Tools   Select Another Resource Report Type

https://cnprc.ucdavis.edu/

Center for investigators studying human health and disease, offering the opportunity to assess the causes of disease, and new treatment methods in nonhuman primate models that closely recapitulate humans. Its mission is to provide interdisciplinary programs in biomedical research on significant human health-related problems in which nonhuman primates are the models of choice.

Proper citation: California National Primate Research Center (RRID:SCR_006426) Copy   

•   Source: SciCrunch Registry

https://www.ars-grin.gov/npgs/

Cooperative effort by U.S. state and federal government and private organizations to preserve the genetic diversity of plants. The NPGS aids scientists and the need for genetic diversity by acquiring, preserving, evaluating, documenting and distributing crop germplasm. The NPGS is managed by the Agricultural Research Service (ARS), the in-house research agency of the United States Department of Agriculture (USDA). Funding for the NPGS comes primarily through appropriations from the U.S. Congress.

Proper citation: National Plant Germplasm System (NPGS) (RRID:SCR_016785) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

http://ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 23, 2019.BGMUT was database that provided publicly accessible platform for DNA sequences and curated set of blood mutation information. Data Archive are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/rbc/Final Archive.

Proper citation: Blood Group Antigen Gene Mutation Database (RRID:SCR_002297) Copy   

•   Source: SciCrunch Registry

http://www.ark-genomics.org/

Portal for studies of genome structure and genetic variation, gene expression and gene function. Provides services including DNA sequencing of model and non-model genomes using both Next Generation and Sanger sequencing , Gene expression analysis using both microarrays and Next Generation Sequencing, High throughput genotyping of SNP and copy number variants, Data collection and analysis supported in-house high performance computing facilities and expertise, Extensive EST clone collections for a number of animal species, all of commercially available microarray tools from Affymetrix, Illumina, Agilent and Nimblegen, Parentage testing using microsatellites and smaller SNP panels. ARK-Genomics has developed network of researchers whom they support through each stage of their genomics research, from grant application, experimental design and technology selection, performing wet laboratory protocols, through to analysis of data often in conjunction with commercial partners.

Proper citation: ARK-Genomics: Centre for Functional Genomics (RRID:SCR_002214) Copy   

•   Source: SciCrunch Registry

https://www.drugabuse.gov/publications/drugfacts/genetics-epigenetics-addiction

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. An archived video on the web providing comprehensive and hands-on training in genetics and epigenetic methodology. The purpose of the course is to provide an introduction to approaches and tools for identifying genes that confer vulnerability to addiction and individual differences in responses to treatments. The course is targeted to those who are new to the field of addiction genetics. The course was held over 5 days with lectures and hands-on demonstrations given each day. Viewers of the course will gain familiarity with conceptual and practical approaches to complex disorders using relevant genetic and epigenetic databases, and appropriate statistical and empirical approaches. Topics covered Behavioral genetics, genetic epidemiology, twin and adoption studies, statistical genetic concepts and approaches for mapping complex traits, haplotype based approaches for association mapping, genome-wide scans for addictive disorders, application of linkage for mapping genes and genetic loci for addictive disorders, pharmacogenomics of treatment of addictive disorders, Baysian Methods for identifying gene-gene interactions, analysis of copy number variation, practical use of genetic databases, mapping of complex traits in mice, methods for analyzing gene expression, and methods for doing epigenetic analysis are covered. The course was held April 4, 2008, at the Bethesda North Marriott Hotel and Conference Center, 5701 Marinelli Road, Bethesda, MD 20852.

Proper citation: Short Course on the Genetics and Epigenetics of Addiction National Institute on Drug Abuse: Archived Video (RRID:SCR_002783) Copy   

•   Source: SciCrunch Registry

https://www.ddbj.nig.ac.jp/jga/index-e.html

A service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects. The JGA contains exclusive data collected from individuals whose consent agreements authorize data release only for specific research use or to bona fide researchers. Strict protocols govern how information is managed, stored and distributed by the JGA. Once processed, all data are encrypted. The JGA accepts only de-identified data approved by JST-NBDC. The JGA implements access-granting policy whereby the decisions of who will be granted access to the data resides with the JST-NBDC. After data submission the JGA team will process the data into databases and archive the original data files. The accepted data types include manufacturer-specific raw data formats from the array-based and new sequencing platforms. The processed data such as the genotype and structural variants or any summary level statistical analyses from the original study authors are stored in databases. The JGA also accepts and distributes any phenotype data associated with the samples. For other human biological data, please contact the NBDC human data ethical committee.

Proper citation: Japanese Genotype-phenotype Archive (JGA) (RRID:SCR_003118) Copy   

•   Source: SciCrunch Registry

http://www.genome.gov/Glossary/

Glossary of Genetic Terms to help everyone understand the terms and concepts used in genetic research. In addition to definitions, specialists in the field of genetics share their descriptions of terms, and many terms include images, animation and links to related terms.

