A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer
| العنوان: | A panel of DNA methylation markers for the classification of consensus molecular subtypes 2 and 3 in patients with colorectal cancer |
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| المؤلفون: | Inge van den Berg, Jan N. M. Ijzermans, Vanja de Weerd, John W.M. Martens, Carolien H.M. van Deurzen, Mark A. van de Wiel, Saskia M. Wilting, Robert R. J. Coebergh van den Braak, Marcel Smid |
| المساهمون: | Surgery, Medical Oncology, Pathology |
| المصدر: | Molecular Oncology, 15(12), 3348-3362. John Wiley & Sons Ltd. Molecular Oncology, Vol 15, Iss 12, Pp 3348-3362 (2021) Molecular Oncology |
| سنة النشر: | 2021 |
| مصطلحات موضوعية: | Elastic net regularization, Oncology, Cancer Research, medicine.medical_specialty, consensus molecular subtypes, Colorectal cancer, Computational biology, Biology, SDG 3 - Good Health and Well-being, Internal medicine, Genetics, Biomarkers, Tumor, medicine, Humans, In patient, Stage (cooking), marker panel, Research Articles, RC254-282, business.industry, Neoplasms. Tumors. Oncology. Including cancer and carcinogens, General Medicine, Methylation, DNA Methylation, medicine.disease, Regression, CpG site, colon cancer, DNA methylation, Molecular Medicine, CpG Islands, methylation, Colorectal Neoplasms, business, Research Article |
| الوصف: | Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). We aim to identify methylation markers to distinguish between CMS2 and CMS3 in patients with CRC, for which an easy test is currently lacking. To this aim, fresh‐frozen tumor tissue of 239 patients with stage I‐III CRC was analyzed. Methylation profiles were obtained using the Infinium HumanMethylation450 BeadChip. We performed adaptive group‐regularized logistic ridge regression with post hoc group‐weighted elastic net marker selection to build prediction models for classification of CMS2 and CMS3. The Cancer Genome Atlas (TCGA) data were used for validation. Group regularization of the probes was done based on their location either relative to a CpG island or relative to a gene present in the CMS classifier, resulting in two different prediction models and subsequently different marker panels. For both panels, even when using only five markers, accuracies were > 90% in our cohort and in the TCGA validation set. Our methylation marker panel accurately distinguishes between CMS2 and CMS3. This enables development of a targeted assay to provide a robust and clinically relevant classification tool for CRC patients. Consensus molecular subtypes (CMSs) can guide precision treatment of colorectal cancer (CRC). However, an easy test to distinguish between CMS2 and CMS3 in patients with colorectal cancer is currently lacking. We developed two methylation marker panels distinguishing between CMS2 and CMS3, both with accuracies > 90% in our cohort and in TCGA validation set. This enables development of a targeted assay to provide a robust and clinically relevant classification tool for CRC patients. |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 1574-7891 |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f0e8f8fe20b0d67022743c2f3d8eb2b2 https://pure.eur.nl/en/publications/53e3a05f-2db5-4aa6-a931-1635d6c1b5dc |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....f0e8f8fe20b0d67022743c2f3d8eb2b2 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 15747891 |
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