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Genome Biol. 2019 Mar 21;20(1):60. doi: 10.1186/s13059-019-1666-7.

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

Author information

1
Genome Center, UC Davis, Davis, USA.
2
Genome Center, UC Davis, Davis, USA. fhormozd@ucdavis.edu.
3
UC Davis MIND Institute, Sacramento, USA. fhormozd@ucdavis.edu.
4
Department of Biochemistry and Molecular Medicine, UC Davis, Sacramento, USA. fhormozd@ucdavis.edu.

Abstract

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 .

PMID:
30898144
PMCID:
PMC6427865
DOI:
10.1186/s13059-019-1666-7
[Indexed for MEDLINE]
Free PMC Article

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