Assessment of patient clinical descriptions and pathogenic variants from gene panel sequences in the CAGI-5 intellectual disability challenge
Marco Carraro
Department of Biomedical Sciences, University of Padua, Padua, Italy
These authors contributed equally to this study.
Search for more papers by this authorAlexander Miguel Monzon
Department of Biomedical Sciences, University of Padua, Padua, Italy
These authors contributed equally to this study.
Search for more papers by this authorLuigi Chiricosta
Department of Biomedical Sciences, University of Padua, Padua, Italy
Search for more papers by this authorFrancesco Reggiani
Department of Biomedical Sciences, University of Padua, Padua, Italy
Department of Information Engineering, University of Padua, Padua, Italy
Search for more papers by this authorMaria Cristina Aspromonte
Department of Woman and Child Health, University of Padua, Padua, Italy
Search for more papers by this authorMariagrazia Bellini
Department of Woman and Child Health, University of Padua, Padua, Italy
Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
Search for more papers by this authorKymberleigh Pagel
Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
Search for more papers by this authorYuxiang Jiang
Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
Search for more papers by this authorPredrag Radivojac
Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
Search for more papers by this authorKunal Kundu
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
Search for more papers by this authorLipika R. Pal
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Search for more papers by this authorYizhou Yin
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
Search for more papers by this authorGaia Andreoletti
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
Search for more papers by this authorJohn Moult
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
Search for more papers by this authorStephen J. Wilson
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Search for more papers by this authorPanagiotis Katsonis
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Search for more papers by this authorOlivier Lichtarge
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Search for more papers by this authorJingqi Chen
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorYaqiong Wang
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorZhiqiang Hu
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorSteven E. Brenner
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorCarlo Ferrari
Department of Information Engineering, University of Padua, Padua, Italy
Search for more papers by this authorAlessandra Murgia
Department of Woman and Child Health, University of Padua, Padua, Italy
Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
Search for more papers by this authorCorresponding Author
Silvio C.E. Tosatto
Department of Biomedical Sciences, University of Padua, Padua, Italy
Institute of Neuroscience, National Research Council (CNR), Padua, Italy
These authors contributed equally to this study.
Correspondence Silvio Tosatto, Department of Biomedical Sciences, University of Padua. Viale G. Colombo 3, 35131, Padua, Italy. Email: [email protected]
Emanuela Leonardi, Department of Woman and Child Health, University of Padua, Padua. Corso Stati Uniti, 4, 35127, Padua, Italy. Email: [email protected]
Search for more papers by this authorCorresponding Author
Emanuela Leonardi
Department of Woman and Child Health, University of Padua, Padua, Italy
Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
These authors contributed equally to this study.
Correspondence Silvio Tosatto, Department of Biomedical Sciences, University of Padua. Viale G. Colombo 3, 35131, Padua, Italy. Email: [email protected]
Emanuela Leonardi, Department of Woman and Child Health, University of Padua, Padua. Corso Stati Uniti, 4, 35127, Padua, Italy. Email: [email protected]
Search for more papers by this authorMarco Carraro
Department of Biomedical Sciences, University of Padua, Padua, Italy
These authors contributed equally to this study.
Search for more papers by this authorAlexander Miguel Monzon
Department of Biomedical Sciences, University of Padua, Padua, Italy
These authors contributed equally to this study.
Search for more papers by this authorLuigi Chiricosta
Department of Biomedical Sciences, University of Padua, Padua, Italy
Search for more papers by this authorFrancesco Reggiani
Department of Biomedical Sciences, University of Padua, Padua, Italy
Department of Information Engineering, University of Padua, Padua, Italy
Search for more papers by this authorMaria Cristina Aspromonte
Department of Woman and Child Health, University of Padua, Padua, Italy
Search for more papers by this authorMariagrazia Bellini
Department of Woman and Child Health, University of Padua, Padua, Italy
Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
Search for more papers by this authorKymberleigh Pagel
Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
Search for more papers by this authorYuxiang Jiang
Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
Search for more papers by this authorPredrag Radivojac
Khoury College of Computer and Information Sciences, Northeastern University, Boston, Massachusetts
Search for more papers by this authorKunal Kundu
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
Search for more papers by this authorLipika R. Pal
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Search for more papers by this authorYizhou Yin
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Computational Biology, Bioinformatics and Genomics, Biological Sciences Graduate Program, University of Maryland, College Park, Maryland
Search for more papers by this authorGaia Andreoletti
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
Search for more papers by this authorJohn Moult
Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, Maryland
Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, Maryland
Search for more papers by this authorStephen J. Wilson
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Search for more papers by this authorPanagiotis Katsonis
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Search for more papers by this authorOlivier Lichtarge
Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
Search for more papers by this authorJingqi Chen
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorYaqiong Wang
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorZhiqiang Hu
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorSteven E. Brenner
Department of Plant and Microbial Biology, University of California, Berkeley, California
Search for more papers by this authorCarlo Ferrari
Department of Information Engineering, University of Padua, Padua, Italy
Search for more papers by this authorAlessandra Murgia
Department of Woman and Child Health, University of Padua, Padua, Italy
Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
Search for more papers by this authorCorresponding Author
Silvio C.E. Tosatto
Department of Biomedical Sciences, University of Padua, Padua, Italy
Institute of Neuroscience, National Research Council (CNR), Padua, Italy
These authors contributed equally to this study.
Correspondence Silvio Tosatto, Department of Biomedical Sciences, University of Padua. Viale G. Colombo 3, 35131, Padua, Italy. Email: [email protected]
Emanuela Leonardi, Department of Woman and Child Health, University of Padua, Padua. Corso Stati Uniti, 4, 35127, Padua, Italy. Email: [email protected]
Search for more papers by this authorCorresponding Author
Emanuela Leonardi
Department of Woman and Child Health, University of Padua, Padua, Italy
Fondazione Istituto di Ricerca Pediatrica (IRP), Città della Speranza, Padova, Italy
These authors contributed equally to this study.
Correspondence Silvio Tosatto, Department of Biomedical Sciences, University of Padua. Viale G. Colombo 3, 35131, Padua, Italy. Email: [email protected]
Emanuela Leonardi, Department of Woman and Child Health, University of Padua, Padua. Corso Stati Uniti, 4, 35127, Padua, Italy. Email: [email protected]
Search for more papers by this authorAbstract
The Critical Assessment of Genome Interpretation-5 intellectual disability challenge asked to use computational methods to predict patient clinical phenotypes and the causal variant(s) based on an analysis of their gene panel sequence data. Sequence data for 74 genes associated with intellectual disability (ID) and/or autism spectrum disorders (ASD) from a cohort of 150 patients with a range of neurodevelopmental manifestations (i.e. ID, autism, epilepsy, microcephaly, macrocephaly, hypotonia, ataxia) have been made available for this challenge. For each patient, predictors had to report the causative variants and which of the seven phenotypes were present. Since neurodevelopmental disorders are characterized by strong comorbidity, tested individuals often present more than one pathological condition. Considering the overall clinical manifestation of each patient, the correct phenotype has been predicted by at least one group for 93 individuals (62%). ID and ASD were the best predicted among the seven phenotypic traits. Also, causative or potentially pathogenic variants were predicted correctly by at least one group. However, the prediction of the correct causative variant seems to be insufficient to predict the correct phenotype. In some cases, the correct prediction has been supported by rare or common variants in genes different from the causative one.
Supporting Information
| Filename | Description |
|---|---|
| humu23823-sup-0001-Suppl_mat_CAGI5_ID_Monzon_Carraro_R1_clean.pdf1.3 MB | Supplementary information |
Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
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