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http://www.georgiahealth.edu/cancer/shared/tumor/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 31, 2016. The MCG Tumor Tissue and Serum Repository or tumor bank, located in the Department of Pathology, Murphey Pathology Building, was established with support from the Georgia Cancer Coalition (GCC). Its mission is to provide researchers access to high quality annotated specimens, an essential requirement for cancer research. The repository collection includes a variety of specimen types, such as tumor tissue and cells, blood and other biofluids as well as normal specimens used as controls. The quality of all specimens is reviewed by a pathologist, and the information is captured in the tumor bank''s database. An imaging system will be used in the future to capture this information. Human-derived specimens are a very precious resource, and therefore the operations of the tumor bank are overseen by an advisory board, representing GHSU and other stakeholders, to ensure that the specimens are properly utilized and the privacy of specimen donors is protected.

Proper citation: Medical College of Georgia Tumor Bank (RRID:SCR_004336) Copy   

•   Source: SciCrunch Registry

http://www.tumorbank.unibe.ch/

Tumorbank Bern - TBB collects high quality clinical samples since 2003 for translational research selected by expert pathologists under controlled conditions of normal and diseased tissue from different origin. The Tumor Bank is approved by the Ethical Commission of Bern, we only collect samples with written informed patient consent. Origin of Tissue: Thoracic Surgery, Gynecology, Urology, Visceral Surgery, Orthopedic Surgery, Head and Neck Surgery, Neurosurgery Tumorbank Bern TBB holds 12,000 samples from 3600 Patients. Please contact us to check if we have samples for your field of research.

Proper citation: Tumorbank Bern (RRID:SCR_004611) Copy   

•   Source: SciCrunch Registry

http://www.ontariotumourbank.ca/

The Ontario Tumour Bank is a province-wide biorepository and data bank focused on collection of tumor-related human biospecimens. It provides academic and industry cancer researchers with a diverse selection of high quality tumor-related specimens and data obtained directly by dedicated tumour bank staff, who follow a stringent set of procedures and ethical guidelines. The biospecimens and clinical data are an important resource for scientists engaged in translational research who are developing better diagnostic tools and new drug therapies. Researchers depend on the Ontario Tumour Bank to provide research biospecimens of high quality, diversity, and integrity. Operating at state-of-the-art hospitals and cancer centers across Ontario, the Ontario Tumour Bank coordinates the collection, storage, analysis, annotation, and distribution of tumor and peripheral blood samples. Working in collaboration with local pathologists, medical oncologists, surgeons and other hospital personnel, specially trained staff obtain patient consent, collect tissues and assemble comprehensive clinical information about each donor and the corresponding samples.

Proper citation: Ontario Tumour Bank (RRID:SCR_004732) Copy   

•   Source: SciCrunch Registry

http://www.biobank-gso.org/apex/f?p=200:1:2527679222961463

The Virtual Tumour Bank of the Canceropole Grand Sud-Ouest''s mission is to federate the cancer research of four French regions: Aquitaine, Languedoc-Roussillon, Limousin and Midi-Pyrenees. This site allows access to an inventory of the specimens stored in the tumor banks of the Greater South-West region, within the laboratories of Pathology of the University Hospital Centers and Cancer Centers of Bordeaux, Limoges, Montpellier, Nimes and Toulouse. You may search by disease or multiple criteria. These specimens are removed from patients primarily to confirm and accurately characterize their cancer diagnosis, and are therefore stored by the tumor bank for diagnostic and/or therapeutic purposes. These samples can be re-qualified for scientific research pending that a number of conditions are met, including the absence of refusal from the person (in compliance with French regulations). So far, the tumor bank is a major tool for cancer treatment and research. This inventory is a further evidence of the coordination effort between the eight concerned tumor banks that have been mobilized at the service of patients and research within the framework of the Canceropole Grand Sud-Ouest programs. These biological resources are made available to research groups that conduct basic or translational programs in the field of oncology. They will not be made available for projects in fields other than oncology.

