Journal of Pathology and Translational Medicine

Original Articles

Effects of Fixation and Storage of Human Tissue Samples on Nucleic Acid Preservation: Soo Kyung Nam, Joon Im, Yoonjin Kwak, Nayoung Han, Kyung Han Nam, An Na Seo, Hye Seung Lee; Korean J Pathol. 2014;48(1):36-42. Published online February 25, 2014; DOI: https://doi.org/10.4132/KoreanJPathol.2014.48.1.36

11,480 View
174 Download
38 Crossref

Background

Because of recent advances in the molecular diagnosis of cancer patients, tissue quality has become more important in daily practice.

Methods

To evaluate the effects of fixative, duration of fixation, decalcification, and storage periods on nucleic acid integrity, DNA and RNA were extracted from gastrointestinal cancer tissue. The yield and purity were analyzed, and polymerase chain reaction (PCR) for glyceraldehyde 3-phosphate dehydrogenase (GAPDH; 60 bp), β-actin (148 bp), and human growth hormone (hGH; 434 bp) and real-time reverse transcription-PCR for β-actin (97 bp) were performed.

Results

All formalin-fixed paraffin-embedded (FFPE) and methacarn-fixed paraffin-embedded (MFPE) samples tested positive for GAPDH and β-actin by PCR. hGH was successfully detected in all MFPE samples, but in only 46.7% of the FFPE samples. Prolonged formalin fixation resulted in fewer GAPDH and β-actin PCR products, and amplification of hGH was not successful. The PCR and reverse transcription-PCR results were significantly affected by the duration of decalcification. The yield, purity, and integrity of mRNA progressively decreased with increased storage periods of paraffin blocks.

Conclusions

Fixation and storage should therefore be standardized in order to improve the quality of molecular pathologic diagnosis.

