Quality Assessment of DNA Extraction Methods from Formalin-Fixed Paraffin-Embedded Tissues

被引：0
作者：
Ferchichi, Marwa [1 ,2 ]
Jouini, Raja [1 ,3 ]
Ayari, Imen [1 ,2 ]
Khanchal, Fatma [2 ]
Koubaa, Wafa [2 ]
Chadli-Debbiche, Aschraf [2 ]
BenBrahim, Ehsen [2 ]
机构：
[1] Univ Sci, Farhat Hached Campus, Tunis El Manar, Tunisia
[2] Habib Thameur Hosp, Pathol Dept, Tunis, Tunisia
[3] Univ Med, Farhat Hached Campus, Tunis El Manar, Tunisia
来源：
INTERNATIONAL JOURNAL OF HUMAN GENETICS | 2019年 / 19卷 / 03期
关键词：
DNA; DNA Extraction; Formalin Fixed Tissues; Pathology; Tumors; PATHOLOGISTS;
D O I：
10.31901/24566330.2019/19.03.733
中图分类号：
Q3 [遗传学];
学科分类号：
071007 ; 090102 ;
摘要：
DNA extraction from archived formalin-fixed paraffin-embedded (FFPE) tissues represent a great source of information. However, till date, it shows some challenges due to its fragmentation and degradation by formalin. The aim of this study was to assess 3 extraction methods used with 651 FFPE namely QIAamp (R) DNA FFPE Tissue Qiagen Kit (80%), MagaZorb (R) DNA Mini-Prep Kit Promega (17.8%) and phenol-chloroform classical extraction (2.2%). Extract concentration mean was 240.05 ng/mu l (7-1985 ng/mu l) and DNA purity (A260/ A280) mean was 1.98 (1.2 - 4). The classical phenol-chloroform method had the most successful DNA concentration (P < 0.001) but had the worst DNA purity ratio while the Promega and Qiagen kits DNA purity ratio were within the norms (P < 0.001). This assessment showed that even with commercial kits, we should always adjust some parameters to have good DNA extracts which is the first step towards a successful molecular analysis.
引用
收藏
页码：134 / 137
页数：4
相关论文
共 8 条
[1]  
[Anonymous], DRUG INVENTION TODAY
[2]   Multicentre validation study of nucleic acids extraction from FFPE tissues [J].
Bonin, Serena ;
Hlubek, Falk ;
Benhattar, Jean ;
Denkert, Carsten ;
Dietel, Manfred ;
Fernandez, Pedro L. ;
Hoefler, Gerald ;
Kothmaier, Hannelore ;
Kruslin, Bozo ;
Mazzanti, Chiara Maria ;
Perren, Aurel ;
Popper, Helmuth ;
Scarpa, Aldo ;
Soares, Paula ;
Stanta, Giorgio ;
Groenen, Patricia J. T. A. .
VIRCHOWS ARCHIV, 2010, 457 (03) :309-317
[3]   Challenges Posed to Pathologists in the Detection of KRAS Mutations in Colorectal Cancers [J].
Dudley, Jonathan ;
Tseng, Li-Hui ;
Rooper, Lisa ;
Harris, Marco ;
Haley, Lisa ;
Chen, Guoli ;
Gocke, Christopher D. ;
Eshleman, James R. ;
Lin, Ming-Tseh .
ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE, 2015, 139 (02) :211-218
[4]   Archived Formalin-Fixed Paraffin-Embedded (FFPE) Blocks: A Valuable Underexploited Resource for Extraction of DNA, RNA, and Protein [J].
Kokkat, Theresa J. ;
Patel, Miral S. ;
McGarvey, Diane ;
LiVolsi, Virginia A. ;
Baloch, Zubair W. .
BIOPRESERVATION AND BIOBANKING, 2013, 11 (02) :101-106
[5]   Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples [J].
Kresse, Stine H. ;
Namlos, Heidi M. ;
Lorenz, Susanne ;
Berner, Jeanne-Marie ;
Myklebost, Ola ;
Bjerkehagen, Bodil ;
Meza-Zepeda, Leonardo A. .
PLOS ONE, 2018, 13 (05)
[6]   Molecular Testing Guideline for Selection of Lung Cancer Patients for EGFR and ALK Tyrosine Kinase Inhibitors Guideline from the College of American Pathologists, International Association for the Study of Lung Cancer, and Association for Molecular Pathology [J].
Lindeman, Neal I. ;
Cagle, Philip T. ;
Beasley, Mary Beth ;
Chitale, Dhananjay Arun ;
Dacic, Sanja ;
Giaccone, Giuseppe ;
Jenkins, Robert Brian ;
Kwiatkowski, David J. ;
Saldivar, Juan-Sebastian ;
Squire, Jeremy ;
Thunnissen, Erik ;
Ladanyi, Marc .
JOURNAL OF THORACIC ONCOLOGY, 2013, 8 (07) :823-859
[7]   DNA Extraction from Paraffin Embedded Material for Genetic and Epigenetic Analyses [J].
Pikor, Larissa A. ;
Enfield, Katey S. S. ;
Cameron, Heryet ;
Lam, Wan L. .
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, 2011, (49)
[8]   DNA extraction from archival formalin-fixed, paraffin-embedded tissues: heat-induced retrieval in alkaline solution [J].
Shi, SR ;
Datar, R ;
Liu, C ;
Wu, L ;
Zhang, Z ;
Cote, RJ ;
Taylor, CR .
HISTOCHEMISTRY AND CELL BIOLOGY, 2004, 122 (03) :211-218
1