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The Human Variome Project (HVP) is the global initiative to collect and curate all human genetic variation affecting human health. [1] Its mission is to improve health outcomes by facilitating the unification of data on human genetic variation and its impact on human health.[ citation needed ]
The HVP concept was conceived by Richard Cotton, a leader in the field of human genetic variation. His group, the Genomic Disorders Research Centre, based at the University of Melbourne and St. Vincent's Hospital, has established a consortium that covers genomic variation and its health implications in a comprehensive form. This consortium has encouraged the creation and supported many of the 571 gene specific variation databases currently available on the internet. However, these databases are of varying completeness and individualistic, so the Human Variome Project was born to establish a central project to encourage the collection and sourcing of this data, verifying it and ultimately using it for improved health outcomes.
Geneticists, diagnosticians, researchers and bioinformatics scientists came together in June 2006 at the Human Variome Project Meeting, organized by Cotton’s team, and agreed to take on the task of organising data collection and unifying the systems of data access and storage. This initiative builds on substantial pilot work and achievements of the Human Genome Variation Society. The authority of those initiating this project is evidenced by the fact that major international bodies were present. These included WHO, OECD, European Commission, UNESCO, March of Dimes (US), Centers for Disease Control and Prevention (US), Google, representatives of two dozen international genetics bodies, numerous genetics journals, 20 countries and Australian State and Federal Governments.
This major international project, a natural partner to the Human Genome Project, will require substantial funding to get it to a sustainable position. A five-year secure budget period of approximately US$12m per year has been proposed to initiate the project. This will enable the project to be organized and find operational funds for the tasks of system development, informatics, database curation and clinical access as well as collection systems that are open and accessible to all.
The Human Variome Project seeks to provide open access to the full realm of genetic variation for the benefit of everyone. [2]
The Centre for Arab Genomic Studies (CAGS) has initiated efforts to proceed with the Arab Human Variome Project under the Human Variome Project. CAGS was one of the participants of the HVP meeting in Melbourne. Since then, several meetings have been held between officials of HVP and CAGS members to discuss the nature of work involved.
The Human Genome Organisation (HUGO) is a non-profit organization founded in 1988. HUGO represents an international coordinating scientific body in response to initiatives such as the Human Genome Project. HUGO has four active committees, including the HUGO Gene Nomenclature Committee (HGNC), and the HUGO Committee on Ethics, Law and Society (CELS).
The International HapMap Project was an organization that aimed to develop a haplotype map (HapMap) of the human genome, to describe the common patterns of human genetic variation. HapMap is used to find genetic variants affecting health, disease and responses to drugs and environmental factors. The information produced by the project is made freely available for research.
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.
The Rat Genome Database (RGD) is a database of rat genomics, genetics, physiology and functional data, as well as data for comparative genomics between rat, human and mouse. RGD is responsible for attaching biological information to the rat genome via structured vocabulary, or ontology, annotations assigned to genes and quantitative trait loci (QTL), and for consolidating rat strain data and making it available to the research community. They are also developing a suite of tools for mining and analyzing genomic, physiologic and functional data for the rat, and comparative data for rat, mouse, human, and five other species.
The Human Genome Project (HGP) was an international scientific research project with the goal of determining the base pairs that make up human DNA, and of identifying, mapping and sequencing all of the genes of the human genome from both a physical and a functional standpoint. It started in 1990 and was completed in 2003. It remains the world's largest collaborative biological project. Planning for the project started after it was adopted in 1984 by the US government, and it officially launched in 1990. It was declared complete on April 14, 2003, and included about 92% of the genome. Level "complete genome" was achieved in May 2021, with a remaining only 0.3% bases covered by potential issues. The final gapless assembly was finished in January 2022.
The variome is the whole set of genetic variations found in populations of species that have gone through a relatively short evolution change. For example, among humans, about 1 in every 1,200 nucleotide bases differ. The size of human variome in terms of effective population size is claimed to be about 10,000 individuals. This variation rate is comparatively small compared to other species. For example, the effective population size of tigers which perhaps has the whole population size less than 10,000 in the wild is not much smaller than the human species indicating a much higher level of genetic diversity although they are close to extinction in the wild. In practice, the variome can be the sum of the single nucleotide polymorphisms (SNPs), indels, and structural variation (SV) of a population or species. The Human Variome Project seeks to compile this genetic variation data worldwide. Variomics is the study of variome and a branch of bioinformatics.
Public health genomics is the use of genomics information to benefit public health. This is visualized as more effective preventive care and disease treatments with better specificity, tailored to the genetic makeup of each patient. According to the Centers for Disease Control and Prevention (U.S.), Public Health genomics is an emerging field of study that assesses the impact of genes and their interaction with behavior, diet and the environment on the population's health.