Proper citation: Southwest France Tumour Bank (RRID:SCR_004574) Copy   

•   Source: SciCrunch Registry

http://www.bccrc.ca/dept/ttr

A provincial biobank resource to support translational cancer research at the BC Cancer Agency, across Canada and internationally. This biobank collects biospecimens (tissues and blood), and clinical information and processes these to create anonymous cases that can be studied by cancer researchers to understand how cancer develops, how it grows, how it spreads, and how it responds to treatment. These tissues and data are obtained from patients who undergo surgery to treat a tumor and who have generously provided their consent for the TTR to collect tissues that are unused after diagnosis has been completed. The TTR is a provincial program that currently comprises a core biobank at the Vancouver Island Center, Victoria, that offers participation in the program to patients in Victoria and Nanaimo. The TTR works with other banks and expert translational research groups in BC, to create expanded capacity for collection and opportunities for research access to tissue resources. The TTR operates under the management and oversight of the director, a scientific advisory board, and the UBC BCCA Research Ethics Board. The TTR operates within organizational policies and a commitment to protection of donor privacy that is embodied in all standard operating procedures and aspects of the repository. The TTR is also a founding member and contributor to the development of provincial (BC BioLibrary) and national (CTRNet) initiatives to promote biobanking.

Proper citation: British Columbia Tumour Tissue Repository (RRID:SCR_004597) Copy   

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https://moffitt.org/research-science/shared-resources/tissue/

A central tissue repository at Moffitt specializing in protocol-driven human tissue collection, storage, processing and dissemination. Tissue Core provides investigators with access to high quality, well-annotated human specimens obtained from representative of the patient populations. The advent of powerful molecular technologies has opened the door to developing more effective treatments of patients with cancer. Access to high quality specimens with associated clinical, treatment, recurrence outcome data will be critical to developing and validating the tests needed for diagnosis and prediction of response to therapy. Since its commencement in 1993, the Tissue Core has collected more than 8,000 cases of human liquid cancers and solid primary and metastatic tumors both malignant and benign with adjacent normal, from variety of sites and diagnoses. Collected samples are mostly remnant tissues obtained from patients undergoing therapeutic surgical procedures at the Center. The core also ensures tissue release compliance with USF-IRB and Privacy Board recommendations. * Protocol driven sample collection, processing and distribution * Collection of sample and patient demographic information. * Nucleic acid extractions from tissue sections, FNA, core biopsies blood and bone marrow. * Histology services: H&E slides, staining, sectioning, paraffin blocks, OCT blocks, sample microdissection * WBC, plasma and serum isolation. * Project development and support: Facility staff provides advice and guidance to researchers.

Proper citation: Moffitt Cancer Center Tissue Core (RRID:SCR_004406) Copy   

•   Source: SciCrunch Registry

http://www.rbta.es/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 16, 2013. Located in Spain, the Andalusian Regional Tumour Bank is a regional tumor bank. In the last decades cancer knowledge is growing exponentially due human genome knowledge and technological advantages. However, this disease is the biggest problem of health in Europe, with more than 2,5 million new cases per year. The diagnosis and treatment of cancer is now allowing to identify the characteristics that the disease has on each person. The next step is meant to be a great revolution in the treatment of cancer. This scientific development is dependent on the availability of human tumour samples preserved in demanding conditions. Current technology requires the availability of tissue morphological and molecular conditions similar to those that had the sample before being removed. Tumor banks are responsible for these new quality requirements to foster the development of research and health care of patients.

Proper citation: Andalusian Regional Tumour Bank (RRID:SCR_004885) Copy   

•   Source: SciCrunch Registry

https://github.com/Illumina/strelka/

Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. Strelka2 germline and somatic small variant caller.

