Assessing predictions of the impact of variants on splicing in CAGI5

Mount SM, Avsec Z, Carmel L, Casadio R, Celik MH, Chen K, Cheng J, Cohen NE, Fairbrother WG, Fenesh T, Gagneur J, Gotea V, Holzer T, Lin CF, Martelli PL, Naito T, Thi Yen Duong Nguyen , Savojardo C, Unger R, Warig R, Yang Y, Zhao H (2019)

Publication Type: Journal article

Publication year: 2019

Journal

Human Mutation Wiley-Blackwell

Book Volume: 40

Pages Range: 1215-1224

Journal Issue: 9

DOI: 10.1002/humu.23869

Abstract

Precision medicine and sequence-based clinical diagnostics seek to predict disease risk or to identify causative variants from sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. In the past, few CAGI challenges have addressed the impact of sequence variants on splicing. In CAGI5, two challenges (Vex-seq and MaPSY) involved prediction of the effect of variants, primarily single-nucleotide changes, on splicing. Although there are significant differences between these two challenges, both involved prediction of results from high-throughput exon inclusion assays. Here, we discuss the methods used to predict the impact of these variants on splicing, their performance, strengths, and weaknesses, and prospects for predicting the impact of sequence variation on splicing and disease phenotypes.

Involved external institutions

University of Maryland US United States (USA) (US) Technische Universität München (TUM) DE Germany (DE) Hebrew University of Jerusalem IL Israel (IL) University of Bologna / Università di Bologna IT Italy (IT) Sun Yat-Sen University CN China (CN) Brown University US United States (USA) (US) Bar-Ilan University IL Israel (IL) National Human Genome Research Institute (NHGRI) US United States (USA) (US) DNAnexus US United States (USA) (US) University of Tokyo JP Japan (JP) University of California, Berkeley US United States (USA) (US)

How to cite

APA:

Mount, S.M., Avsec, Z., Carmel, L., Casadio, R., Celik, M.H., Chen, K.,... Zhao, H. (2019). Assessing predictions of the impact of variants on splicing in CAGI5. Human Mutation, 40(9), 1215-1224. https://dx.doi.org/10.1002/humu.23869

MLA:

Mount, Stephen M., et al. "Assessing predictions of the impact of variants on splicing in CAGI5." Human Mutation 40.9 (2019): 1215-1224.

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