Challenges in using liquid biopsies for gene expression profiling

Oncotarget
Tania PorrasJulie E Lang

Abstract

Circulating tumor cells (CTCs) have potential utility as a surrogate biomarker of tumor biology via a liquid biopsy. The aim of this study was to evaluate if the nCounter NanoString assay could be used for accurate gene expression profiling of CTCs using the PAM50 research-use-only CodeSet. Analysis was performed on CTCs isolated by the ANGLE Parsortix system from healthy blood spiked with the breast cancer cell lines Hs578T, SkBr3, MDA-MB-231 or MCF7. Using cell lines as gold standard positive controls and Parsortix processed blood without spiking (unspiked) as negative controls, we found an average of 12 significantly differentially expressed genes among spiked samples versus unspiked controls. We validated our findings with the NanoStringDiff differential expression statistical method. The NanoString recommended targeted pre-amplification introduced false positive results due to pre-amplification bias, and the amplification of non-cancer genes from normal leukocytes confounded gene expression profiling of CTCs. Pre-amplification bias is a concern for other similar assays that may be used as discovery tools or target validation of transcripts of interest in gene expression profiling of CTCs. We recommend the use of an unspike...Continue Reading

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Aug 15, 2018·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·M Craig MillerDaniel J O'Shannessy
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Methods Mentioned

BETA
flow cytometry
FACS
RNA-seq
biopsy
blood draw
PCR
RNA Seq
blood draws
genotyping

Software Mentioned

NanoString PAM50
NanoString
NanoString nSolver Analysis
ANGLE Parsortix System
GraphPad Prism
Parsortix
nCounter
nCounter NanoString PAM50
nSolver Analysis
nSolver

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