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A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials 期刊论文

编号：

3427AEAC73B0F32CC3DF7DD8EC80DE42
作者：

Wang, Duo(王铎)#^[1,2,3]Liu, Yaqing#^[4,5]Zhang, Yuanfeng(张远峰)^[1,2,3]Chen, Qingwang^[4,5];Han, Yanxi(韩彦熙)^[1,2,3]Hou, Wanwan^[4,5];Liu, Cong(刘聪)^[1,2,3]Yu, Ying^[4,5];Li, Ziyang^[6];Li, Ziqiang(李自强)^[1,2,3]Zhao, Jiaxin(赵佳昕)^[1,2,3]Shi, Leming*^[4,5,7]Zheng, Yuanting*^[4,5,7]Li, Jinming(李金明)*^[1,2,3]Zhang, Rui(张瑞)*^[1,2,3]
语种：

英文
期刊：

NATURE COMMUNICATIONS ISSN：2041-1723 2024 年 15 卷 1 期 ; JUL 22
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摘要：

Translating RNA-seq into clinical diagnostics requires ensuring the reliability and cross-laboratory consistency of detecting clinically relevant subtle differential expressions, such as those between different disease subtypes or stages. As part of the Quartet project, we present an RNA-seq benchmarking study across 45 laboratories using the Quartet and MAQC reference samples spiked with ERCC controls. Based on multiple types of ''ground truth'', we systematically assess the real-world RNA-seq performance and investigate the influencing factors involved in 26 experimental processes and 140 bioinformatics pipelines. Here we show greater inter-laboratory variations in detecting subtle differential expressions among the Quartet samples. Experimental factors including mRNA enrichment and strandedness, and each bioinformatics step, emerge as primary sources of variations in gene expression. We underscore the profound influence of experimental execution, and provide best practice recommendations for experimental designs, strategies for filtering low-expression genes, and the optimal gene annotation and analysis pipelines. In summary, this study lays the foundation for developing and quality control of RNA-seq for clinical diagnostic purposes. Here the authors report on an RNA-seq benchmarking study that demonstrates greater inter-lab variations in detecting subtle differential expression. The study reveals the impact of experimental execution, experimental designs, low-expression gene filtering, and analysis tool selection.
推荐引用方式
GB/T 7714：

Wang Duo,Liu Yaqing,Zhang Yuanfeng, et al. A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials [J].NATURE COMMUNICATIONS,2024,15(1).
APA：

Wang Duo,Liu Yaqing,Zhang Yuanfeng,Chen Qingwang,&Zhang Rui.(2024).A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials .NATURE COMMUNICATIONS,15(1).
MLA：

Wang Duo, et al. "A real-world multi-center RNA-seq benchmarking study using the Quartet and MAQC reference materials" .NATURE COMMUNICATIONS 15,1(2024).
入库时间：

2024/8/6 15:14:58
更新时间：

2024/8/6 15:14:58
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