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Integration of clinical and genomic data to enhance precision medicine: a case of study applied to the retina-macula

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Integration of clinical and genomic data to enhance precision medicine: a case of study applied to the retina-macula

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Reyes Román, JF.; León-Palacio, A.; García-Simón, A.; Cabrera Beyrouti, R.; Pastor López, O. (2023). Integration of clinical and genomic data to enhance precision medicine: a case of study applied to the retina-macula. Software & Systems Modeling. 22(1):159-174. https://doi.org/10.1007/s10270-022-01039-4

Por favor, use este identificador para citar o enlazar este ítem: http://hdl.handle.net/10251/195755

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Title: Integration of clinical and genomic data to enhance precision medicine: a case of study applied to the retina-macula
Author: REYES ROMÁN, JOSÉ FABIÁN León-Palacio, Ana García-Simón, Alberto Cabrera Beyrouti, Ruben Pastor López, Oscar
UPV Unit: Universitat Politècnica de València. Escola Tècnica Superior d'Enginyeria Informàtica
Issued date:
Abstract:
[EN] Age-related macular degeneration is a complex, multifactorial, and neurodegenerative disease that is the third cause of blindness after cataracts and glaucoma. To date, there are no effective remedies available for ...[+]
Subjects: Conceptual modeling , Information systems , Precision medicine , Age-related macular degeneration , Genomics
Copyrigths: Reserva de todos los derechos
Source:
Software & Systems Modeling. (issn: 1619-1366 )
DOI: 10.1007/s10270-022-01039-4
Publisher:
Springer-Verlag
Publisher version: https://doi.org/10.1007/s10270-022-01039-4
Project ID:
info:eu-repo/grantAgreement/AGENCIA ESTATAL DE INVESTIGACION//PDC2021-121243-I00//PLATAFORMA DELFOS: SISTEMA DE INFORMACIÓN PARA LA GESTIÓN DE VARIACIONES GENOMICAS/
info:eu-repo/grantAgreement/AGENCIA VALENCIANA DE LA INNOVACION//INNEST%2F2021%2F57//SISTEMA INTELIGENTE DE APOYO A LA TOMA DE DECISIONES CLÍNICAS EN MEDICINA DE PRECISIÓN/
info:eu-repo/grantAgreement/GENERALITAT VALENCIANA//CIPROM%2F2021%2F023//Combining Explainable Artificial Intelligence and Conceptual Modelling for Data Intensive Domains Management/
info:eu-repo/grantAgreement/AEI//PID2021-123824OB-I00//DESARROLLO ÁGIL DE SISTEMAS DESDE REQUISITOS A CÓDIGO/
info:eu-repo/grantAgreement/UPV//A36-G-MAC, 2019//Preparatory Action-UPVFISABIO/
Thanks:
The authors would like to thank the members of the PROS Research Center Genome group for the fruitful discussions regarding the application of CM in the medical field. This work was supported by the Valencian Innovation ...[+]
Type: Artículo

References

National Eye Institute: Age-related macular degeneration (2021) https://www.nei.nih.gov/learn-about-eye-health/eye-conditions-and-diseases/age-related-macular-degeneration

de Jong, E.K., Geerlings, M.J., den Hollander, A.I.: Age-related macular degeneration. Genet. Genom. Eye Dis. 1, 155–180 (2020). https://doi.org/10.1016/B978-0-12-816222-4.00010-1

Katta, S., Kaur, I., Chakrabarti, S.: The molecular genetic basis of age-related macular degeneration: an overview. J. Genet. 88(4), 425–449 (2009). https://doi.org/10.1007/s12041-009-0064-4 [+]
National Eye Institute: Age-related macular degeneration (2021) https://www.nei.nih.gov/learn-about-eye-health/eye-conditions-and-diseases/age-related-macular-degeneration

de Jong, E.K., Geerlings, M.J., den Hollander, A.I.: Age-related macular degeneration. Genet. Genom. Eye Dis. 1, 155–180 (2020). https://doi.org/10.1016/B978-0-12-816222-4.00010-1

