American Association for Cancer Research
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Supplementary Figure-2 from Development and Validation of a Gene Signature Classifier for Consensus Molecular Subtyping of Colorectal Carcinoma in a CLIA-Certified Setting

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posted on 2023-03-31, 22:26 authored by Jeffrey S. Morris, Rajyalakshmi Luthra, Yusha Liu, Dzifa Y. Duose, Wonyul Lee, Neelima G. Reddy, Justin Windham, Huiqin Chen, Zhimin Tong, Baili Zhang, Wei Wei, Manyam Ganiraju, Bradley M. Broom, Hector A. Alvarez, Alicia Mejia, Omkara Veeranki, Mark J. Routbort, Van K. Morris, Michael J. Overman, David Menter, Riham Katkhuda, Ignacio I. Wistuba, Jennifer S. Davis, Scott Kopetz, Dipen M. Maru

Classification accuracy for training data V1 (based on 4-fold cross val-idation, 2A) and the full validation data V2 (2B) for various methods as function of number

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NCI

MD Anderson Cancer Center

NIH

EMD Serono

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ARTICLE ABSTRACT

Consensus molecular subtyping (CMS) of colorectal cancer has potential to reshape the colorectal cancer landscape. We developed and validated an assay that is applicable on formalin-fixed, paraffin-embedded (FFPE) samples of colorectal cancer and implemented the assay in a Clinical Laboratory Improvement Amendments (CLIA)-certified laboratory. We performed an in silico experiment to build an optimal CMS classifier using a training set of 1,329 samples from 12 studies and validation set of 1,329 samples from 14 studies. We constructed an assay on the basis of NanoString CodeSets for the top 472 genes, and performed analyses on paired flash-frozen (FF)/FFPE samples from 175 colorectal cancers to adapt the classifier to FFPE samples using a subset of genes found to be concordant between FF and FFPE, tested the classifier's reproducibility and repeatability, and validated in a CLIA-certified laboratory. We assessed prognostic significance of CMS in 345 patients pooled across three clinical trials. The best classifier was weighted support vector machine with high accuracy across platforms and gene lists (>0.95), and the 472-gene model outperforming existing classifiers. We constructed subsets of 99 and 200 genes with high FF/FFPE concordance, and adapted FFPE-based classifier that had strong classification accuracy (>80%) relative to “gold standard” CMS. The classifier was reproducible to sample type and RNA quality, and demonstrated poor prognosis for CMS1–3 and good prognosis for CMS2 in metastatic colorectal cancer (P < 0.001). We developed and validated a colorectal cancer CMS assay that is ready for use in clinical trials, to assess prognosis in standard-of-care settings and explore as predictor of therapy response.