暗示:利用个性化参考图谱提高细胞类型解卷积的准确性

IF 10.4 1区 生物学 Q1 GENETICS & HEREDITY
Guanqun Meng, Yue Pan, Wen Tang, Lijun Zhang, Ying Cui, Fredrick R. Schumacher, Ming Wang, Rui Wang, Sijia He, Jeffrey Krischer, Qian Li, Hao Feng
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引用次数: 0

摘要

利用计算工具,可以对大容量转录组学进行解卷积,以估计组成细胞类型的丰度。然而,现有的解卷积方法是以假设整个研究人群都由一个参考面板提供服务为条件的,忽略了人与人之间的异质性。在这里,我们提出了一种利用个性化参考面板来解卷积细胞类型比例的新型算法 imply。模拟研究表明,与现有方法相比,偏差有所减少。对纵向联盟的真实数据分析显示,细胞类型比例的差异与 1 型糖尿病和帕金森病的几种疾病表型有关。imply 可通过 R/Bioconductor 软件包 ISLET 获得,网址是 https://bioconductor.org/packages/ISLET/ 。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
imply: improving cell-type deconvolution accuracy using personalized reference profiles
Using computational tools, bulk transcriptomics can be deconvoluted to estimate the abundance of constituent cell types. However, existing deconvolution methods are conditioned on the assumption that the whole study population is served by a single reference panel, ignoring person-to-person heterogeneity. Here, we present imply, a novel algorithm to deconvolute cell type proportions using personalized reference panels. Simulation studies demonstrate reduced bias compared with existing methods. Real data analyses on longitudinal consortia show disparities in cell type proportions are associated with several disease phenotypes in Type 1 diabetes and Parkinson’s disease. imply is available through the R/Bioconductor package ISLET at https://bioconductor.org/packages/ISLET/ .
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来源期刊
Genome Medicine
Genome Medicine GENETICS & HEREDITY-
CiteScore
20.80
自引率
0.80%
发文量
128
审稿时长
6-12 weeks
期刊介绍: Genome Medicine is an open access journal that publishes outstanding research applying genetics, genomics, and multi-omics to understand, diagnose, and treat disease. Bridging basic science and clinical research, it covers areas such as cancer genomics, immuno-oncology, immunogenomics, infectious disease, microbiome, neurogenomics, systems medicine, clinical genomics, gene therapies, precision medicine, and clinical trials. The journal publishes original research, methods, software, and reviews to serve authors and promote broad interest and importance in the field.
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