 2012, Vol. 21, Page 114-9
PubMed ID: 22555094 PubMed Review Paper? No
Purpose of Paper
Conclusion of Paper
Studies
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Study Purpose
The purpose of this study was to determine the effects of automated versus manual DNA and RNA extraction from 5 different FFPE tissues on yield. Nucleic acids were extracted from 5 um sections of FFPE blocks that had been stored between 2 months and 6 years.
Summary of Findings:
With the exception of 1 liver section, PAEP DNA and RPL37A RNA were amplified from all 68 sections from each tissue extracted using the automated method. Amplification success using the manual method was not investigated. 44 of 45 specimens extracted using both methods allowed for KRAS sequencing, and the sequences were consistent between extraction methods for all but 1 specimen which showed an additional peak for the sample extracted by the automated method. The authors report the automated method of DNA and RNA extracted was almost twice as fast as the manual method.
Biospecimens
Preservative Types
- Formalin
Diagnoses:
- Neoplastic - Carcinoma
- Not specified
Platform:
Analyte Technology Platform DNA Real-time qPCR DNA DNA sequencing RNA Real-time qRT-PCR Pre-analytical Factors:
Classification Pre-analytical Factor Value(s) Biospecimen Acquisition Biospecimen location Cervix
Colon
Liver
Lymph node
Lung
Analyte Extraction and Purification Analyte isolation method Manual with Qia VAC
Automated with VERSANT
Real-time qPCR Specific Targeted nucleic acid PAEP
Real-time qRT-PCR Specific Targeted nucleic acid RPL37A
DNA sequencing Specific Targeted nucleic acid KRAS codon 12-13