Citations

Citations to this article as recorded by

A nanoscale quality control framework for assessing FFPE DNA integrity in cancer research
Zixuan Huang, Yunpei Si, Yi Zhang, Zicheng Huang, Xuehao Xiu, Yunshan Wang, YuDong Wang, Chunhai Fan, Ping Song
Nanoscale Horizons.2025;[Epub] CrossRef
InDEL instability in two different tumoral tissues and its forensic significance
İpek Gürel, Faruk Aşıcıoğlu, Gökhan Ersoy, Özlem Bülbül, Tülin Öztürk, Gönül Filoğlu
Forensic Science, Medicine and Pathology.2024; 20(4): 1241. CrossRef
Utility of bronchoscopically obtained frozen cytology pellets for next-generation sequencing
Chihiro Mimura, Rei Takamiya, Shodai Fujimoto, Takafumi Fukui, Atsuhiko Yatani, Jun Yamada, Mizuki Takayasu, Naoya Takata, Hiroki Sato, Kiyoko Fukuda, Koichi Furukawa, Daisuke Hazama, Naoko Katsurada, Masatsugu Yamamoto, Shingo Matsumoto, Koichi Goto, Mot
BMC Cancer.2024;[Epub] CrossRef
Predictive molecular pathology after prolonged fixation: A study on tissue from anatomical body donors
Anja Böckers, Leon Schurr, Michael Schön, Tatjana Scholl, Tobias M. Böckers, Konrad Steinestel, Annette Arndt
Experimental and Molecular Pathology.2024; 137: 104899. CrossRef
Tiempos y condiciones de almacenamiento de las muestras en anatomía patológica. Recomendaciones de la Sociedad Española de Anatomía Patológica parte 1: muestras destinadas al diagnóstico
Francesc Tresserra Casas, Esther Rosello Sastre, María Jesús Fernández Aceñero, Lara Zaragoza Macián, Javier Azúa Romeo, Clara Alfaro-Cervelló, Samuel Navarro Fos, Eugenia García Fernández, Jordi Temprana-Salvador, Mar Iglesias Coma, Francesc Olivares Veg
Revista Española de Patología.2024; 57(4): 235. CrossRef
RNA-Seq Analysis in Non-Small Cell Lung Cancer: What Is the Best Sample from Clinical Practice?
Lorenzo Nibid, Giovanna Sabarese, Luca Andreotti, Benedetta Canalis, Daniela Righi, Filippo Longo, Margherita Grazi, Pierfilippo Crucitti, Giuseppe Perrone
Journal of Personalized Medicine.2024; 14(8): 851. CrossRef
A Study on the Stainability and DNA Conservation of Tissue Slides according to Fixation Time and Temperature
Da-som JEONG
Korean Journal of Clinical Laboratory Science.2024; 56(3): 217. CrossRef
Selection and Evaluation of mRNA and miRNA Reference Genes for Expression Studies (qPCR) in Archived Formalin-Fixed and Paraffin-Embedded (FFPE) Colon Samples of DSS-Induced Colitis Mouse Model
Ana Unkovič, Emanuela Boštjančič, Aleš Belič, Martina Perše
Biology.2023; 12(2): 190. CrossRef
The quality of DNA isolated from autopsy formalin-fixed and formalin-fixed paraffin-embedded tissues: study of 1662 samples
Katarina Vitošević, Danijela Todorović, Živana Slović, Tatjana Varljen, Ivana Radaković, Dušan Radojević, Vanja Čanović, Miloš Todorović
Molecular Biology Reports.2023; 50(8): 6323. CrossRef
Morphometric and Molecular Analysis of Five-Spine Epidinium Morphotypes Taken from the Rumen of European Bison, Bison bonasus
Silvia Ivorová, Anna Kopčaková, Peter Pristaš, Svetlana Kišidayová
Life.2023; 13(12): 2350. CrossRef
Retrieving high-quality genomic DNA from formalin-fixed paraffin-embedded tissues for multiple molecular analyses
Ha Thi Nguyen, Vinay Bharadwaj Tatipamula, Duy Ngoc Do, Thien Chi Huynh, Mai Kim Dang
Preparative Biochemistry & Biotechnology.2022; 52(1): 48. CrossRef
Evaluation of DNA Isolation and Amplification from Various Organs Preserved through Frozen, Formalin-Fixed and Paraffin-Embedded Tissue Sample method
Mifta Rizqina Amalia, Anna Roosdiana, Yudit Oktanella, Andreas Bandang Hardian, Dini Agusti Paramanandi, Kharisma Kurnia Utami, Andi Tri Rakhmat Akbar, Made Venika Nareswari, Fajar Shodiq Permata
Journal of Experimental Biology and Agricultural Sciences.2022; 10(3): 643. CrossRef
DNA isolated from formalin-fixed paraffin-embedded healthy tissue after 30 years of storage can be used for forensic studies
Katarina Vitošević, Miloš Todorović, Živana Slović, Tatjana Varljen, Stevan Matić, Danijela Todorović
