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https://www.synapse.org/

A cloud-based collaborative platform which co-locates data, code, and computing resources for analyzing genome-scale data and seamlessly integrates these services allowing scientists to share and analyze data together. Synapse consists of a web portal integrated with the R/Bioconductor statistical package and will be integrated with additional tools. The web portal is organized around the concept of a Project which is an environment where you can interact, share data, and analysis methods with a specific group of users or broadly across open collaborations. Projects provide an organizational structure to interact with data, code and analyses, and to track data provenance. A project can be created by anyone with a Synapse account and can be shared among all Synapse users or restricted to a specific team. Public data projects include the Synapse Commons Repository (SCR) (syn150935) and the metaGenomics project (syn275039). The SCR provides access to raw data and phenotypic information for publicly available genomic data sets, such as GEO and TCGA. The metaGenomics project provides standardized preprocessed data and precomputed analysis of the public SCR data.

Proper citation: Synapse (RRID:SCR_006307) Copy   

•   Source: SciCrunch Registry

https://dcc.icgc.org/

Portal provides tools for visualizing, querying, and downloading cancer data, which is released on quarterly schedule.

Proper citation: ICGC Data Portal (RRID:SCR_021722) Copy   

•   Source: SciCrunch Registry

https://www.ucl.ac.uk/biobank/physicalbloom

The UCL/UCLH Biobank for Studying Health and Disease has been primarily established to support the Research Programme and scientific needs, of the Pathology Department UCLH & the UCL Cancer Institute. The establishment of the core programme enables a centralised approach to the management and integration of all research groups working within these institutions, providing appropriate structure and support. The biobank has policies and guidelines to guarantee compliance with HTA legislation and to ensure quality standards will be maintained. The biobank stores normal and pathological specimens, surplus to diagnostic requirements, from relevant tissues and bodily fluids, as well as human tissue used in xenograft experiments. Stored tissues include; snap-frozen or cryopreserved tissue, formalin-fixed tissue, paraffin-embedded tissues, and slides prepared for histological examination. Tissues include resection specimens obtained surgically or by needle core biopsy. Bodily fluids include; whole blood, serum, plasma, urine, cerebrospinal fluid, milk, saliva and buccal smears and cytological specimens such as sputum and cervical smears. Fine needle aspirates obtained from tissues and bodily cavities (eg. pleura and peritoneum) are also collected. Where appropriate the biobank also stores separated cells, protein, DNA and RNA isolated from collected tissues and bodily fluids described above. Some of the tissue and aspirated samples are stored in the diagnostic archive.

Proper citation: UCL/UCLH Biobank for Studying Health and Disease (RRID:SCR_004610) Copy   

•   Source: SciCrunch Registry

http://www.shca.org.cn/english/content/11540

The Institutional Tissue Bank (ITB) of Fudan University Shanghai Cancer Center was established in 2006 with the goal of serving as a central repository for human tissue samples for cancer research and possible personalized medicine for the institution. The Institutional Research Board oversees the fulfilling of informed consent of each patient whose samples are collected. The ITB''s collection procedures meet the global quality standards and provide high quality tissue samples. The quality control for morphology, RNA, DNA and protein has been set up to ensure the sample quality. Routine frozen section from tissue aliquot is made for every piece of sample to ensure the component of tumor tissue and the pathological feature is the same as the diagnosed tumor. Agilent 2100 Bioanalyzer was used to provide RNA and DNA quality parameters. The Tissue Bank occupies 500 m2, with sufficient space for sample preparation and storage, data registration, data tracking/access, related equipments and monitor system. Variant samples including blood, tumor tissue, and body fluids are collected and serve as alternative permanent patient tissue records. Annotation of collected samples is captured through linking the medical record and pathological report system to tissue bank software. Frequent tumor types such as lung cancer, breast cancer, gastric cancer, urological tumors, gynecological tumors and esophageal cancers, head & neck cancers, as well as infrequent cancer types such as malignant soft tissue sarcomas, pancreatic cancer, gall bladder cancer, and other rare cancers are all collected and stored. Tumor tissues are stored with matched normal tissues. Serum and plasma are isolated from coagulation plus and coagulation minus blood samples. White blood cells are stored as well. Tissues are stored both in RNALater at -20 degrees C and -80 degrees C after snap frozen. Samples have been increased from 4,000 in 2008 to 10,783 in 2009. To the end of September 2010, over 30,000 samples has been processed and stored in our tissue bank. As planned, 50,000 samples will be stored dynamically. Over 50 funded projects have used the samples from our tissue bank. Productive papers have been published in the past years by using the samples. More and more projects will be approved to get research resources from tissue bank in the future. The tissue bank of FUSCC has been designated as the key subject and successful model by Shanghai municipal government.

