Literature DB >> 25640584

Comparison of eight commercially available kits for DNA extraction from formalin-fixed paraffin-embedded tissues.

Anna Janecka1, Agnieszka Adamczyk2, Anna Gasińska2.   

Abstract

A proper extraction method from formalin-fixed paraffin-embedded (FFPE) blocks is essential to obtain DNA of satisfactory quality/quantity. We compared the effectiveness of eight commercially available kits for DNA extraction based on 10 FFPE tissues. Kits differed significantly in terms of DNA yield, purity, and quality. Using the QIAamp DNA FFPE Tissue Kit (Qiagen) and the ReliaPrep FFPE gDNA Miniprep System (Promega), we obtained DNA of the highest quality and acceptable quantity. We also demonstrated that overnight digestion of samples usually improved DNA yield and/or purity. For precious or limited material, double elution is recommended for obtaining up to 42% higher amount of DNA.
Copyright © 2015 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Commercially available kit; DNA extraction; DNA yield and purity; FFPE tissue; Real-time PCR

Mesh：

Substances：

Year:  2015        PMID： 25640584     DOI： 10.1016/j.ab.2015.01.019

Source DB:  PubMed          Journal:  Anal Biochem        ISSN： 0003-2697            Impact factor:   3.365


  18 in total

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Authors:  Beth A Marosy; Brian D Craig; Kurt N Hetrick; P Dane Witmer; Hua Ling; Sean M Griffith; Benjamin Myers; Elaine A Ostrander; Janet L Stanford; Lawrence C Brody; Kimberly F Doheny
Journal:  Curr Protoc Hum Genet       Date:  2017-01-11

2.  Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer.

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Journal:  Cancer Genomics Proteomics       Date:  2016 09-10       Impact factor: 4.069

3.  Validation of a standardized extraction method for formalin-fixed paraffin-embedded tissue samples.

Authors:  Camilla Lagheden; Carina Eklund; Sara Nordqvist Kleppe; Elizabeth R Unger; Joakim Dillner; Karin Sundström
Journal:  J Clin Virol       Date:  2016-04-27       Impact factor: 3.168

4.  Effect of Different Proteinase K Digest Protocols and Deparaffinization Methods on Yield and Integrity of DNA Extracted From Formalin-fixed, Paraffin-embedded Tissue.

Authors:  Zoe Frazer; Changyoung Yoo; Manveer Sroya; Camille Bellora; Brian L DeWitt; Ignacio Sanchez; Geraldine A Thomas; William Mathieson
Journal:  J Histochem Cytochem       Date:  2020-02-11       Impact factor: 2.479

5.  Extracorporeal life support survival in a pediatric hematopoietic cellular transplant recipient with presumed GvHD-related fulminant myocarditis.

Authors:  M S Zinter; B D Barrows; P C Ursell; K Kowalek; K Kalantar; N Cambronero; J L DeRisi; P Oishi; C C Dvorak
Journal:  Bone Marrow Transplant       Date:  2017-06-05       Impact factor: 5.483

6.  Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples.

Authors:  Eric Bonnet; Marie-Laure Moutet; Céline Baulard; Delphine Bacq-Daian; Florian Sandron; Lilia Mesrob; Bertrand Fin; Marc Delépine; Marie-Ange Palomares; Claire Jubin; Hélène Blanché; Vincent Meyer; Anne Boland; Robert Olaso; Jean-François Deleuze
Journal:  PLoS One       Date:  2018-04-05       Impact factor: 3.240

7.  Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS): Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples.

Authors:  Gladys Arreaza; Ping Qiu; Ling Pang; Andrew Albright; Lewis Z Hong; Matthew J Marton; Diane Levitan
Journal:  Int J Mol Sci       Date:  2016-09-20       Impact factor: 5.923

8.  Validation of a Multiplex Allele-Specific Polymerase Chain Reaction Assay for Detection of KRAS Gene Mutations in Formalin-Fixed, Paraffin-Embedded Tissues from Colorectal Cancer Patients.

Authors:  Sirirat Seekhuntod; Paninee Thavarungkul; Nuntaree Chaichanawongsaroj
Journal:  PLoS One       Date:  2016-01-26       Impact factor: 3.240

9.  Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers.

Authors:  Suet-Feung Chin; Angela Santonja; Marta Grzelak; Soomin Ahn; Stephen-John Sammut; Harry Clifford; Oscar M Rueda; Michelle Pugh; Mae A Goldgraben; Helen A Bardwell; Eun Yoon Cho; Elena Provenzano; Federico Rojo; Emilio Alba; Carlos Caldas
Journal:  Exp Mol Pathol       Date:  2018-03-31       Impact factor: 3.362

10.  Evaluation of commercial DNA and RNA extraction methods for high-throughput sequencing of FFPE samples.

Authors:  Stine H Kresse; Heidi M Namløs; Susanne Lorenz; Jeanne-Marie Berner; Ola Myklebost; Bodil Bjerkehagen; Leonardo A Meza-Zepeda
Journal:  PLoS One       Date:  2018-05-17       Impact factor: 3.240
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