The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. Members of each of eight sessions the clinic and phenotype. The human genome project delivered a template against which all human genetic variation can be compared. Human variome project united nations educational, scientific and. The aim of the human variome project is to ensure that all information on genetic variation can be collected, curated, interpreted and shared freely and openly. The hvp established a working group for variant database quality assessment in 2012. Special article human mutation initiating a human variome project country node jumana alaama,1 timothy d. To ensure that this contributes to improving global health outcomes, the human variome project focusses on increasing both the quality and quantity of genomic knowledge that is collected, curated, interpreted and shared for clinical practice. The human variome project hvp is an international consortium of scientists and. The human variome project is an international nongovernmental organisation working to build capacity in the practice of responsible genomics. The first version of the variome annotation schema was constructed by analysing the database schema for the existing insight mutation database. The malaysian node of the human variome project myhvp database used open source software in the development of the variation and mutation databases.
Lsdbs should be accredited by the human variome project and use an agreed reference sequence, nomenclature and database standard, and they should accommodate highquality clinical. Arthur lian chi hsu, renate marquisnicholson, sebastian lunke, clare love, kym pham, olga kondrashova, matt wakefield, tiffany cowie, barney rudzki and paul waring human variome project tim smith, alan lo, melvyn leong, david perkins, heather. Facilitate the development of software to collect and exchange human variation data in a federation of genespecific locusspecific, country specific, diseasespecific, and general databases. An ngo maintaining operational relations with the united nations educational, scientific and cultural organisation unesco. For hvp, rare mutations in a population open the possibility of identifying the research participant. Myhvpdb provides only information about the genetic variations and mutations found in the malays. The human variome database in australia in 2014 graham taylor. Hgvsnomenclature is used to report and exchange information regarding variants found in. The human variome project beijing meeting journal of. Dec 01, 2005 toward a human variome project toward a human variome project cotton, richard g. Mar 28, 2007 lsdbs should be accredited by the human variome project and use an agreed reference sequence, nomenclature and database standard, and they should accommodate highquality clinical and phenotype. The human variome project beijing meeting, a joint meeting of the human variome project consortium and the human variome project chinese node, was held in beijing, 8th12th of december, 2011. Since the 1st variant effect prediction training course veptc in 2016, the human variome project hvp has held yearly training courses in variant effect prediction as part of its mission to build capacity in the practice of responsible genomics and contribute to improving global health outcomes.
The human variome project is complementary to the massive resequencing projects that contribute on a daily basis to variation databases such as dbsnp and the increasing information from genomewide. Global variome human variome project home facebook. Annotating the biomedical literature for the human variome. Sep 24, 2019 the human variome project is an international nongovernmental organisation working to build capacity in the practice of responsible genomics. Hgvsnomenclature is used to report and exchange information regarding variants found in dna, rna and protein sequences and serves as an international standard. The human variome project 18 april 2007 research on variation in the human genome and its clinical consequences has spawned a bewildering number and variety of databases, including the human. Nov 01, 2012 3 the human variome project establish guidelines for disease.
In the six years that have passed since that meeting, the concept of the human variome project has evolved and matured. So, the question therefore arises as to whether hgmd can be dovetailed into the human variome project. Strategies need to be developed and appropriate software created and put in place in the next 3 years that will enable the seamless, effortless, and lowcost collection of data from laboratories. His group developed the freely available lsdbinabox software package lovd, the mutalyzer tool hgvs. Harmonizing the interpretation of genetic variants across. Collection of variation causing disease the human variome project richard g. Vihinen m1, hancock jm2, maglott dr3, landrum mj 3. The vision of the human variome project is to be a catalyst for reduction in human. Characterization of the microbiomes of healthy human subjects at five major body sites, using 16s and metagenomic shotgun sequencing. Although much knowledge of human diversity has been accumulated, estimates suggest that 90% of genetic variation has not yet been characterized. The human variome project 18 april 2007 research on variation in the human genome and its clinical consequences has spawned a bewildering number and variety of databases, including the human gene mutation database hgmd, dbsnp and tsc databases of single nucleotide polymorphisms, the hapmap database, and omim online mendelian inheritance. Connecting the human variome project to nutrigenomics. Cotton rg, phillips k, horaitis o 2007 a survey of locusspeci. The project sparked the immediate interest of those present, but the participants realized that to expand its global reach the project would need a formal structure and commitment at the governmental level.
Lovd leiden open variation database human variome project. The human variome project takes a global approach to sharing. A specialized database was developed to store and manage the data based on genetic variations which also associated with health and disease of malaysian ethnic groups. Cotton 1, 2 human genomics volume 3, article number. The human variome project beijing meeting, a joint meeting of the human variome project consortium and the human variome project chinese node, was held in beijing, 8th12th of.
