CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Autores
Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; Repo, Susanna; Hoskins, Roger A.; Andreoletti, Gaia; Barsky, Daniel; Chellapan, Ajithavalli; Chu, Hoyin; Dabbiru, Navya; Kollipara, Naveen K.; Ly, Melissa; Neumann, Andrew J.; Pal, Lipika R.; Odell, Eric; Pandey, Gaurav; Peters Petrulewicz, Robin C.; Srinivasan, Rajgopal; Yee, Stephen F.; Yeleswarapu, Sri Jyothsna; Zuhl, Maya; Adebali, Ogun; Fornasari, Maria Silvina; Patra, Ayoti; O'Donnell Luria, Anne; Ng, Pauline C.; Shon, John; Veltman, Joris; Zook, Justin M.
Año de publicación
2024
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. Results Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. Conclusions Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
Fil: Jain, Shantanu. No especifíca;
Fil: Bakolitsa, Constantina. No especifíca;
Fil: Brenner, Steven E.. No especifíca;
Fil: Radivojac, Predrag. No especifíca;
Fil: Moult, John. No especifíca;
Fil: Repo, Susanna. No especifíca;
Fil: Hoskins, Roger A.. No especifíca;
Fil: Andreoletti, Gaia. No especifíca;
Fil: Barsky, Daniel. No especifíca;
Fil: Chellapan, Ajithavalli. No especifíca;
Fil: Chu, Hoyin. No especifíca;
Fil: Dabbiru, Navya. No especifíca;
Fil: Kollipara, Naveen K.. No especifíca;
Fil: Ly, Melissa. No especifíca;
Fil: Neumann, Andrew J.. No especifíca;
Fil: Pal, Lipika R.. No especifíca;
Fil: Odell, Eric. No especifíca;
Fil: Pandey, Gaurav. No especifíca;
Fil: Peters Petrulewicz, Robin C.. No especifíca;
Fil: Srinivasan, Rajgopal. No especifíca;
Fil: Yee, Stephen F.. No especifíca;
Fil: Yeleswarapu, Sri Jyothsna. No especifíca;
Fil: Zuhl, Maya. No especifíca;
Fil: Adebali, Ogun. No especifíca;
Fil: Fornasari, Maria Silvina. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Patra, Ayoti. No especifíca;
Fil: O'Donnell Luria, Anne. No especifíca;
Fil: Ng, Pauline C.. No especifíca;
Fil: Shon, John. No especifíca;
Fil: Veltman, Joris. No especifíca;
Fil: Zook, Justin M.. No especifíca;
Materia
Variant impact
Disease
Computational Biology
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/240041

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oai_identifier_str oai:ri.conicet.gov.ar:11336/240041
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methodsJain, ShantanuBakolitsa, ConstantinaBrenner, Steven E.Radivojac, PredragMoult, JohnRepo, SusannaHoskins, Roger A.Andreoletti, GaiaBarsky, DanielChellapan, AjithavalliChu, HoyinDabbiru, NavyaKollipara, Naveen K.Ly, MelissaNeumann, Andrew J.Pal, Lipika R.Odell, EricPandey, GauravPeters Petrulewicz, Robin C.Srinivasan, RajgopalYee, Stephen F.Yeleswarapu, Sri JyothsnaZuhl, MayaAdebali, OgunFornasari, Maria SilvinaPatra, AyotiO'Donnell Luria, AnneNg, Pauline C.Shon, JohnVeltman, JorisZook, Justin M.Variant impactDiseaseComputational Biologyhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. Results Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. Conclusions Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.Fil: Jain, Shantanu. No especifíca;Fil: Bakolitsa, Constantina. No especifíca;Fil: Brenner, Steven E.. No especifíca;Fil: Radivojac, Predrag. No especifíca;Fil: Moult, John. No especifíca;Fil: Repo, Susanna. No especifíca;Fil: Hoskins, Roger A.. No especifíca;Fil: Andreoletti, Gaia. No especifíca;Fil: Barsky, Daniel. No especifíca;Fil: