Loading...
Publication
TAD-GConTool and CNV-ConTool to assist prediction of phenotypic outcome of chromosomal rearrangements
| Name: | Description: | Size: | Format: | |
|---|---|---|---|---|
| 1.17 MB | Adobe PDF |
Authors
Advisor(s)
Abstract(s)
With the advance of genome sequencing technologies, it is currently possible to identify a large
number of chromosomal or genomic structural variants in a single individual. Therefore, the
validation and manual assessment of structural variants clinical significance becomes
unpractical and time consuming when performed with previous methodologies.
In order to assist the validation process, we developed two clinically inspired bioinformatics
tools - TADGConTool and CNV-ConTool. They were developed in python with a Common
Gateway Interface that allows easy and user-friendly access through any standards compliant
web browser (available at: http://dgrctools.insa.min- saude.pt/).
TAD-GConTool collects genomic information of breakpoint regions, using topological
associated domains (TADs) as reference. It then accesses public databases to retrieve elements
found inside TADs, and the associated clinical phenotypes, highlighting those causing
dominant disorders.
CNV-ConTool searches for overlaps between patient-specific breakpoints and CNVs, and
those reported in several public databases.
These tools were already successfully applied to about 40 cases studied under the project
“Next-gen cytogenetics enters clinical care and annotates the human genome” (HMSPICT/0016/2013) and are now being made available to the broader scientific community. These
tools allowed a faster and more informed evaluation of the genomic structural variants, helping
select potential pathogenic variants, either by identifying phenotype- associated genes, or by
overlapping deletions and duplications with already described benign or pathogenic CNVs.
As genome sequencing is becoming more and more a routine method for identification of
chromosomal and genomic structural variants, such clinically oriented bioinformatics tools are
crucial and represent the first level of analysis toward personalized genomic medicine.
This research was supported by national funds through FCT - Fundação para a Ciência e a
Tecnologia, Research Grant HMSP-ICT/0016/2013.
Description
Keywords
Bioinformatic Tools Genomics Structural Variants Phenotypic Outcome Prediction Genómica Funcional e Estrutural
Pedagogical Context
Citation
Fino J, David D. TAD-GConTool and CNV-ConTool to assist prediction of phenotypic outcome of chromosomal rearrangements. Bioinformatic Open Days, Braga - Portugal, 2020