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

PloS One
Eric BonnetJean-François Deleuze

Abstract

Next-generation sequencing (NGS) studies are becoming routinely used for the detection of novel and clinically actionable DNA variants at a pangenomic scale. Such analyses are now used in the clinical practice to enable precision medicine. Formalin-fixed paraffin-embedded (FFPE) tissues are still one of the most abundant source of cancer clinical specimen, unfortunately this method of preparation is known to degrade DNA and therefore compromise subsequent analysis. Some studies have reported that variant detection can be performed on FFPE samples sequenced with NGS techniques, but few or none have done an in-depth coverage analysis and compared the influence of different state-of-the-art FFPE DNA extraction kits on the quality of the variant calling. Here, we generated 42 human whole-exome sequencing data sets from fresh-frozen (FF) and FFPE samples. These samples include normal and tumor tissues from two different organs (liver and colon), that we extracted with three different FFPE extraction kits (QIAamp DNA FFPE Tissue kit and GeneRead DNA FFPE kit from Qiagen, Maxwell™ RSC DNA FFPE Kit from Promega). We determined the rate of concordance of called variants between matched FF and FFPE samples on all common variants (represe...Continue Reading

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Mar 22, 2019·Personalized Medicine·Yuxian BaiShunchang Jiao
Apr 12, 2019·PloS One·Samantha J McDonoughJulie M Cunningham
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Related Concepts

Whole Exome Sequencing
Taenia Coli
Malignant Tumor of Colon
DNA, Double-Stranded
DNA, Neoplasm
Fixatives
Formalin
Liver
Malignant Neoplasm of Liver
Cryonic Suspension

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