Chellapan, Ajithavalli. No especifíca;Fil: Chu, Hoyin. No especifíca;Fil: Dabbiru, Navya. No especifíca;Fil: Kollipara, Naveen K.. No especifíca;Fil: Ly, Melissa. No especifíca;Fil: Neumann, Andrew J.. No especifíca;Fil: Pal, Lipika R.. No especifíca;Fil: Odell, Eric. No especifíca;Fil: Pandey, Gaurav. No especifíca;Fil: Peters Petrulewicz, Robin C.. No especifíca;Fil: Srinivasan, Rajgopal. No especifíca;Fil: Yee, Stephen F.. No especifíca;Fil: Yeleswarapu, Sri Jyothsna. No especifíca;Fil: Zuhl, Maya. No especifíca;Fil: Adebali, Ogun. No especifíca;Fil: Fornasari, Maria Silvina. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Patra, Ayoti. No especifíca;Fil: O'Donnell Luria, Anne. No especifíca;Fil: Ng, Pauline C.. No especifíca;Fil: Shon, John. No especifíca;Fil: Veltman, Joris. No especifíca;Fil: Zook, Justin M.. No especifíca;BioMed Central2024-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/240041Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; et al.; CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods; BioMed Central; Genome Biology; 25; 1; 2-2024; 1-461474-760XCONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-023-03113-6info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03113-6info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T10:16:11Zoai:ri.conicet.gov.ar:11336/240041instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 10:16:12.046CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
title CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
spellingShingle CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
Jain, Shantanu
Variant impact
Disease
Computational Biology
title_short CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
title_full CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
title_fullStr CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
title_full_unstemmed CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
title_sort CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods
dc.creator.none.fl_str_mv Jain, Shantanu
Bakolitsa, Constantina
Brenner, Steven E.
Radivojac, Predrag
Moult, John
Repo, Susanna
Hoskins, Roger A.
Andreoletti, Gaia
Barsky, Daniel
Chellapan, Ajithavalli
Chu, Hoyin
Dabbiru, Navya
Kollipara, Naveen K.
Ly, Melissa
Neumann, Andrew J.
Pal, Lipika R.
Odell, Eric
Pandey, Gaurav
Peters Petrulewicz, Robin C.
Srinivasan, Rajgopal
Yee, Stephen F.
Yeleswarapu, Sri Jyothsna
Zuhl, Maya
Adebali, Ogun
Fornasari, Maria Silvina
Patra, Ayoti
O'Donnell Luria, Anne
Ng, Pauline C.
Shon, John
Veltman, Joris
Zook, Justin M.
author Jain, Shantanu
author_facet Jain, Shantanu
Bakolitsa, Constantina
Brenner, Steven E.
Radivojac, Predrag
Moult, John
Repo, Susanna
Hoskins, Roger A.
Andreoletti, Gaia
Barsky, Daniel
Chellapan, Ajithavalli
Chu, Hoyin
Dabbiru, Navya
Kollipara, Naveen K.
Ly, Melissa
Neumann, Andrew J.
Pal, Lipika R.
Odell, Eric
Pandey, Gaurav
Peters Petrulewicz, Robin C.
Srinivasan, Rajgopal
Yee, Stephen F.
Yeleswarapu, Sri Jyothsna
Zuhl, Maya
Adebali, Ogun
Fornasari, Maria Silvina
Patra, Ayoti
O'Donnell Luria, Anne
Ng, Pauline C.
Shon, John
Veltman, Joris
Zook, Justin M.
author_role author
author2 Bakolitsa, Constantina
Brenner, Steven E.
Radivojac, Predrag
Moult, John
Repo, Susanna
Hoskins, Roger A.
Andreoletti, Gaia
Barsky, Daniel
Chellapan, Ajithavalli
Chu, Hoyin
Dabbiru, Navya
Kollipara, Naveen K.
