Assessing the digenic model in rare disorders using population sequencing data
An important fraction of patients with rare disorders remains with no clear genetic diagnostic, even after whole-exome or whole-genome sequencing, posing a difficulty in giving adequate treatment and genetic counseling. The analysis of genomic data in rare disorders mostly considers the presence of single gene variants in coding regions that follow a concrete monogenic mode of inheritance. A digenic inheritance, with variants in two functionally-related genes in the same individual, is a plausible alternative that might explain the genetic basis of the disease in some cases. In this case, digenic disease combinations should be absent or underrepresented in healthy individuals. We develop a framework to evaluate the significance of digenic combinations and test its statistical power in different scenarios. We suggest that this approach will be relevant with the advent of new sequencing efforts including hundreds of thousands of samples.
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Springer Nature
2022-10-03
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Subjects: | Diseases, Genetic interaction, Population genetics, |
Online Access: | http://hdl.handle.net/10261/289423 http://dx.doi.org/10.13039/100004440 http://dx.doi.org/10.13039/501100011033 http://dx.doi.org/10.13039/501100000276 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100000265 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100000272 https://api.elsevier.com/content/abstract/scopus_id/85139249603 |
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Diseases Genetic interaction Population genetics Diseases Genetic interaction Population genetics Moreno-Ruiz, Nerea Lao, Oscar Arostegui, Juan Ignacio Laayouni, Hafid Casals, Ferran Genomics England Research Consortium Assessing the digenic model in rare disorders using population sequencing data |
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An important fraction of patients with rare disorders remains with no clear genetic diagnostic, even after whole-exome or whole-genome sequencing, posing a difficulty in giving adequate treatment and genetic counseling. The analysis of genomic data in rare disorders mostly considers the presence of single gene variants in coding regions that follow a concrete monogenic mode of inheritance. A digenic inheritance, with variants in two functionally-related genes in the same individual, is a plausible alternative that might explain the genetic basis of the disease in some cases. In this case, digenic disease combinations should be absent or underrepresented in healthy individuals. We develop a framework to evaluate the significance of digenic combinations and test its statistical power in different scenarios. We suggest that this approach will be relevant with the advent of new sequencing efforts including hundreds of thousands of samples. |
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Ministerio de Ciencia e Innovación (España) |
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Ministerio de Ciencia e Innovación (España) Moreno-Ruiz, Nerea Lao, Oscar Arostegui, Juan Ignacio Laayouni, Hafid Casals, Ferran Genomics England Research Consortium |
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Diseases Genetic interaction Population genetics |
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Moreno-Ruiz, Nerea Lao, Oscar Arostegui, Juan Ignacio Laayouni, Hafid Casals, Ferran Genomics England Research Consortium |
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Moreno-Ruiz, Nerea |
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Assessing the digenic model in rare disorders using population sequencing data |
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Assessing the digenic model in rare disorders using population sequencing data |
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Assessing the digenic model in rare disorders using population sequencing data |
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Assessing the digenic model in rare disorders using population sequencing data |
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Assessing the digenic model in rare disorders using population sequencing data |
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assessing the digenic model in rare disorders using population sequencing data |
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Springer Nature |
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2022-10-03 |
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http://hdl.handle.net/10261/289423 http://dx.doi.org/10.13039/100004440 http://dx.doi.org/10.13039/501100011033 http://dx.doi.org/10.13039/501100000276 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100000265 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100000272 https://api.elsevier.com/content/abstract/scopus_id/85139249603 |
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dig-ibe-es-10261-2894232024-05-16T20:42:40Z Assessing the digenic model in rare disorders using population sequencing data Moreno-Ruiz, Nerea Lao, Oscar Arostegui, Juan Ignacio Laayouni, Hafid Casals, Ferran Genomics England Research Consortium Ministerio de Ciencia e Innovación (España) Agencia Estatal de Investigación (España) European Commission Generalitat de Catalunya Department of Health & Social Care (UK) National Institute for Health Research (UK) National Health Service (UK) Wellcome Trust Medical Research Council (UK) Moreno-Ruiz, Nerea [0000-0002-9636-0179] Lao, Oscar [0000-0002-8525-9649] Arostegui, Juan Ignacio [0000-0003-4757-504X] Laayouni, Hafid [0000-0003-1297-5078] Casals, Ferran [0000-0002-8941-0369] Diseases Genetic interaction Population genetics An important fraction of patients with rare disorders remains with no clear genetic diagnostic, even after whole-exome or whole-genome sequencing, posing a difficulty in giving adequate treatment and genetic counseling. The analysis of genomic data in rare disorders mostly considers the presence of single gene variants in coding regions that follow a concrete monogenic mode of inheritance. A digenic inheritance, with variants in two functionally-related genes in the same individual, is a plausible alternative that might explain the genetic basis of the disease in some cases. In this case, digenic disease combinations should be absent or underrepresented in healthy individuals. We develop a framework to evaluate the significance of digenic combinations and test its statistical power in different scenarios. We suggest that this approach will be relevant with the advent of new sequencing efforts including hundreds of thousands of samples. This study was funded by grants RTI2018-096824-B-C22 (FC), PID2021-125106OB-C32 (FC), RTI2018-096824-B-C21 (JIA) and PID2021-125106OB-C31 (JIA) funded by MCIN/ AEI /10.13039/501100011033/ and FEDER Una manera de hacer Europa; Direcció General de Recerca- Generalitat de Catalunya (2017SGR-702) (FC); and CERCA Programme/Generalitat de Catalunya (JIA). NMR was supported by grant 2021 FI_B_00296 from Agència de Gestió d’Ajuts Universitaris i de Recerca, Generalitat de Catalunya. This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. Peer reviewed 2023-02-15T12:09:47Z 2023-02-15T12:09:47Z 2022-10-03 artículo http://purl.org/coar/resource_type/c_6501 European Journal of Human Genetics 30: 1439-1443 (2022) 1018 4813 http://hdl.handle.net/10261/289423 10.1038/s41431-022-01191-x 1476-5438 http://dx.doi.org/10.13039/100004440 http://dx.doi.org/10.13039/501100011033 http://dx.doi.org/10.13039/501100000276 http://dx.doi.org/10.13039/501100000780 http://dx.doi.org/10.13039/501100002809 http://dx.doi.org/10.13039/501100000265 http://dx.doi.org/10.13039/501100004837 http://dx.doi.org/10.13039/501100000272 36192439 2-s2.0-85139249603 https://api.elsevier.com/content/abstract/scopus_id/85139249603 en #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# #PLACEHOLDER_PARENT_METADATA_VALUE# info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-096824-B-C22/ES/IDENTIFICACION DE NUEVOS MECANISMOS MOLECULARES EN ENFERMEDADES AUTOINFLAMATORIAS/ info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2021-125106OB-C32 info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/RTI2018-096824-B-C21/ES/IDENTIFICACION DE NUEVOS MECANISMOS MOLECULARES EN ENFERMEDADES AUTOINFLAMATORIAS/ info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica, Técnica y de Innovación 2021-2023/PID2021-125106OB-C31 European journal of human genetics : EJHG Publisher's version The underlying dataset has been published as supplementary material of the article in the publisher platform at 10.1038/s41431-022-01191-x http://dx.doi.org/10.1038/s41431-022-01191-x Sí open application/pdf Springer Nature |