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 …

Computational prediction of human deep intronic variation

P Barbosa, R Savisaar, M Carmo-Fonseca… - …, 2023 - academic.oup.com
Background The adoption of whole-genome sequencing in genetic screens has facilitated
the detection of genetic variation in the intronic regions of genes, far from annotated splice …

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 …

Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome

D Garrido-Martín, B Borsari, M Calvo, F Reverter… - Nature …, 2021 - nature.com
Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we
develop an efficient and reproducible pipeline for the discovery of genetic variants that affect …

MMSplice: modular modeling improves the predictions of genetic variant effects on splicing

J Cheng, TYD Nguyen, KJ Cygan, MH Çelik… - Genome biology, 2019 - Springer
Predicting the effects of genetic variants on splicing is highly relevant for human genetics.
We describe the framework MMSplice (modular modeling of splicing) with which we built the …

Benchmarking deep learning splice prediction tools using functional splice assays

TV Riepe, M Khan, S Roosing, FPM Cremers… - Human …, 2021 - Wiley Online Library
Hereditary disorders are frequently caused by genetic variants that affect pre‐messenger
RNA splicing. Though genetic variants in the canonical splice motifs are almost always …

VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases

D Huang, Y Zhou, X Yi, X Fan, J Wang… - Nucleic acids …, 2022 - academic.oup.com
Interpreting the molecular mechanism of genomic variations and their causal relationship
with diseases/traits are important and challenging problems in the human genetic study. To …

Genome-wide detection of human variants that disrupt intronic branchpoints

P Zhang, Q Philippot, W Ren, WT Lei… - Proceedings of the …, 2022 - National Acad Sciences
Pre-messenger RNA splicing is initiated with the recognition of a single-nucleotide intronic
branchpoint (BP) within a BP motif by spliceosome elements. Forty-eight rare variants in 43 …

Interpretable prioritization of splice variants in diagnostic next-generation sequencing

D Danis, JOB Jacobsen, LC Carmody… - The American Journal of …, 2021 - cell.com
A critical challenge in genetic diagnostics is the computational assessment of candidate
splice variants, specifically the interpretation of nucleotide changes located outside of the …

Analysis of transcript-deleterious variants in Mendelian disorders: implications for RNA-based diagnostics

S Maddirevula, H Kuwahara, N Ewida, HE Shamseldin… - Genome biology, 2020 - Springer
Background At least 50% of patients with suspected Mendelian disorders remain
undiagnosed after whole-exome sequencing (WES), and the extent to which non-coding …