Forensic Science, Medicine and Pathology.2021; 17(1): 47. CrossRef
Extraction of DNA and RNA from Formalin-fixed Paraffin-embedded Tissue Specimens
NIdhi Shukla, Narmadhaa Siva, Madhu Sivakumar, Rabia Parveen, Ashwani Mishra, Avadh Shah, Krishna Medicherla, Prashanth Suravajhala
BIO-PROTOCOL.2021;[Epub] CrossRef
Cyclin dependent kinase inhibitor 2A and miR-671-5p expression profile in Iranian glioblastoma multiforme
Tayyebali Salmani, Sayyed Mohammad Hossein Ghaderian, Mohammadreza Hajiesmaeili, Omidvar Rezaei Mirghaed, Azadeh Rakhshan, Mohammad Javad Nasiri, Mahan Mohammadi
Gene Reports.2020; 19: 100620. CrossRef
Comparison between Fluorescence in-situ Hybridization (FISH), Reverse Transcriptase PCR (RT-PCR) and fragment analysis, for detection of t (X; 18) (p11; q11) translocation in synovial sarcomas
Omshree Shetty, Trupti Pai, Mamta Gurav, Bharat Rekhi
Indian Journal of Pathology and Microbiology.2020; 63(1): 64. CrossRef
Comparison of HPV detection rate in formalin‐fixed paraffin‐embedded tissues of head and neck carcinoma using two DNA extraction kits and three amplification methods
Ljiljana Božić, Tanja Jovanović, Aleksandra Šmitran, Marko Janković, Aleksandra Knežević
European Journal of Oral Sciences.2020; 128(6): 501. CrossRef
Formalin Fixation of Human Healthy Autopsied Tissues: The Influence of Type of Tissue, Temperature and Incubation Time on the Quality of Isolated DNA
Danijela Todorovic, Katarina Vitosevic, Milos Todorovic, Zivana Slovic
Serbian Journal of Experimental and Clinical Research .2020; 21(4): 307. CrossRef
Detection of Disease-specific Fusion Genes of Soft Tissue Tumors Using Formalin-fixed Paraffin-embedded Tissues; Its Diagnostic Usefulness and Factors Affecting the Detection Rates
Takahiro Matsushige, Satoshi Kuwamoto, Michiko Matsushita, Lusi Oka Wardhani, Yasushi Horie, Kazuhiko Hayashi, Yukisato Kitamura
Yonago Acta Medica.2019; 62(1): 115. CrossRef
The Biospecimen Preanalytical Variables Program: A Multiassay Comparison of Effects of Delay to Fixation and Fixation Duration on Nucleic Acid Quality
Latarsha J. Carithers, Rachana Agarwal, Ping Guan, Hana Odeh, Michael C. Sachs, Kelly B. Engel, Sarah R. Greytak, Mary Barcus, Conrado Soria, Chih-Jian (Jason) Lih, P. Mickey Williams, Philip A. Branton, Leslie Sobin, Benjamin Fombonne, Therese Bocklage,
Archives of Pathology & Laboratory Medicine.2019; 143(9): 1106. CrossRef
Pathobiology and innate immune responses of gallinaceous poultry to clade 2.3.4.4A H5Nx highly pathogenic avian influenza virus infection
Kateri Bertran, Mary J. Pantin-Jackwood, Miria F. Criado, Dong-Hun Lee, Charles L. Balzli, Erica Spackman, David L. Suarez, David E. Swayne
Veterinary Research.2019;[Epub] CrossRef
Optimized Storage Methods of RNA Extraction from Formalin Fixed Paraffin Embedded Tissue
Mehdi Barati, Mahdieh Shokrollahi Barough, Fatemeh Pak, Vahid Semnani, Mehrnoosh Pashaei, Parviz Kokhaei
Middle East Journal of Rehabilitation and Health.2018;[Epub] CrossRef
Effect of formalin fixation on pcr amplification of DNA isolated from healthy autopsy tissues
Katarina Vitošević, Miloš Todorović, Tatjana Varljen, Živana Slović, Stevan Matić, Danijela Todorović
Acta Histochemica.2018; 120(8): 780. CrossRef
Evaluation of the optimal provision of formalin-fixed, paraffin-embedded material for reverse transcription-PCR in soft-tissue tumour diagnosis
Khin Thway, Dorte Wren, Jasmin Lee, Lisa Thompson, Cyril Fisher, David Gonzalez
Journal of Clinical Pathology.2017; 70(1): 20. CrossRef
Molecular Testing for Gastrointestinal Cancer
Hye Seung Lee, Woo Ho Kim, Yoonjin Kwak, Jiwon Koh, Jeong Mo Bae, Kyoung-Mee Kim, Mee Soo Chang, Hye Seung Han, Joon Mee Kim, Hwal Woong Kim, Hee Kyung Chang, Young Hee Choi, Ji Y. Park, Mi Jin Gu, Min Jin Lhee, Jung Yeon Kim, Hee Sung Kim, Mee-Yon Cho
Journal of Pathology and Translational Medicine.2017; 51(2): 103. CrossRef
