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N Biotechnol. 2020 Jan 25;54:52-61. doi: 10.1016/j.nbt.2019.07.005. Epub 2019 Aug 6.

Standardization of the preanalytical phase of DNA extraction from fixed tissue for next-generation sequencing analyses.

Author information

1
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: olga.kofanova@ibbl.lu.
2
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: camille.bellora@ibbl.lu.
3
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: sonia.frasquilho@ibbl.lu.
4
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: laurent.antunes@lns.etat.lu.
5
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: gael.hamot@ibbl.lu.
6
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: conny.mathay@asta.etat.lu.
7
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: kathleen.mommaerts@ibbl.lu.
8
LIH (Luxembourg Institute for Health), 1 A-B Rue Thomas Edison, 1445 Strassen, Luxembourg. Electronic address: arnaud.muller@lih.lu.
9
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: brian.dewitt@ibbl.lu.
10
IBBL (Integrated BioBank of Luxembourg), 1 rue Louis Rech, L-3555 Dudelange, Luxembourg. Electronic address: fay.betsou@ibbl.lu.

Abstract

Next-generation sequencing (NGS) analyses on DNA derived from archived Formalin-Fixed Paraffin-Embedded (FFPE) clinical material can provide a powerful tool in oncology research and clinical diagnostics. Although several studies have established that NGS can be performed using DNA from FFPE tissue, the accuracy and reproducibility of such analyses, as well as their robustness to the biomolecular quality of the samples used, remains a matter of debate. Excellent reviews have recently been published, providing evidence-based best practices for FFPE DNA extraction. Alternative fixatives exist, although their implementation in clinical practice is difficult. In this article, we present (i) a review of fixed tissue DNA preanalytics with a special focus on DNA extraction and fixed tissue sample qualification and (ii) results from comparisons between different methods of DNA extraction from tissue samples that have been fixed or stabilized by different methods, in terms of NGS metrics and different DNA quality metrics.

KEYWORDS:

DNA extraction; FFPE; Next-Generation sequencing; Preanalytics; Quality control; Tissue

PMID:
31398512
DOI:
10.1016/j.nbt.2019.07.005
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