Ly, Melissa
Neumann, Andrew J.
Pal, Lipika R.
Odell, Eric
Pandey, Gaurav
Peters Petrulewicz, Robin C.
Srinivasan, Rajgopal
Yee, Stephen F.
Yeleswarapu, Sri Jyothsna
Zuhl, Maya
Adebali, Ogun
Fornasari, Maria Silvina
Patra, Ayoti
O'Donnell Luria, Anne
Ng, Pauline C.
Shon, John
Veltman, Joris
Zook, Justin M.
author2_role author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Variant impact
Disease
Computational Biology
topic Variant impact
Disease
Computational Biology
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.6
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. Results Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. Conclusions Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
Fil: Jain, Shantanu. No especifíca;
Fil: Bakolitsa, Constantina. No especifíca;
Fil: Brenner, Steven E.. No especifíca;
Fil: Radivojac, Predrag. No especifíca;
Fil: Moult, John. No especifíca;
Fil: Repo, Susanna. No especifíca;
Fil: Hoskins, Roger A.. No especifíca;
Fil: Andreoletti, Gaia. No especifíca;
Fil: Barsky, Daniel. No especifíca;
Fil: Chellapan, Ajithavalli. No especifíca;
Fil: Chu, Hoyin. No especifíca;
Fil: Dabbiru, Navya. No especifíca;
Fil: Kollipara, Naveen K.. No especifíca;
Fil: Ly, Melissa. No especifíca;
Fil: Neumann, Andrew J.. No especifíca;
Fil: Pal, Lipika R.. No especifíca;
Fil: Odell, Eric. No especifíca;
Fil: Pandey, Gaurav. No especifíca;
Fil: Peters Petrulewicz, Robin C.. No especifíca;
Fil: Srinivasan, Rajgopal. No especifíca;
Fil: Yee, Stephen F.. No especifíca;
Fil: Yeleswarapu, Sri Jyothsna. No especifíca;
Fil: Zuhl, Maya. No especifíca;
Fil: Adebali, Ogun. No especifíca;
Fil: Fornasari, Maria Silvina. Universidad Nacional de Quilmes; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina
Fil: Patra, Ayoti. No especifíca;
Fil: O'Donnell Luria, Anne. No especifíca;
Fil: Ng, Pauline C.. No especifíca;
Fil: Shon, John. No especifíca;
Fil: Veltman, Joris. No especifíca;
Fil: Zook, Justin M.. No especifíca;
description Background The Critical Assessment of Genome Interpretation (CAGI) aims to advance the state-of-the-art for computational prediction of genetic variant impact, particularly where relevant to disease. The five complete editions of the CAGI community experiment comprised 50 challenges, in which participants made blind predictions of phenotypes from genetic data, and these were evaluated by independent assessors. Results Performance was particularly strong for clinical pathogenic variants, including some difficult-to-diagnose cases, and extends to interpretation of cancer-related variants. Missense variant interpretation methods were able to estimate biochemical effects with increasing accuracy. Assessment of methods for regulatory variants and complex trait disease risk was less definitive and indicates performance potentially suitable for auxiliary use in the clinic. Conclusions Results show that while current methods are imperfect, they have major utility for research and clinical applications. Emerging methods and increasingly large, robust datasets for training and assessment promise further progress ahead.
publishDate 2024
dc.date.none.fl_str_mv 2024-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/240041
Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; et al.; CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods; BioMed Central; Genome Biology; 25; 1; 2-2024; 1-46
1474-760X
CONICET Digital
CONICET
url http://hdl.handle.net/11336/240041
identifier_str_mv Jain, Shantanu; Bakolitsa, Constantina; Brenner, Steven E.; Radivojac, Predrag; Moult, John; et al.; CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods; BioMed Central; Genome Biology; 25; 1; 2-2024; 1-46
1474-760X
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1186/s13059-023-03113-6
info:eu-repo/semantics/altIdentifier/url/https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-03113-6
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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