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http://www2.le.ac.uk/

Public research university based in Leicester, England. Famous for the discovery of genetic fingerprinting and contributing to the discovery and identification of the remains of King Richard III.

Proper citation: University of Leicester; Leicester; United Kingdom (RRID:SCR_004900) Copy   

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http://smart.embl.de/

Software tool for identification and annotation of genetically mobile domains and analysis of domain architectures.

Proper citation: SMART (RRID:SCR_005026) Copy   

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http://www.gene.com/

A biotechnology corporation that uses human genetic information to discover, develop, manufacture and commercialize medicines to treat patients with serious or life-threatening medical conditions.

Proper citation: Genentech (RRID:SCR_003997) Copy   

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http://www.alz.org/research/funding/alzheimers_research_roundtable.asp

A consortium aiming to facilitate the development and implementation of new treatments for Alzheimer's disease by collectively addressing obstacles to research and development, clinical care and public health education. The Roundtable convenes twice each year for a two-day presentation and discussion of specific topics within Alzheimer's research. Topics are selected from a list proposed and voted on by members. Roundtable members explore a broad range of Alzheimer's science topics, including: * New data and technologies that may improve the diagnosis of Alzheimer's disease, especially in its earliest and mildest stages. * Neuropsychological testing, genetic factors, and biochemical and neuroimaging biomarkers that could contribute to an earlier and more accurate Alzheimer's diagnosis. * Lessons learned about clinical trial design that may help shape future clinical trials of drugs aimed at slowing or stopping the progression of Alzheimer's. * The pros and cons of various scales as outcomes measures of clinical trials. The outputs of Roundtable meetings are published as articles in the Alzheimer's Association's journal, Alzheimer's & Dementia. The Research Roundtable also sponsors Alzheimer's Association grants. The chosen project is named Research Roundtable Sponsored Grant and the principal investigator of the project is invited to give a progress report at a Roundtable meeting.

Proper citation: Alzheimers Association Research Roundtable (RRID:SCR_004007) Copy   

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http://www.geuvadis.org/web/geuvadis/home

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 6,2023. A European Medical Sequencing Consortium committed to gaining insights into the human genome and its role in health and medicine by sharing data, experience and expertise in high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GEUVADIS (RRID:SCR_000684) Copy   

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http://www.genet.sickkids.on.ca/cftr/

Collection of mutations in CFTR gene for international cystic fibrosis genetics research community. Provides up to date information about individual mutations in CFTR gene. All known CFTR mutations and sequence variants have been converted to standard nomenclature recommended by Human Genome Variation Society. On line process for submission of new mutations has been added.While they continue to ensure quality of data, they urge international community to give them feedback and suggestions. Clinical information in this database relates only to details of discovery of specific mutations. As part of 2010 upgrade, CFTR1 joined new project called CFTR2 - Clinical and Functional TRanslation of CFTR. Links to CFTR2 for many mutations in CFTR1 will provide up-to-date summaries of genotype-phenotype information from patient registries around the world.

Proper citation: Cystic Fibrosis Mutation Database (RRID:SCR_000685) Copy   

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http://www.asperbio.com

A genetic testing company for rare and complex disorders and syndromes. The company specializes in retinal disorders, reproductive medicine and oncology. They also offer custom genotyping services.

Proper citation: Asper Biotech (RRID:SCR_000700) Copy   

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http://csg.sph.umich.edu//abecasis/MACH/index.html

A Markov Chain based software tool for haplotyping, genotype imputation and disease association analysis that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

