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dc.contributor.authorLiu, Mingmingen_US
dc.contributor.authorWatson, Layne T.en_US
dc.contributor.authorZhang, Liqingen_US
dc.date.accessioned2015-07-31T16:40:53Z
dc.date.available2015-07-31T16:40:53Z
dc.date.issued2015-07-30
dc.identifier.citationHuman Genomics. 2015 Jul 30;9(1):18en_US
dc.identifier.urihttp://hdl.handle.net/10919/55026
dc.description.abstractBackground Many genetic variants have been identified in the human genome. The functional effects of a single variant have been intensively studied. However, the joint effects of multiple variants in the same genes have been largely ignored due to their complexity or lack of data. This paper uses HMMvar, a hidden Markov model based approach, to investigate the combined effect of multiple variants from the 1000 Genomes Project. Two tumor suppressor genes, TP53 and phosphatase and tensin homolog (PTEN), are also studied for the joint effect of compensatory indel variants. Results Results show that there are cases where the joint effect of having multiple variants in the same genes is significantly different from that of a single variant. The deleterious effect of a single indel variant can be alleviated by their compensatory indels in TP53 and PTEN. Compound mutations in two genes, β-MHC and MyBP-C, leading to severer cardiovascular disease compared to single mutations, are also validated. Conclusions This paper extends the functionality of HMMvar, a tool for assigning a quantitative score to a variant, to measure not only the deleterious effect of a single variant but also the joint effect of multiple variants. HMMvar is the first tool that can predict the functional effects of both single and general multiple variations on proteins. The precomputed scores for multiple variants from the 1000 Genomes Project and the HMMvar package are available at https://bioinformatics.cs.vt.edu/zhanglab/HMMvar/en_US
dc.format.mimetypeapplication/pdfen_US
dc.language.isoen_US
dc.rightsCreative Commons Attribution 4.0 International*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titlePredicting the combined effect of multiple genetic variantsen_US
dc.typeArticle - Refereeden_US
dc.date.updated2015-07-31T16:40:53Z
dc.description.versionPeer Reviewed
dc.rights.holderLiu et al.en_US
dc.contributor.departmentAerospace and Ocean Engineeringen_US
dc.contributor.departmentComputer Scienceen_US
dc.contributor.departmentMathematicsen_US
dc.title.serialHuman Genomics
dc.identifier.doihttps://doi.org/10.1186/s40246-015-0040-4
dc.type.dcmitypeTexten_US


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Creative Commons Attribution 4.0 International
License: Creative Commons Attribution 4.0 International