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Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia
BACKGROUND: Machine learning (ML) algorithms and methods offer great tools to analyze large complex genomic datasets. Our goal was to compare the genomic architecture of schizophrenia (SCZ) and autism spectrum disorder (ASD) using ML. METHODS: In this paper, we used regularized gradient boosted mach...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049199/ https://www.ncbi.nlm.nih.gov/pubmed/32111185 http://dx.doi.org/10.1186/s12888-020-02503-5 |
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author | Sardaar, Sameer Qi, Bill Dionne-Laporte, Alexandre Rouleau, Guy. A. Rabbany, Reihaneh Trakadis, Yannis J. |
author_facet | Sardaar, Sameer Qi, Bill Dionne-Laporte, Alexandre Rouleau, Guy. A. Rabbany, Reihaneh Trakadis, Yannis J. |
author_sort | Sardaar, Sameer |
collection | PubMed |
description | BACKGROUND: Machine learning (ML) algorithms and methods offer great tools to analyze large complex genomic datasets. Our goal was to compare the genomic architecture of schizophrenia (SCZ) and autism spectrum disorder (ASD) using ML. METHODS: In this paper, we used regularized gradient boosted machines to analyze whole-exome sequencing (WES) data from individuals SCZ and ASD in order to identify important distinguishing genetic features. We further demonstrated a method of gene clustering to highlight which subsets of genes identified by the ML algorithm are mutated concurrently in affected individuals and are central to each disease (i.e., ASD vs. SCZ “hub” genes). RESULTS: In summary, after correcting for population structure, we found that SCZ and ASD cases could be successfully separated based on genetic information, with 86–88% accuracy on the testing dataset. Through bioinformatic analysis, we explored if combinations of genes concurrently mutated in patients with the same condition (“hub” genes) belong to specific pathways. Several themes were found to be associated with ASD, including calcium ion transmembrane transport, immune system/inflammation, synapse organization, and retinoid metabolic process. Moreover, ion transmembrane transport, neurotransmitter transport, and microtubule/cytoskeleton processes were highlighted for SCZ. CONCLUSIONS: Our manuscript introduces a novel comparative approach for studying the genetic architecture of genetically related diseases with complex inheritance and highlights genetic similarities and differences between ASD and SCZ. |
format | Online Article Text |
id | pubmed-7049199 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-70491992020-03-05 Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia Sardaar, Sameer Qi, Bill Dionne-Laporte, Alexandre Rouleau, Guy. A. Rabbany, Reihaneh Trakadis, Yannis J. BMC Psychiatry Research Article BACKGROUND: Machine learning (ML) algorithms and methods offer great tools to analyze large complex genomic datasets. Our goal was to compare the genomic architecture of schizophrenia (SCZ) and autism spectrum disorder (ASD) using ML. METHODS: In this paper, we used regularized gradient boosted machines to analyze whole-exome sequencing (WES) data from individuals SCZ and ASD in order to identify important distinguishing genetic features. We further demonstrated a method of gene clustering to highlight which subsets of genes identified by the ML algorithm are mutated concurrently in affected individuals and are central to each disease (i.e., ASD vs. SCZ “hub” genes). RESULTS: In summary, after correcting for population structure, we found that SCZ and ASD cases could be successfully separated based on genetic information, with 86–88% accuracy on the testing dataset. Through bioinformatic analysis, we explored if combinations of genes concurrently mutated in patients with the same condition (“hub” genes) belong to specific pathways. Several themes were found to be associated with ASD, including calcium ion transmembrane transport, immune system/inflammation, synapse organization, and retinoid metabolic process. Moreover, ion transmembrane transport, neurotransmitter transport, and microtubule/cytoskeleton processes were highlighted for SCZ. CONCLUSIONS: Our manuscript introduces a novel comparative approach for studying the genetic architecture of genetically related diseases with complex inheritance and highlights genetic similarities and differences between ASD and SCZ. BioMed Central 2020-02-28 /pmc/articles/PMC7049199/ /pubmed/32111185 http://dx.doi.org/10.1186/s12888-020-02503-5 Text en © The Author(s) 2020 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Sardaar, Sameer Qi, Bill Dionne-Laporte, Alexandre Rouleau, Guy. A. Rabbany, Reihaneh Trakadis, Yannis J. Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
title | Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
title_full | Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
title_fullStr | Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
title_full_unstemmed | Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
title_short | Machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
title_sort | machine learning analysis of exome trios to contrast the genomic architecture of autism and schizophrenia |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049199/ https://www.ncbi.nlm.nih.gov/pubmed/32111185 http://dx.doi.org/10.1186/s12888-020-02503-5 |
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