Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting

African Journal of Laboratory Medicine

 
 
Field Value
 
Title Practical tips to using formalin-fixed paraffin-embedded tissue archives for molecular diagnostics in a South African setting
 
Creator van Deventer, Barbara S. du Toit-Prinsloo, Lorraine van Niekerk, Chantal
 
Subject Health Sciences, Pathology; Chemical Pathology; Forensic Medicine Autopsy; deoxyribonucleic acid; formalin-fixed paraffin-embedded tissue; formalin-fixed paraffin-embedded tissue archive; high-resolution melt analysis; molecular diagnostics; polymerase chain reaction; post-mortem genetic testing; sequencing
Description Background: Formalin-fixed paraffin-embedded (FFPE) tissue archives in hospitals, biobanks, and others offer a vast collection of extensive, readily available specimens for molecular testing. Unfortunately, the use of tissue samples for molecular diagnostic applications is challenging; thus, the forensic pathology FFPE tissue archives in Africa have been a largely unexploited genetic resource, with the usability of DNA obtainable from these samples being unknown.Intervention: The study, conducted from January 2015 to August 2016, determined the usefulness of FFPE tissue as a reliable source of genetic material for successful post-mortem molecular applications and diagnostics. Formalin-fixed paraffin-embedded tissue samples were collected and archived from autopsies conducted over 13 years in the forensic medicine department of the University of Pretoria (Pretoria, South Africa). Deoxyribonucleic acid from FFPE tissue samples and control blood samples was amplified by high-resolution melt real-time polymerase chain reaction before sequencing. The procurement parameters and fixation times were compared with the quantity and quality of the extracted DNA and the efficiency of its subsequent molecular applications.Lessons learnt: This study has shown that FFPE samples are still usable in molecular forensics, despite inadequate sample preparation, and offer immense value to forensic molecular diagnostics.Recommendations: FFPE samples fixed in formalin for more than 24 h should still be used in molecular diagnostics or research, as long as the primer design targets amplicons not exceeding 300 base pairs. 
 
Publisher AOSIS
 
Contributor Genomics Research Institute, University of Pretoria for funding this project. National Research Foundation for funding part of this project. The authors would also like to thank Mr. Tobie de Witt for all FFPE tissue sample preparation.
Date 2022-06-23
 
Type info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion — Laboratory experiment
Format text/html application/epub+zip text/xml application/vnd.openxmlformats-officedocument.spreadsheetml.sheet application/vnd.openxmlformats-officedocument.spreadsheetml.sheet application/vnd.openxmlformats-officedocument.spreadsheetml.sheet application/vnd.openxmlformats-officedocument.spreadsheetml.sheet application/pdf
Identifier 10.4102/ajlm.v11i1.1587
 
Source African Journal of Laboratory Medicine; Vol 11, No 1 (2022); 6 pages 2225-2010 2225-2002
 
Language eng
 
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Rights Copyright (c) 2022 Barbara S. van Deventer, Lorraine du Toit-Prinsloo, Chantal van Niekerk https://creativecommons.org/licenses/by/4.0
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