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Updated: Jun 22, 2026
11:35
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
Published on: August 21, 2016
Semantic prioritization of novel causative genomic variants
Imane Boudellioua1, Rozaimi B Mahamad Razali1, Maxat Kulmanov1
1King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia.
Plos Computational Biology
|April 18, 2017
Summary
Identifying disease-causing genetic variants is challenging. The PhenomeNET Variant Predictor (PVP) system uses automated reasoning to prioritize variants from whole exome and whole genome sequencing, aiding genetic diagnosis.
Area of Science:
- Clinical genetics
- Bioinformatics
- Computational biology
Background:
- Distinguishing causative genetic variants from benign ones is a major challenge in clinical genetics.
- Current computational methods for variant prioritization often rely on machine learning with diverse features.
Purpose of the Study:
- To introduce the PhenomeNET Variant Predictor (PVP) system for filtering and prioritizing genetic variants.
- To leverage semantic technologies and automated reasoning over genotype-phenotype relationships.
Main Methods:
- Developed the PhenomeNET Variant Predictor (PVP) system.
- Utilized semantic technologies and automated reasoning for variant prioritization.
- Applied PVP to synthetic whole exome and whole genome sequencing datasets.
Main Results:
- PVP demonstrated effective performance in identifying causative variants across various diseases and syndromes.
- A retrospective study showed PVP's accuracy in interpreting whole exome sequencing data for congenital hypothyroidism patients.
- PVP successfully identified causative variants in both synthetic and patient data.
Conclusions:
- The PhenomeNET Variant Predictor (PVP) system accurately identifies causative genetic variants.
- PVP is a powerful resource for variant discovery in whole exome and whole genome sequencing.
- The system aids the clinical genetics community in diagnosing inherited and de novo mutations.
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