Proper citation: Cancer Center Tissue Bank - Fudan University (RRID:SCR_004596) Copy   

•   Source: SciCrunch Registry

http://www.fccc.edu/prevention/studies/biosample/about.html

Fox Chase has developed a facility dedicated to the collection and distribution of human subject biosamples and supporting personal and family cancer history data. In response to announcement (CA-00-025; P30 CA06927S2), the Fox Chase Cancer Center''s Biosample Repository (BR) and Tumor Bank Facility (TBF) is making blood specimens (i.e., whole blood, plasma, platelet-rich plasma, platelet homogenates, red blood cells, leukocytes, lymphoblastoid cell lines, and DNA isolated from leukocytes) and tumor tissues (i.e., multi-tissue microarrays and tumor DNAs) collected by our facilities available for research. Request for blood and tissue will be reviewed by a panel of scientists and ranked. Priority will be given to those investigators with current NIGH/NCI funding, but will be made available as recommended by the internal and external advisory committees. * Blood Inventory: Plasma, Serum, Whole Blood, Lymphocytes, DNA * Tissue Inventory: Tumor and Normal Adjacent Tissue, Fresh-Frozen, Formalin-Fixed Paraffin-Embedded Tissue, OCT Embedded Tissue, Ethanol-fixed Tissue

Proper citation: Fox Chase Biosample Repository Core Facility (RRID:SCR_004746) Copy   

•   Source: SciCrunch Registry

http://cancer.case.edu/sharedresources/tissue/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 11, 2023. The Case Comprehensive Cancer Center''s Biorepository and Tissue Processing Core Facility (BTPC) serves two primary functions: 1. To build an inventory of remnant human tissues, blood and other body fluids (collectively termed biospecimens) targeted towards cancer and other medical research, for later assignment to investigators; and 2. To provide long term, controlled storage of biospecimens for specific researchers. These samples are for research purposes only and may not be used for clinical diagnosis or implantation into humans. Clinical information relating to the samples and donors are collected and maintained in a secure database. Samples and data are de-identified or de-linked before release to the researcher unless he/she has specific IRB approval to gain access to this information. Remnant biospecimens are prospectively collected from surgical procedures, autopsies and clinical laboratories for the BTPC by the Human Tissue Procurement Facility (HTPF), which operates under UH-IRB Protocol 01-02-45. Blood and bone marrow specimens are collected for the BTPC by the Hematopoietic Stem Cell Core Facility (HSCC), which operates under UH-IRB Protocol 09-90-195. The Division of Surgical Pathology at University Hospitals Case Medical Center (UHCMC) has clinical archives of paraffin blocks that can be made available through the BTPC for retrospective research studies under the approval of the Vice Chair for Clinical Affairs at UHCMC. Surgical Pathologists associated with the BTPC are responsible for determining which blocks can be made available and how much material can be removed from the blocks. Types of Tissue Available * Malignant, benign, diseased, normal and normal human tissues * Normal adjacent tissues available paired with tumor specimens in many cases * Tissues are collected from over 50 anatomic sites * Frozen specimens, OCT-embedded and paraffin-embedded tissues * Large array of paraffin-embedded specimens from clinical archives of paraffin blocks and QC research blocks maintained by the HTPF * Peripheral blood and bone marrow samples from initial visits and follow-up procedures are processed to obtain serum and cell fractions for storage * No samples are collected from individuals with known infectious illnesses * Fetal biospecimens are not collected due to state and local statutes

Proper citation: Case Comprehensive Cancer Center Biorepository and Tissue Processing Core Facility (RRID:SCR_004382) Copy   

