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• W3087029191 abstract "Background:​ Non-coding variants have emerged as important contributors to the pathogenesis of human diseases, not only as common susceptibility alleles but also as rare high-impact variants. Despite recent advances in the study of regulatory elements and the availability of specialized data collections, the systematic annotation of non-coding variants from genome sequencing remains challenging. Results: ​ We integrated 24 data sources to develop a standardized collection of 2.4 million regulatory elements in the human genome, transcription factor binding sites, DNase peaks, ultra-conserved non-coding elements, and super-enhancers. Information on controlled gene(s), tissue(s) and associated phenotype(s) are provided for regulatory elements when possible. We also calculated a variation constraint metric for regulatory regions and showed that genes controlled by constrained regions are more likely to be disease-associated genes and essential genes from mouse knock-out screenings. Finally, we evaluated 16 non-coding impact prediction scores providing suggestions for variant prioritization. The companion tool allows for annotation of VCF files with information about the regulatory regions as well as non-coding prediction scores to inform variant prioritization. The proposed annotation framework was able to capture previously published disease-associated non-coding variants and its integration in a routine prioritization pipeline increased the number of candidate genes, including genes potentially correlated with patient phenotype, and established clinically relevant genes. Conclusion: ​ We have developed a resource for the annotation and prioritization of regulatory variants in WGS analysis to support the discovery of candidate disease-associated variants in the non-coding genome." @default.
• W3087029191 created "2020-09-25" @default.
• W3087029191 creator A5076049770 @default.
• W3087029191 creator A5078452635 @default.
• W3087029191 creator A5091819421 @default.
• W3087029191 date "2020-09-19" @default.
• W3087029191 modified "2023-10-15" @default.
• W3087029191 title "GREEN-DB: a framework for the annotation and prioritization of non-coding regulatory variants in whole-genome sequencing" @default.
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• W3087029191 doi "https://doi.org/10.1101/2020.09.17.301960" @default.
• W3087029191 hasPublicationYear "2020" @default.
• W3087029191 type Work @default.
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