Benchmarking splice variant prediction algorithms using massively parallel splicing assays

C Smith, JO Kitzman - Genome Biology, 2023 - Springer
Background Variants that disrupt mRNA splicing account for a sizable fraction of the
pathogenic burden in many genetic disorders, but identifying splice-disruptive variants …

SPiP: Splicing Prediction Pipeline, a machine learning tool for massive detection of exonic and intronic variant effects on mRNA splicing

R Leman, B Parfait, D Vidaud, E Girodon… - Human …, 2022 - Wiley Online Library
Modeling splicing is essential for tackling the challenge of variant interpretation as each
nucleotide variation can be pathogenic by affecting pre‐mRNA splicing via …

Introme accurately predicts the impact of coding and noncoding variants on gene splicing, with clinical applications

PJ Sullivan, V Gayevskiy, RL Davis, M Wong, C Mayoh… - Genome Biology, 2023 - Springer
Predicting the impact of coding and noncoding variants on splicing is challenging,
particularly in non-canonical splice sites, leading to missed diagnoses in patients. Existing …

Machine learning approaches for the prioritization of genomic variants impacting pre-mRNA splicing

CF Rowlands, D Baralle, JM Ellingford - Cells, 2019 - mdpi.com
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the
advent of next-generation sequencing, allowing a deeper insight into a patient's variant …

CI-SpliceAI—improving machine learning predictions of disease causing splicing variants using curated alternative splice sites

Y Strauch, J Lord, M Niranjan, D Baralle - PLoS One, 2022 - journals.plos.org
Background It is estimated that up to 50% of all disease causing variants disrupt splicing.
Due to its complexity, our ability to predict which variants disrupt splicing is limited, meaning …

Performance evaluation of computational methods for splice-disrupting variants and improving the performance using the machine learning-based framework

H Liu, J Dai, K Li, Y Sun, H Wei, H Wang… - Briefings in …, 2022 - academic.oup.com
A critical challenge in genetic diagnostics is the assessment of genetic variants associated
with diseases, specifically variants that fall out with canonical splice sites, by altering …

Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies

MJ Cormier, BS Pedersen, P Bayrak-Toydemir… - BMC …, 2022 - Springer
Background Despite numerous molecular and computational advances, roughly half of
patients with a rare disease remain undiagnosed after exome or genome sequencing. A …

Using secondary structure to predict the effects of genetic variants on alternative splicing

R Wang, Y Wang, Z Hu - Human mutation, 2019 - Wiley Online Library
Accurate interpretation of genomic variants that alter RNA splicing is critical to precision
medicine. We present a computational framework, Prediction of variant Effect on Percent …

Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences

C Xu, S Bao, Y Wang, W Li, H Chen, Y Shen… - Genome …, 2024 - genome.cshlp.org
Alternative splicing plays a crucial role in protein diversity and gene expression regulation in
higher eukaryotes and mutations causing dysregulated splicing underlie a range of genetic …

CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores

P Rentzsch, M Schubach, J Shendure, M Kircher - Genome medicine, 2021 - Springer
Background Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate
synthesis of human proteins. Genetic variants impacting splicing underlie a substantial …