Literature DB >> 26173844

Innovative genomic collaboration using the GENESIS (GEM.app) platform.

Michael Gonzalez1, Marni J Falk2, Xiaowu Gai3, Richard Postrel1, Rebecca Schüle4,5,6, Stephan Zuchner6.   

Abstract

Next-generation sequencing has led to an unparalleled pace of Mendelian disease gene discovery in recent years. To address the challenges of analysis and sharing of large datasets, we had previously introduced the collaborative web-based GEM.app software [Gonzalez et al., ]. Here, we are presenting the results of using GEM.app over nearly 3 years and introducing the next generation of this platform. First, GEM.app has been renamed to GENESIS since it is now part of "The Genesis Project" (501c3), a not-for-profit foundation that is committed to providing the best technology to enable research scientists and to connecting patients and clinicians to genomic information. Second, GENESIS (GEM.app) has grown to nearly 600 registered users from 44 countries, who have collectively achieved 62 gene identifications or published studies that have expanded phenotype/genotype correlations. Our concept of user-driven data sharing and matchmaking is now the main cause for gene discoveries within GENESIS. In many of these findings, researchers from across the globe have been connected, which gave rise to the genetic evidence needed to successfully pinpoint-specific gene mutations that explained patients' disease. Here, we present an overview of the various novel insights that have been made possible through the data-sharing capabilities of GENESIS/GEM.app.
© 2015 WILEY PERIODICALS, INC.

Entities:  

Keywords:  Mendelian disease; data sharing; exome; matchmaker exchange; next-generation sequencing

Mesh:

Year:  2015        PMID: 26173844      PMCID: PMC4682547          DOI: 10.1002/humu.22836

Source DB:  PubMed          Journal:  Hum Mutat        ISSN: 1059-7794            Impact factor:   4.878


  9 in total

Review 1.  Monogenic mitochondrial disorders.

Authors:  Werner J H Koopman; Peter H G M Willems; Jan A M Smeitink
Journal:  N Engl J Med       Date:  2012-03-22       Impact factor: 91.245

2.  The NCBI dbGaP database of genotypes and phenotypes.

Authors:  Matthew D Mailman; Michael Feolo; Yumi Jin; Masato Kimura; Kimberly Tryka; Rinat Bagoutdinov; Luning Hao; Anne Kiang; Justin Paschall; Lon Phan; Natalia Popova; Stephanie Pretel; Lora Ziyabari; Moira Lee; Yu Shao; Zhen Y Wang; Karl Sirotkin; Minghong Ward; Michael Kholodov; Kerry Zbicz; Jeffrey Beck; Michael Kimelman; Sergey Shevelev; Don Preuss; Eugene Yaschenko; Alan Graeff; James Ostell; Stephen T Sherry
Journal:  Nat Genet       Date:  2007-10       Impact factor: 38.330

3.  PNPLA6 mutations cause Boucher-Neuhauser and Gordon Holmes syndromes as part of a broad neurodegenerative spectrum.

Authors:  Matthis Synofzik; Michael A Gonzalez; Charles Marques Lourenco; Marie Coutelier; Tobias B Haack; Adriana Rebelo; Didier Hannequin; Tim M Strom; Holger Prokisch; Christoph Kernstock; Alexandra Durr; Ludger Schöls; Marcos M Lima-Martínez; Amjad Farooq; Rebecca Schüle; Giovanni Stevanin; Wilson Marques; Stephan Züchner
Journal:  Brain       Date:  2013-12-19       Impact factor: 13.501

4.  Neuropathy target esterase gene mutations cause motor neuron disease.

Authors:  Shirley Rainier; Melanie Bui; Erin Mark; Donald Thomas; Debra Tokarz; Lei Ming; Colin Delaney; Rudy J Richardson; James W Albers; Nori Matsunami; Jeff Stevens; Hilary Coon; Mark Leppert; John K Fink
Journal:  Am J Hum Genet       Date:  2008-02-28       Impact factor: 11.025

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

Authors:  Michael A Gonzalez; Rafael F Acosta Lebrigio; Derek Van Booven; Rick H Ulloa; Eric Powell; Fiorella Speziani; Mustafa Tekin; Rebecca Schüle; Stephan Züchner
Journal:  Hum Mutat       Date:  2013-04-03       Impact factor: 4.878

Review 6.  Mitochondrial Disease Sequence Data Resource (MSeqDR): a global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities.

Authors:  Marni J Falk; Lishuang Shen; Michael Gonzalez; Jeremy Leipzig; Marie T Lott; Alphons P M Stassen; Maria Angela Diroma; Daniel Navarro-Gomez; Philip Yeske; Renkui Bai; Richard G Boles; Virginia Brilhante; David Ralph; Jeana T DaRe; Robert Shelton; Sharon F Terry; Zhe Zhang; William C Copeland; Mannis van Oven; Holger Prokisch; Douglas C Wallace; Marcella Attimonelli; Danuta Krotoski; Stephan Zuchner; Xiaowu Gai
Journal:  Mol Genet Metab       Date:  2014-12-04       Impact factor: 4.797

Review 7.  RD-Connect: an integrated platform connecting databases, registries, biobanks and clinical bioinformatics for rare disease research.

