We previously classified colorectal cancer (CRC) into five distinctive subtypes (CRCAssigner) and later into four consensus molecular subtypes (CMS) based on microarray or RNAseq gene expression profiles. The goal of this study was to develop a less expensive multiplex biomarker assay to stratify patient samples into CRC subtypes using the nCounter platform (NanoString Technologies) with short turn-around time for potential clinical use.
We used three cohorts of primary untreated CRC samples (n = 51) with two microarray (Del Rio; Montpellier Cancer Research Institute, France and OriGene; OriGene, Rockville, MD, USA) and one RNAseq (SG; Singapore General Hospital, Singapore) gene expression profiles. We reduced our published 786-gene CRCAssigner signature (CRCAssigner-786) into a short gene panel (CRC-panel). Initially, we compared CMS subtypes with CRCAssigner-786 subtypes, followed by CRCAssigner-786 subtypes with that of the microarray/RNAseq-based CRC-panel. We then developed a customized nCounter CRC-panel and compared to different subtype classifications. To assess reproducibility, we generated technical replicates.
There was an average of 70% concordance between CMS and CRCAssigner subtypes across different cohorts. 94% of predicted subtypes were concordant using microarray CRCAssigner-786 versus microarray CRC-panel signatures in both the Del Rio (16/17) and OriGene (16/17) cohorts. nCounter CRC-panel assay classified 82% (14/17) Del Rio and 65% (11/17) OriGene samples consistently with microarray-based CRC-panel classification. In the SG cohort, nCounter CRC-panel classified 76% (13/17) and 94% (16/17) of samples consistently with RNAseq-786 and RNAseq CRC-panel, respectively. Pearson’s correlation coefficient between five pairs of technical replicates was 0.98.
nCounter assay stratified CRC samples into subtypes to known classifications. Given the high reproducibility and reduced costs, nCounter platform has been tested in formalin-fixed paraffin-embedded samples (ESMO-2017 Abstract-#3467). This assay may facilitate prospective validation of CRC subtypes in the clinic.
Clinical trial identification
Legal entity responsible for the study
Institute of Cancer Research (ICR), London
NIHR Biomedical Research Centre
A. Sadanandam: Entitled to a share of royalties received by the licensor for a patent number PCT/IB2013/060416 in colorectal cancer subtypes. Research funding from Bristol-Myers Squibb for pancreatic cancer. All other authors have declared no conflicts of interest.