SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation
Abstract 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...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | Human Genomics |
| Online Access: | https://doi.org/10.1186/s40246-023-00451-1 |
| _version_ | 1811165775031959552 |
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| author | Jean-Madeleine de Sainte Agathe Mathilde Filser Bertrand Isidor Thomas Besnard Paul Gueguen Aurélien Perrin Charles Van Goethem Camille Verebi Marion Masingue John Rendu Mireille Cossée Anne Bergougnoux Laurent Frobert Julien Buratti Élodie Lejeune Éric Le Guern Florence Pasquier Fabienne Clot Vasiliki Kalatzis Anne-Françoise Roux Benjamin Cogné David Baux |
| author_facet | Jean-Madeleine de Sainte Agathe Mathilde Filser Bertrand Isidor Thomas Besnard Paul Gueguen Aurélien Perrin Charles Van Goethem Camille Verebi Marion Masingue John Rendu Mireille Cossée Anne Bergougnoux Laurent Frobert Julien Buratti Élodie Lejeune Éric Le Guern Florence Pasquier Fabienne Clot Vasiliki Kalatzis Anne-Françoise Roux Benjamin Cogné David Baux |
| author_sort | Jean-Madeleine de Sainte Agathe |
| collection | DOAJ |
| description | Abstract 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 ). Graphical abstract |
| first_indexed | 2024-04-10T15:42:45Z |
| format | Article |
| id | doaj.art-6a70fd35d3034a74859689ebbe00f9a6 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-10T15:42:45Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | Human Genomics |
| spelling | doaj.art-6a70fd35d3034a74859689ebbe00f9a62023-02-12T12:17:51ZengBMCHuman Genomics1479-73642023-02-0117111610.1186/s40246-023-00451-1SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretationJean-Madeleine de Sainte Agathe0Mathilde Filser1Bertrand Isidor2Thomas Besnard3Paul Gueguen4Aurélien Perrin5Charles Van Goethem6Camille Verebi7Marion Masingue8John Rendu9Mireille Cossée10Anne Bergougnoux11Laurent Frobert12Julien Buratti13Élodie Lejeune14Éric Le Guern15Florence Pasquier16Fabienne Clot17Vasiliki Kalatzis18Anne-Françoise Roux19Benjamin Cogné20David Baux21Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne UniversitéDépartement de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne UniversitéNantes Université, CHU Nantes, Service de Génétique MédicaleNantes Université, CHU Nantes, Service de Génétique MédicaleLaboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/)Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de MontpellierLaboratoire de Génétique Moléculaire, CHU de Montpellier, Université de MontpellierService de Médecine Génomique, Maladies de Système et d’Organe, Fédération de Génétique et de Médecine Génomique, DMU BioPhyGen, APHP Centre-Université Paris Cité, Hôpital CochinCentre de référence des maladies neuromusculaires Nord/Est/Ile de France, Hôpital Pitié-Salpêtrière, APHPInserm, U1216, CHU Grenoble Alpes, Grenoble Institut Neurosciences, Université Grenoble AlpesLaboratoire de Génétique Moléculaire, CHU de Montpellier, Université de MontpellierLaboratoire de Génétique Moléculaire, CHU de Montpellier, Université de MontpellierLaboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/)Département de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne UniversitéDépartement de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne UniversitéDépartement de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne UniversitéCentre mémoire, Inserm U1172 DistALZ, Licend, Univ Lille, CHU LilleDépartement de Génétique Médicale, Groupe Hospitalier Universitaire de la Pitié Salpêtrière, AP-HP.Sorbonne Université, Laboratoire de Médecine Génomique Sorbonne UniversitéINM, Univ Montpellier, INSERMLaboratoire de Génétique Moléculaire, CHU de Montpellier, Université de MontpellierLaboratoire de Biologie Médicale Multi-Sites SeqOIA (laboratoire-seqoia.fr/)Laboratoire de Génétique Moléculaire, CHU de Montpellier, Université de MontpellierAbstract 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 ). Graphical abstracthttps://doi.org/10.1186/s40246-023-00451-1 |
| spellingShingle | Jean-Madeleine de Sainte Agathe Mathilde Filser Bertrand Isidor Thomas Besnard Paul Gueguen Aurélien Perrin Charles Van Goethem Camille Verebi Marion Masingue John Rendu Mireille Cossée Anne Bergougnoux Laurent Frobert Julien Buratti Élodie Lejeune Éric Le Guern Florence Pasquier Fabienne Clot Vasiliki Kalatzis Anne-Françoise Roux Benjamin Cogné David Baux SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation Human Genomics |
| title | SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation |
| title_full | SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation |
| title_fullStr | SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation |
| title_full_unstemmed | SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation |
| title_short | SpliceAI-visual: a free online tool to improve SpliceAI splicing variant interpretation |
| title_sort | spliceai visual a free online tool to improve spliceai splicing variant interpretation |
| url | https://doi.org/10.1186/s40246-023-00451-1 |
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