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http://www.iro.umontreal.ca/~csuros/quadgt/

Software package for calling single-nucleotide variants in four sequenced genomes comprising a normal-tumor pair and the two parents. Genotypes are inferred using a joint model of parental variant frequencies, de novo germline mutations, and somatic mutations. The model quantifies the descent-by-modification relationships between the unknown genotypes by using a set of parameters in a Bayesian inference setting. Note that you can use it on any subset of the four related genomes, including parent-offspring trios, and normal-tumor pairs without parental samples.

Proper citation: QuadGT (RRID:SCR_000073) Copy   

•   Source: SciCrunch Registry

http://www.epo-berlin.com/

A small and medium-sized enterprise (SME) that has expertise in preclinical pharmacology, pharmacokinetics, and toxicology for the characterization of novel anticancer therapeutics and predictive biomarkers like: cytostatics, biologicals (peptides, antibodies), (anti)-hormones, immunomodulators (cytokines), and gene therapeutics. EPO has modern laboratories licensed for animal experiments and gene technology (S2) and a broad panel of murine and human tumor models growing in immunocompetent (SPF-quality, syngeneic strains) or immunodeficient mice (nude, SCID, NOD/SCID). EPO has established imaging technologies to monitor in vivo tumor growth.

Proper citation: Experimental Pharmacology and Oncology Berlin-Buch (RRID:SCR_003954) Copy   

•   Source: SciCrunch Registry

http://www.alacris.de/

Commercial organization that uses next generation sequencing technologies coupled with computational modeling of tumor and somatic tissues in order to identify individualized therapies for cancer patients. The company also uses these technologies to help pharmaceutical partners stratify patients for their clinical trials. Alacris has an exclusive worldwide commercial license for the computational modeling of tumors and somatic tissues using proprietary computational systems modeling technologies ModCell developed at the Max Planck Institute for Molecular Genetics (MPI-MG) in Berlin coupled with next generation sequencing and genotyping technology developed at Harvard Medical School in Boston. The company also is building up the first next generation sequencing center in Europe for clinical operations.

Proper citation: Alacris Theranostics (RRID:SCR_003953) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/destruct/

A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing.

Proper citation: deStruct (RRID:SCR_004747) Copy   

•   Source: SciCrunch Registry

http://www.althia.es/

A biomedical company in Spain focused on the development of new tools for diagnosis and personalized treatment of oncological diseases and precancerous. It has three areas of activity in permanent innovation: Assistance in Diagnosis / Prognosis in solid and hematological tumors, Translational Research covering the gap between basic and clinical research and advanced radiotherapy treatments based image-guided single dose (SD-IGRT). Their objectives are: * Provide an integrated tissue and tumor molecular phenotype analysis using the most advanced technologies in diagnosis, to guide the most appropriate treatment for each patient. * Discover and validate molecular patterns by molecular systems and platforms including pathology, to generate predictive algorithms through computational biology, evolution and determining the response of patients with a particular tumor profile. Althia has laboratories equipped with the most advanced equipment and technologies in Barcelona and Granada Genyo Center, with offices in Madrid.

Proper citation: Althia (RRID:SCR_003918) Copy   

•   Source: SciCrunch Registry

http://compbio.bccrc.ca/software/mutationseq/

A software suite using feature-based classifiers for somatic mutation prediction from paired tumour/normal next-generation sequencing data. mutationSeq has the advantages of integrating different features (e.g., base qualities, mapping qualities, strand bias, and tailed distance features), and validated somatic mutations to make predictions. Given paired normal/tumour bam files, mutationSeq will output the probability of each candidate site being somatic.

Proper citation: mutationSeq (RRID:SCR_006815) Copy   

•   Source: SciCrunch Registry

http://pstiing.icr.ac.uk/

A publicly accessible knowledgebase about protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast. The knowledgebase allowing users to search and to dynamically generate visual representations of protein-protein interactions and transcriptional regulatory networks. Signalling and transcriptional modules can also be displayed singly or in combination. This allow users to identify important "cross-talks" between signalling modules via connections with key components or "hubs". The knowledgebase will facilitate a "systems-wide" understanding across many protein, signalling and transcriptional regulatory networks triggered by multiple environmental cues, and also serve as a platform for future efforts to computationally and mathematically model the system behavior of inflammatory processes and tumourigenesis.

