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 …

Predicting the effect of variants on splicing using Convolutional Neural Networks

T Thanapattheerakul, W Engchuan, JH Chan - PeerJ, 2020 - peerj.com
Mutations that cause an error in the splicing of a messenger RNA (mRNA) can lead to
diseases in humans. Various computational models have been developed to recognize the …

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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 …