GEnomes Management Application (GEM.app): A New Software Tool for Large-Scale Collaborative Genome Analysis

Michael A. Gonzalez, Rafael F Acosta Lebrigio, Derek Van Booven, Rick H. Ulloa, Eric Powell, Fiorella Speziani, Mustafa Tekin, Rebecca Schüle, Stephan L Zuchner

Research output: Contribution to journalArticle

60 Citations (Scopus)

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/">https://genomics.med.miami.edu/">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. The web-based tool Genomes Management Application is used in 15 different countries and provides easy to use yet powerful and fast analysis over hundreds of exomes.

Original languageEnglish
Pages (from-to)842-846
Number of pages5
JournalHuman Mutation
Volume34
Issue number6
DOIs
StatePublished - Jun 1 2013

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Exome
Software
Genomics
Genome
Phenotype
Medical Genetics
Genes
Research Personnel
Research
Datasets

Keywords

  • Exome sequencing
  • Next-generation sequencing
  • Next-generation sequencing analysis

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Gonzalez, M. A., Lebrigio, R. F. A., Van Booven, D., Ulloa, R. H., Powell, E., Speziani, F., ... Zuchner, S. L. (2013). GEnomes Management Application (GEM.app): A New Software Tool for Large-Scale Collaborative Genome Analysis. Human Mutation, 34(6), 842-846. https://doi.org/10.1002/humu.22305

GEnomes Management Application (GEM.app) : A New Software Tool for Large-Scale Collaborative Genome Analysis. / Gonzalez, Michael A.; Lebrigio, Rafael F Acosta; Van Booven, Derek; Ulloa, Rick H.; Powell, Eric; Speziani, Fiorella; Tekin, Mustafa; Schüle, Rebecca; Zuchner, Stephan L.

In: Human Mutation, Vol. 34, No. 6, 01.06.2013, p. 842-846.

Research output: Contribution to journalArticle

Gonzalez, MA, Lebrigio, RFA, Van Booven, D, Ulloa, RH, Powell, E, Speziani, F, Tekin, M, Schüle, R & Zuchner, SL 2013, 'GEnomes Management Application (GEM.app): A New Software Tool for Large-Scale Collaborative Genome Analysis', Human Mutation, vol. 34, no. 6, pp. 842-846. https://doi.org/10.1002/humu.22305
Gonzalez MA, Lebrigio RFA, Van Booven D, Ulloa RH, Powell E, Speziani F et al. GEnomes Management Application (GEM.app): A New Software Tool for Large-Scale Collaborative Genome Analysis. Human Mutation. 2013 Jun 1;34(6):842-846. https://doi.org/10.1002/humu.22305
Gonzalez, Michael A. ; Lebrigio, Rafael F Acosta ; Van Booven, Derek ; Ulloa, Rick H. ; Powell, Eric ; Speziani, Fiorella ; Tekin, Mustafa ; Schüle, Rebecca ; Zuchner, Stephan L. / GEnomes Management Application (GEM.app) : A New Software Tool for Large-Scale Collaborative Genome Analysis. In: Human Mutation. 2013 ; Vol. 34, No. 6. pp. 842-846.
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