Proper citation: pSTIING (RRID:SCR_002045) Copy   

•   Source: SciCrunch Registry

http://www.braintumourbank.ca/pages/about.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. The mission of the Canadian Virtual Brain Tumour Bank (CVBTB) is to facilitate clinical, molecular and translational research through the provision of well-characterized tissue linked to clinical data and to become a standardized national tissue resource whereby scientific needs are met, addressed and accelerated through a common public accessible core the CVBTB. Recognizing the need to encourage systemic banking of brain tumor tissues throughout the country and to link banks of brain tumor tissue samples with academic and scientific institutions that require these samples, the CVBTB was established. Under the sponsorship of Schering Plough Canada Inc. and in association with the Canadian Brain Tumour Consortium (CBTC), the CVBTB looks to act as a resource for all researchers to provide them with information on the types of brain tumor tissue samples available and to direct them to the tumor tissue banking sites holding these samples. The CVBTB also looks to provide information on standard operating procedures regarding aspects of tumor tissue banking such as tissue accrual, storage and shipment and the processing of blood samples such as serum and lymphocytes. The CVBTB currently consists of four brain tumour tissue banking sites (Toronto Western Hospital - Toronto, Ontario; London Health Sciences Centre - London, Ontario; McGill University - Montreal, Quebec; University of Calgary - Calgary, Alberta) and is continuously looking for more institutions to be a part of the CVBTB. If your institution would like to become a part of the CVBTB, please contact the CVBTB coordinator.

Proper citation: Canadian Virtual Brain Tumour Bank (RRID:SCR_004221) 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://sourceforge.net/projects/mutascope/

Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

Proper citation: Mutascope (RRID:SCR_001265) Copy   

•   Source: SciCrunch Registry

http://www.dtp.nci.nih.gov

Portal for preclinical information and research materials, including web-accessible data and tools, NCI-60 Tumor Cell Line Screen, compounds in vials and plates, tumor cells, animals, and bulk drugs for investigational new drug (IND)-directed studies. DTP has been involved in the discovery or development of more than 70 percent of the anticancer therapeutics on the market today, and will continue helping the academic and private sectors to overcome various therapeutic development barriers, particularly through supporting high-risk projects and therapeutic development for rare cancers. Initially DTP made its drug discovery and development services and the results from the human tumor cell line assay publicly accessible to researchers worldwide. At first, the site offered in vitro human cell line data for a few thousand compounds and in vitro anti-HIV screening data for roughly 42,000 compounds. Today, visitors can find: * Downloadable in vitro human tumor cell line data for some 43,500 compounds and 15,000 natural product extracts * Results for 60,000 compounds evaluated in the yeast assay * In vivo animal model results for 30,000 compounds * 2-D and 3-D chemical structures for more than 200,000 compounds * Molecular target data, including characterizations for at least 1,200 targets, plus data from multiple cDNA microarray projects In addition to browsing DTP's databases and downloading data, researchers can request individual samples or sets of compounds on 96-well plates for research, or they can submit their own compounds for consideration for screening via DTP's online submission form. Once a compound is submitted for screening, researchers can follow its progress and retrieve data using a secure web interface. The NCI has collected information on almost half a million chemical structures in the past 50 years. DTP has made this information accessible and useful for investigators through its 3-D database, a collection of three-dimensional structures for more than 200,000 drugs. Investigators use the 3-D database to screen compounds for anticancer therapeutic activity. Also available on DTP's website are 127,000 connection tables for anticancer agents. A connection table is a convenient way of depicting molecular structures without relying on drawn chemical structures. As unique lists of atoms and their connections, the connection tables can be indexed and stored in computer databases where they can be used for patent searches, toxicology studies, and precursor searching, for example., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Developmental Therapeutics Program (RRID:SCR_003057) Copy   

•   Source: SciCrunch Registry

http://www.georgiacancer.org/res-tissue.php

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013.
The Georgia Cancer Specimen and Tissue Bank is committed to a safe and reliable supply of tissue and cell products for research purposes. Work has begun already to build the state tumor bank initiative with operating sites in several locations through the state. We are confident that our results will yield a strong program that will benefit all Georgians and contribute to significant advances in cancer research and knowledge.

Proper citation: Biorepository Alliance of Georgia for Oncology (RRID:SCR_004184) Copy   

•   Source: SciCrunch Registry

https://scicrunch.org/browse/resourcesedit/SCR_004214

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 18, 2022. A tumor bank that provides a large collection of cancer specimens, from breast and other cancers, annotated with clinical information. The CBCF TB enables researchers to address unanswered questions concerning the prognosis and treatment of breast cancer and other cancers. The CBCF TB website is also directed to participants interested in donating tumor tissue or blood. Biological specimens such as blood, urine, bone marrow, and ascites (fluid that sometimes collects in the abdomen) contain genetic information, just as tumor tissue does. These samples can be used in studies that may help researchers see how people with certain genetic make-ups respond to certain treatments. It can also explain why different people have different health problems. CBCF TB, formerly ARTB, was created by a merger of components of two existing Tumor-banking initiatives, the CLS Repository in Calgary and the Tumor bank of the PolyomX Program in Edmonton.

