SNUH methylation classifier for CNS tumors.

IF 4.8 2区 医学 Q1 GENETICS & HEREDITY
Kwanghoon Lee, Jaemin Jeon, Jin Woo Park, Suwan Yu, Jae-Kyung Won, Kwangsoo Kim, Chul-Kee Park, Sung-Hye Park
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引用次数: 0

Abstract

Background: Methylation profiling of central nervous system (CNS) tumors, pioneered by the German Cancer Research Center, has significantly improved diagnostic accuracy. This study aimed to further enhance the performance of methylation classifiers by leveraging publicly available data and innovative machine-learning techniques.

Results: Seoul National University Hospital Methylation Classifier (SNUH-MC) addressed data imbalance using the Synthetic Minority Over-sampling Technique (SMOTE) algorithm and incorporated OpenMax within a Multi-Layer Perceptron to prevent labeling errors in low-confidence diagnoses. Compared to two published CNS tumor methylation classification models (DKFZ-MC: Deutsches Krebsforschungszentrum Methylation Classifier v11b4: RandomForest, 767-MC: Multi-Layer Perceptron), our SNUH-MC showed improved performance in F1-score. For 'Filtered Test Data Set 1,' the SNUH-MC achieved higher F1-micro (0.932) and F1-macro (0.919) scores compared to DKFZ-MC v11b4 (F1-micro: 0.907, F1-macro: 0.627). We evaluated the performance of three classifiers; SNUH-MC, DKFZ-MC v11b4, and DKFZ-MC v12.5, using specific criteria. We set established 'Decisions' categories based on histopathology, clinical information, and next-generation sequencing to assess the classification results. When applied to 193 unknown SNUH methylation data samples, SNUH-MC notably improved diagnosis compared to DKFZ-MC v11b4. Specifically, 17 cases were reclassified as 'Match' and 34 cases as 'Likely Match' when transitioning from DKFZ-MC v11b4 to SNUH-MC. Additionally, SNUH-MC demonstrated similar results to DKFZ-MC v12.5 for 23 cases that were unclassified by v11b4.

Conclusions: This study presents SNUH-MC, an innovative methylation-based classification tool that significantly advances the field of neuropathology and bioinformatics. Our classifier incorporates cutting-edge techniques such as the SMOTE and OpenMax resulting in improved diagnostic accuracy and robustness, particularly when dealing with unknown or noisy data.

中枢神经系统肿瘤SNUH甲基化分类器。
背景:由德国癌症研究中心首创的中枢神经系统(CNS)肿瘤的甲基化分析,显著提高了诊断的准确性。本研究旨在通过利用公开可用的数据和创新的机器学习技术进一步提高甲基化分类器的性能。结果:首尔国立大学医院甲基化分类器(SNUH-MC)使用合成少数过采样技术(SMOTE)算法解决数据不平衡问题,并将OpenMax纳入多层感知器中,以防止低置信度诊断中的标记错误。与两种已发表的中枢神经系统肿瘤甲基化分类模型(DKFZ-MC: Deutsches Krebsforschungszentrum methylation Classifier v11b4: RandomForest, 767-MC: Multi-Layer Perceptron)相比,我们的SNUH-MC在f1评分上表现更好。对于“过滤测试数据集1”,与DKFZ-MC v11b4 (F1-micro: 0.907, F1-macro: 0.627)相比,SNUH-MC获得了更高的F1-micro(0.932)和F1-macro(0.919)分数。我们评估了三个分类器的性能;snh - mc, DKFZ-MC v11b4和DKFZ-MC v12.5,使用特定的标准。我们根据组织病理学、临床信息和下一代测序来评估分类结果,建立了“决策”分类。当应用于193个未知SNUH甲基化数据样本时,与DKFZ-MC v11b4相比,SNUH- mc显著提高了诊断。具体来说,从DKFZ-MC v11b4过渡到SNUH-MC时,17例被重新归类为“匹配”,34例被重新归类为“可能匹配”。此外,SNUH-MC在23例未被v11b4分类的病例中显示出与DKFZ-MC v12.5相似的结果。结论:这项研究提出了SNUH-MC,一个创新的基于甲基化的分类工具,显著推进了神经病理学和生物信息学领域。我们的分类器结合了SMOTE和OpenMax等尖端技术,从而提高了诊断的准确性和鲁棒性,特别是在处理未知或有噪声的数据时。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
自引率
5.30%
发文量
150
期刊介绍: Clinical Epigenetics, the official journal of the Clinical Epigenetics Society, is an open access, peer-reviewed journal that encompasses all aspects of epigenetic principles and mechanisms in relation to human disease, diagnosis and therapy. Clinical trials and research in disease model organisms are particularly welcome.
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