Published quality assessment criteria for variation databases. Members of each of eight sessions the clinic and phenotype, the diagnostic laboratory, the research laboratory, curation and collection, informatics, relevance to the emerging world, integration and. The success of whole exome sequencing wes for highly heterogeneous disorders, such as mitochondrial disease, is limited by substantial technical and bioinfor. The human variome project is an international nongovernmental. Recommendations of the 2006 human variome project meeting. The human variome project was initiated to ensure collection of all mutations and associated clinical data in all genes worldwide and to ensure free and open access to this important data to assist in. Pdf the human variome project pilot project and progress. Since the 1st variant effect prediction training course veptc in 2016, the human variome project hvp has held yearly training courses in variant effect prediction as part of its mission to build. Oct 15, 2010 a key ethical concern for the human variome project and eventually for data generated from individuals in nutrigenomics research is the accessibility of research data on public websites. Nutrigenomics is the science of analyzing and understanding genenutrient interactions, which because of the genetic heterogeneity, varying degrees of interaction among gene products, and the environmental diversity is a complex science. The human variome project europe pmc article europe. This meeting addressed all areas of human genetics relevant to collection of information on variation and its effects. The human variome project hvp was initiated in 2006 to foster discussion around how patient outcomes could be improved by connecting and promoting the disparate work of genetic variation. Connecting the human variome project to nutrigenomics genes.
Nutrigenomics is the science of analyzing and understanding genenutrient interactions, which because of the genetic heterogeneity, varying degrees of interaction among gene products, and. Quality genedisease specific databases of genetic variation lsdbs are highly desired. His legacy will live on in the many people he inspired, and the work of the human variome project and other allied activities such as the global alliance for genomics and health. They would integrate the information, propose common guidelines, discuss common coding issues, and facilitate navigation from one database to another. The database was created to organise, store and distribute variations and mutations that are related to population specific malaysian ethnic groups. The human variome project is an international nongovernmental organisation working to. Human variome project quality assessment criteria for. His legacy will live on in the many people he inspired, and the work of the human variome project and other allied activities such as the global. Collection of mutations defined as variation causing disease in this paper causing disease began soon after the cause of thalassaemia as a mutation in the.
The human variome project hvp has an established process for development and acceptance of guidelines and standards for variation data smith and vihinen, 2015. As part of these efforts he currently curates over 50 gene sequence variant databases. Human variome project quality assessment criteria for variation. Human variome project australian node information the human variome project is an international nongovernmental organisation that is working to ensure that all information on genetic variation and its effect on human health can be collected, curated, interpreted and shared freely and openly. Typically, human mitochondrial dna has various features such as hvsi, hvsii, singlenucleotide polymorphism snp, restriction enzyme sites, and short tandem repeat str. The human variome project was initiated to ensure collection of all mutations and associated clinical data in all genes worldwide and to ensure free and open access to this important data to assist in interpreting the clinical significance of these mutations in patients. For example, the utility of the datasets for genome wide association studies, hapmap projects, diagnostics for personalized nutrition and medicine.
A key ethical concern for the human variome project and eventually for data generated from individuals in nutrigenomics research is the accessibility of research data on public websites. May 29, 2014 the human variome database in australia in 2014 graham taylor 1. The hvp was featured recently in relation to neurogenetic databases in. In the near future, it will expand for the other malaysian ethnics as well. The role of the human variome project will be to foster such a strategy, to get diseasecentered networks involved, and to promote or host coordination forums. To ensure that this contributes to improving global health. Not easily, given the current thinking of the project organisers.
Using international scientific databases as a tool in science. Applications of ngs, the human variome project and data. Human variome project quality assessment criteria for variation databases. Apparently sequencing two white males of european extraction does not make for a very good sample of mankind, and that if we really want to get a good view of what we are really like, we need to sequence a couple more. This led to the founding in 2010 of the human variome project international limited, a nonprofit australian public company. Sequence variant nomenclature human genetic variation. Lovd is a flexible, freely available tool for the collection and display of dna variants. At a gathering of experts in human genetics in 2006, the human variome project. The human variome project hvp was initiated in 2006 to foster discussion around how patient outcomes could be improved by connecting and promoting the disparate work of genetic variation database curators. Harmonizing the interpretation of genetic variants across the. The human variome project is an international nongovernmental organisation that is working to ensure that all information on genetic variation and its effect on human health can be collected, curated, interpreted and shared freely and openly. Not easily, given the current thinking of the project.
Many of the objectives of the human variome project are certainly laudable. Evaluate the need for a term or body such as the human variome organisation huvo and examine whether human proteome organization. Collection of variation causing disease the human variome. Global variome human variome project, newcastle upon tyne.
Characterization of microbiome and human host from three cohorts of microbiomeassociated conditions, using multiple omics technologies. Human variome project australian node genetic and rare. The human variome database in australia in 2014 graham taylor 1. Abstract numerous databases containing information about dna, rna, and protein variations are available. Nov 07, 2008 they would integrate the information, propose common guidelines, discuss common coding issues, and facilitate navigation from one database to another. The human variome database in australia in 2014 graham. Thus, variome aims to add value to databases such as omim, genbank, dbsnp, dbgap and the hapmap and organizations including ncbi and the european. However, these databases are of varying completeness and individualistic, so the human variome project was born to establish a central project to encourage. The human variome project hvp established a working group for variant database quality assessment.
Capturing all diseasecausing mutations for clinical and. Toward a human variome project toward a human variome project cotton, richard g. The human variome project is complementary to the massive resequencing projects that contribute on a daily basis to variation databases such as dbsnp and the increasing information from genomewide association studies. Applications of ngs, the human variome project and data sharing. The melbourne meeting will formally initiate the human variome project.
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