Proper citation: MACH 1.0 (RRID:SCR_001759) Copy   

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https://pmsf.org/

The Phelan-McDermid Syndrome Foundation, established in 2002, is a 501(c)3 nonprofit group that provides support services for those who have family members affected by 22q13 Deletion Syndrome / Phelan-McDermid Syndrome. It also raises money to further awareness of the syndrome through research and sponsoring an international conference every two years that brings together families, researchers and therapists. The Foundation facilitates connections between families through networking, communications and support services. We also build alliances with other rare diseases groups to expand our reach and exposure. The syndrome, which affects families worldwide, is a rare genetic occurrence and is the result of a damaged or missing protein on the 22nd chromosome. Our Foundation works with researchers who are looking into the cause and possible cure for the syndrome. PMSF's grants and fellowships program is intended to encourage research projects that will advance the development of treatments and cures for PMS. Our mission is to bring together everyone affected by 22q13 Deletion Syndrome/Phelan-McDermid Syndrome to help them through the challenges they face every day and to raise awareness in the medical and research communities.

Proper citation: Phelan-McDermid Syndrome Foundation (RRID:SCR_001707) Copy   

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http://www.emory.edu/LIVING_LINKS/

The primary mission of the Living Links Center is to study human evolution by investigating our close genetic, anatomical, cognitive, and behavioral similarities with great apes. The Living Links Center was established for primate studies that shed light on human behavioral evolution. It is an integrated part of the Yerkes National Primate Research Center, which is the nation's oldest and largest primate center. The Living Links Center is home to two socially housed groups of chimpanzees and two socially housed groups of capuchin monkeys. The research conducted in this center is broken down into four categories: - Chimpanzees: Chimpanzee research at the Living Links Center is conducted at the Yerkes Field Station, which is home to two socially housed chimpanzee groups known as FS1 and FS2. Each mixed gender group of 12 individuals lives in a large outdoor enclosure with wooden climbing structures and play objects attached to an indoor sleeping area. FS1 and FS2 can hear, but not see each other because their enclosures are ~200m apart and separated by a small hill. Chimpanzee research is conducted on a volunteer basis with members of each group. - Elephants: This newly found presence of mirror self-recognition in elephants, previously predicted due to their well-known social complexity, is thought to relate to empathetic tendencies and the ability to distinguish oneself from others. As a result of this study, the elephant now joins a cognitive elite among animals commensurate with its well-known complex social life and high level of intelligence. Although elephants are far more distantly related to us than the great apes, they seem to have evolved similar social and cognitive capacities making complex social systems and intelligence part of this picture. These parallels between humans and elephants suggest a convergent cognitive evolution possibly related to complex sociality and cooperation. - Capuchin Monkeys: Though there are several different species of capuchin monkey, the one most widely studied in captivity by Living Links, is the brown, or tufted, capuchin (Cebus apella). - Collaborative Projects: projects with collaborators around the world. Sponsors: This center is supported by the Yerkes National Primate Research Center.

Proper citation: Living Links: Center for the Advanced Study of Ape and Human Evolution (RRID:SCR_001776) Copy   

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https://software.broadinstitute.org/gatk/

A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

Proper citation: GATK (RRID:SCR_001876) Copy   

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http://mousecyc.jax.org/

A manually curated database of both known and predicted metabolic pathways for the laboratory mouse. It has been integrated with genetic and genomic data for the laboratory mouse available from the Mouse Genome Informatics database and with pathway data from other organisms, including human. The database records for 1,060 genes in Mouse Genome Informatics (MGI) are linked directly to 294 pathways with 1,790 compounds and 1,122 enzymatic reactions in MouseCyc. (Aug. 2013) BLAST and other tools are available. The initial focus for the development of MouseCyc is on metabolism and includes such cell level processes as biosynthesis, degradation, energy production, and detoxification. MouseCyc differs from existing pathway databases and software tools because of the extent to which the pathway information in MouseCyc is integrated with the wealth of biological knowledge for the laboratory mouse that is available from the Mouse Genome Informatics (MGI) database.

