GRIPT: a novel case-control analysis method for Mendelian disease gene discovery

Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes an...

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Autores principales: Wang, Jun, Zhao, Li, Wang, Xia, Chen, Yong, Xu, Mingchu, Soens, Zachry T., Ge, Zhongqi, Wang, Peter Ronghan, Wang, Fei, Chen, Rui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258408/
https://www.ncbi.nlm.nih.gov/pubmed/30477545
http://dx.doi.org/10.1186/s13059-018-1579-x
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author Wang, Jun
Zhao, Li
Wang, Xia
Chen, Yong
Xu, Mingchu
Soens, Zachry T.
Ge, Zhongqi
Wang, Peter Ronghan
Wang, Fei
Chen, Rui
author_facet Wang, Jun
Zhao, Li
Wang, Xia
Chen, Yong
Xu, Mingchu
Soens, Zachry T.
Ge, Zhongqi
Wang, Peter Ronghan
Wang, Fei
Chen, Rui
author_sort Wang, Jun
collection PubMed
description Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1579-x) contains supplementary material, which is available to authorized users.
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spelling pubmed-62584082018-11-29 GRIPT: a novel case-control analysis method for Mendelian disease gene discovery Wang, Jun Zhao, Li Wang, Xia Chen, Yong Xu, Mingchu Soens, Zachry T. Ge, Zhongqi Wang, Peter Ronghan Wang, Fei Chen, Rui Genome Biol Method Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1579-x) contains supplementary material, which is available to authorized users. BioMed Central 2018-11-26 /pmc/articles/PMC6258408/ /pubmed/30477545 http://dx.doi.org/10.1186/s13059-018-1579-x Text en © The Author(s). 2018 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 Method
Wang, Jun
Zhao, Li
Wang, Xia
Chen, Yong
Xu, Mingchu
Soens, Zachry T.
Ge, Zhongqi
Wang, Peter Ronghan
Wang, Fei
Chen, Rui
GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
title GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
title_full GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
title_fullStr GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
title_full_unstemmed GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
title_short GRIPT: a novel case-control analysis method for Mendelian disease gene discovery
title_sort gript: a novel case-control analysis method for mendelian disease gene discovery
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258408/
https://www.ncbi.nlm.nih.gov/pubmed/30477545
http://dx.doi.org/10.1186/s13059-018-1579-x
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