Proper citation: Talking Glossary of Genetic Terms (RRID:SCR_003215) Copy   

•   Source: SciCrunch Registry

http://cbl-gorilla.cs.technion.ac.il/

A tool for identifying and visualizing enriched GO terms in ranked lists of genes. It can be run in one of two modes: * Searching for enriched GO terms that appear densely at the top of a ranked list of genes or * Searching for enriched GO terms in a target list of genes compared to a background list of genes.

Proper citation: GOrilla: Gene Ontology Enrichment Analysis and Visualization Tool (RRID:SCR_006848) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/node/252

THIS RESOURCE IS NO LONGER IN SERVICE,documented on January,18, 2022. FaceBase Biorepository is now collecting biological samples from people with cleft lip/palate and their family members. Information for Prospective Cases: Clefts of the lip and/or palate can be caused by a wide range of genetic, environmental and other factors. The FaceBase Biorepository will serve as a common source of both biological samples and information that can be made available to investigators trying to determine the underlying cause of these common birth defects. Genetic studies, in particular, will benefit from both family history information and having samples from affected individuals as well as their family members. DNA is the information containing molecules found in all the cells of our body and can be easily obtained from material such as blood or saliva samples. As part of the FaceBase Biorepository, we are requesting families to submit biological samples from specific family members as well as information from other family members that might be affected with either the same condition or a similar condition. The medical and family history information that is collected includes other relevant information such as exposure to possible environmental causes during pregnancy. The biorepository is managed by Nichole Nidey, a research study coordinator, and Jeff Murray, a pediatric clinical geneticist and researcher. They are available to speak with family members regarding questions they may have, including providing information about the biorepository and making arrangements for the collection of samples for those who wish to participate. All participation is voluntary. Your name or other personally identifiable information (name, address, etc) will be removed before information is placed in the biorepository. Summary data to show how the database itself has been used overall as well as updates on whether specific findings might have been made using this database will be available on the FaceBase website at www.facebase.org. A newsletter containing this information will also be given to families and referring clinicians so that they may discuss the specifics with the families if there appears to be information that might be relevant in a particular case. Families will also need to sign a consent form that has been approved by the Institutional Review Board at the University of Iowa. Also, any submitted samples or data can also be removed from the database at any time should the family no longer wish to participate. Investigators interested in requesting DNA samples or for more information, please contact cleftresearch (at) uiowa.edu, Nichole Nidey, nichole-nidey (at) uiowa.edu or (319) 353-4365, or Jeff Murray, jeff-murray (at) uiowa.edu.

Proper citation: FaceBase Biorepository (RRID:SCR_006001) Copy   

•   Source: SciCrunch Registry

http://www.homepages.ed.ac.uk/pmckeigu/pooling/poolscore.htm

Software program for analysis of case-control genetic association studies using allele frequency measurements on DNA pools (entry from Genetic Analysis Software)

Proper citation: POOLSCORE (RRID:SCR_007514) Copy   

•   Source: SciCrunch Registry

http://www003.upp.so-net.ne.jp/pub/publications.html#sl

Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)

Proper citation: LDGROUP (RRID:SCR_006282) Copy   

•   Source: SciCrunch Registry

http://www.geenivaramu.ee/en/

The Estonian Biobank is the population-based biobank of the EGCUT. The project is conducted in accordance with the Estonian Genes Research Act and all participants have signed a broad informed consent form (www.biobank.ee and Metspalu 2004, Drug Dev. Res.). As of December 2011, the biobank contains 51,515 participants (gene donors). The database of genotypic, phenotypic, health and genealogical information represents about 5% of Estonia''s adult population, and is the largest cohort ever gathered in Estonia. The age, sex and geographical distribution of this cohort reflect the structure of the adult population in Estonia. The database enables to conduct research in order to find links between genes, environmental factors, lifestyles and complex diseases or other traits. Active use of the biobank has started and although the first users are researchers all over the world with hundreds of different projects currently underway, industry is also interested. At the international level, the EGCUT will join the BBMRI follow-up program (ERIC) and through this channel provide service (biobanking, genotyping, sequencing and data analysis) for the centers in Europe who need it. Currently, the first follow-up study is underway and the molecular information of the cohort will be increased. For example, we have over 12 000 DNA samples analyzed by high density genotyping arrays and over 10 000 plasma samples analyzed by NMR scans, over 1000 individuals with RNA expression arrays, 2000 individuals with clinical laboratory analysis (over 40 tests) and over 60 full genomes are under deep sequencing. The infrastructure of the EGCUT includes a laboratory for DNA genotyping and next generation sequencing all based on Illumina platforms (HiScanSQ, HiSeq2000 and robotics), an IT unit (databases) with required computing power and storage space (1.2PB), data analysis team (bioinformatics and statistical genetics) and last but not least, a patient recruitment unit (health records, lifestyle and environmental information and biological samples ����?����������?? DNA, plasma and WBC from all 51515 gene donors). This is all located on 1000m2 in a brand new laboratory building, Riia str 23, Tartu, Estonia.

