Planning the Human Variome Project: The Spain report

Abstract

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; http://www.humanvariomeproject.org/) 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.

Beyond the genomics blueprint: the 4th Human Variome Project Meeting, UNESCO, Paris, 2012

“…5 In 2009, the group was charged with conducting a needs assessment, and the findings were presented at an HVP forum in November 2010. The assessment found that the most frequently chosen category for unmet needs was methods to interpret variants.…”

Databases for neurogenetics: Introduction, overview, and challenges

“…These and other issues are being discussed with a multidisciplinary approach within the HVP consortium and recommendations are being produced [Kaput et al, 2009;Povey et al, 2010]. However, specific characteristics of neurological disorders call for the confluence of experts in the clinical aspects, as well as in neuropathology, neurophysiology, neuroimaging, genetics, and molecular and cell biology [Haworth et al, 2011].…”

Connecting the Human Variome Project to nutrigenomics

“…The Human Variome Project (HVP; http://www.human variomeproject.org/) is an international effort to systematically identify genes, their mutations, and their variants associated with phenotypic variability and indications of human disease or phenotype [15,16,33,51]. The goal of the HVP is to link clinical, medical, and research laboratories for developing knowledge.…”

“…The HVP faces additional challenges since clinics and service laboratories describe pathogenicity and genetic variation, but academic incentives to publish are not paramount for these professions. Novel approaches for attribution have been proposed [23,33,43] and are starting to be applied by some databases and continue to be developed by the HVP. A public debate is also in progress among the editors of genetics journals to coordinate efforts toward the attribution of data deposition and database linking (http://www.gen2phen.org/wiki/hvppublication-credit-and-incentives-recommendations).…”