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. 2013 Jun;34(6):842-6.
doi: 10.1002/humu.22305. Epub 2013 Apr 3.

GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis

Michael A Gonzalez  1 , Rafael F Acosta Lebrigio, Derek Van Booven, Rick H Ulloa, Eric Powell, Fiorella Speziani, Mustafa Tekin, Rebecca Schüle, Stephan Züchner
Affiliations

GEnomes Management Application (GEM.app): a new software tool for large-scale collaborative genome analysis

Michael A Gonzalez et al. Hum Mutat. 2013 Jun.

Abstract

Novel genes are now identified at a rapid pace for many Mendelian disorders, and increasingly, for genetically complex phenotypes. However, new challenges have also become evident: (1) effectively managing larger exome and/or genome datasets, especially for smaller labs; (2) direct hands-on analysis and contextual interpretation of variant data in large genomic datasets; and (3) many small and medium-sized clinical and research-based investigative teams around the world are generating data that, if combined and shared, will significantly increase the opportunities for the entire community to identify new genes. To address these challenges, we have developed GEnomes Management Application (GEM.app), a software tool to annotate, manage, visualize, and analyze large genomic datasets (https://genomics.med.miami.edu/). GEM.app currently contains ∼1,600 whole exomes from 50 different phenotypes studied by 40 principal investigators from 15 different countries. The focus of GEM.app is on user-friendly analysis for nonbioinformaticians to make next-generation sequencing data directly accessible. Yet, GEM.app provides powerful and flexible filter options, including single family filtering, across family/phenotype queries, nested filtering, and evaluation of segregation in families. In addition, the system is fast, obtaining results within 4 sec across ∼1,200 exomes. We believe that this system will further enhance identification of genetic causes of human disease.

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Figures

Figure 1
Figure 1. GEM.app pipeline and Graphical User Interface
A) Starting page with currently seven analysis modules. B) Example of “Variants within families” filter module. There are at least 13 context-specific different filter categories available. Preset filters auto-fill a number variables and allow for a “three click” search. C) Results screen of a GEM.app query. Different control options are detailed.
Figure 2
Figure 2. Current usage of GEM.app
A) Geographical scheme of principle investigators with data in GEM.app. B) The number of registered users has grown to >103 in the past 6 months. C) The usage of GEM.app has increased significantly since its release. ASHG – American Society for Human Genetics annual meeting.
Figure 3
Figure 3. Performance of GEM.app
Average search times over 10,000 queries from over 60 different users. By far the most popular module is “Variants within families” which returns results in ~4 second across 1,200 exomes. Individual families are typically instantly returned.
See this image and copyright information in PMC

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