Prioritization and functional assessment of noncoding variants associated with complex diseases

Unraveling functional noncoding variants associated with complex diseases is still a great challenge. We present a novel algorithm, Prioritization And Functional Assessment (PAFA), that prioritizes and assesses the functionality of genetic variants by introducing population differentiation measures...

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Bibliographic Details
Published in:Genome medicine 2018-07, Vol.10 (1), p.53-53, Article 53
Main Authors: Zhou, Lin, Zhao, Fangqing
Format: Article
Language:English
Subjects:
Algorithms
Annotations
Bioinformatics
Complex disease
Computational biology
Diabetes
Disease
Functional annotation
Genetic diversity
Genetic variant
Genetic variation
Genomes
Genomics
Macular degeneration
Method
Noncoding variant
Population
Population differentiation
Population genetics
Prostate cancer
Systematic review
Variant prioritization
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Summary:Unraveling functional noncoding variants associated with complex diseases is still a great challenge. We present a novel algorithm, Prioritization And Functional Assessment (PAFA), that prioritizes and assesses the functionality of genetic variants by introducing population differentiation measures and recalibrating training variants. Comprehensive evaluations demonstrate that PAFA exhibits much higher sensitivity and specificity in prioritizing noncoding risk variants than existing methods. PAFA achieves improved performance in distinguishing both common and rare recurrent variants from non-recurrent variants by integrating multiple annotations and metrics. An integrated platform was developed, providing comprehensive functional annotations for noncoding variants by integrating functional genomic data, which can be accessed at http://159.226.67.237:8080/pafa .
ISSN:1756-994X
1756-994X
DOI:10.1186/s13073-018-0565-y