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TAD fusion score: discovery and ranking the contribution of deletions to genome structure

Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show th...

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Detalles Bibliográficos
Autores principales: Huynh, Linh, Hormozdiari, Fereydoun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427865/
https://www.ncbi.nlm.nih.gov/pubmed/30898144
http://dx.doi.org/10.1186/s13059-019-1666-7
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author Huynh, Linh
Hormozdiari, Fereydoun
author_facet Huynh, Linh
Hormozdiari, Fereydoun
author_sort Huynh, Linh
collection PubMed
description Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders, including developmental disorders and cancer, in comparison to the deletions reported in the 1000 Genomes Project. The TAD fusion score tool is publicly available at https://github.com/HormozdiariLab/TAD-fusion-score. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1666-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-64278652019-04-01 TAD fusion score: discovery and ranking the contribution of deletions to genome structure Huynh, Linh Hormozdiari, Fereydoun Genome Biol Method Deletions that fuse two adjacent topologically associating domains (TADs) can cause severe developmental disorders. We provide a formal method to quantify deletions based on their potential disruption of the three-dimensional genome structure, denoted as the TAD fusion score. Furthermore, we show that deletions that cause TAD fusion are rare and under negative selection in the general population. Finally, we show that our method correctly gives higher scores to deletions reported to cause various disorders, including developmental disorders and cancer, in comparison to the deletions reported in the 1000 Genomes Project. The TAD fusion score tool is publicly available at https://github.com/HormozdiariLab/TAD-fusion-score. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1666-7) contains supplementary material, which is available to authorized users. BioMed Central 2019-03-21 /pmc/articles/PMC6427865/ /pubmed/30898144 http://dx.doi.org/10.1186/s13059-019-1666-7 Text en © The Author(s) 2019 Open Access This 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 Method
Huynh, Linh
Hormozdiari, Fereydoun
TAD fusion score: discovery and ranking the contribution of deletions to genome structure
title TAD fusion score: discovery and ranking the contribution of deletions to genome structure
title_full TAD fusion score: discovery and ranking the contribution of deletions to genome structure
title_fullStr TAD fusion score: discovery and ranking the contribution of deletions to genome structure
title_full_unstemmed TAD fusion score: discovery and ranking the contribution of deletions to genome structure
title_short TAD fusion score: discovery and ranking the contribution of deletions to genome structure
title_sort tad fusion score: discovery and ranking the contribution of deletions to genome structure
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6427865/
https://www.ncbi.nlm.nih.gov/pubmed/30898144
http://dx.doi.org/10.1186/s13059-019-1666-7
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