Proper citation: MouseCyc (RRID:SCR_001791) Copy   

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http://rgp.dna.affrc.go.jp/E/index.html

Rice Genome Research Program (RGP) is an integral part of the Japanese Ministry of Agriculture, Forestry and Fisheries (MAFF) Genome Research Project. RGP now aims to completely sequence the entire rice genome and subsequently to pursue integrated goals in functional genomics, genome informatics and applied genomics. It is jointly coordinated by the National Institute of Agrobiological Sciences (NIAS), a government research institute under MAFF and the Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), a semi-private research organization managed and supported by MAFF and a consortium of some twenty Japanese companies. The research is funded with yearly grants from MAFF and additional funds from the Japan Racing Association (JRA). It is now the leading member of the International Rice Genome Sequencing Project (IRGSP), a consortium of ten countries sharing the sequencing of the 12 rice chromosomes. The IRGSP adopts the clone-by-clone shotgun sequencing strategy so that each sequenced clone can be associated with a specific position on the genetic map and adheres to the policy of immediate release of the sequence data to the public domain. In December 2004, the IRGSP completed the sequencing of the rice genome. The high-quality and map-based sequence of the entire genome is now available in public databases.

Proper citation: Rice Genome Research Project (RRID:SCR_002268) Copy   

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http://www.broadinstitute.org/rat/public/index_main.html

Data set of pictures representing genetic linkage maps of the rat resulting from the integration of two F2 intercrosses (SHRSP x BN and FHH x ACI). Markers in common between the two crosses are connected by a line to define integration points. There are a total of 4,786 markers on these maps; 4375 WIBR/MIT CGR markers; 223 markers from the previously released Mit/Mgh rat maps and 188 markers from the National Institute of Arthritis and Musculoskeletal and Skin Diseases Arb rat maps. Pictures are drawn to a scale of 5cm (Kosombi) per inch. The changes in color of the backbone of the chromosome for each cross represents the space between any two framework loci. Markers in blue type are framework loci. Markers in green type are unique placement loci. Markers in black type are bouncy placement loci.

Proper citation: Genetic Maps of the Rat Genome (RRID:SCR_002266) Copy   

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https://github.com/transmart

tranSMART is a knowledge management platform that enables scientists to develop and refine research hypotheses by investigating correlations between genetic and phenotypic data, and assessing their analytical results in the context of published literature and other work. tranSMART is licensed through GPL 3. The integration, normalization, and alignment of data in tranSMART permits users to explore data very efficiently to formulate new research strategies. Some of tranSMART''s specific applications include: * Revalidating previous hypotheses * Testing and refining novel hypotheses * Conducting cross-study meta-analysis * Searching across multiple data sources to find associations of concepts, such as a gene''s involvement in biological processes or experimental results * Comparing biological processes and pathways among multiple data sets from related diseases or even across multiple therapeutic areas Data Repository The tranSMART Data Repository combines a data warehouse with access to federated sources of open and commercial databases. tranSMART accommodates: * Phenotypic data, such as demographics, clinical observations, clinical trial outcomes, and adverse events * High content biomarker data, such as gene expression, genotyping, pharmacokinetic and pharmaco-dynamics markers, metabolomics data, and proteomics data * Unstructured text-data, such as published journal articles, conference abstracts and proceedings, and internal studies and white papers * Reference data from sources such as MeSH, UMLS, Entrez, GeneGo, Ingenuity, etc. * Metadata providing context about datasets, allowing users to assess the relevance of results delivered by tranSMART Data in tranSMART is aligned to allow identification and analysis of associations between phenotypic and biomarker data, and it is normalized to conform with CDISC and other standards to facilitate search and analysis across different data sources. tranSMART also enables investigators to search published literature and other text sources to evaluate their analysis in the context of the broader universe of reported research. External data can also be integrated into the tranSMART data repository, either from open data projects like GEO, EBI Array Express, GCOD, or GO, or from commercially available data sources. Making data accessible in tranSMART enables organizations to leverage investments in manual curation, development costs of automated ETL tools, or commercial subscription fees across multiple research groups. Dataset Explorer tranSMART''s Dataset Explorer provides flexible, powerful search and analysis capabilities. The core of the Dataset Explorer integrates and extends the open source i2b2 application, Lucene text indexing, and GenePattern analytical tools. Connections to other open source and commercial analytical tools such as Galaxy, Integrative Genomics Viewer, Plink, Pathway Studio, GeneGo, Spotfire, R, and SAS can be established to expand tranSMART''s capabilities. tranSMART''s design allows organizations flexibility in selecting analytical tools accessible through the Dataset Explorer, and provides file export capabilities to enable researchers to use tools not accessible in the tranSMART portal.