Proper citation: Strelka2 (RRID:SCR_005109) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/ibsr

Data set of manually-guided expert segmentation results along with magnetic resonance brain image data. Its purpose is to encourage the development and evaluation of segmentation methods by providing raw test and image data, human expert segmentation results, and methods for comparing segmentation results. Please see the MediaWiki for more information. This repository is meant to contain standard test image data sets which will permit a standardized mechanism for evaluation of the sensitivity of a given analysis method to signal to noise ratio, contrast to noise ratio, shape complexity, degree of partial volume effect, etc. This capability is felt to be essential to further development in the field since many published algorithms tend to only operate successfully under a narrow range of conditions which may not extend to those experienced under the typical clinical imaging setting. This repository is also meant to describe and discuss methods for the comparison of results.

Proper citation: Internet Brain Segmentation Repository (RRID:SCR_001994) Copy   

•   Source: SciCrunch Registry

http://ranchobiosciences.com/gse4922/

Curated data set of a study that investigated the expression profiles of 347 primary invasive breast tumors on Affymetrix microarrays. Three separate breast cancer cohorts were analyzed: 1) Uppsala (n=249), 2) Stockholm (n=58), 3) Singapore (n=40). The Uppsala and Singapore data can be accessed in GSE4922. The Stockholm cohort data can be accessed at GEO Series GSE1456.

Proper citation: GSE4922 (RRID:SCR_003557) Copy   

•   Source: SciCrunch Registry

http://www.centreducancer.be/en/show/index/section/8/page/34

When a patient suffering or thought to be suffering from cancer is cared for, samples are often taken to determine the precise diagnosis and to determine any treatment necessary. After this essential stage of the patient''s care, unused biological material is sometimes left over. This material is an essential and precious tool for research into cancer. For this reason, patients can decide to make the material available to researchers the world over who study either the development mechanism of cancer or the new treatments available. Residual samples are centralized and stored in the Tumor Bank at the Cliniques Universitaires Saint-Luc Cancer Centre. The research carried out on this material primarily benefits cancer patients. It can help improve existing treatments or discover new drugs, and also allows new diagnostic tools to be tested. Any financial profits obtained from assessing the results obtained are entirely reinvested in the work of the Cancer Centre''s Tumour Bank and in new research projects at the Catholic University of Louvain. Using and sharing material, and verification and retrospective analysis of clinical data, all comply with strict rules. As with donations of blood, marrow or organs, an Ethics Committee oversees the operations of the Tumour Bank and research projects. This committee is responsible for ensuring compliance with current Belgian and legal texts, especially those concerning the protection of patient privacy and rights.

Proper citation: Saint-Luc Tumour Bank (RRID:SCR_008714) Copy   

•   Source: SciCrunch Registry

https://www.urmc.rochester.edu/neurosurgery/specialties/neurooncology.aspx

Collaborative neuro-oncology research program with a tissue repository (tumor bank) containing a wide range of clinical specimens, which they make available to researchers in order to study the effects of new drugs on a large number and wide range of tumor specimens. They provide highly coordinated, complex care in neurosurgery, radiation oncology, medical oncology, and neurology to patients afflicted with tumors of the brain and spine by combining the newest technologies and treatments available anywhere in the world. The program is formed from a multidisciplinary group with a goal of helping patients navigate the complex issues surrounding brain and spinal cancer care. The researchers are working to increase the number of targets that could be considered for anti-angiogenesis therapy. Many of their studies focus on the blood vessel cells (endothelial cells) themselves, which, unlike tumor cells, rarely mutate and so might be less likely to become resistant to therapy and are also more easily reached through the bloodstream. Their researchers are also attempting to better understand the changes in the blood-brain barrier (BBB) that are associated with fluid accumulation and brain swelling (edema) in neuro-oncology patients. Normal brain tissue is shielded from the rest of the body by the BBB. This barrier is composed of very tight blood vessels that prevent most substances from entering the brain. Brain tumors have a leaky BBB ����?? this feature can be used to identify tumors on MRI scans. They have identified specific molecules that appear to be associated with the leaky, abnormal vessels while the normal blood vessels with intact BBB produce these molecules at very low levels or not at all. Inhibiting the function of these molecules may help control or prevent disruption of the BBB and limit cerebral edema in brain tumor patients, as well as patients suffering from stroke or traumatic brain injury.

