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A crowdsourcing database for the copy-number variation of the spanish population

Identificadores del recurso

López-López, D., Roldán, G., Fernández-Rueda, J. L., Bostelmann, G., Carmona, R., Aquino, V., Perez-Florido, J., Ortuño, F., Pita, G., Núñez-Torres, R., González-Neira, A., CSVS Crowdsourcing Group, Alonso, A., Salgado-Garrido, J., Pasalodos-Sanchez, S., Ayuso, C., Minguez, P., Avila-Fernandez, A., Corton, M., … Dopazo, J. (2023). A crowdsourcing database for the copy-number variation of the Spanish population. Human Genomics, 17(1), 20. https://doi.org/10.1186/s40246-023-00466-8

1473-9542

https://hdl.handle.net/2454/45578

10.1186/s40246-023-00466-8

Procedència

(Academica-e: repositorio digital de la Universidad Pública de Navarra)

Fitxa

Títol:: A crowdsourcing database for the copy-number variation of the spanish population
Tema:: Copy-number variation; Spanish population
Descripció:: Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.; This work is supported by Grants PID2020-117979RB-I00 from the Spanish Ministry of Science and Innovation; by the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019, IMP/00009 and PI20/01305), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”).
Idioma:: English
Relació:: Human Genomics, (2023) 17:20; info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117979RB-I00/ES/; info:eu-repo/grantAgreement/ISCIII/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 (ISCIII)/PI20%2F01305/ES/; https://doi.org/10.1186/s40246-023-00466-8
Autor/Productor:: López-López, Daniel; Roldán, Gema; Fernández-Rueda, José L.; Bostelmann, Gerrit; Carmona, Rosario; Aquino, Virginia; Pérez-Florido, Javier; Ortuño, Francisco; Pita, Guillermo; Núñez-Torres, Rocío; González Neira, Anna; Alonso Sánchez, Ángel Miguel; Salgado Garrido, Josefa; Pasalodos Sánchez, Sara; Ayuso, C.; Mínguez, P.; Ávila-Fernández, A.; Cortón, M.; 0000-0001-7701-7706; Borrego, S.; Antiñolo, G.; Carracedo, A.; Amigo, J.; Castaño, L. A.; Tejada, I.; Delmiro, A.; Espinos, C.; Grinberg, D.; Guillén, E.; Lapunzin, A. P.; López-Escámez, J. A.; Gallego-Martínez, A.; Martí, R.; Rovira, E.; Millán, J. M.; Moreno, M. A.; Morin, M.; Moreno-Galdó, A.; Fernández-Cancio, M.; Morte, B.; Mulero, V.; García, D.; Nunes, V.; Palau, F.; Pérez, B.; Jurado, L. P.; Perona, R.; Pujol, A.; Ramos, F.; López, E.; Ribes, A.; Rosell, J.; Surrallés, J.; Peña-Chilet, María; Dopazo, J.
Editor:: BMC
Otros colaboradores/productores:: Universidad Pública de Navarra. Departamento de Ciencias de la Salud; Nafarroako Unibertsitate Publikoa. Osasun Zientziak Saila
Drets:: © The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License.; http://creativecommons.org/licenses/by/4.0/; Acceso abierto / Sarbide irekia; info:eu-repo/semantics/openAccess
Data:: 2023
Tipo de recurso:: info:eu-repo/semantics/article; info:eu-repo/semantics/publishedVersion
Format:: application/pdf; application/zip