•   Source: SciCrunch Registry

http://www.clinicbiobanc.org/en_index.html

A biobank of repositories which works to obtain, store, manage and distribute large collections of human biological samples of phenotypes and diseases of marked interest for researchers. The biobank sample collection is made up of three extensive repositories. The Neurological Tissue Biobank is a nervous tissue repository (brain and spinal cord) created from donations from cadavers with or without neurological conditions. It helps facilitate research in neurological illnesses. The Tumour Biobank and Anatomical Pathologies Collections is a repository of tumorous tissue and samples from cancer patients. The Blood and Fluid Biobank is a repository which contains samples of metabolic, inflammatory bowel, hepatic, digestive and maternal and foetal diseases, among others. It houses a large range of samples of scientific interest, primarily DNA, serum and plasma.

Proper citation: Biobank of Hospital Clinic - IDIBAPS (RRID:SCR_004530) Copy   

•   Source: SciCrunch Registry

http://www.jtcancercenter.org/clinical_trials/the_tissue_bank2/

The Tissue Bank stores tissue, blood, and bone marrow samples that have been taken from patients who have given their consent after they have undergone biopsies, surgery, or other procedures for cancer at the John Theurer Cancer Center. Our scientists use these samples to analyze and study multiple types of human cancer, with a goal toward learning more about how cancer develops, developing innovative new treatments, and determining how well a treatment is working. Our Tissue Bank is overseen by our program and medical director, Andre Goy, M.D., M.S., who is also deputy director of the Cancer Center and chief of the Division of Lymphoma; and our scientific director, K. Stephen Suh, Ph.D. Currently, 30 percent of our Tissue Bank team members work in our clinics, and 70 percent of our team works ����?��������??behind the scenes,����?��������?? conducting important scientific research without meeting patients.

Proper citation: Hackensack University Tissue Bank (RRID:SCR_004956) Copy   

•   Source: SciCrunch Registry

https://research.kssg.ch/Projekte/nach-Projekttyp/48182/L-en

St. Gallen Lung Biopsy Biobank is a tissue and blood sample collation (biobank) of all patients willing to give informed consent, who are undergoing bronchoscopy and/or surgical lung resection in their diagnostic pathway for any pulmonary disease. The special feature of the proposed biobank is the collection of endobronchial biopsies, blood, and molecularly defined cell populations from tumor tissue in a quality suitable for mRNA and other protein expression techniques, which is not possible by standard biobanks.

Proper citation: St. Gallen Lung Biopsy Biobank (RRID:SCR_004971) Copy   

•   Source: SciCrunch Registry

http://frederick.cancer.gov/

A federally funded research and development center dedicated to biomedical research. NCI-Frederick partners with university, government, and corporate scientists to speed the translation of laboratory research into new diagnostic tests and treatments for cancer and HIV/AIDS. NCI-Frederick is comprised of more than 2,800 government- and contractor-employed biomedical researchers, laboratory technicians, and support staff and several cancer research centers. The FNLCR provides quick response capabilities and meets special long-term research and development needs for NCI that cannot be met as effectively by existing in-house or contractor resources.

Proper citation: NCI-Frederick (RRID:SCR_004880) Copy   

•   Source: SciCrunch Registry

http://www.utmb.edu/scccb/htbc/htbc.htm

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016.

Proper citation: University of Texas Tumor Bank (RRID:SCR_005048) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/oncotator

A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed.

Proper citation: Oncotator (RRID:SCR_005183) Copy   

•   Source: SciCrunch Registry

http://lomalindahealth.org/medical-center/our-services/cancer-center/cancer-resource-center/biospecimen-laboratory.html

The Loma Linda University Cancer Center Biospecimen Laboratory provides specimens for researchers as they search for the causes of cancer, and look for new means of prevention and treatment. The specimens include tissues, blood products (blood cell, plasma and serum) and bone marrow cells. Researchers interested in gaining access to the Biospecimen Laboratory''s samples should email Dr. Saied Mirshahidi, requesting access. The number and types of samples we have available for research can be viewed, http://www.llu.edu/catissuesummary/. Use the Biospecimen Laboratory Tissue Request Form to request specimens for research studies.

