Genomic pan-cancer classification using image-based deep learning

被引:0
|
作者
Ye, Taoyu [1 ]
Li, Sen [1 ]
Zhang, Yang [1 ]
机构
[1] Harbin Inst Technol Shenzhen, Shenzhen 518055, Guangdong, Peoples R China
关键词
Pan-cancer classification; Genetic mutation map; Image-based deep learning; Guided Grad-CAM visualization; Tumor-type-specific genes; Pathway analysis; RENIN-ANGIOTENSIN SYSTEM; FOCAL-ADHESION KINASE; PROSTATE-CANCER; ANDROGEN RECEPTOR; GENE FUSIONS; CELL-GROWTH; ACTIVATION; PATHWAY; TARGETS; BIOLOGY;
D O I
10.1016/j.csbj.2021.01.0102
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Accurate cancer type classification based on genetic mutation can significantly facilitate cancer-related diagnosis. However, existing methods usually use feature selection combined with simple classifiers to quantify key mutated genes, resulting in poor classification performance. To circumvent this problem, a novel image-based deep learning strategy is employed to distinguish different types of cancer. Unlike conventional methods, we first convert gene mutation data containing single nucleotide polymorphisms, insertions and deletions into a genetic mutation map, and then apply the deep learning networks to classify different cancer types based on the mutation map. We outline these methods and present results obtained in training VGG-16, Inception-v3, ResNet-50 and Inception-ResNet-v2 neural networks to classify 36 types of cancer from 9047 patient samples. Our approach achieves overall higher accuracy (over 95%) compared with other widely adopted classification methods. Furthermore, we demonstrate the application of a Guided Grad-CAM visualization to generate heatmaps and identify the top-ranked tumor-type-specific genes and pathways. Experimental results on prostate and breast cancer demonstrate our method can be applied to various types of cancer. Powered by the deep learning, this approach can potentially provide a new solution for pan-cancer classification and cancer driver gene discovery. The source code and datasets supporting the study is available at https://github.com/yetaoyu/Genomic-pancancer-classification. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.
引用
收藏
页码:835 / 846
页数:12
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