Katta, S., Kaur, I., Chakrabarti, S.: The molecular genetic basis of age-related macular degeneration: an overview. J. Genet. 88(4), 425–449 (2009). https://doi.org/10.1007/s12041-009-0064-4

Resnikoff, S., Pascolini, D., Etya’Ale, D., Kocur, I., Pararajasegaram, R., Pokharel, G.P., Mariotti, S.P.: Global data on visual impairment in the year 2002. Bull. World Health Organ. 82, 844–851 (2004)

Velez-Montoya, R., Oliver, S.C., Olson, J.L., Fine, S.L., Quiroz-Mercado, H., Mandava, N.: Current knowledge and trends in age-related macular degeneration: genetics, epidemiology, and prevention. Retina 34(3), 423–441 (2014). https://doi.org/10.1097/IAE.0000000000000036

Loewenstein, A.: The significance of early detection of age-related macular degeneration: Richard and Hinda Rosenthal foundation lecture, the macula society 29th annual meeting. Retina 27(7), 873–878 (2007). https://doi.org/10.1097/IAE.0b013e318050d2ec

Boyer, D.S., Antoszyk, A.N., Awh, C.C., Bhisitkul, R.B., Shapiro, H., Acharya, N.R., MARINA Study Group: Subgroup analysis of the MARINA study of ranibizumab in neovascular age-related macular degeneration. Ophthalmology 114(2), 246–252 (2007). https://doi.org/10.1016/j.ophtha.2006.10.045

Olivé, A.: Conceptual Modeling of Information Systems. Springer Science and Business Media, Berlin (2007). https://doi.org/10.1007/978-3-540-39390-0

Reyes Román, J. F., Marco-Palomares, A., García S. A., Pastor, O.: A model-based application for the effective and efficient management of data associated with retina-macula pathology. In: Enterprise, Business-Process and Information Systems Modeling, pp. 366–379. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-79186-5_24

León, A., Pastor, Ó.: Enhancing precision medicine: a big data-driven approach for the management of genomic data. Big Data Res. 26, 100253 (2021). https://doi.org/10.1016/j.bdr.2021.100253

Reyes Román, J. F. (2018). Diseño y desarrollo de un sistema de información genómica basado en un modelo conceptual holístico del genoma humano (Doctoral dissertation, Universitat Politècnica de València). https://doi.org/10.4995/Thesis/10251/99565

García, A., León Palacio, A., Reyes Román, J.F., Casamayor, J.C., Pastor, O.: Towards the understanding of the human genome: a holistic conceptual modeling approach. IEEE Access 8, 197111–197123 (2020). https://doi.org/10.1109/ACCESS.2020.3034793

Aguilera, D., Gómez, C., Olivé, A.: Enforcement of conceptual schema quality issues in current integrated development environments. In: International Conference on Advanced Information Systems Engineering, pp. 626–640. Springer, Berlin, Heidelberg (2013). https://doi.org/10.1007/978-3-642-38709-8_40

Delcambre, L.M., Liddle, S.W., Pastor, O., Storey, V.C.: A reference framework for conceptual modeling. In: International Conference on Conceptual Modeling, pp. 27–42. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00847-5_4

Paton, N.W., Khan, S.A., Hayes, A., Moussouni, F., Brass, A., Eilbeck, K., Oliver, S.G.: Conceptual modelling of genomic information. Bioinformatics 16(6), 548–557 (2000). https://doi.org/10.1093/bioinformatics/16.6.548

Bornberg-Bauer, E., Paton, N.W.: Conceptual data modelling for bioinformatics. Brief. Bioinform. 3(2), 166–180 (2002). https://doi.org/10.1093/bib/3.2.166

Ram, S., Wei, W.: Modeling the semantics of 3D protein structures. In: International Conference on Conceptual Modeling, pp. 696–708. Springer, Berlin, Heidelberg (2004. https://doi.org/10.1007/978-3-540-30464-7_52

Eilbeck, K., Lewis, S.E., Mungall, C.J., et al.: The sequence ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44 (2005). https://doi.org/10.1186/gb-2005-6-5-r44

Vihinen, M.: Variation ontology for annotation of variation effects and mechanisms. Genome Res. 24(2), 356–364 (2014). https://doi.org/10.1101/gr.157495.113

