MADloy

Accurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male di...

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Autores: González, Juan Ramón|||0000-0003-3267-2146, López Sánchez, Marcos|||0000-0002-1517-5968, Cáceres, Alejandro|||0000-0001-8551-6695, Puig, Pedro|||0000-0002-6607-9642, Esko, Tõnu, Pérez-Jurado, Luis Alberto|||0000-0002-1988-3005
Tipo de recurso: artículo
Fecha de publicación:2020
País:España
Institución:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:238659
Acceso en línea:https://ddd.uab.cat/record/238659
https://dx.doi.org/urn:doi:10.1186/s12859-020-03768-z
Access Level:acceso abierto
Palabra clave:Loss of chromosome Y
SNP array
Bioconductor
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repository_id_str
spelling MADloyrobust detection of mosaic loss of chromosome Y from genotype-array-intensity dataGonzález, Juan Ramón|||0000-0003-3267-2146López Sánchez, Marcos|||0000-0002-1517-5968Cáceres, Alejandro|||0000-0001-8551-6695Puig, Pedro|||0000-0002-6607-9642Esko, TõnuPérez-Jurado, Luis Alberto|||0000-0002-1988-3005Loss of chromosome YSNP arrayBioconductorAccurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male disease. However, discrepancies of reported findings can be due to the uncertainty and variability of the methods used for mLOY detection and to the differences in the tissue-matrix used. We created a publicly available software tool called MADloy (Mosaic Alteration Detection for LOY) that incorporates existing methods and includes a new robust approach, allowing efficient calling in large studies and comparisons between methods. MADloy optimizes mLOY calling by correctly modeling the underlying reference population with no-mLOY status and incorporating B-deviation information. We observed improvements in the calling accuracy to previous methods, using experimentally validated samples, and an increment in the statistical power to detect associations with disease and mortality, using simulation studies and real dataset analyses. To understand discrepancies in mLOY detection across different tissues, we applied MADloy to detect the increment of mLOY cellularity in blood on 18 individuals after 3 years and to confirm that its detection in saliva was sub-optimal (41%). We additionally applied MADloy to detect the down-regulation genes in the chromosome Y in kidney and bladder tumors with mLOY, and to perform pathway analyses for the detection of mLOY in blood. MADloy is a new software tool implemented in R for the easy and robust calling of mLOY status across different tissues aimed to facilitate its study in large epidemiological studies. 22020-01-0120202020-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/238659https://dx.doi.org/urn:doi:10.1186/s12859-020-03768-zreponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengAgencia Estatal de Investigación https://doi.org/10.13039/501100011033 RTI2018-100789-B-I00Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2014/SGR-1468Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2017/SGR-1974Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 MDM-2014-0370Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 CEX2018-000806-Sopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:2386592026-06-06T12:50:31Z
dc.title.none.fl_str_mv MADloy
robust detection of mosaic loss of chromosome Y from genotype-array-intensity data
title MADloy
spellingShingle MADloy
González, Juan Ramón|||0000-0003-3267-2146
Loss of chromosome Y
SNP array
Bioconductor
title_short MADloy
title_full MADloy
title_fullStr MADloy
title_full_unstemmed MADloy
title_sort MADloy
dc.creator.none.fl_str_mv González, Juan Ramón|||0000-0003-3267-2146
López Sánchez, Marcos|||0000-0002-1517-5968
Cáceres, Alejandro|||0000-0001-8551-6695
Puig, Pedro|||0000-0002-6607-9642
Esko, Tõnu
Pérez-Jurado, Luis Alberto|||0000-0002-1988-3005
author González, Juan Ramón|||0000-0003-3267-2146
author_facet González, Juan Ramón|||0000-0003-3267-2146
López Sánchez, Marcos|||0000-0002-1517-5968
Cáceres, Alejandro|||0000-0001-8551-6695
Puig, Pedro|||0000-0002-6607-9642
Esko, Tõnu
Pérez-Jurado, Luis Alberto|||0000-0002-1988-3005
author_role author
author2 López Sánchez, Marcos|||0000-0002-1517-5968
Cáceres, Alejandro|||0000-0001-8551-6695
Puig, Pedro|||0000-0002-6607-9642
Esko, Tõnu
Pérez-Jurado, Luis Alberto|||0000-0002-1988-3005
author2_role author
author
author
author
author
dc.subject.none.fl_str_mv Loss of chromosome Y
SNP array
Bioconductor
topic Loss of chromosome Y
SNP array
Bioconductor
description Accurate protocols and methods to robustly detect the mosaic loss of chromosome Y (mLOY) are needed given its reported role in cancer, several age-related disorders and overall male mortality. Intensity SNP-array data have been used to infer mLOY status and to determine its prominent role in male disease. However, discrepancies of reported findings can be due to the uncertainty and variability of the methods used for mLOY detection and to the differences in the tissue-matrix used. We created a publicly available software tool called MADloy (Mosaic Alteration Detection for LOY) that incorporates existing methods and includes a new robust approach, allowing efficient calling in large studies and comparisons between methods. MADloy optimizes mLOY calling by correctly modeling the underlying reference population with no-mLOY status and incorporating B-deviation information. We observed improvements in the calling accuracy to previous methods, using experimentally validated samples, and an increment in the statistical power to detect associations with disease and mortality, using simulation studies and real dataset analyses. To understand discrepancies in mLOY detection across different tissues, we applied MADloy to detect the increment of mLOY cellularity in blood on 18 individuals after 3 years and to confirm that its detection in saliva was sub-optimal (41%). We additionally applied MADloy to detect the down-regulation genes in the chromosome Y in kidney and bladder tumors with mLOY, and to perform pathway analyses for the detection of mLOY in blood. MADloy is a new software tool implemented in R for the easy and robust calling of mLOY status across different tissues aimed to facilitate its study in large epidemiological studies.
publishDate 2020
dc.date.none.fl_str_mv 2
2020-01-01
2020
2020-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/238659
https://dx.doi.org/urn:doi:10.1186/s12859-020-03768-z
url https://ddd.uab.cat/record/238659
https://dx.doi.org/urn:doi:10.1186/s12859-020-03768-z
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.relation.none.fl_str_mv Agencia Estatal de Investigación https://doi.org/10.13039/501100011033 RTI2018-100789-B-I00
Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2014/SGR-1468
Agència de Gestió d'Ajuts Universitaris i de Recerca https://doi.org/10.13039/501100003030 2017/SGR-1974
Ministerio de Economía y Competitividad https://doi.org/10.13039/501100003329 MDM-2014-0370
Ministerio de Ciencia e Innovación https://doi.org/10.13039/501100004837 CEX2018-000806-S
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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