Mouse Genome Informatics (MGI) is a free, online database and bioinformatics resource hosted by The Jackson Laboratory, with funding by the National Human Genome Research Institute (NHGRI), the National Cancer Institute (NCI), and the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). MGI provides access to data on the genetics, genomics and biology of the laboratory mouse to facilitate the study of human health and disease. The database integrates multiple projects, with the two largest contributions coming from the Mouse Genome Database and Mouse Gene Expression Database (GXD). As of 2018, MGI contains data curated from over 230,000 publications.
The Centre for Arab Genomic Studies (CAGS) is a not-for-profit study centre aimed at the characterization and prevention of genetic disorders in the Arab World. The Centre is closely associated with the Sheikh Hamdan Award for Medical Sciences. One of the major projects of CAGS is the Catalogue for Transmission Genetics in Arabs (CTGA), an online, freely accessible database of genetic disorders reported from the Arab World. CAGS has been involved in the Human Variome Project as a representative of the Arab region and has been one of the first organizations to take an active lead in working on the project. CAGS organizes the Pan Arab Human Genetics Conference every alternate year, to provide a platform for discussion and education on genetic issues in the region.
The 1000 Genomes Project, launched in January 2008, was an international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists planned to sequence the genomes of at least one thousand anonymous participants from a number of different ethnic groups within the following three years, using newly developed technologies which were faster and less expensive. In 2010, the project finished its pilot phase, which was described in detail in a publication in the journal Nature. In 2012, the sequencing of 1092 genomes was announced in a Nature publication. In 2015, two papers in Nature reported results and the completion of the project and opportunities for future research.
P3G (Public Population Project in Genomicsand Society) is a not-for-profit international consortium dedicated to facilitating collaboration between researchers and biobanks working in the area of human population genomics. P3G is member-based and composed of experts from the different disciplines in the areas of and related to genomics, including epidemiology, law, ethics, technology, biomolecular science, etc. P3G and its members are committed to a philosophy of information sharing with the goal of supporting researchers working in areas that will improve the health of people around the world.
DECIPHER is a web-based resource and database of genomic variation data from analysis of patient DNA. It documents submicroscopic chromosome abnormalities and pathogenic sequence variants, from over 25000 patients and maps them to the human genome using Ensembl or UCSC Genome Browser. In addition it catalogues the clinical characteristics from each patient and maintains a database of microdeletion/duplication syndromes, together with links to relevant scientific reports and support groups.
Genetic studies on Arabs refers to the analyses of the genetics of ethnic Arab people in the Middle East and North Africa. Arabs are genetically diverse as a result of their intermarriage and mixing with indigenous people of the pre-Islamic Middle East and North Africa following the Arab and Islamic expansion. Genetic ancestry components related to the Arabian Peninsula display an increasing frequency pattern from west to east over North Africa. A similar frequency pattern exist across northeastern Africa with decreasing genetic affinities to groups of the Arabian Peninsula along the Nile river valley across Sudan and the more they go south. This genetic cline of admixture is dated to the time of Arab expansion and immigration to North Africa (Maghreb) and northeast Africa.
In bioinformatics, a Gene Disease Database is a systematized collection of data, typically structured to model aspects of reality, in a way to comprehend the underlying mechanisms of complex diseases, by understanding multiple composite interactions between phenotype-genotype relationships and gene-disease mechanisms. Gene Disease Databases integrate human gene-disease associations from various expert curated databases and text mining derived associations including Mendelian, complex and environmental diseases.
Richard Cotton AM was an Australian medical researcher and founder of the Murdoch Institute and the Human Variome Project. Cotton focused on the prevention and treatment of genetic disorders and birth defects.
Genomic and medical data refers to an area within genetics that concerns the recording, sequencing and analysis of an organism's genome.
Donna R. Maglott is a staff scientist at the National Center for Biotechnology Information known for her research on large-scale genomics projects, including the mouse genome and development of databases required for genomics research.
Nicole Soranzo is an Italian-British senior group leader in human genetics at the Wellcome Sanger Institute, Professor of Human Genetics at the University of Cambridge. She is an internationally recognised Human Geneticist who has focused on the application of cutting edge genomic technologies to study the spectrum of human genetic variation associated with cardio-metabolic and immune diseases. She has led many large-scale discovery efforts including more than 1,000 novel genetic variants associated with cardio-metabolic diseases and their risk factors as well as establishing the HaemGen consortium, which is a worldwide effort to discover genetic determinants of blood cell formation and also interpretation of the downstream consequences of sequence variation through a host of integrative analyses and functional approaches.
Human Heredity and Health in Africa, or H3Africa, is an initiative to study the genomics and medical genetics of African people. Its goals are to build the continent's research infrastructure, train researchers and clinicians, and to study questions of scientific and medical interest to Africans. The H3Africa Consortium was formally launched in 2012 in Addis Ababa and has grown to include research projects across 32 countries, a pan-contintental bioinformatics network, and the first whole genome sequencing of many African ethnolinguistic groups.