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 …

[HTML][HTML] 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 …

[HTML][HTML] 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 …

[HTML][HTML] 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 …

[HTML][HTML] 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 …

Mechanism and modeling of human disease-associated near-exon intronic variants that perturb RNA splicing

HL Chiang, YT Chen, JY Su, HN Lin, CHA Yu… - Nature Structural & …, 2022 - nature.com
Abstract It is estimated that 10%–30% of disease-associated genetic variants affect splicing.
Splicing variants may generate deleteriously altered gene product and are potential …

Rules and tools to predict the splicing effects of exonic and intronic mutations

K Ohno, J Takeda, A Masuda - Wiley Interdisciplinary Reviews …, 2018 - Wiley Online Library
Development of next generation sequencing technologies has enabled detection of
extensive arrays of germline and somatic single nucleotide variations (SNVs) in human …

[HTML][HTML] What's wrong in a jump? Prediction and validation of splice site variants

G Riolo, S Cantara, C Ricci - Methods and Protocols, 2021 - mdpi.com
Alternative splicing (AS) is a crucial process to enhance gene expression driving organism
development. Interestingly, more than 95% of human genes undergo AS, producing multiple …

Comparison of In Silico Tools for Splice‐Altering Variant Prediction Using Established Spliceogenic Variants: An End‐User's Point of View

W Jang, J Park, H Chae, M Kim - International Journal of …, 2022 - Wiley Online Library
Assessing the impact of variants of unknown significance on splicing has become a critical
issue and a bottleneck, especially with the widespread implementation of whole‐genome or …

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

K Li, T Luo, Y Zhu, Y Huang, A Wang… - Nucleic Acids …, 2022 - academic.oup.com
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 …