Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods

Samantha J. Mcdonough, Aditya Bhagwate, Zhifu Sun, Chen Wang, Michael Zschunke, Joshua A. Gorman, Karla J. Kopp, Julie M. Cunninghamid

Research output: Contribution to journalArticlepeer-review

20 Scopus citations


Archival tissues represent a rich resource for clinical genomic studies, particularly when coupled with comprehensive medical records. Use of these in next generation sequencing (NGS) is a priority. Nine formalin-fixed paraffin-embedded (FFPE) DNA extraction methods were evaluated using twelve FFPE samples of varying tissue types. Quality assessment included total yield, percent dsDNA, fragment analysis and multiplex PCR. After assessment, three tissue types from four FFPE DNA methods were selected for NGS downstream evaluation, targeted and whole exome sequencing. In addition, two low input library protocols were evaluated for WES. Analysis revealed average coverage across the target regions for WES was ~20-30X for all four FFPE DNA extraction methods. For the targeted panels, the highest molecular tag coverage was obtained with the Kingfisher FFPE extraction method. The genotype concordance was 99% for the commonly called variant positions between all four extraction methods with the targeted PCR NGS panel and 96% with WES. Assessing quality of extracted DNA AIDS in selecting the optimal NGS approach, and the choice of both DNA extraction and library preparation approaches can impact the performance of archival tissue in NGS.

Original languageEnglish (US)
Article numbere0211400
JournalPloS one
Issue number4
StatePublished - Apr 2019

ASJC Scopus subject areas

  • General


Dive into the research topics of 'Use of FFPE-derived DNA in next generation sequencing: DNA extraction methods'. Together they form a unique fingerprint.

Cite this