# Colorectal Cancer Molecular Subtype Assay Development and Validation

> **NIH NIH UH3** · UNIVERSITY OF TX MD ANDERSON CAN CTR · 2021 · $297,095

## Abstract

ABSTRACT
Stage III colorectal cancer (CRC) demonstrates substantial variability in tumor biology and clinical outcomes and
there is a need to understand prognosis for patients in order to gauge risk benefit for chemotherapy and intensity
of chemotherapy administration. These features are not well recapitulated by the current biomarkers in use in
the clinic, majority of them are DNA based mutation assays. RNA expression patterns have been described by
various investigators and may more fully recapitulate tumor biology. The clinical utility of these findings have
been limited by the apparent conflicting subgrouping efforts and lack of a validated gene expression signature
as a clinical grade assay applicable on formalin fixed paraffin embedded (FFPE) tissue. In our international
collaboration with several academic leaders who have previously published in this field, we have identified a
robust consensus subgroup classification based on clustering approaches independent of clinical
outcomes. Remarkably, this classification system, termed consensus molecular subtypes (CMS), identified 4
subgroups that provide novel insights into the classification of CRC. One subgroup with mesenchymal, TGF-β,
and angiogenic features (CMS4) is associated with a hazard ratio for death of 2.26 (95% CI of 1.41 to 3.61,
P=.001), significantly higher than other subgroups, in a multivariate model inclusive of current clinical and
pathologic risk factors and genetic signature (Oncotype Dx). We hypothesize that a gene expression
signature classifier can be developed and validated for determining the CMS in FFPE tissues, and that
this classifier can be implemented to improve prognostication of stage III CRC by classifying them in
CMS 4 vs. other subtypes. We have developed a support-vector-machine classifier with very high accuracy for
classification based on an Affymetrix array from fresh frozen specimens. We have demonstrated good
classification accuracy (>90%) using customized Nanostring codesets on FFPE tumor samples of 85
patients with stage III CRC. We have also demonstrated good technical reproducibility in six of those 85
samples. In this application, we will transfer the assay using the Nanostring Codeset to fresh frozen (FF) and
FFPE using a set of paired samples, while maintaining classifier performance. We will then pursue technical and
analytic validation of the assay, including precision in repeatability, reproducibility between sample types, inter-
lab reproducibility, and impact of RNA quality/quantity. In the UH3 portion of the grant, we will clinically validate
the prognostic utility of the gene expression signature assay in single-institution cohort, and then in a completed
prospective study of FOLFOX chemotherapy (NRG/NSABPC-08), in a CLIA certified laboratory. Additional data
will be used in predicting response to various standard of care therapeutics, which represents a series of future
potential applications of the assay. By utilizing an assay developed ...

## Key facts

- **NIH application ID:** 10334569
- **Project number:** 4UH3CA207101-03
- **Recipient organization:** UNIVERSITY OF TX MD ANDERSON CAN CTR
- **Principal Investigator:** Scott Kopetz
- **Activity code:** UH3 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2021
- **Award amount:** $297,095
- **Award type:** 4N
- **Project period:** 2018-09-21 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10334569

## Citation

> US National Institutes of Health, RePORTER application 10334569, Colorectal Cancer Molecular Subtype Assay Development and Validation (4UH3CA207101-03). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10334569. Licensed CC0.

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