Proper citation: Estonian Genome Center (RRID:SCR_004467) Copy   

•   Source: SciCrunch Registry

http://ccr.coriell.org/Sections/Collections/NINDS/?SsId=10

Open resource of biological samples (DNA, cell lines, and other biospecimens) and corresponding phenotypic data to promote neurological research. Samples from more than 34,000 unique individuals with cerebrovascular disease, dystonia, epilepsy, Huntington's Disease, motor neuron disease, Parkinsonism, and Tourette Syndrome, as well as controls (population control and unaffected relatives) have been collected. The mission of the NINDS Repository is to provide 1) genetics support for scientists investigating pathogenesis in the central and peripheral nervous systems through submissions and distribution; 2) information support for patients, families, and advocates concerned with the living-side of neurological disease and stroke.

Proper citation: NINDS Repository (RRID:SCR_004520) Copy   

•   Source: SciCrunch Registry

http://epi.helmholtz-muenchen.de/kora-gen/index_e.php

KORA-gen is infrastructure to provide phenotypes, genotypes and biosamples for collaborative genetic epidemiological research. From all four surveys that have been conducted so far, the following biological material is on hand: genomic DNA, blood serum, blood plasma and EBV immortalized cell lines (form KORA S4 only). These have been extracted from blood samples and are stored in nitrogen tanks and -80 degrees C refrigerators. Genomic DNA from more than 18.000 adult subjects from Augsburg and the surrounding counties is available at present. So far, EBV immortalized cell lines from 1.600 participants are cultivated. To meet the manifold demands of researchers with genetic and molecular questions KORA-gen fulfills the following prerequisites for successful genetic-epidemiological research: * representative samples from the general population, * well characterized disease phenotypes and intermediate phenotypes, * information on environmental factors, * availability of genomic DNA, serum, plasma and urine, as well as EBV immortalized cell lines. In total, four population based health surveys have been conducted between 1984 and 2000 with 18000 participants in the age range of 25 to 74 years, and a biological specimen bank was established in order to enable scientists to perform epidemiologic research with respect to molecular and genetic questions. The KORA study center conducts regular follow-up investigations and has collected a wealth of information on sociodemography, general medical history, environmental factors, smoking, nutrition, alcohol consumption, and various laboratory parameters. This unique resource will be increased further by follow-up studies of the cohort. The assessment of statistical questions covers the definition of the study design and the calculation of statistical power. Furthermore, we offer assistance in data analysis. Kora-gen can be used by external partners. Interested parties can inform themselves interactively via internet about the available data and rules of access. The genotypic data base is a common resource to all partners.

Proper citation: KORA-gen (RRID:SCR_004510) Copy   

•   Source: SciCrunch Registry

http://www.genomeutwin.org/index.htm

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Study of genetic and life-style risk factors associated with common diseases based on analysis of European twins. The population cohorts used in the Genomeutwin study consist of Danish, Finnish, Italian, Dutch, English, Australian and Swedish twins and the MORGAM population cohort. This project will apply and develop new molecular and statistical strategies to analyze unique European twin and other population cohorts to define and characterize the genetic, environmental and life-style components in the background of health problems like obesity, migraine, coronary heart disease and stroke, representing major health care problems worldwide. The participating 8 twin cohorts form a collection of over 0.6 million pairs of twins. Tens of thousands of DNA samples with informed consents for genetic studies of common diseases have already been stored from these population-based twin cohorts. Studies targeted to cardiovascular traits are now being undertaken in MORGAM, a prospective case-cohort study. MORGAM cohorts include approximately 6000 individuals, drawn from population-based cohorts consisting of more than 80 000 participants who have donated DNA samples.

Proper citation: GenomEUtwin (RRID:SCR_002843) Copy   

•   Source: SciCrunch Registry

https://www.apbenson.com/cyrillic-downloads

Software application for pedigree drawing with fully integrated risk analysis and support for industry standard databases (MS Access and Corel Paradox). It is designed for genetic counselors and others who work with patients. Cyrillic 2 draws pedigrees, works with genetic marker data, lets you do haplotyping and allows exports to a range of linkage analysis packages.

Proper citation: CYRILLIC (RRID:SCR_001823) Copy   

•   Source: SciCrunch Registry

http://www.depressiontools.org/

Online instrument that estimates whether a biomarker predicting outcome of depression treatment is likely to be clinically significant.

Proper citation: DepressionTools.org Clinical Significance Calculator (RRID:SCR_003873) Copy   

•   Source: SciCrunch Registry

http://www.homozygositymapper.org/

A web-based approach of homozygosity mapping that can handle tens of thousands markers. User can upload their own SNP genotype files to the database. Intuitive graphic interface is provided to view the homozygous stretches, with the ability of zooming into single chromosomes or user-defined chromosome regions. The underlying genotypes in all samples are displayed. The software is also integrated with our candidate gene search engine, GeneDistiller, so that users can interactively determine the most promising gene. (entry from Genetic Analysis Software)

Proper citation: HOMOZYGOSITYMAPPER (RRID:SCR_001714) Copy   

•   Source: SciCrunch Registry

http://analysis2.bio-x.cn/myAnalysis.php

A powerful web-based platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci.

Proper citation: SHEsis: Analysis Tools For Random Samples (RRID:SCR_002958) Copy   

•   Source: SciCrunch Registry