Proper citation: University of Rochester Program for Brain Tumors and Spinal Tumors (RRID:SCR_005343) Copy   

•   Source: SciCrunch Registry

http://ucneuroscience.com/

Leading treatment, research and teaching center for complex neurological conditions based at the University Hospital and the UC College of Medicine. Its physicians and researchers have created national models for evidence-based treatment and research of complex conditions, including ischemic and hemorrhagic stroke, brain aneurysms, brain and spinal cord trauma, brain tumors, Parkinson's disease, epilepsy and seizure disorders, multiple sclerosis, trigeminal neuralgia, Alzheimer's disease and memory disorders, mood disorders, and neuromuscular disorders. UCNI includes a team of more than 100 experts from 15 specialties who collaborate across disciplines to provide the most comprehensive diagnoses and treatments possible.

Proper citation: University of Cincinnati Neuroscience Institute (RRID:SCR_005345) Copy   

•   Source: SciCrunch Registry

https://github.com/ding-lab/msisensor

A C++ software program for automatically detecting somatic and germline variants at microsatellite regions. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples.

Proper citation: MSIsensor (RRID:SCR_006418) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/socrates/

Software for detecting genomic rearrangements in tumors that utilizes only split-read data. It features single nucleotide resolution, high sensitivity, and high specificity in simulated data. It takes advantage of parallelism for efficient use of resources.

Proper citation: Socrates (RRID:SCR_006411) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.oxfordjournals.org/content/early/2014/01/02/bioinformatics.btt759.abstract?sid=e62f3c2b-26dc-428b-ba24-99e92a277d77

Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.

Proper citation: AbsCN-seq (RRID:SCR_006409) Copy   

•   Source: SciCrunch Registry

http://www.proteinatlas.org/

Open access resource for human proteins. Used to search for specific genes or proteins or explore different resources, each focusing on particular aspect of the genome-wide analysis of the human proteins: Tissue, Brain, Single Cell, Subcellular, Cancer, Blood, Cell line, Structure and Interaction. Swedish-based program to map all human proteins in cells, tissues, and organs using integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology. All the data in the knowledge resource is open access to allow scientists both in academia and industry to freely access the data for exploration of the human proteome.

Proper citation: The Human Protein Atlas (RRID:SCR_006710) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/science/programs/genome-biology/computational-rd/somaticcall-manual

Software program that finds single-base differences (substitutions) between sequence data from tumor and matched normal samples. It is designed to be highly stringent, so as to achieve a low false positive rate. It takes as input a BAM file for each sample, and produces as output a list of differences (somatic mutations). Note: This software package is no longer supported and information on this page is provided for archival purposes only.

Proper citation: SomaticCall (RRID:SCR_001196) Copy   

•   Source: SciCrunch Registry

http://patchwork.r-forge.r-project.org/

Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data.

Proper citation: Patchwork (RRID:SCR_000072) Copy   

•   Source: SciCrunch Registry

http://www.oncotest.com/

A contract research organization (CRO) specializing in preclinical oncology services. As a pioneer in the field of patient derived tumor xenografts (PDX), they provide tailored solutions to the problems faced by preclinical oncology researchers. They assist with the identification of the best drug candidates and the validation of their targets and deliver in-depth bioinformatics analyses, laying the groundwork for the successful planning of clinical trials. Their diverse tumor model collection enables them to recommend the right assays and models to answer their customers' questions. Their AAALAC accredited facilities with IVC system, separate model development unit, large cage capacity of over 14,500 mice and proprietary electronic measurement system with an integrated database and by continuously maintaining important PDX models in mice, they are able to provide the highest standard of testing within a reasonable timeframe.

Proper citation: Oncotest (RRID:SCR_000489) Copy   

•   Source: SciCrunch Registry