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2. <dc:creator>López-López, Daniel</dc:creator>
3. <dc:creator>Roldán, Gema</dc:creator>
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39. <dc:creator>Moreno-Galdó, A.</dc:creator>
40. <dc:creator>Fernández-Cancio, M.</dc:creator>
41. <dc:creator>Morte, B.</dc:creator>
42. <dc:creator>Mulero, V.</dc:creator>
43. <dc:creator>García, D.</dc:creator>
44. <dc:creator>Nunes, V.</dc:creator>
45. <dc:creator>Palau, F.</dc:creator>
46. <dc:creator>Pérez, B.</dc:creator>
47. <dc:creator>Jurado, L. P.</dc:creator>
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51. <dc:creator>López, E.</dc:creator>
52. <dc:creator>Ribes, A.</dc:creator>
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54. <dc:creator>Surrallés, J.</dc:creator>
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56. <dc:creator>Dopazo, J.</dc:creator>
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58. <dc:contributor>Nafarroako Unibertsitate Publikoa. Osasun Zientziak Saila</dc:contributor>
59. <dc:subject>Copy-number variation</dc:subject>
60. <dc:subject>Spanish population</dc:subject>
61. <dc:description>Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.</dc:description>
62. <dc:description>This work is supported by Grants PID2020-117979RB-I00 from the Spanish Ministry of Science and Innovation; by the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019, IMP/00009 and PI20/01305), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”).</dc:description>
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  61. <dc:description>Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.</dc:description>
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6. <description>Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.</description>
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7. <dc:description>Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.</dc:description>
8. <dc:description>This work is supported by Grants PID2020-117979RB-I00 from the Spanish Ministry of Science and Innovation; by the Institute of Health Carlos III (project IMPaCT-Data, exp. IMP/00019, IMP/00009 and PI20/01305), co-funded by the European Union, European Regional Development Fund (ERDF, “A way to make Europe”).</dc:description>
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1. <dc:title>A crowdsourcing database for the copy-number variation of the spanish population</dc:title>
2. <dc:creator>López-López, Daniel</dc:creator>
3. <dc:creator>Roldán, Gema</dc:creator>
4. <dc:creator>Fernández-Rueda, José L.</dc:creator>
5. <dc:creator>Bostelmann, Gerrit</dc:creator>
6. <dc:creator>Carmona, Rosario</dc:creator>
7. <dc:creator>Aquino, Virginia</dc:creator>
8. <dc:creator>Pérez-Florido, Javier</dc:creator>
9. <dc:creator>Ortuño, Francisco</dc:creator>
10. <dc:creator>Pita, Guillermo</dc:creator>
11. <dc:creator>Núñez-Torres, Rocío</dc:creator>
12. <dc:creator>González Neira, Anna</dc:creator>
13. <dc:creator>Alonso Sánchez, Ángel Miguel</dc:creator>
14. <dc:creator>Salgado Garrido, Josefa</dc:creator>
15. <dc:creator>Pasalodos Sánchez, Sara</dc:creator>
16. <dc:creator>Ayuso, C.</dc:creator>
17. <dc:creator>Mínguez, P.</dc:creator>
18. <dc:creator>Ávila-Fernández, A.</dc:creator>
19. <dc:creator>Cortón, M.</dc:creator>
20. <dc:creator>Artuch Garde, Raquel</dc:creator>
21. <dc:creator>Borrego, S.</dc:creator>
22. <dc:creator>Antiñolo, G.</dc:creator>
23. <dc:creator>Carracedo, A.</dc:creator>
24. <dc:creator>Amigo, J.</dc:creator>
25. <dc:creator>Castaño, L. A.</dc:creator>
26. <dc:creator>Tejada, I.</dc:creator>
27. <dc:creator>Delmiro, A.</dc:creator>
28. <dc:creator>Espinos, C.</dc:creator>
29. <dc:creator>Grinberg, D.</dc:creator>
30. <dc:creator>Guillén, E.</dc:creator>
31. <dc:creator>Lapunzin, A. P.</dc:creator>
32. <dc:creator>López-Escámez, J. A.</dc:creator>
33. <dc:creator>Gallego-Martínez, A.</dc:creator>
34. <dc:creator>Martí, R.</dc:creator>
35. <dc:creator>Rovira, E.</dc:creator>
36. <dc:creator>Millán, J. M.</dc:creator>
37. <dc:creator>Moreno, M. A.</dc:creator>
38. <dc:creator>Morin, M.</dc:creator>
39. <dc:creator>Moreno-Galdó, A.</dc:creator>
40. <dc:creator>Fernández-Cancio, M.</dc:creator>
41. <dc:creator>Morte, B.</dc:creator>
42. <dc:creator>Mulero, V.</dc:creator>
43. <dc:creator>García, D.</dc:creator>
44. <dc:creator>Nunes, V.</dc:creator>
45. <dc:creator>Palau, F.</dc:creator>
46. <dc:creator>Pérez, B.</dc:creator>
47. <dc:creator>Jurado, L. P.</dc:creator>
48. <dc:creator>Perona, R.</dc:creator>
49. <dc:creator>Pujol, A.</dc:creator>
