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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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EDIR: exome database of interspersed repeats
Laura D T Vo Ngoc1, Randy Osei1, Katrin Dohr2
1Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Clinical Sciences, Research Group Reproduction and Genetics, Centre for Medical Genetics, Brussels 1090, Belgium.
Bioinformatics (Oxford, England)
|December 1, 2022
Summary
Intragenic exonic deletions, often caused by homologous regions, can lead to genetic diseases. We created the Exome Database of Interspersed Repeats (EDIR) to map these structures within the human exome for better disease research.
Area of Science:
- Genomics
- Human Genetics
- Bioinformatics
Background:
- Intragenic exonic deletions are associated with genetic disorders.
- These deletions are frequently bordered by homologous regions.
- Understanding interspersed repeats within coding sequences is crucial for genetic disease research.
Purpose of the Study:
- To develop a comprehensive resource for identifying homology-flanked sequences within the human exome.
- To facilitate the study of intragenic exonic deletions and their role in genetic diseases.
Main Methods:
- An inductive strategy was employed to build the Exome Database of Interspersed Repeats (EDIR).
- The database maps the positions of interspersed repeats within the human exome.
- The EDIR database is accessible via an R/Bioconductor package and a web interface.
Main Results:
- The Exome Database of Interspersed Repeats (EDIR) has been successfully compiled.
- EDIR provides rapid, per-gene extraction of homology-flanked sequences across the human exome.
- The database enables a clearer view of interspersed repeats within coding sequences.
Conclusions:
- EDIR serves as a valuable resource for researchers studying genetic diseases linked to intragenic deletions.
- The developed tools (R package, web interface) facilitate easy access and querying of the EDIR dataset.
- This work enhances the understanding of genomic structures contributing to human genetic variation and disease.
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