Ashburner, M., Ball, C., Blake, J., et al.: Gene ontology: tool for the unification of biology. Nat. Genet. 25, 25–29 (2000). https://doi.org/10.1038/75556

Pastor, Ó., León, A., Reyes Román, J.F., García, A.S., Casamayor, J.C.: Using conceptual modeling to improve genome data management. Brief. Bioinform. 22(1), 45–54 (2021). https://doi.org/10.1093/bib/bbaa100

Burriel Coll, V. (2017). Diseño y desarrollo de un sistema de información para la gestión de información sobre Cáncer de mama (Doctoral dissertation, Universitat Politècnica de València). https://doi.org/10.4995/Thesis/10251/86158

Arevshatyan, S., Reyes Román, J.F., Burriel, V., Cañete, A., Castel, V., Pastor, Ó.: Integration and analysis of clinical and genomic data of neuroblastoma applying conceptual modeling. (2019)

Wieringa, R.: Design Science Methodology for Information Systems and Software Engineering, pp. 1–332. Springer-Verlag, Berlin Heidelberg (2014). https://doi.org/10.1007/978-3-662-43839-8

Marco Palomares, A.: Desarrollo dirigido por modelos para el análisis y gestión de los datos asociados a la patología macular. (Master Thesis, Universitat Politècnica de València) (2020). http://hdl.handle.net/10251/151886

Jenny Preece, H.S., Rogers, Y.: Interaction design: beyond human-computer interaction. (2015)

Seddon, J.M., Reynolds, R., Maller, J., Fagerness, J.A., Daly, M.J., Rosner, B.: Prediction model for prevalence and incidence of advanced age-related macular degeneration based on genetic, demographic, and environmental variables. Investig. Ophthalmol. Vis. Sci. 50(5), 2044–2053 (2009). https://doi.org/10.1167/iovs.08-3064

Fritsche, L.G., Fariss, R.N., Stambolian, D., Abecasis, G.R., Curcio, C.A., Swaroop, A.: Age-related macular degeneration: genetics and biology coming together. Annu. Rev. Genom. Hum. Genet. 15, 151–171 (2014). https://doi.org/10.1146/annurev-genom-090413-025610

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., et al.: The complete sequence of a human genome. Science 376(6588), 44–53 (2022). https://doi.org/10.1126/science.abj6987

Bonnans, C., Chou, J., Werb, Z.: Remodelling the extracellular matrix in development and disease. Nat. Rev. Mol. Cell Biol. 15(12), 786–801 (2014). https://doi.org/10.1038/nrm3904

Folkman, J.: Angiogenesis. Annu. Rev. Med. 57, 1–18 (2006). https://doi.org/10.1146/annurev.med.57.121304.131306

Beatty, S., Koh, H.H., Phil, M., Henson, D., Boulton, M.: The role of oxidative stress in the pathogenesis of age-related macular degeneration. Surv. Ophthalmol. 45(2), 115–134 (2000). https://doi.org/10.1016/S0039-6257(00)00140-5

Vavvas, D.G., Small, K.W., Awh, C.C., Zanke, B.W., Tibshirani, R.J., Kustra, R.: CFH and ARMS2 genetic risk determines progression to neovascular age-related macular degeneration after antioxidant and zinc supplementation. Proc. Natl. Acad. Sci. 115(4), E696–E704 (2018). https://doi.org/10.1073/pnas.1718059115

Seddon, J.M., Silver, R.E., Rosner, B.: Response to AREDS supplements according to genetic factors: survival analysis approach using the eye as the unit of analysis. Br. J. Ophthalmol. 100(12), 1731–1737 (2016). https://doi.org/10.1136/bjophthalmol-2016-308624

Brown, D.M., Michels, M., Kaiser, P.K., Heier, J.S., Sy, J.P., Ianchulev, T.: Ranibizumab versus verteporfin photodynamic therapy for neovascular age-related macular degeneration: two-year results of the ANCHOR study. Ophthalmology 116(1), 57–65 (2009). https://doi.org/10.1016/j.ophtha.2008.10.018