Proper citation: Canadian Breast Cancer Foundation Tumor Bank (RRID:SCR_004214) Copy   

•   Source: SciCrunch Registry

http://www.azcc.arizona.edu/research/shared-services/tacmass/tissue-acquisition

TACMASS collects, preserves, and banks biospecimens obtained from Arizona Cancer Center surgical patients who are seen by University Medical Center surgeons and oncologists. Biospecimens collected at the time of surgery include fresh surgical tissue, blood and urine. Serum, plasma and genomic DNA are harvested from the whole blood. AZCC Members and collaborators may request the use of banked biospecimens through TACMASS. The patient's surgeon or oncologist is responsible for consenting the patient for submission of surgical specimens to the AZCC BioRepository (IRB #06-0609-04, Setsuko Chambers, PI). The surgeon and the Department of Pathology attending physicians and residents are responsible for identifying appropriate tissue for banking that will not compromise pathological diagnosis. Tumor and/or normal adjacent tissue, identified by gross examination, that will not be needed for pathological diagnosis are preserved by fixing in formalin, snap freezing, and/or fixing in RNALater. Histological diagnosis is rendered on each piece of formalin-fixed and snap frozen tissue by Hematoxylin and Eosin staining (H&E). Everyone involved in submitting specimens to the Tumor Bank must maintain a current CITI Certification.

Proper citation: Arizona Cancer Center Tumor Bank (RRID:SCR_003544) Copy   

•   Source: SciCrunch Registry

https://www.ctrnet.ca/

The Canadian Tumour Repository Network (CTRNet) is a not-for-profit consortium of leading provincial tumor banks and programs that furthers Canadian health research. CTRNet provides interested researchers with a streamlined process to obtain quality human tissue and human tissue products from member tumor banks. The benefits of working with CTRNet.ca include: * The ability for researchers to search for quality controlled tissue samples from Canada''''s leading tumor banks in one central location and for biobanks to display and make their biospecimens available for research users. * Learning opportunities in tissue handling, research design and relevant technology training and innovations. * Invitation to CTRNet workshops and conferences. * A resource for current news links and discussion forums about cancer research and tumor banking. The vision of CTRNet is to create new opportunities for translational cancer research that will improve cancer outcomes in Canada and beyond. Through the creation and maintenance of an online pan-Canadian network, researchers will gain unprecedented access to a new and comprehensive source of tissue and clinical data. The network is a sustainable resource and operates according to the highest scientific and ethical standards for research to benefit all Canadians. Currently CTRNet has the following member banks: * CBCF Tumor Bank Alberta * Manitoba Tumour Bank * Ontario Tumour Bank * British Columbia Cancer Agency Tumour Tissue Repository (BCCA-TTR) * Le r��seau de recherche en cancer du FRSQ * NCIC Clinical Trials Group

Proper citation: Canadian Tumour Repository Network (RRID:SCR_004192) Copy   

•   Source: SciCrunch Registry

http://sunnybrook.ca/research/?page=sri_core_tbank_home

Sunnybrook Research Institute''s tumour bank provides a mechanism for the optimal collection, storage and distribution of human tissue for investigative purposes. We collect both freshly frozen and formalin-fixed paraffin-embedded tumour and normal samples, retrospectively and prospectively (informed consent and confidential consent is obtained from patients before sample collection). We offer the 1. Distribution of tissue and data to interested investigators after approval from the institutional research ethics board and 2. Collaboration with various research investigators. Our mandate is to design, implement and manage the structures and processes to ensure the timely provision of tissue samples and associated data. We are currently building bank on four disease sites: breast, prostate, colorectal, gynecological. We are also creating and maintaining a database with a tissue tracking and inventory system, using TissueMetrix software.

Proper citation: Sunnybrook Tumour Bank (RRID:SCR_004138) Copy   

•   Source: SciCrunch Registry

http://toc.lbg.ac.at/en/research-program/project-tumor-bank

As a basis for the experimental cluster projects, and for further future projects a collection of various biological specimens of cancer patients shall be established. All participating Ludwig Boltzmann Institutes (LBIs) are supplying biological specimens from tumor patients and clinical documentation. At the LBI for Gynecology and Gynecologic Oncology a tumor bank for biological specimens from gynecologic cancer patients already exists. All the procedures for sample processing and storage are well established. Existing equipment for storing tissue specimens at -196 degrees C can be used. Materials from the following malignant diseases are collected: Breast cancer Colorectal cancer Neuroendocrine tumors (NET) (Small cell lung cancer (SCLC) and Carcinoid tumors) Types of biological materials: Tissue (fresh frozen) Bone marrow Blood (serum/plasma/cell fractions) Pleural effusions Ascitic fluids Sputum Bronchial lavage Stool The biological specimens are initially processed at the respective LBIs or at their connected lab facilities. Enrichment of blood samples for disseminated tumor cells is done at the LBI for Gynecology and Gynecologic oncology. Long time storage of all materials is done at appropriate temperatures at the same institution. This LBI also coordinates the logistics. All relevant sample-specific and clinical data are surveyed at the respective LBIs and stored centralized in an on-line data bank in anonymized form, respecting all relevant regulations on data protection and security.

Proper citation: Ludwig Boltzman Tumour Bank (RRID:SCR_004322) Copy   

•   Source: SciCrunch Registry

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