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Title: | Identification of biological mechanisms underlying a multidimensional ASD phenotype using machine learning | Authors: | Asif, Muhammad Martiniano, Hugo F. M. C. Marques, Ana Rita Santos, João Xavier Vilela, Joana Rasga, Celia Oliveira, Guiomar Couto, Francisco M. Vicente, Astrid M. |
Issue Date: | 28-Jan-2020 | Publisher: | Springer Nature | Project: | UID/Multi/04046/2013 UID/CEC/00408/2019 PTDC/CCI-BIO/28685/2017 PD/BD/52485/2014 PD/BD/113773/2015 PD/BD/114386/2016 PD/BD/131390/2017 POCI- 01-0145-FEDER-016428 |
Serial title, monograph or event: | Translational Psychiatry | Volume: | 10 | Issue: | 1 | Abstract: | The complex genetic architecture of Autism Spectrum Disorder (ASD) and its heterogeneous phenotype makes molecular diagnosis and patient prognosis challenging tasks. To establish more precise genotype-phenotype correlations in ASD, we developed a novel machine-learning integrative approach, which seeks to delineate associations between patients' clinical profiles and disrupted biological processes, inferred from their copy number variants (CNVs) that span brain genes. Clustering analysis of the relevant clinical measures from 2446 ASD cases in the Autism Genome Project identified two distinct phenotypic subgroups. Patients in these clusters differed significantly in ADOS-defined severity, adaptive behavior profiles, intellectual ability, and verbal status, the latter contributing the most for cluster stability and cohesion. Functional enrichment analysis of brain genes disrupted by CNVs in these ASD cases identified 15 statistically significant biological processes, including cell adhesion, neural development, cognition, and polyubiquitination, in line with previous ASD findings. A Naive Bayes classifier, generated to predict the ASD phenotypic clusters from disrupted biological processes, achieved predictions with a high precision (0.82) but low recall (0.39), for a subset of patients with higher biological Information Content scores. This study shows that milder and more severe clinical presentations can have distinct underlying biological mechanisms. It further highlights how machine-learning approaches can reduce clinical heterogeneity by using multidimensional clinical measures, and establishes genotype-phenotype correlations in ASD. However, predictions are strongly dependent on patient's information content. Findings are therefore a first step toward the translation of genetic information into clinically useful applications, and emphasize the need for larger datasets with very complete clinical and biological information. | URI: | https://hdl.handle.net/10316/106751 | ISSN: | 2158-3188 | DOI: | 10.1038/s41398-020-0721-1 | Rights: | openAccess |
Appears in Collections: | I&D IBILI - Artigos em Revistas Internacionais |
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