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2015 ; 7
(3
): 1699-715
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Analysis of Pre-Analytic Factors Affecting the Success of Clinical
Next-Generation Sequencing of Solid Organ Malignancies
#MMPMID26343728
Chen H
; Luthra R
; Goswami RS
; Singh RR
; Roy-Chowdhuri S
Cancers (Basel)
2015[Aug]; 7
(3
): 1699-715
PMID26343728
show ga
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.