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首页> 外文期刊>IEEE/ACM transactions on computational biology and bioinformatics >CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression
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CNAPE: A Machine Learning Method for Copy Number Alteration Prediction from Gene Expression

机译：CNAPE：基因表达复制数改变预测的机器学习方法

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摘要

Detection of DNA copy number alteration in cancer cells is critical to understanding cancer initiation and progression. Widely used methods, such as DNA arrays and genomic DNA sequencing, are relatively expensive and require DNA samples at a microgram level, which are not avaiblable in certain situations like clinical biopsies or single-cell genomes. Here, we developed an alternative method-CNAPE to computationally infer copy number alterations from gene expression data. A prior knowledge-aided machine learning model was proposed, trained and tested on 9,740 cancer samples from The Cancer Genome Atlas. We then applied CNAPE to study gliomas, the most common and aggressive brain cancer in adult. Particularly, using RNA sequencing data, CNAPE respectively predicted DNA copy number of chromosomes, chromosomal arms, and 12 commonly altered genes, and achieved over 80 percent accuracy in almost all broad regions and some focal regions. CNAPE was developed as an easy-to-use tool at https://github.com/WangLabHKUST/CNAPE.
机译：癌细胞中DNA拷贝数改变的检测对于了解癌症启动和进展至关重要。广泛使用的方法（例如DNA阵列和基因组DNA测序）相对昂贵，并且需要在微克水平下进行DNA样品，其在某些情况下不可避免，如临床活组织检查或单细胞基因组。在这里，我们开发了一种替代方法-CNAPE，用于计算来自基因表达数据的拷贝数改变。提出了一种先前的知识辅助机器学习模型，从癌症基因组地图集的9,740个癌症样本上培训和测试。然后我们应用CNAPE学习胶质瘤，是成年人中最常见和最富有侵袭性的脑癌。特别地，使用RNA测序数据，CNAPE分别预测的DNA拷贝数的染色体，染色体臂和12个常见改变的基因，并且在几乎所有宽的地区和一些焦点区域中实现了超过80％的准确性。 CNAPE是在https://github.com/wanglabhkust/cnape的易于使用工具。

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    Mu Quanhua; Wang Jiguang;

  • 作者单位

    Hong Kong Univ Sci & Technol Dept Chem & Biol Engn Div Life Sci Ctr Syst Biol & Human Hlth Clear Water Bay Kowloon Hong Kong Peoples R China|Hong Kong Univ Sci & Technol State Key Lab Mol Neurosci Clear Water Bay Kowloon Hong Kong Peoples R China;

    Hong Kong Univ Sci & Technol Dept Chem & Biol Engn Div Life Sci Ctr Syst Biol & Human Hlth Clear Water Bay Kowloon Hong Kong Peoples R China|Hong Kong Univ Sci & Technol State Key Lab Mol Neurosci Clear Water Bay Kowloon Hong Kong Peoples R China;

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  • 正文语种 eng
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  • 关键词

    Copy number alteration; gene expression; cancer; machine learning; bioinformatics;

    机译：拷贝数改变;基因表达;癌症;机器学习;生物信息学;

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