Authors:  Rachel Thompson; Louise Johnston; Domenica Taruscio; Lucia Monaco; Christophe Béroud; Ivo G Gut; Mats G Hansson; Peter-Bram A 't Hoen; George P Patrinos; Hugh Dawkins; Monica Ensini; Kurt Zatloukal; David Koubi; Emma Heslop; Justin E Paschall; Manuel Posada; Peter N Robinson; Kate Bushby; Hanns Lochmüller
Journal:  J Gen Intern Med       Date:  2014-08       Impact factor: 5.128

8.  Statistical guidance for experimental design and data analysis of mutation detection in rare monogenic mendelian diseases by exome sequencing.

Authors:  Degui Zhi; Rui Chen
Journal:  PLoS One       Date:  2012-02-10       Impact factor: 3.240

9.  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Authors:  Sebastian Köhler; Sandra C Doelken; Christopher J Mungall; Sebastian Bauer; Helen V Firth; Isabelle Bailleul-Forestier; Graeme C M Black; Danielle L Brown; Michael Brudno; Jennifer Campbell; David R FitzPatrick; Janan T Eppig; Andrew P Jackson; Kathleen Freson; Marta Girdea; Ingo Helbig; Jane A Hurst; Johanna Jähn; Laird G Jackson; Anne M Kelly; David H Ledbetter; Sahar Mansour; Christa L Martin; Celia Moss; Andrew Mumford; Willem H Ouwehand; Soo-Mi Park; Erin Rooney Riggs; Richard H Scott; Sanjay Sisodiya; Steven Van Vooren; Ronald J Wapner; Andrew O M Wilkie; Caroline F Wright; Anneke T Vulto-van Silfhout; Nicole de Leeuw; Bert B A de Vries; Nicole L Washingthon; Cynthia L Smith; Monte Westerfield; Paul Schofield; Barbara J Ruef; Georgios V Gkoutos; Melissa Haendel; Damian Smedley; Suzanna E Lewis; Peter N Robinson
Journal:  Nucleic Acids Res       Date:  2013-11-11       Impact factor: 16.971

  9 in total
  44 in total

1.  FAHN/SPG35: a narrow phenotypic spectrum across disease classifications.

Authors:  Tim W Rattay; Tobias Lindig; Jonathan Baets; Katrien Smets; Tine Deconinck; Anne S Söhn; Konstanze Hörtnagel; Kathrin N Eckstein; Sarah Wiethoff; Jennifer Reichbauer; Marion Döbler-Neumann; Ingeborg Krägeloh-Mann; Michaela Auer-Grumbach; Barbara Plecko; Alexander Münchau; Bernd Wilken; Marc Janauschek; Anne-Katrin Giese; Jan L De Bleecker; Els Ortibus; Martine Debyser; Adolfo Lopez de Munain; Aurora Pujol; Maria Teresa Bassi; Maria Grazia D'Angelo; Peter De Jonghe; Stephan Züchner; Peter Bauer; Ludger Schöls; Rebecca Schüle
Journal:  Brain       Date:  2019-06-01       Impact factor: 13.501

2.  Severe axonal Charcot-Marie-Tooth disease with proximal weakness caused by de novo mutation in the MORC2 gene.

Authors:  Petra Laššuthová; Dana Šafka Brožková; Marcela Krůtová; Radim Mazanec; Stephan Züchner; Michael A Gonzalez; Pavel Seeman
Journal:  Brain       Date:  2016-02-11       Impact factor: 13.501

3.  Truncating Mutations in UBAP1 Cause Hereditary Spastic Paraplegia.

Authors:  Mohammad Ali Farazi Fard; Adriana P Rebelo; Elena Buglo; Hamid Nemati; Hassan Dastsooz; Ina Gehweiler; Selina Reich; Jennifer Reichbauer; Beatriz Quintáns; Andrés Ordóñez-Ugalde; Andrea Cortese; Steve Courel; Lisa Abreu; Eric Powell; Matt C Danzi; Nicole B Martuscelli; Dana M Bis-Brewer; Feifei Tao; Fariba Zarei; Parham Habibzadeh; Majid Yavarian; Farzaneh Modarresi; Mohammad Silawi; Zahra Tabatabaei; Masoume Yousefi; Hamid Reza Farpour; Christoph Kessler; Elisabeth Mangold; Xenia Kobeleva; Ivailo Tournev; Teodora Chamova; Amelie J Mueller; Tobias B Haack; Mark Tarnopolsky; Ziv Gan-Or; Guy A Rouleau; Matthis Synofzik; María-Jesús Sobrido; Albena Jordanova; Rebecca Schüle; Stephan Zuchner; Mohammad Ali Faghihi
Journal:  Am J Hum Genet       Date:  2019-03-28       Impact factor: 11.025