Proper citation: Loma Linda University Cancer Center Biospecimen Laboratory (RRID:SCR_004767) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/jax-mice-and-services/in-vivo-pharmacology/mouse-tumor-biology-database

Database supports use of mouse model system for human cancer by providing comprehensive resource for data and information on various tumor models.

Proper citation: Mouse Tumor Biology Database (RRID:SCR_006517) Copy   

•   Source: SciCrunch Registry

http://srv00.recas.ba.infn.it/ASPicDB/

A database to access reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano et al. 2006), and to the functional annotation of predicted isoforms. Users may select and extract specific sets of data related to genes, transcripts and introns fulfilling a combination of user-defined criteria. Several tabular and graphical views of the results are presented, providing a comprehensive assessment of the functional implication of alternative splicing in the gene set under investigation. ASPicDB also includes information on tissue-specific splicing patterns of normal and cancer cells, based on available EST data and their library source annotation.

Proper citation: ASPicDB (RRID:SCR_002102) Copy   

•   Source: SciCrunch Registry

http://ncim.nci.nih.gov/ncimbrowser/

A wide-ranging biomedical terminology database that covers most terminologies used by NCI for clinical care, translational and basic research, and public information and administrative activities. NCIm features: * Maps 4,000,000 terms from more than 75 sources into 2,000,000 biomedical concepts that represent their meaning. * Displays preferred terms, synonyms, definitions, and other information from each source. * Links to NCI Thesaurus and other related information sources. * Contains 22,000,000 cross-links between content elements. * Updated frequently by a team of biomedical terminology and subject matter experts. NCIm contains most public domain terminologies from the National Library of Medicine's UMLS Metathesaurus, as well as many other biomedical terminologies created by or of interest to NCI and its partners. Some propriety terminologies are included, with permission, and have restrictions on their use. The current version of the NCI Metathesaurus, based on the UMLS build 2013AA, covers up to National Cancer Institute Thesaurus, 13.12d. A viewer for the UMLS changes document can be downloaded.

Proper citation: NCI Metathesaurus (RRID:SCR_003565) Copy   

•   Source: SciCrunch Registry

http://www.tubafrost.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. In this web site you will find the central European database of OECI-TuBaFrost collecting the information of biobanks or in the project support environment on human material; i.e., frozen tumor tissue specimens, pathology blocks, blood samples in different forms, cell lines, Tissue Micro Arrays, etc. Our goal is by centralizing the tumor tissues information to facilitate the search of doctors / researchers for tumor materials, which they need for their cancer research there with facilitating cancer research. OECI members only can participate in the OECI-TuBaFrost exchange platform, or those introduced by an OECI member. We are a group of pathology and research departments as well as bio-bankers in clinical based biobanking based in comprehensive cancer centers or hospitals with a competence in comprehensive cancer care across Europe. Each participating institute is involved in cancer research resulting in innovative procedures, new drugs, improved diagnosis and new insights in disease development. The overall result is better care and treatment for cancer patients. To maximize the scientific value of the human tissue samples, information about the clinical status of the patient in combination with the quality and type of samples is very important. A TuBaFrost electronic database will securely store all this information. Within the closed project supporting environments, the data collected will include: * Diagnosis - identification of the type of cancer * Type of tissue collected - the origin, i.e. breast, skin, colorectal * Quality of tissue collected - collection and storage details The tissue is stored in the hospital where the donor was diagnosed/treated. It stays there until it is used or sent to another hospital or research center within the TuBaFrost group. The electronic database will track samples throughout the network. The tissue is not sold. The exchange of tissue to other hospitals is regulated by a contract, which uses the national regulations of the country supplying the tissue. Tissue samples within the TuBaFrost collection will only be used for research, which has been approved by ethics committees. This ensures that the tissue is only used for the best quality research and only for the specific reasons given to the ethics committee.

