CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice

Cheng Jun; ?elik Muhammed Hasan; Nguyen Thi Yen Duong; Avsec ?iga; Gagneur Julien

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CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice

机译：Cagi 5拼接挑战：利用MMSPLICE改善外显子跳跃和内含子保留预测

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Abstract Pathogenic genetic variants often primarily affect splicing. However, it remains difficult to quantitatively predict whether and how genetic variants affect splicing. In 2018, the fifth edition of the Critical Assessment of Genome Interpretation proposed two splicing prediction challenges based on experimental perturbation assays: Vex‐seq, assessing exon skipping, and MaPSy, assessing splicing efficiency. We developed a modular modeling framework, MMSplice, the performance of which was among the best on both challenges. Here we provide insights into the modeling assumptions of MMSplice and its individual modules. We furthermore illustrate how MMSplice can be applied in practice for individual genome interpretation, using the MMSplice VEP plugin and the Kipoi variant interpretation plugin, which are directly applicable to VCF files.

机译：摘要致病性遗传变异通常主要影响拼接。然而，它仍然难以定量预测是否以及遗传变异如何影响拼接。 2018年，基于实验扰动测定的基因组解释的第五版批判性评估提出了两个拼接预测挑战：VEX-SEQ，评估外显子跳跃和Mapsy，评估剪接效率。我们开发了一个模块化建模框架，MMSPLICE，其性能在这两项挑战中是最佳的。在这里，我们提供了对MMSPLICE的建模假设及其各个模块的见解。我们此外，我们如何使用MMSPLICE VEP插件和KIPOI VELIANT解释插件在实践中应用MMSPLICE如何应用于单个基因组解释，这些解释插件直接适用于VCF文件。

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《Human mutation》 |2019年第9期|共9页
作者
Cheng Jun; ?elik Muhammed Hasan; Nguyen Thi Yen Duong; Avsec ?iga; Gagneur Julien;
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作者单位

Department of InformaticsTechnical University of MunichGarching Germany;

Department of InformaticsTechnical University of MunichGarching Germany;

Department of InformaticsTechnical University of MunichGarching Germany;

Department of InformaticsTechnical University of MunichGarching Germany;

Department of InformaticsTechnical University of MunichGarching Germany;

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原文格式 PDF
正文语种 eng
中图分类医学遗传学;
关键词
artificial neural network; splicing; variant effect; variant interpretation;

机译：人工神经网络;拼接;变异效果;变体解释;

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专利

1. CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice [J] . Cheng Jun, ?elik Muhammed Hasan, Nguyen Thi Yen Duong, Human mutation . 2019,第9期

机译：Cagi 5拼接挑战：利用MMSPLICE改善外显子跳跃和内含子保留预测
2. Splicing Defects in the AAAS Gene Leading to both Exon Skipping and Partial Intron Retention in a Tunisian Patient with Allgrove Syndrome [J] . Kallabi Fakhri, Ben Rhouma Bochra, Baklouti Siwar, Hormone research in p?diatrics . 2016,第2期

机译：AAAS基因的剪接缺陷会导致突尼斯患有Allgrove综合征的患者外显子跳跃和部分内含子保留
3. Splicing defects in ABCD1 gene leading to both exon skipping and partial intron retention in X-linked adrenoleukodystrophy Tunisian patient [J] . Kallabi Fakhri, Salem Ikhlass Hadj, Ben Chehida Amel, Neuroscience Research: The Official Journal of the Japan Neuroscience Society . 2015,第Null期

机译：X联肾上腺白质营养不良患者突尼斯患者中ABCD1基因的剪接缺陷导致外显子跳跃和部分内含子保留
4. Classic Cryptanalysis Applied to Exons and Introns Prediction [C] . Manuel Aguilar R., Hector Praire H., Laura Cruz R., International Conference on Computational Science and Its Applications(ICCSA 2007) pt.3; 20070826-29; Kuala Lumpur(MY) . 2007

机译：经典密码分析应用于外显子和内含子的预测
5. Statistical models for exon and intron content, with an application to genetic structure prediction [D] . Lusby, Fiona 2000

机译：外显子和内含子含量的统计模型，在遗传结构预测中的应用
6. Non-EST based prediction of exon skipping and intron retention events using Pfam information [O] . Michael Hiller, Klaus Huse, Matthias Platzer, 2005

机译：使用Pfam信息基于非EST预测外显子跳跃和内含子保留事件
7. Non-EST based prediction of exon skipping and intron retention events using Pfam information [O] . Michael Hiller, Klaus Huse, Matthias Platzer, 2005

机译：使用pfam信息的非基于EsT的外显子跳跃和内含子保留事件的预测

CAGI 5 splicing challenge: Improved exon skipping and intron retention predictions with MMSplice

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