50. <dc:creator>Ramos, F.</dc:creator>
51. <dc:creator>López, E.</dc:creator>
52. <dc:creator>Ribes, A.</dc:creator>
53. <dc:creator>Rosell, J.</dc:creator>
54. <dc:creator>Surrallés, J.</dc:creator>
55. <dc:creator>Peña-Chilet, María</dc:creator>
56. <dc:creator>Dopazo, J.</dc:creator>
57. <dc:contributor>Universidad Pública de Navarra. Departamento de Ciencias de la Salud</dc:contributor>
58. <dc:contributor>Nafarroako Unibertsitate Publikoa. Osasun Zientziak Saila</dc:contributor>
59. <dc:subject>Copy-number variation</dc:subject>
60. <dc:subject>Spanish population</dc:subject>
61. <dcterms:abstract>Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.</dcterms:abstract>
62. <dcterms:issued>2023</dcterms:issued>
63. <dc:type>Artículo / Artikulua</dc:type>
64. <dc:type>info:eu-repo/semantics/article</dc:type>
65. <dc:identifier>López-López, D., Roldán, G., Fernández-Rueda, J. L., Bostelmann, G., Carmona, R., Aquino, V., Perez-Florido, J., Ortuño, F., Pita, G., Núñez-Torres, R., González-Neira, A., CSVS Crowdsourcing Group, Alonso, A., Salgado-Garrido, J., Pasalodos-Sanchez, S., Ayuso, C., Minguez, P., Avila-Fernandez, A., Corton, M., … Dopazo, J. (2023). A crowdsourcing database for the copy-number variation of the Spanish population. Human Genomics, 17(1), 20. https://doi.org/10.1186/s40246-023-00466-8</dc:identifier>
66. <dc:identifier>1473-9542</dc:identifier>
67. <dc:identifier>https://hdl.handle.net/2454/45578</dc:identifier>
68. <dc:identifier>10.1186/s40246-023-00466-8</dc:identifier>
69. <dc:language>eng</dc:language>
70. <dc:relation>Human Genomics, (2023) 17:20</dc:relation>
71. <dc:relation>info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-117979RB-I00/ES/</dc:relation>
72. <dc:relation>info:eu-repo/grantAgreement/ISCIII/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020 (ISCIII)/PI20%2F01305/ES/</dc:relation>
73. <dc:relation>https://doi.org/10.1186/s40246-023-00466-8</dc:relation>
74. <dc:rights>http://creativecommons.org/licenses/by/4.0/</dc:rights>
75. <dc:rights>Acceso abierto / Sarbide irekia</dc:rights>
76. <dc:rights>info:eu-repo/semantics/openAccess</dc:rights>
77. <dc:rights>© The Author(s) 2023. This article is licensed under a Creative Commons Attribution 4.0 International License.</dc:rights>
78. <dc:publisher>BMC</dc:publisher>
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  1. <dc:title>A crowdsourcing database for the copy-number variation of the spanish population</dc:title>
  2. <dc:contributor>Universidad Pública de Navarra. Departamento de Ciencias de la Salud</dc:contributor>
  3. <dc:contributor>Nafarroako Unibertsitate Publikoa. Osasun Zientziak Saila</dc:contributor>
  4. <dc:subject>Copy-number variation</dc:subject>
  5. <dc:subject>Spanish population</dc:subject>
  6. <dc:description>Background: Despite being a very common type of genetic variation, the distribution of copy-number variations (CNVs) in the population is still poorly understood. The knowledge of the genetic variability, especially at the level of the local population, is a critical factor for distinguishing pathogenic from non-pathogenic variation in the discovery of new disease variants. Results: Here, we present the SPAnish Copy Number Alterations Collaborative Server (SPACNACS), which currently contains copy number variation profiles obtained from more than 400 genomes and exomes of unrelated Spanish individuals. By means of a collaborative crowdsourcing effort whole genome and whole exome sequencing data, produced by local genomic projects and for other purposes, is continuously collected. Once checked both, the Spanish ancestry and the lack of kinship with other individuals in the SPACNACS, the CNVs are inferred for these sequences and they are used to populate the database. A web interface allows querying the database with different filters that include ICD10 upper categories. This allows discarding samples from the disease under study and obtaining pseudo-control CNV profiles from the local population. We also show here additional studies on the local impact of CNVs in some phenotypes and on pharmacogenomic variants. SPACNACS can be accessed at: http://csvs.clinbioinfosspa.es/spacnacs/. Conclusion: SPACNACS facilitates disease gene discovery by providing detailed information of the local variability of the population and exemplifies how to reuse genomic data produced for other purposes to build a local reference database.</dc:description>
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xoai

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