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

• Published in: Nucleic acids research Vol. 50; no. 16; pp. 9115 - 9126
• Main Authors: Li, Kuokuo, Luo, Tengfei, Zhu, Yan, Huang, Yuanfeng, 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, Xia, Kun, He, Xiaojin, Li, Jinchen, Zhao, Guihu
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 09.09.2022
• Subjects: Data Resources and Analyses; Gene Frequency; Humans; Molecular Sequence Annotation; RNA Splicing - genetics
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkac686

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 ∼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.