Reference genes for studies in infectious parasitic diseases in five types of human tissues
Cristina Silva Meira-Strejevitch, Vera Lucia Pereira-Chioccola, Marta Marques Maia, Daise Damaris Carnietto de Hippolito, Hui-Tzu Lin Wang, Gabriela Motoie, Aparecida Helena de Souza Gomes, Cristina Takami Kanamura, Roosecelis Brasil Martines, Cinara Cáss
Gene Reports.2017; 7: 98. CrossRef
Establishment of a primary culture of polymorphous low grade adenocarcinoma cells
Lucas Novaes Teixeira, Victor Angelo Martins Montalli, Silvia Borges Pimentel de Oliveira, Thais Fernanda Santos Toledo, Elizabeth Ferreira Martinez, Vera Cavalcanti de Araújo
Archives of Oral Biology.2017; 82: 188. CrossRef
DNA degrades during storage in formalin-fixed and paraffin-embedded tissue blocks
Alice Guyard, Alice Boyez, Anaïs Pujals, Cyrielle Robe, Jeanne Tran Van Nhieu, Yves Allory, Julien Moroch, Odette Georges, Jean-Christophe Fournet, Elie-Serge Zafrani, Karen Leroy
Virchows Archiv.2017; 471(4): 491. CrossRef
Prevalence of exon 11 internal tandem duplications in the C‐KIT proto‐oncogene in Australian canine mast cell tumours
VS Tamlin, AE Kessell, RJ Mccoy, EC Dobson, TS Smith, M Hebart, L Brown, D Mitrovic, AE Peaston
Australian Veterinary Journal.2017; 95(10): 386. CrossRef
Robust transcriptional tumor signatures applicable to both formalin-fixed paraffin-embedded and fresh-frozen samples
Rou Chen, Qingzhou Guan, Jun Cheng, Jun He, Huaping Liu, Hao Cai, Guini Hong, Jiahui Zhang, Na Li, Lu Ao, Zheng Guo
Oncotarget.2017; 8(4): 6652. CrossRef
Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system
Sayaka Yuzawa, Hiroshi Nishihara, Shigeru Yamaguchi, Hiromi Mohri, Lei Wang, Taichi Kimura, Masumi Tsuda, Mishie Tanino, Hiroyuki Kobayashi, Shunsuke Terasaka, Kiyohiro Houkin, Norihiro Sato, Shinya Tanaka
Modern Pathology.2016; 29(7): 708. CrossRef
Comparison of the Diagnostic Value Between Real-Time Reverse Transcription-Polymerase Chain Reaction Assay and Histopathologic Examination in Sentinel Lymph Nodes for Patients With Gastric Carcinoma
Yoonjin Kwak, Soo Kyung Nam, Eun Shin, Sang-Hoon Ahn, Hee Eun Lee, Do Joong Park, Woo Ho Kim, Hyung-Ho Kim, Hye Seung Lee
American Journal of Clinical Pathology.2016; 145(5): 651. CrossRef
WITHDRAWN: Selection of reference genes in five types of human tissues for normalization of gene expression studies in infectious diseases
Cristina Silva Meira-Strejevitch, Vera Lucia Pereira-Chioccola, Marta Marques Maia, Daise Damaris Carnietto de Hipólito, Hui-Tzu Lin Wang, Gabriela Motoie, Aparecida Helena de Souza Gomes, Cristina Takami Kanamura, Roosecelis Brasil Martines, Cinara Cássi
Gene.2016;[Epub] CrossRef
A Comparison of Fresh Frozen vs. Formalin-Fixed, Paraffin-Embedded Specimens of Canine Mammary Tumors via Branched-DNA Assay
Florenza Lüder Ripoli, Annika Mohr, Susanne Conradine Hammer, Saskia Willenbrock, Marion Hewicker-Trautwein, Silvia Hennecke, Hugo Murua Escobar, Ingo Nolte
International Journal of Molecular Sciences.2016; 17(5): 724. CrossRef
Expression of caspase-3 predicts prognosis in advanced noncardia gastric cancer
Sousana Amptoulach, Andreas C. Lazaris, Ioanna Giannopoulou, Nikolaos Kavantzas, Efstratios Patsouris, Nikolaos Tsavaris
Medical Oncology.2015;[Epub] CrossRef
The Importance of Reference Gene Analysis of Formalin-Fixed, Paraffin-Embedded Samples from Sarcoma Patients — An Often Underestimated Problem
Ninna Aggerholm-Pedersen, Akmal Safwat, Steen Bærentzen, Marianne Nordsmark, Ole Steen Nielsen, Jan Alsner, Brita S. Sørensen
Translational Oncology.2014; 7(6): 687. CrossRef
Comparison of histomorphology and DNA preservation produced by fixatives in the veterinary diagnostic laboratory setting
William F. Craft, Julia A. Conway, Michael J. Dark
PeerJ.2014; 2: e377. CrossRef
Histotechnical solutions for quality improvement of nucleic acid specimens extracted from paraffin blocks
A. N Vaganova
Genes & Cells.2014; 9(2): 96. CrossRef