4.  The Matchmaker Exchange: a platform for rare disease gene discovery.

Authors:  Anthony A Philippakis; Danielle R Azzariti; Sergi Beltran; Anthony J Brookes; Catherine A Brownstein; Michael Brudno; Han G Brunner; Orion J Buske; Knox Carey; Cassie Doll; Sergiu Dumitriu; Stephanie O M Dyke; Johan T den Dunnen; Helen V Firth; Richard A Gibbs; Marta Girdea; Michael Gonzalez; Melissa A Haendel; Ada Hamosh; Ingrid A Holm; Lijia Huang; Matthew E Hurles; Ben Hutton; Joel B Krier; Andriy Misyura; Christopher J Mungall; Justin Paschall; Benedict Paten; Peter N Robinson; François Schiettecatte; Nara L Sobreira; Ganesh J Swaminathan; Peter E Taschner; Sharon F Terry; Nicole L Washington; Stephan Züchner; Kym M Boycott; Heidi L Rehm
Journal:  Hum Mutat       Date:  2015-10       Impact factor: 4.878

5.  Mutations in ATP1A1 Cause Dominant Charcot-Marie-Tooth Type 2.

Authors:  Petra Lassuthova; Adriana P Rebelo; Gianina Ravenscroft; Phillipa J Lamont; Mark R Davis; Fiore Manganelli; Shawna M Feely; Chelsea Bacon; Dana Šafka Brožková; Jana Haberlova; Radim Mazanec; Feifei Tao; Cima Saghira; Lisa Abreu; Steve Courel; Eric Powell; Elena Buglo; Dana M Bis; Megan F Baxter; Royston W Ong; Lorna Marns; Yi-Chung Lee; Yunhong Bai; Daniel G Isom; René Barro-Soria; Ki W Chung; Steven S Scherer; H Peter Larsson; Nigel G Laing; Byung-Ok Choi; Pavel Seeman; Michael E Shy; Lucio Santoro; Stephan Zuchner
Journal:  Am J Hum Genet       Date:  2018-03-01       Impact factor: 11.025

6.  Substrate interaction defects in histidyl-tRNA synthetase linked to dominant axonal peripheral neuropathy.

Authors:  Jamie A Abbott; Rebecca Meyer-Schuman; Vincenzo Lupo; Shawna Feely; Inès Mademan; Stephanie N Oprescu; Laurie B Griffin; M Antonia Alberti; Carlos Casasnovas; Sharon Aharoni; Lina Basel-Vanagaite; Stephan Züchner; Peter De Jonghe; Jonathan Baets; Michael E Shy; Carmen Espinós; Borries Demeler; Anthony Antonellis; Christopher Francklyn
Journal:  Hum Mutat       Date:  2017-12-26       Impact factor: 4.878

7.  Loss-of-function mutations in the ATP13A2/PARK9 gene cause complicated hereditary spastic paraplegia (SPG78).

Authors:  Alejandro Estrada-Cuzcano; Shaun Martin; Teodora Chamova; Matthis Synofzik; Dagmar Timmann; Tine Holemans; Albena Andreeva; Jennifer Reichbauer; Riet De Rycke; Dae-In Chang; Sarah van Veen; Jean Samuel; Ludger Schöls; Thorsten Pöppel; Danny Mollerup Sørensen; Bob Asselbergh; Christine Klein; Stephan Zuchner; Albena Jordanova; Peter Vangheluwe; Ivailo Tournev; Rebecca Schüle
Journal:  Brain       Date:  2017-02       Impact factor: 13.501

8.  A recurrent WARS mutation is a novel cause of autosomal dominant distal hereditary motor neuropathy.

Authors:  Pei-Chien Tsai; Bing-Wen Soong; Inès Mademan; Yen-Hua Huang; Chia-Rung Liu; Cheng-Tsung Hsiao; Hung-Ta Wu; Tze-Tze Liu; Yo-Tsen Liu; Yen-Ting Tseng; Kon-Ping Lin; Ueng-Cheng Yang; Ki Wha Chung; Byung-Ok Choi; Garth A Nicholson; Marina L Kennerson; Chih-Chiang Chan; Peter De Jonghe; Tzu-Hao Cheng; Yi-Chu Liao; Stephan Züchner; Jonathan Baets; Yi-Chung Lee
Journal:  Brain       Date:  2017-05-01       Impact factor: 13.501

9.  De novo ITPR1 variants are a recurrent cause of early-onset ataxia, acting via loss of channel function.

Authors:  Matthis Synofzik; Katherine L Helbig; Florian Harmuth; Tine Deconinck; Pranoot Tanpaiboon; Bo Sun; Wenting Guo; Ruiwu Wang; Erika Palmaer; Sha Tang; G Bradley Schaefer; Janina Gburek-Augustat; Stephan Züchner; Ingeborg Krägeloh-Mann; Jonathan Baets; Peter de Jonghe; Peter Bauer; S R Wayne Chen; Ludger Schöls; Rebecca Schüle
Journal:  Eur J Hum Genet       Date:  2018-06-20       Impact factor: 4.246

10.  A novel MFN2 mutation causes variable clinical severity in a multi-generational CMT2 family.

Authors:  Lois Dankwa; Jessica Richardson; William W Motley; Mena Scavina; Steve Courel; Tanya Bardakjian; Stephan Züchner; Steven S Scherer
Journal:  Neuromuscul Disord       Date:  2018-12-21       Impact factor: 4.296

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