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 …

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 …

A systematic analysis of splicing variants identifies new diagnoses in the 100,000 Genomes Project

AJM Blakes, HA Wai, I Davies, HE Moledina, A Ruiz… - Genome Medicine, 2022 - Springer
Background Genomic variants which disrupt splicing are a major cause of rare genetic
diseases. However, variants which lie outside of the canonical splice sites are difficult to …

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 …

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 …

AVISPA: a web tool for the prediction and analysis of alternative splicing

Y Barash, J Vaquero-Garcia, J González-Vallinas… - Genome biology, 2013 - Springer
Transcriptome complexity and its relation to numerous diseases underpins the need to
predict in silico splice variants and the regulatory elements that affect them. Building upon …

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 …

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 …

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 …