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Planning the Human Variome Project: The Spain Report

By Jim Kaput, Richard G.H. Cotton, Lauren Hardman, Michael Watson, Aida I. Al Aqeel, Jumana Y. Al-Aama, Fahd Al-Mulla, Santos Alonso, Stefan Aretz, Arleen D. Auerbach, Bharati Bapat, Dagmar G. Scheible, Rodney J. Scott, Daniela Seminara, Elizabeth A. Shephard, Rolf H. Sijmons, Timothy D. Smith, María-Jesús Sobrido, Toshihiro Tanaka, Sean V. Tavtigian, Graham R. Taylor, Jon Teague, Thoralf Töpel, Mollie Ullman-Cullere, Joji Utsunomiya, Henk J. van Kranen, Mauno Vihinen, Elizabeth Webb, Thomas K. Weber, Meredith Yeager, Young I. Yeom, Seon-Hee Yim, Hyang-Sook Yoo, Inge T. Bernstein, Jong Bhak, Stacey L. Bleoo, Helmut Blöcker, Steven E. Brenner, John Burn, Mariona Bustamante, Rita Calzone, Anne Cambon-Thomsen, Michele Cargill, Paola Carrera, Lawrence Cavedon, Yoon Shin Cho, Yeun-Jun Chung, Mireille Claustres, Garry Cutting, Raymond Dalgleish, Johan T. den Dunnen, Carlos Díaz, Steven Dobrowolski, M. Rosário N. dos Santos, Rosemary Ekong, Simon B. Flanagan, Paul Flicek, Yoichi Furukawa, Maurizio Genuardi, Ho Ghang, Maria V. Golubenko, Marc S. Greenblatt, Ada Hamosh, John M. Hancock, Ross Hardison, Terence M. Harrison, Robert Hoffmann, Rania Horaitis, Heather J. Howard, Carol Isaacson Barash, Neskuts Izagirre, Jongsun Jung, Toshio Kojima, Sandrine Laradi, Yeon-Su Lee, Jong-Young Lee, Vera L. Gil-da-Silva-Lopes, Finlay A. Macrae, Donna Maglott, Makia J. Marafie, Steven G.E. Marsh, Yoichi Matsubara, Ludwine M. Messiaen, Gabriela Möslein, Mihai G. Netea, Melissa L. Norton, Peter J. Oefner, William S. Oetting, James C. O'Leary, Ana Maria Oller de Ramirez, Mark H. Paalman, Jillian Parboosingh, George P. Patrinos, Giuditta Perozzi, Ian R. Phillips, Sue Povey, Suyash Prasad, Ming Qi, David J. Quin, Rajkumar S. Ramesar, C. Sue Richards and Judith Savige


This is the pre-peer reviewed version of the following article: Dalgleish, R. et al., Planning the Human Variome Project: The Spain Report, Human Mutation, 2009, 30(4), pp. 496-510, which has been published in final form at, Doi: 10.1002/humu.20972.The remarkable progress in characterizing the human genome sequence, exemplified by the Human Genome Project and the HapMap Consortium, has led to the perception that knowledge and the tools (e.g., microarrays) are sufficient for many if not most biomedical research efforts. A large amount of data from diverse studies proves this perception inaccurate at best, and at worst, an impediment for further efforts to characterize the variation in the human genome. Since variation in genotype and environment are the fundamental basis to understand phenotypic variability and heritability at the population level, identifying the range of human genetic variation is crucial to the development of personalized nutrition and medicine. The Human Variome Project (HVP; was proposed initially to systematically collect mutations that cause human disease and create a cyber infrastructure to link locus specific databases (LSDB). We report here the discussions and recommendations from the 2008 HVP planning meeting held in San Feliu de Guixols, Spain, in May 2008

Topics: variome, genome, mutation, database, genetic disease
Publisher: Wiley-Blackwell
Year: 2009
DOI identifier: 10.1002/humu.20972
OAI identifier:

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  1. communication, interaction and research networks between the developing and the developed countries. doi
  2. Consider ethical issues arising from transferring data from LSDB to web browsers; refer to the
  3. Define conditions for removal from database.
  4. Demonstrate feasibility and productivity of approaches before application (pilot projects). The most notable at present is the InSiGHT collaboration and the “Adopt a gene” approach.
  5. Determine the appropriate limits to access within LSDBs to prevent individual identification.
  6. Disclosure of additional data, even for clinical reasons to medical professionals, cannot occur unless prior authorization given by donor in original consent.
  7. Ensure against harms to vulnerable individuals or groups of individuals, including groups defined on the basis of data findings.
  8. Ensure strict protection of privacy in cases of rare mutations in rare disease or unique combinations of clinical features, where identification of individuals is at risk.
  9. Examine overall governance strategy outside the facilitating activities of the coordinating office.
  10. How ought data which is not tied to consent be handled? That is, in the absence of explicit approval or refusal can data be used and if so, ought it to be de-identified or anonymized, or not used?
  11. In fostering standardization, there is a need to consistently define ‘de-identified’ and ‘anonymized’ and ensure consistent use across the LSDBs.
  12. Is access to deceased individuals’ information ethically appropriate? Is familial consent required if individuals did not authorize access prior to their death?
  13. Lobby for general support of the HVP as well as for individual grants.
  14. Planning the Human Variome Project: The Spain Report
  15. Proceed with systematical implementation of the Adopt a Gene approach, which has now been initiated, for funding of curators.
  16. specific and disease specific programs can be developed when applying for funding (i.e. the InSiGHT colon cancer project).
  17. To keep abreast of new analytical methods that may impact or influence the ability to maintain confidentiality of data. Box 7 Ethics Sub-Group Recommendations and Remaining Issues
  18. Virtual or actual medical relationships with an enquirer are unwise and are discouraged (e.g., a company or person who performs the genetic test should not provide advice on the use of the results).
  19. What constitutes appropriate consent for prospective data collection?

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