Proper citation: OECI - Tubafrost: The European Human Frozen Tissue Bank (RRID:SCR_004280) Copy   

•   Source: SciCrunch Registry

http://www.rrcancer.ca/en/publique/accueil

An infrastructure to allow Quebec researchers to have at their disposal tumor banks and the services that support large scale research in genomics and proteomics. The database and the tissue bank of the research network was created to allow rapid access to biological samples and their clinical data. It is spread out over many hospital institutions (in Montreal, Quebec and Sherbrooke). The members of the RRCancer-BTD supply normal, benign and malignant samples from routine surgeries and blood tests. Blood and tissue samples are collected by the provincial biobanks on a regular basis and are coded, classified and stored. The samples can be supplied to a researcher either fresh or frozen or blocks of paraffin or on slices. The sharing of information and biological material is managed according to ethical rules and contributes to increasing the value of research in Quebec. The network has mobilized a significant number of researchers in the area of cancer that unite their efforts to pursue high caliber multidisciplinary research. They are a group of researchers from many different Qu��bec Universities all working in the branch of cancer research. They are located in four hospital centers in Quebec, namely the University of Montreal Hospital Centre (CHUM), the University of Quebec Hospital Centre (CHUQ), the University of Sherbrooke Hospital Centre (CHUS) and the McGill University Hospital Centre (CUSM), as well as in the affiliated research and university centers (Sacr��-Coeur, Maisonneuve-Rosemont and the Montreal Jewish Hospital). The collaborative efforts created and maintained in this network have allowed transfer of knowledge and the sharing of cutting edge technologies. RRCancer favors multidisciplinary cancer research in both fundamental and clinical scopes. The network is based on the desire researchers to work together to prevent cancer and improve therapeutic strategies, all the while continuing the very important task of raining new specialists and graduate students.

Proper citation: Cancer Research Network of the FRSQ (RRID:SCR_004225) Copy   

•   Source: SciCrunch Registry

http://www.ibbl.lu/

An independent, not-for-profit biobanking and biotechnology foundation designed to facilitate new, high quality medical research. The IBBL collects, stores, and analyzes biological samples and associated data, which are then made available to research organizations investigating new treatments for diseases. It houses a biospecimen collection and biorepository that contains high quality tissues and maintains quality control of the specimens and the clinical data associated with the tissue samples, while maintaining biobanking ethical standards. It also provides biorefinery analyses and research services that can make analytes from tissues (e.g. DNA, RNA and protein), maintains technology for high throughput gene sequencing and gene expression, and conducts biospecimen research. An informatics platform maintains the clinical and biospecimens data in a secure fashion for additional analysis. Samples are collected by IBBL personnel from hospitals in a targeted manner. The IBBL collaborates with research and health organizations in North America, Europe and the Middle East, and with the major international biobanking societies.

Proper citation: Integrated Biobank of Luxembourg (RRID:SCR_004211) Copy   

•   Source: SciCrunch Registry

http://www.itor-ghs.org/biorepository.php

From the type of mutation causing cancer to specific gene expression levels, genetic biomarkers are becoming an indispensable tool for developing new treatment models for cancer. The ITOR Biorepository Services tissue bank initiatives are critical to the continued development of an organized research infrastructure that will attract leading biotechnology and pharmaceutical companies interested in developing the next generation of cancer therapies. Ultimately, by linking the laboratory and clinical settings through innovative research investigations, USC, Greenville Hospital System University Medical Center, and private partners can identify the most novel ways to find and couple these biomarkers to patient drug trials and eventually, the most effective treatments & cures for cancer. The ITOR Biorepository Services Department ����?����������?? in conjunction with the Greenville Hospital System''s surgical oncologists, pathologists and staff ����?����������?? have developed tissue bank sample processing guidelines for frozen tissue, fresh tissue and peripheral blood and include flash freezing in liquid nitrogen within 15 minutes of harvest to maximize cell viability for basic science research. The department has a dedicated staff, including two research nurses and a data coordinator, which facilitate the logistics of tissue handling and submit outcomes data on participating patients. The ITOR Biorepository staff is in the process of adopting a universal consent for all patients of the Greenville Hospital System to have the option of donating excess tissue for research, should they desire. ITOR of GHS has several tissue-based patient initiatives & programs under development and ongoing. At the forefront of cancer care are two specific programs, Total Cancer Care and Caris Target Now.

Proper citation: ITOR Biorepository Services (RRID:SCR_004191) Copy   

•   Source: SciCrunch Registry