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Int. J. Mol. Sci. 2016, 17(9), 1579; doi:10.3390/ijms17091579

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

1
Translational Medicine, Merck Research Laboratories, Merck & Co., Inc., Kenilworth, NJ 07033, USA
2
Translational Biomarkers, Merck Research Laboratories, Merck Sharp & Dohme, Singapore 609927, Singapore
*
Author to whom correspondence should be addressed.
Academic Editor: William Chi-shing Cho
Received: 8 August 2016 / Revised: 8 September 2016 / Accepted: 13 September 2016 / Published: 20 September 2016
(This article belongs to the Special Issue Next-Generation Sequencing for Clinical Application)
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Abstract

In cancer drug discovery, it is important to investigate the genetic determinants of response or resistance to cancer therapy as well as factors that contribute to adverse events in the course of clinical trials. Despite the emergence of new technologies and the ability to measure more diverse analytes (e.g., circulating tumor cell (CTC), circulating tumor DNA (ctDNA), etc.), tumor tissue is still the most common and reliable source for biomarker investigation. Because of its worldwide use and ability to preserve samples for many decades at ambient temperature, formalin-fixed, paraffin-embedded tumor tissue (FFPE) is likely to be the preferred choice for tissue preservation in clinical practice for the foreseeable future. Multiple analyses are routinely performed on the same FFPE samples (such as Immunohistochemistry (IHC), in situ hybridization, RNAseq, DNAseq, TILseq, Methyl-Seq, etc.). Thus, specimen prioritization and optimization of the isolation of analytes is critical to ensure successful completion of each assay. FFPE is notorious for producing suboptimal DNA quality and low DNA yield. However, commercial vendors tend to request higher DNA sample mass than what is actually required for downstream assays, which restricts the breadth of biomarker work that can be performed. We evaluated multiple genomics service laboratories to assess the current state of NGS pre-analytical processing of FFPE. Significant differences in pre-analytical capabilities were observed. Key aspects are highlighted and recommendations are made to improve the current practice in translational research. View Full-Text
Keywords: next-generation sequencing (NGS); formalin-fixed and paraffin-embedded tumor tissue (FFPE); pre-analytics; DNA extraction; DNA amplifiability next-generation sequencing (NGS); formalin-fixed and paraffin-embedded tumor tissue (FFPE); pre-analytics; DNA extraction; DNA amplifiability
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Arreaza, G.; Qiu, P.; Pang, L.; Albright, A.; Hong, L.Z.; Marton, M.J.; Levitan, D. Pre-Analytical Considerations for Successful Next-Generation Sequencing (NGS): Challenges and Opportunities for Formalin-Fixed and Paraffin-Embedded Tumor Tissue (FFPE) Samples. Int. J. Mol. Sci. 2016, 17, 1579.

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