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Canadian Journal of Cardiology

Proprietary Considerations in the Use of Cardiovascular Genetic Data

  • Mladen Kolovic
    Affiliations
    Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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  • John F. Robinson
    Affiliations
    Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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  • Robert A. Hegele
    Correspondence
    Corresponding author: Dr Robert A. Hegele, Robarts Research Institute, 4288A - 1151 Richmond St N, London, Ontario N6A 5B7, Canada. Tel.: +1-519-931-5271; fax: +1-519-931-5218.
    Affiliations
    Department of Medicine and Robarts Research Institute, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
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Published:February 11, 2016DOI:https://doi.org/10.1016/j.cjca.2016.02.033

      Abstract

      Cardiovascular researchers and clinicians who analyze next-generation sequencing data often search databases of previously reported mutations to determine if an observed mutation is pathogenic. In 2012 we created a database of all reported mutations causing human dyslipidemia syndromes. In 2015, we were advised that some information in our database was now proprietary, after the acquisition of a human disease genetic database by a private biotechnology company. To make our dyslipidemia database and tables of mutations compliant with this new reality, we wrote custom computer scripts to remove certain data fields from the previously reported tables. Data columns in the revised tables now include: accession number, gene name and symbol, mutation type, exon number, inheritance pattern, minor allele frequencies, predictive functional scores, reported functional effects, and additional patient information. The revised mutation tables provide a comprehensive qualitative and quantitative description of genetic variants causing monogenic dyslipidemias, but do not have complete information on all mutations. This experience indicates that free and unlimited access to human disease mutation data should not be taken for granted. Investigators or clinicians who require additional data that is not within the revised tables can still access the data through academic institutions that hold subscriptions to proprietary human mutation databases.

      Résumé

      Les chercheurs et les cliniciens spécialisés en santé cardiovasculaire qui analysent les données de séquençage de nouvelle génération interrogent souvent les bases de données à la recherche de mutations déjà rapportées afin de déterminer si l’une d’elles serait pathogène. En 2012, nous avons constitué une base de données regroupant toutes les mutations rapportées à ce jour à l’origine de syndromes de dyslipidémie chez l’humain. En 2015, on nous a informés que certaines de ces données relevaient maintenant du domaine privé, à la suite de l’acquisition, par une entreprise de biotechnologie privée, d’une base de données sur les maladies génétiques humaines. Pour ajuster notre base de données sur la dyslipidémie et nos tableaux de mutations en conséquence, nous avons dû ajouter des scripts informatiques sur mesure afin d’éliminer certains champs de données. Les colonnes de données des tableaux révisés sont maintenant les suivantes : numéro de référence, nom et symbole du gène, type de mutation, numéro d’exon, modalités de transmission héréditaire, fréquence des allèles minoritaires, scores fonctionnels prédictifs, effets fonctionnels observés et renseignements additionnels sur les patients. La version révisée des tableaux offre désormais une description qualitative et quantitative détaillée des variantes génétiques à l’origine des dyslipidémies monogéniques sans toutefois afficher toute l’information relative à toutes les mutations. Cette expérience nous apprend que l’accès gratuit et illimité aux données sur les mutations génétiques pathogènes ne doit pas être tenu pour acquis. Les chercheurs et les cliniciens qui ont besoin de données supplémentaires qui n’apparaissent pas dans nos nouveaux tableaux peuvent encore y avoir accès par l’intermédiaire des établissements universitaires abonnés aux bases de données privées.
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      References

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      2. UNESCO. Report of the IBC on Updating Its Reflection on the Human Genome and Human Rights. Available at: http://unesdoc.unesco.org/images/0023/002332/233258E.pdf. Accessed November 6, 2015.

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