Proper citation: tranSMART (RRID:SCR_005586) Copy   

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http://www.mirecc.va.gov/visn6/

The VISN 6 MIRECC is organized as a translational medicine multi-site center focused on post deployment mental health issues. The overarching goals are improving clinical assessment and treatment and development of novel interventions through basic and clinical research. This MIRECC aims: (1) To determine whether early intervention in post-deployment mental health is effective in forestalling the development or decreasing the severity of post-deployment mental illness, (2) To determine what neuroimaging, genetic, neurocognitive, or other characteristics predict the development of post-deployment mental illness, and (3) To assess the longitudinal course of post-deployment mental illness.

Proper citation: Mid-Atlantic (VISN 6) Mental Illness Research, Education and Clinical Center (RRID:SCR_008077) Copy   

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http://www.cephb.fr/

The Centre d''Etude du Polymorphisme Humain (CEPH) is a research laboratory, the main activities of which are the setting up, storage, processing and distribution of DNA collections for the identification of genetic factors conferring susceptibility to complex disorders. These collections are established in partnership and full collaboration with external French or international research groups. The Foundation currently hosts the CEPH reference panel, the HGDP panel (Human genome Diversity Cell Line Panel) and several collections amounting mid-2008 to more than 250 000 samples. The goal of CEPH is to understand complex multifactorial disorders necessitates the establishment of structures facilitating access to large and integrated collection of individuals, characterized by a large number of variables emanating from different technologies and platforms. To achieve this goal, CEPH facilitates the setting up of integrated analyses combining clinical, genetic and environmental data, for the identification of susceptibility factors to complex multifactorial disorders Additionally, CEHP allows the reception, storage, processing and distribution of biological sample collections. At the same time, it promotes and participates in the design and setting up of genetic studies: - in partnership and full collaboration with external research groups - giving access to a large number of variables - in a sufficient number of subjects - allowing large scale integrated analyses

Proper citation: Centre dEtude du Polymorphisme Humain (RRID:SCR_008026) Copy   

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http://www.dnaftb.org/dnaftb/

An animated primer on the basics of DNA, genes, and heredity organized around three key concepts: Classical Genetics, Molecules of Genetics, and Genetic Organization and Control. The science behind each concept is explained by: animation, image gallery, video interviews, problem, biographies, and links.

Proper citation: DNA From The Beginning: AN Animated Primer on the Basics of DNA, Genes, and Heredity (RRID:SCR_008028) Copy   

