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VARPRISM: incorporating variant prioritization in tests of de novo mutation association
BACKGROUND: Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. RESULTS: We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization i...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997702/ https://www.ncbi.nlm.nih.gov/pubmed/27562213 http://dx.doi.org/10.1186/s13073-016-0341-9 |
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author | Hu, Hao Coon, Hilary Li, Man Yandell, Mark Huff, Chad D. |
author_facet | Hu, Hao Coon, Hilary Li, Man Yandell, Mark Huff, Chad D. |
author_sort | Hu, Hao |
collection | PubMed |
description | BACKGROUND: Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. RESULTS: We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk. VARPRISM evaluates the consequence of any given exonic mutation on the protein sequence to estimate the likelihood that the mutation is benign or damaging and conducts a likelihood ratio test on the gene level. We analyzed the Simons Simplex Collection of 2508 parent-offspring autism trios using VARPRISM, replicating 44 genes previously implicated in autism susceptibility and identifying 20 additional candidate genes, including MYO1E, KCND3, PDCD1, DLX3, and TSPAN4 (false discovery rate < 0.3). CONCLUSION: By incorporating functional predictions, VARPRISM improved the statistical power to identify de novo mutations increasing disease risks. VARPRISM is available at http://www.hufflab.org/software/VARPRISM. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-016-0341-9) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4997702 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-49977022016-08-26 VARPRISM: incorporating variant prioritization in tests of de novo mutation association Hu, Hao Coon, Hilary Li, Man Yandell, Mark Huff, Chad D. Genome Med Software BACKGROUND: Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. RESULTS: We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk. VARPRISM evaluates the consequence of any given exonic mutation on the protein sequence to estimate the likelihood that the mutation is benign or damaging and conducts a likelihood ratio test on the gene level. We analyzed the Simons Simplex Collection of 2508 parent-offspring autism trios using VARPRISM, replicating 44 genes previously implicated in autism susceptibility and identifying 20 additional candidate genes, including MYO1E, KCND3, PDCD1, DLX3, and TSPAN4 (false discovery rate < 0.3). CONCLUSION: By incorporating functional predictions, VARPRISM improved the statistical power to identify de novo mutations increasing disease risks. VARPRISM is available at http://www.hufflab.org/software/VARPRISM. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-016-0341-9) contains supplementary material, which is available to authorized users. BioMed Central 2016-08-25 /pmc/articles/PMC4997702/ /pubmed/27562213 http://dx.doi.org/10.1186/s13073-016-0341-9 Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Hu, Hao Coon, Hilary Li, Man Yandell, Mark Huff, Chad D. VARPRISM: incorporating variant prioritization in tests of de novo mutation association |
title | VARPRISM: incorporating variant prioritization in tests of de novo mutation association |
title_full | VARPRISM: incorporating variant prioritization in tests of de novo mutation association |
title_fullStr | VARPRISM: incorporating variant prioritization in tests of de novo mutation association |
title_full_unstemmed | VARPRISM: incorporating variant prioritization in tests of de novo mutation association |
title_short | VARPRISM: incorporating variant prioritization in tests of de novo mutation association |
title_sort | varprism: incorporating variant prioritization in tests of de novo mutation association |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4997702/ https://www.ncbi.nlm.nih.gov/pubmed/27562213 http://dx.doi.org/10.1186/s13073-016-0341-9 |
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