Nucleic Acids Research2022，Vol.50Issue(16) ：12.DOI:10.1093/nar/gkac686

Performance evaluation of differential splicing analysis methods and splicing analytics platform construction

Li, Kuokuo Luo, Tengfei Zhu, Yan Wang, An Zhang, Di Dong, Lijie Wang, Yujian Wang, Rui Tang, Dongdong Yu, Zhen Shen, Qunshan Lv, Mingrong Ling, Zhengbao Fang, Zhenghuan Yuan, Jing Li, Bin He, Xiaojin Li, Jinchen Zhao, Guihu Huang, Yuanfeng Xia, Kun
Nucleic Acids Research2022，Vol.50Issue(16) ：12.DOI:10.1093/nar/gkac686
✕
  • NSTL
  • Oxford Univ Press

Performance evaluation of differential splicing analysis methods and splicing analytics platform construction

Li, Kuokuo 1Luo, Tengfei 2Zhu, Yan 2Wang, An 1Zhang, Di 1Dong, Lijie 2Wang, Yujian 2Wang, Rui 2Tang, Dongdong 1Yu, Zhen 1Shen, Qunshan 1Lv, Mingrong 1Ling, Zhengbao 2Fang, Zhenghuan 2Yuan, Jing 1Li, Bin 2He, Xiaojin 1Li, Jinchen 2Zhao, Guihu 2Huang, Yuanfeng 2Xia, Kun2
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作者信息

  • 1. Anhui Med Univ
  • 2. Cent South Univ
  • 折叠

Abstract

A proportion of previously defined benign variants or variants of uncertain significance in humans, which are challenging to identify, may induce an abnormal splicing process. An increasing number of methods have been developed to predict splicing variants, but their performance has not been completely evaluated using independent benchmarks. Here, we manually sourced similar to 50 000 positive/negative splicing variants from > 8000 studies and selected the independent splicing variants to evaluate the performance of prediction methods. These methods showed different performances in recognizing splicing variants in donor and acceptor regions, reminiscent of different weight coefficient applications to predict novel splicing variants. Of these methods, 66.67% exhibited higher specificities than sensitivities, suggesting that more moderate cut-off values are necessary to distinguish splicing variants. Moreover, the high correlation and consistent prediction ratio validated the feasibility of integration of the splicing prediction method in identifying splicing variants. We developed a splicing analytics platform called SPCards, which curates splicing variants from publications and predicts splicing scores of variants in genomes. SPCards also offers variant-level and gene-level annotation information, including allele frequency, non-synonymous prediction and comprehensive functional information. SPCards is suitable for high-throughput genetic identification of splicing variants, particularly those located in non-canonical splicing regions.

Key words

PRE-MESSENGER-RNA/PREDICTION/VARIANTS/GENE/JUNCTIONS/RESOURCE/ELEMENTS/DATABASE/DISEASE/CODE

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出版年

2022
Nucleic Acids Research

Nucleic Acids Research

SCI
ISSN：0305-1048
被引量4
参考文献量69
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