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CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)

In the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6), the Genetics of Neurodevelopmental Disorders Lab in Padua proposed a new ID-challenge to give the opportunity of developing computational methods for predicting patient’s phenotype and the causal variants. E...

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Autores principales: Aspromonte, Maria Cristina, Conte, Alessio Del, Zhu, Shaowen, Tan, Wuwei, Shen, Yang, Zhang, Yexian, Li, Qi, Wang, Maggie Haitian, Babbi, Giulia, Bovo, Samuele, Martelli, Pier Luigi, Casadio, Rita, Althagafi, Azza, Toonsi, Sumyyah, Kulmanov, Maxat, Hoehndorf, Robert, Katsonis, Panagiotis, Williams, Amanda, Lichtarge, Olivier, Xian, Su, Surento, Wesley, Pejaver, Vikas, Mooney, Sean D., Sunderam, Uma, Srinivasan, Rajgopal, Murgia, Alessandra, Piovesan, Damiano, Tosatto, Silvio C. E., Leonardi, Emanuela
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Journal Experts 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418555/
https://www.ncbi.nlm.nih.gov/pubmed/37577579
http://dx.doi.org/10.21203/rs.3.rs-3209168/v1
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author Aspromonte, Maria Cristina
Conte, Alessio Del
Zhu, Shaowen
Tan, Wuwei
Shen, Yang
Zhang, Yexian
Li, Qi
Wang, Maggie Haitian
Babbi, Giulia
Bovo, Samuele
Martelli, Pier Luigi
Casadio, Rita
Althagafi, Azza
Toonsi, Sumyyah
Kulmanov, Maxat
Hoehndorf, Robert
Katsonis, Panagiotis
Williams, Amanda
Lichtarge, Olivier
Xian, Su
Surento, Wesley
Pejaver, Vikas
Mooney, Sean D.
Sunderam, Uma
Srinivasan, Rajgopal
Murgia, Alessandra
Piovesan, Damiano
Tosatto, Silvio C. E.
Leonardi, Emanuela
author_facet Aspromonte, Maria Cristina
Conte, Alessio Del
Zhu, Shaowen
Tan, Wuwei
Shen, Yang
Zhang, Yexian
Li, Qi
Wang, Maggie Haitian
Babbi, Giulia
Bovo, Samuele
Martelli, Pier Luigi
Casadio, Rita
Althagafi, Azza
Toonsi, Sumyyah
Kulmanov, Maxat
Hoehndorf, Robert
Katsonis, Panagiotis
Williams, Amanda
Lichtarge, Olivier
Xian, Su
Surento, Wesley
Pejaver, Vikas
Mooney, Sean D.
Sunderam, Uma
Srinivasan, Rajgopal
Murgia, Alessandra
Piovesan, Damiano
Tosatto, Silvio C. E.
Leonardi, Emanuela
author_sort Aspromonte, Maria Cristina
collection PubMed
description In the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6), the Genetics of Neurodevelopmental Disorders Lab in Padua proposed a new ID-challenge to give the opportunity of developing computational methods for predicting patient’s phenotype and the causal variants. Eight research teams and 30 models had access to the phenotype details and real genetic data, based on the sequences of 74 genes (VCF format) in 415 pediatric patients affected by Neurodevelopmental Disorders (NDDs). NDDs are clinically and genetically heterogeneous conditions, with onset in infant age. In this study we evaluate the ability and accuracy of computational methods to predict comorbid phenotypes based on clinical features described in each patient and causal variants. Finally, we asked to develop a method to find new possible genetic causes for patients without a genetic diagnosis. As already done for the CAGI5, seven clinical features (ID, ASD, ataxia, epilepsy, microcephaly, macrocephaly, hypotonia), and variants (causative, putative pathogenic and contributing factors) were provided. Considering the overall clinical manifestation of our cohort, we give out the variant data and phenotypic traits of the 150 patients from CAGI5 ID-Challenge as training and validation for the prediction methods development.
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spelling pubmed-104185552023-08-12 CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs) Aspromonte, Maria Cristina Conte, Alessio Del Zhu, Shaowen Tan, Wuwei Shen, Yang Zhang, Yexian Li, Qi Wang, Maggie Haitian Babbi, Giulia Bovo, Samuele Martelli, Pier Luigi Casadio, Rita Althagafi, Azza Toonsi, Sumyyah Kulmanov, Maxat Hoehndorf, Robert Katsonis, Panagiotis Williams, Amanda Lichtarge, Olivier Xian, Su Surento, Wesley Pejaver, Vikas Mooney, Sean D. Sunderam, Uma Srinivasan, Rajgopal Murgia, Alessandra Piovesan, Damiano Tosatto, Silvio C. E. Leonardi, Emanuela Res Sq Article In the context of the Critical Assessment of the Genome Interpretation, 6th edition (CAGI6), the Genetics of Neurodevelopmental Disorders Lab in Padua proposed a new ID-challenge to give the opportunity of developing computational methods for predicting patient’s phenotype and the causal variants. Eight research teams and 30 models had access to the phenotype details and real genetic data, based on the sequences of 74 genes (VCF format) in 415 pediatric patients affected by Neurodevelopmental Disorders (NDDs). NDDs are clinically and genetically heterogeneous conditions, with onset in infant age. In this study we evaluate the ability and accuracy of computational methods to predict comorbid phenotypes based on clinical features described in each patient and causal variants. Finally, we asked to develop a method to find new possible genetic causes for patients without a genetic diagnosis. As already done for the CAGI5, seven clinical features (ID, ASD, ataxia, epilepsy, microcephaly, macrocephaly, hypotonia), and variants (causative, putative pathogenic and contributing factors) were provided. Considering the overall clinical manifestation of our cohort, we give out the variant data and phenotypic traits of the 150 patients from CAGI5 ID-Challenge as training and validation for the prediction methods development. American Journal Experts 2023-08-02 /pmc/articles/PMC10418555/ /pubmed/37577579 http://dx.doi.org/10.21203/rs.3.rs-3209168/v1 Text en https://creativecommons.org/licenses/by/4.0/This work is licensed under a Creative Commons Attribution 4.0 International License (https://creativecommons.org/licenses/by/4.0/) , which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Aspromonte, Maria Cristina
Conte, Alessio Del
Zhu, Shaowen
Tan, Wuwei
Shen, Yang
Zhang, Yexian
Li, Qi
Wang, Maggie Haitian
Babbi, Giulia
Bovo, Samuele
Martelli, Pier Luigi
Casadio, Rita
Althagafi, Azza
Toonsi, Sumyyah
Kulmanov, Maxat
Hoehndorf, Robert
Katsonis, Panagiotis
Williams, Amanda
Lichtarge, Olivier
Xian, Su
Surento, Wesley
Pejaver, Vikas
Mooney, Sean D.
Sunderam, Uma
Srinivasan, Rajgopal
Murgia, Alessandra
Piovesan, Damiano
Tosatto, Silvio C. E.
Leonardi, Emanuela
CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)
title CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)
title_full CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)
title_fullStr CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)
title_full_unstemmed CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)
title_short CAGI6 ID-Challenge: Assessment of phenotype and variant predictions in 415 children with Neurodevelopmental Disorders (NDDs)
title_sort cagi6 id-challenge: assessment of phenotype and variant predictions in 415 children with neurodevelopmental disorders (ndds)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10418555/
https://www.ncbi.nlm.nih.gov/pubmed/37577579
http://dx.doi.org/10.21203/rs.3.rs-3209168/v1
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