A combined functional annotation score for non-synonymous variants.

Autor:	Lopes MC; Wellcome Trust Sanger Institute, Hinxton, Hinxton, UK. ml10@sanger.ac.uk, Joyce C, Ritchie GR, John SL, Cunningham F, Asimit J, Zeggini E
Jazyk:	angličtina
Zdroj:	Human heredity [Hum Hered] 2012; Vol. 73 (1), pp. 47-51. Date of Electronic Publication: 2012 Jan 18.
DOI:	10.1159/000334984
Abstrakt:	Aims: Next-generation sequencing has opened the possibility of large-scale sequence-based disease association studies. A major challenge in interpreting whole-exome data is predicting which of the discovered variants are deleterious or neutral. To address this question in silico, we have developed a score called Combined Annotation scoRing toOL (CAROL), which combines information from 2 bioinformatics tools: PolyPhen-2 and SIFT, in order to improve the prediction of the effect of non-synonymous coding variants. Methods: We used a weighted Z method that combines the probabilistic scores of PolyPhen-2 and SIFT. We defined 2 dataset pairs to train and test CAROL using information from the dbSNP: 'HGMD-PUBLIC' and 1000 Genomes Project databases. The training pair comprises a total of 980 positive control (disease-causing) and 4,845 negative control (non-disease-causing) variants. The test pair consists of 1,959 positive and 9,691 negative controls. Results: CAROL has higher predictive power and accuracy for the effect of non-synonymous variants than each individual annotation tool (PolyPhen-2 and SIFT) and benefits from higher coverage. Conclusion: The combination of annotation tools can help improve automated prediction of whole-genome/exome non-synonymous variant functional consequences. (Copyright © 2012 S. Karger AG, Basel.)
Databáze:	MEDLINE
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