[HTML][HTML] 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
… , CADD-Splice, we show that inclusion of splicing DNN effect … Variants disrupting splicing
are established contributors to … to successfully predict splice variants residing within exonic

[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
… of genomic variants affecting this process (splicing variants in … recent Machine Learning-based
algorithms, for the prediction of … MutPred Splice Impact of coding region substitutions on …

[HTML][HTML] SpliceAPP: an interactive web server to predict splicing errors arising from human mutations

AC Huang, JY Su, YJ Hung, HL Chiang, YT Chen… - BMC genomics, 2024 - Springer
predicting splice site and exonic splicing variants [10,11,12]. Moreover, the inherent limitations
of deepvariant disrupting canonical splicing, and the effect indicates the significance of a …

[PDF][PDF] Interpretable prioritization of splice variants in diagnostic next-generation sequencing

D Danis, JOB Jacobsen, LC Carmody… - The American Journal of …, 2021 - cell.com
… that contextualize predicted effects of variants on splicing to make it easier to interpret …
10% of all exonic variants, including missense and nonsense variants, may alter splicing.However, …

[HTML][HTML] Exon identity influences splicing induced by exonic variants and in silico prediction efficacy

N Martin, A Bergougnoux, N Baatallah… - Journal of Cystic …, 2021 - Elsevier
… of variants affecting 5’ and 3’ splice sites, the impact of variants … performed with Splice AI
[18], a deep learning-based tool … predictions (MutPred Splice and Splice AI) or false positive …

Splicing impact of deep exonic missense variants in CAPN3 explored systematically by minigene functional assay

E Dionnet, A Defour, N Da Silva, A Salvi… - Human …, 2020 - Wiley Online Library
… (deep exonic missense variants) disrupted normal splicing of … machine learning-based
computational tools failed to predictpredicted as splice-affecting by SpliceAI and MutPred Splice (…

The computational approach to variant interpretation: principles, results, and applicability

S Özkan, N Padilla, A Moles-Fernández, O Diez… - Clinical DNA variant …, 2021 - Elsevier
… and those using machine learning principles. For variants affecting splicing, we review the
evolution of computational approaches designed to predict splicing affectation and highlight …

NeoSplice: a bioinformatics method for prediction of splice variant neoantigens

S Chai, CC Smith, TK Kochar… - Bioinformatics …, 2022 - academic.oup.com
MutPred Splice and MiSplice are unique in using DNA-seq data to predict for somatic variants
that may disrupt normal splicing of … a machine learning model to predict exonic nucleotide …

Identification and in-silico characterization of splice-site variants from a large cardiogenetic national registry

K Rayani, B Davies, M Cheung, D Comber… - European Journal of …, 2023 - nature.com
MutPred Splice uses machine learning to predict the potential consequences of exonic changes
on pre-mRNA splicing [… -type and variant sequence features for machine learning-based

All exons are not created equal—exon vulnerability determines the effect of exonic mutations on splicing

LL Holm, TK Doktor, KK Flugt… - Nucleic Acids …, 2024 - academic.oup.com
… 359 mutations were predicted to alter either a … predicting splicing mutations that do not
directly alter splice site sequences. Notably, our exclusion of mutations that generate cryptic splice