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
.jpg)
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/240041
Ver los metadatos del registro completo
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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 Técnicas2025-10-22T11:46:19Zoai: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:34982025-10-22 11:46:20.087CONICET 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 |
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article |
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publishedVersion |
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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 |
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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 |
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eng |
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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 |
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BioMed Central |
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BioMed Central |
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dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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