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http://www.projects.roslin.ac.uk/cdiv/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. The objective of the project is the standardization of micro-satellite markers used within participating laboratories, use of DNA markers to define genetic diversity and to enable monitoring of breeds to promote conservation programs where required, and the determination of diversity present in rare and local breeds across Europe. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project (See BovMaP). Work with micro-satellite markers has shown that they are valuable tools for examining genetic diversity and phylogeny in many species. However, for work carried out in different laboratories to be comparable, it is essential that the same markers are used. To maintain the compatibility of data generated by the various typing labs, it is essential that all laboratories adopt the same markers and typing protocols. It is therefore of paramount importance that the blood typing laboratories and research labs that are examining the genetic structure of the cattle populations adopt a common panel of the best micro-satellite markers available. Some pilot comparative work has been undertaken through the International Society for Animal Genetics, but so far this has only involved the blood typing laboratories. One objective of this project is to facilitate the comparison of the micro-satellite markers currently in use in the different types of laboratory and determine the efficiency of the markers available in revealing genetic differences within and among breeds. It will also be important to compare the use of markers in different laboratories to determine how robust they are and how easily results can be compared. From comparison of the markers, those that are most suitable will be selected to form a panel which will be recommended for pedigree validation and genetic surveys. Cattle are an important source of food in Europe, and intense selection has resulted in the development of specialized breeds. Selection for high-producing dairy cattle has been successful, but one associated drawback is that the cattle population, both in Europe and North America, has been skewed dramatically towards one breed, the Holstein/Friesian. So there has been a decline in the number of individuals of other breeds, and hence a general erosion of the genetic base of the cattle population. The progressive move towards the North American-type Holstein animals has also resulted in the requirement for high input/high output farming and intensive management schemes. The impact of this on the environment has been significant, e.g. pollution problems arising from the need for high nitrogen fertilizers to produce sufficient high quality fodder, and disposal problems associated with slurry waste. Poorer areas of the community have been unable to compete with such farming systems, and are more suited to low input/low output farming using traditional stock. It is however the future perspective that is of greatest concern. It is impossible to predict requirements for cattle production - quality, production type, management systems, etc. The ability to switch rapidly to alternative production will be dependent on the genetic base of the population available to selection programs. It is therefore essential to maintain the greatest genetic diversity possible in the cattle population. Whilst current farming practices are perceived to be both efficient and acceptable, the breeds less favored by commercial farmers will dwindle. It is therefore important that on an European scale efficient management of these breeds maintains the widest genetic base possible. This project aims to carry out a survey of the current genetic base of the European cattle population and to provide the tools to assist breeding programs to maintain a broad base. The blood typing laboratories are now beginning to use micro-satellite markers as an alternative to serology for parentage verification, and are selecting a common set to be used from the several hundred micro-satellite markers available that cover the bovine genome, produced as part of the Bovine genome mapping project. Early work to measure genetic diversity used blood groups to show differences between breeds and the diversity present. Unfortunately, the number of loci available are limited, with only the B system being sufficiently polymorphic to be really useful. However, since there is a wealth of information available from such typing, this information can be used to estimate changes in the genetic structure of cattle populations across Europe over the past twenty years. More recently mini-satellite probes have been used to generate ''genetic fingerprints'' which have been used to show differences between individuals. Such fingerprints have been used to estimate genetic diversity - the greater the number of bands revealed by the fingerprint being equated with greater diversity. This is valid within limits. The main disadvantage of the fingerprint approach is that the chromosomal location and number of loci being sampled, and so the proportion of the genome examined, is unknown. The allelic bands on the gel cannot be easily identified, so allele inheritance cannot be addressed making it impossible to trace ancestry. Through the EC funded BovMaP project, large numbers of highly polymorphic micro-satellite markers have become available, which are being mapped on the bovine genome. These markers are particularly suited to measuring genetic diversity, and markers can be selected to cover the entire genome.

Proper citation: CaDBase: Genetic diversity in cattle (RRID:SCR_008146) Copy   

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http://locus.jouy.inra.fr/cgi-bin/bovmap/intro.pl

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 22, 2016. Database containing information on the cattle genome comprising loci list, phenes list, homology query, cattle maps, gene list, and chromosome homology. The objective of BovMap is to develop a set of anchored loci for the cattle genome map. In total, 58 clones were hybridized with chromosomes and identified loci on 22 of the 31 different bovine chromosomes. Three clones contained satellite DNA. Two or more markers were placed on 12 chromosomes. Sequencing of the microsatellites and flanking regions was performed directly from 43 cosmids, as previously reported. Primers were developed for 39 markers and used to describe the polymorphism associated with the corresponding loci. Users are also allowed to summit their own data for Bovmap. An integrated cytogenetic and meiotic map of the bovine genome has also been developed around the Bovmap database. One objective that Bovmap uses as the mapping strategy for the bovine genome uses large insert clones as a tool for physical mapping and as a source of highly polymorphic microsatellites for genetic typing.

Proper citation: BovMap Database (RRID:SCR_008145) Copy   

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