Comparison of the DNA Preservation in Neutral-Buffered Formalin Fixed Paraffin-Embedded Tissue and in Non-Buffered Formalin Fixed Paraffin-Embedded Tissue.: An Na Seo, Jae Hoon Kim, Dakeun Lee, Ji Yun Jeong, Ji Young Park; Korean J Pathol. 2011;45(6):549-556.; DOI: https://doi.org/10.4132/KoreanJPathol.2011.45.6.549

4,635 View
59 Download
1 Crossref

Abstract PDF

BACKGROUND
The preservation of optimized DNA and its extraction from formalin-fixed, paraffin-embedded (FFPE) tissues are important issues. There has been some doubt over whether 10% neutral-buffered formalin is an ideal fixation solution for DNA preservation over non-buffered formalin, as conventionally recommended. In this study, the correlation between the efficiency of DNA extraction from FFPE tissues and buffered formalin was evaluated.
METHODS
Several tissues with same conditions except fixatives were fixed in four different formalin solution groups and were routinely processed as paraffin-embedding protocols. DNAs were extracted from four different FFPE tissues that were stored for over 3 months and over 9 months. The quantity and quality of the DNAs were assessed with a NanoDrop ND-1000 spectrophotometer, and the polymerase chain reaction (PCR) amplification and degradation were analyzed via microchip electrophoresis. KRAS mutation analysis and microsatellite instability (BAT25) PCR were performed with each sample.
RESULTS
The results showed no remarkable difference in the four groups.
CONCLUSIONS
The study findings demonstrate that DNA preservation is fairly unaffected by a neutral buffer where there is short formalin manufacture period and an adequate formalin fixation time before embedding in paraffin.

Citations

Citations to this article as recorded by

Comparison of Direct Sequencing, PNA Clamping-Real Time Polymerase Chain Reaction, and Pyrosequencing Methods for the Detection ofEGFRMutations in Non-small Cell Lung Carcinoma and the Correlation with Clinical Responses to EGFR Tyrosine Kinase Inhibitor
Hyun Ju Lee, Xianhua Xu, Hyojin Kim, Yan Jin, Pingli Sun, Ji Eun Kim, Jin-Haeng Chung
Korean Journal of Pathology.2013; 47(1): 52. CrossRef

Plastination: An Improved Method for Preservation of Pathology Specimens.: Chong Woo Yoo, Min Ho Choo, Sa Sun Cho, Sang Kook Lee, Je Geun Chi, Woo Ho Kim; Korean J Pathol. 1998;32(7):531-534.

2,083 View
10 Download

Abstract: The gross tissue specimens are a valuable aid to the teaching of pathology and anatomy. However, traditional methods for storage and handling of them are discouragingly difficult and, recently, minimal surgical resections as well as preoperative interventions make it more difficult to have instructive gross specimens. Plastination is a process of tissue preservation by impregnation with silicone polymers or epoxy resins. The process in our study involves dehydration by cryosubstitution in aceton, defatting, forced impregnation of silicon polymer in a vacuum, curing and finishing. We submitted 40 surgically resected specimens to plastination. The resulting specimens are odorless, relatively dry, durable, life-like, non-hazardous, maintenance-free, and do not deteriorate with time. Plastinated specimens are a useful adjunct to the teaching of pathology, particularly suited for use in small groups, and appropriate method of tissue preservation. They are much preferred to wet preparation and conventional pots by both students and teachers owing to their accessibility, superior illustrative powers, and comparative ease of interpretation.

Flush Perfusion, Preservation and Reperfusion Effects in Lung Transplantation: Light Microscopic and Ultrastructural Study.: Kun Young Kwon, Young Keun Lim, Jae Hoon Bae, Chang Kwon Park; Korean J Pathol. 1998;32(11):967-977.

1,750 View
10 Download

Abstract: This study was undertaken to investigate the morphologic changes following flushing, preservation and reperfusion procedures in a canine lung allotransplantation model. Donor lungs were flushed with modified Euro-Collins (MEC) solution, low potassium dextran glucose (LPDG) solution or University of Wisconsin (UW) solution, then stored at 10oC for 20 hours. Light microscopic and electron microscopic features of the lungs were examined after flushing, preservation and 2 hours after reperfusion. After flushing light microscopy showed focal mild alveolar collapse and interstitial edema. After preservation the lung tissue showed multiple foci of alveolar collapse, consolidation, and alveolar epithelial cell damage. After reperfusion the lung tissue showed diffuse alveolar collapse, consolidation and many destroyed cellular debris in the alveolar lumina. After flushing electron microscopy showed focal alveolar collapse and mild swelling of type I epithelial cells. After preservation both type I epithelial cells and endothelial cells were swollen and destroyed focally. Some type I epithelial cells were detached from the basal lamina. The endothelial cells showed luminal protrusion of tactile-like structure and vacuoles of the cytoplasm. After reperfusion the lung tissue showed fibrin material in the alveoli, prominent type I epithelial cell swelling with fragmented cytoplasmic debris and marked endothelial cell swelling with vacuoles or tactile-like projections. The alveolar macrophages showed active phagocytosis. After preservation scanning electron microscopic examination of the pulmonary arteries showed multiple patchy areas of swelling or conglomerated lesions in the inner surface of the pulmonary arteries. In conclusion, the ultrastructural changes associated with flushing were mild in severity, the donor lungs were injured during the preservation, and further damage occurred during the reperfusion.

First
Prev
Page of 1
Next
Last

Search