Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease.

Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease.
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DOI:
10.1186/s13073-022-01012-2
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发表时间:
2022-02-01
期刊:
影响因子:
12.3
通讯作者:
Zhang J
Zhang J
中科院分区:
生物学1区
文献类型:
--
作者:
Johnson TS;Yu CY;Huang Z;Xu S;Wang T;Dong C;Shao W;Zaid MA;Huang X;Wang Y;Bartlett C;Zhang Y;Walker BA;Liu Y;Huang K;Zhang J

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我们提出了DEGAS(单个细胞的诊断证据GAuge),一种新型的深度迁移学习框架,将疾病信息从患者转移到细胞。我们将这种可传递的信息称为“印象”,它允许单个细胞与疾病属性相关联,如诊断,预后和对治疗的反应。使用模拟的数据和10个不同的单细胞和患者的散装组织转录组数据集从多形性胶质母细胞瘤(GBM),阿尔茨海默氏病(AD),多发性骨髓瘤(MM),我们证明了可行性,灵活性和广泛的应用程序的DEGAS框架。骨髓瘤单细胞转录组学的DEGAS分析鉴定了与进展相关的PHF 19高骨髓瘤细胞。可用性:https://github.com/tsteelejohnson91/DEGAS.在线版本包含补充材料,可通过10.1186/s13073-022-01012-2获得。
We propose DEGAS (Diagnostic Evidence GAuge of Single cells), a novel deep transfer learning framework, to transfer disease information from patients to cells. We call such transferrable information “impressions,” which allow individual cells to be associated with disease attributes like diagnosis, prognosis, and response to therapy. Using simulated data and ten diverse single-cell and patient bulk tissue transcriptomic datasets from glioblastoma multiforme (GBM), Alzheimer’s disease (AD), and multiple myeloma (MM), we demonstrate the feasibility, flexibility, and broad applications of the DEGAS framework. DEGAS analysis on myeloma single-cell transcriptomics identified PHF19high myeloma cells associated with progression. Availability: https://github.com/tsteelejohnson91/DEGAS. The online version contains supplementary material available at 10.1186/s13073-022-01012-2.
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