SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation.
Journal
Human genomics
ISSN: 1479-7364
Titre abrégé: Hum Genomics
Pays: England
ID NLM: 101202210
Informations de publication
Date de publication:
10 02 2023
10 02 2023
Historique:
received:
01
12
2022
accepted:
18
01
2023
entrez:
11
2
2023
pubmed:
12
2
2023
medline:
15
2
2023
Statut:
epublish
Résumé
SpliceAI is an open-source deep learning splicing prediction algorithm that has demonstrated in the past few years its high ability to predict splicing defects caused by DNA variations. However, its outputs present several drawbacks: (1) although the numerical values are very convenient for batch filtering, their precise interpretation can be difficult, (2) the outputs are delta scores which can sometimes mask a severe consequence, and (3) complex delins are most often not handled. We present here SpliceAI-visual, a free online tool based on the SpliceAI algorithm, and show how it complements the traditional SpliceAI analysis. First, SpliceAI-visual manipulates raw scores and not delta scores, as the latter can be misleading in certain circumstances. Second, the outcome of SpliceAI-visual is user-friendly thanks to the graphical presentation. Third, SpliceAI-visual is currently one of the only SpliceAI-derived implementations able to annotate complex variants (e.g., complex delins). We report here the benefits of using SpliceAI-visual and demonstrate its relevance in the assessment/modulation of the PVS1 classification criteria. We also show how SpliceAI-visual can elucidate several complex splicing defects taken from the literature but also from unpublished cases. SpliceAI-visual is available as a Google Colab notebook and has also been fully integrated in a free online variant interpretation tool, MobiDetails ( https://mobidetails.iurc.montp.inserm.fr/MD ).
Identifiants
pubmed: 36765386
doi: 10.1186/s40246-023-00451-1
pii: 10.1186/s40246-023-00451-1
pmc: PMC9912651
doi:
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7Informations de copyright
© 2023. The Author(s).
Références
Genet Med. 2020 Aug;22(8):1355-1365
pubmed: 32398771
J Alzheimers Dis. 2014;42(3):939-47
pubmed: 25024321
Cancer Res. 2017 Nov 1;77(21):e31-e34
pubmed: 29092934
Genome Biol. 2016 Jun 06;17(1):122
pubmed: 27268795
Nature. 2020 May;581(7809):434-443
pubmed: 32461654
Nucleic Acids Res. 2022 Sep 9;50(16):9115-9126
pubmed: 35993808
EMBO J. 2016 Apr 1;35(7):706-23
pubmed: 26896445
Orphanet J Rare Dis. 2012 Mar 27;7:18
pubmed: 22452838
Hum Mutat. 2011 Mar;32(3):299-308
pubmed: 21972111
Cell. 2019 Jan 24;176(3):535-548.e24
pubmed: 30661751
Nat Commun. 2022 Mar 29;13(1):1655
pubmed: 35351883
Eur J Hum Genet. 2021 Feb;29(2):356-360
pubmed: 33161418
PLoS Genet. 2010 Oct 07;6(10):
pubmed: 20949073
Int J Mol Sci. 2021 Apr 16;22(8):
pubmed: 33923806
Hum Genet. 2017 Sep;136(9):1155-1172
pubmed: 28597072
PLoS One. 2022 Jun 1;17(6):e0256411
pubmed: 35648796
Nature. 2022 Jul;607(7920):732-740
pubmed: 35859178
Genet Med. 2022 Jan;24(1):130-145
pubmed: 34906502
Hum Mutat. 2018 Nov;39(11):1517-1524
pubmed: 30192042
Genet Med. 2015 May;17(5):405-24
pubmed: 25741868
Nature. 2022 Apr;604(7905):310-315
pubmed: 35388217
Sci Rep. 2021 Oct 18;11(1):20607
pubmed: 34663891
Genome Biol. 2022 Apr 21;23(1):103
pubmed: 35449021
Fly (Austin). 2012 Apr-Jun;6(2):80-92
pubmed: 22728672
Genome Res. 2002 Jun;12(6):996-1006
pubmed: 12045153
FEBS Lett. 2005 Mar 28;579(9):1900-3
pubmed: 15792793
BMC Med Genomics. 2021 Jun 9;14(1):152
pubmed: 34107977
Orphanet J Rare Dis. 2015 Apr 12;10:44
pubmed: 25886057
Clin Genet. 2018 Apr;93(4):752-761
pubmed: 28881385
PLoS One. 2022 Jun 3;17(6):e0269159
pubmed: 35657932
Eur J Hum Genet. 2010 May;18(5):544-52
pubmed: 20029458
Genet Med. 2020 Jun;22(6):1005-1014
pubmed: 32123317
Hum Mol Genet. 2006 Mar 15;15(6):999-1013
pubmed: 16461336
Sci Rep. 2021 Apr 8;11(1):7696
pubmed: 33833316
Eur J Immunol. 2010 Jun;40(6):1778-85
pubmed: 20213738
Am J Hum Genet. 2021 Sep 2;108(9):1564-1577
pubmed: 34289339
Genes (Basel). 2021 Aug 25;12(9):
pubmed: 34573290
Nucleic Acids Res. 2018 Jan 4;46(D1):D1062-D1067
pubmed: 29165669