Tsilimbaris, M.K., López-Gálvez, M.I., Gallego-Pinazo, R., Margaron, P., Lambrou, G.N.: Epidemiological and clinical baseline characteristics as predictive biomarkers of response to anti-VEGF treatment in patients with neovascular AMD. J. Ophthalmol. (2016). https://doi.org/10.1155/2016/4367631

Lorés-Motta, L., de Jong, E.K., den Hollander, A.I.: Exploring the use of molecular biomarkers for precision medicine in age-related macular degeneration. Mol. Diagn. Ther. 22(3), 315–343 (2018). https://doi.org/10.1007/s40291-018-0332-1

García Simón, A., Costa Sánchez, M., Pastor, O.: Characterization and treatment of the temporal dimension of genomic variations: a conceptual model-based approach. In: International Conference on Conceptual Modeling, pp. 104–113. Springer, Cham (2021). https://doi.org/10.1007/978-3-030-88358-4_9

Reyes Román, J.F., Pastor, O., Casamayor, J.C., Valverde, F.: Applying conceptual modeling to better understand the human genome. In: International Conference on Conceptual Modeling, pp. 404–412. Springer, Cham (2016). https://doi.org/10.1007/978-3-319-46397-1_31

García, A., León Palacio, A., Reyes Román, J. F., Casamayor, J. C., Pastor, O.: A conceptual model-based approach to improve the representation and management of omics data in precision medicine. IEEE Access 9, 154071–154085 (2021). https://doi.org/10.1109/ACCESS.2021.3128757

León Palacio, A., Pastor, Ó., Casamayor Ródenas, J.C.: A method to identify relevant genome data: conceptual modeling for the medicine of precision. In: International Conference on Conceptual Modeling, pp. 597–609. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00847-5_44

León Palacio, A., Pastor, Ó.: Smart data for genomic information systems: the SILE method. Complex Syst. Inform. Model. Q. 17, 1–23 (2018). https://doi.org/10.7250/csimq.2018-17.01

Plazzotta, F., Luna, D., Bernaldo, González, de Quirós, F.: Sistemas de información en salud: integrando datos clínicos en diferentes escenarios y usuarios. Rev. Peru. Med. Exp. Salud Públ. 32(2), 343–351 (2015)

Instituto de Microcirugía Ocular: DMAE: Síntomas y tratamientos | IMO. (2018) https://www.imo.es/es/dmae

Pardo, I.C., Varona, D.G., de Miranda Remedios, D.I.: Degeneración macular relacionada con la edad. Arch. Méd. Camagüey 12(2), 1–22 (2008)

Ruiz-Moreno, J.M., Arias-Barquet, L., Armadá-Maresca, F., Boixadera-Espax, A., García-Layana, A., GÚIAS-DE PRÁDE PRÁCTICA CLÍNICA DE LA SERV:Tratamiento de la Degeneración Macular Asociada a la Edad (DMAE) Exudativa y Atrófica”. (Segunda revisión) Arch. Soc. Española Oftalmol. 84(7),333–344 (2009)

García, A., Reyes Román, J.F., Casamayor, J.C., Pastor, O.: Towards an effective and efficient management of genome data: an information systems engineering perspective. In: International Conference on Advanced Information Systems Engineering, pp. 99–110. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-21297-1_9

Baird, P.N., Hageman, G.S., Guymer, R.H.: New era for personalized medicine: the diagnosis and management of age-related macular degeneration. Clin. Exp. Ophthalmol. 37(8), 814–821 (2009). https://doi.org/10.1111/j.1442-9071.2009.02136.x

Senra, H., Macedo, A.F., Nunes, N., Balaskas, K., Aslam, T., Costa, E.: Psychological and psychosocial interventions for depression and anxiety in patients with age-related macular degeneration: a systematic review. Am. J. Geriatr. Psychiatry 27(8), 755–773 (2019). https://doi.org/10.1016/j.jagp.2019.03.001

Mehta, S.: Age-related macular degeneration. Prim. Care Clin. Off. Pract. (2015). https://doi.org/10.1016/j.pop.2015.05.009

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