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Cancers 2015, 7(3), 1699-1715; doi:10.3390/cancers7030859

Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies

1
Department of Pathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
2
Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
Current affiliation: Department of Laboratory Hematology, Toronto General Hospital, University Health Network, 200 Elizabeth Street, 11 Eaton South, Toronto, ON M5G 2C4, Canada
*
Author to whom correspondence should be addressed.
Academic Editors: Camile S. Farah and William Chi-Shing Cho
Received: 3 July 2015 / Revised: 20 August 2015 / Accepted: 21 August 2015 / Published: 28 August 2015
(This article belongs to the Special Issue Next Generation Sequencing Approaches in Cancer)
View Full-Text   |   Download PDF [393 KB, uploaded 28 August 2015]   |  

Abstract

Application of next-generation sequencing (NGS) technology to routine clinical practice has enabled characterization of personalized cancer genomes to identify patients likely to have a response to targeted therapy. The proper selection of tumor sample for downstream NGS based mutational analysis is critical to generate accurate results and to guide therapeutic intervention. However, multiple pre-analytic factors come into play in determining the success of NGS testing. In this review, we discuss pre-analytic requirements for AmpliSeq PCR-based sequencing using Ion Torrent Personal Genome Machine (PGM) (Life Technologies), a NGS sequencing platform that is often used by clinical laboratories for sequencing solid tumors because of its low input DNA requirement from formalin fixed and paraffin embedded tissue. The success of NGS mutational analysis is affected not only by the input DNA quantity but also by several other factors, including the specimen type, the DNA quality, and the tumor cellularity. Here, we review tissue requirements for solid tumor NGS based mutational analysis, including procedure types, tissue types, tumor volume and fraction, decalcification, and treatment effects. View Full-Text
Keywords: next-generation sequencing; targeted hotspot mutation analysis; pre-analytic factors; tissue qualification next-generation sequencing; targeted hotspot mutation analysis; pre-analytic factors; tissue qualification
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

Chen, H.; Luthra, R.; Goswami, R.S.; Singh, R.R.; Roy-Chowdhuri, S. Analysis of Pre-Analytic Factors Affecting the Success of Clinical Next-Generation Sequencing of Solid Organ Malignancies. Cancers 2015, 7, 1699-1715.

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