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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
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
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
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
Biospecimen repository of normal and diseased human material from a variety of tissues and conditions along with clinical annotation. Both frozen aliquots and paraffin embedded tissue are available. Biospecimens are available to qualified researchers with IRB approval. * Preliminary inquires please contact Cheryl Spencer at cheryl.spencer (at) bmc.org
Proper citation: Boston University Biospecimen Archive Research Core (RRID:SCR_005363) Copy
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
http://www.einstein.yu.edu/centers/ictr/
Patient-derived specimens are essential to research in genomics, proteomics, and biomarkers. We provide banking for biological fluid and tissue specimens as well as human DNA and RNA. We provide secure archival sample storage as well as clinically-annotated specimen biobanks for defined research projects. The core serves the human research blood and tissue banking needs of clinical and translational researchers. Samples can be banked by an individual PI or by a consortium of investigators. All samples are tracked and archived using a secure tracking database, the Einstein-Montefiore Bio-Repository Databank (EM-BRED), http://informatics30.aecom.yu.edu/em-bred/default.aspx. EM-BRED provides qualified investigators with a solution to securely link patient specimens to clinical and pathological data. It consists of a user-friendly query engine that allows for comprehensive specimen search, and ultimately to build clinical annotations of relevance. The facility works under the best practices set out by NCI and ISBER (2006) for collection, storage, and retrieval of human biological materials for research.
Proper citation: Einstein-Montefiore Institute for Clinical and Translational Research Biorepository (RRID:SCR_005297) Copy
http://molonc.bccrc.ca/platforms/btb/
The Molecular Oncology department hosts the breast cancer tumour tissue repository (BREAST-TTR), a project within the agency-wide tumour tissue repository. The BREAST-TTR comprises several important banks of breast tissues, contemporaneous as well as archival. The main banks are: * 3000 frozen breast cancers, linked to 15 year outcomes data from the BCCA Breast Cancer Outcomes Unit. This archival bank consists of frozen tissue, DNA and RNA, and a tissue microarray of the cases. * Live-cryopreserved cancers. At present around 50 individual cases of metastatic breast cancer, with tumour material cryopreserved for subsequent cell culture/xenograft work. * Comptemporary bank. Between the TTR in Victoria and the accrual site in Vancouver, approximately 1300 contemporaneous (within last 4 years) breast cancers with matched normal DNA and outcomes linkages.
Proper citation: British Columbia Breast Cancer Tumour Bank (RRID:SCR_006671) Copy
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
http://bioinformatics.oxfordjournals.org/content/early/2012/05/10/bioinformatics.bts271.full.pdf
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 7,2024. Software for somatic single nucleotide variant (SNV) and small indel detection from sequencing data of matched tumor-normal samples. The method employs a novel Bayesian approach which represents continuous allele frequencies for both tumor and normal samples, whilst leveraging the expected genotype structure of the normal. This is achieved by representing the normal sample as a mixture of germline variation with noise, and representing the tumor sample as a mixture of the normal sample with somatic variation. A natural consequence of the model structure is that sensitivity can be maintained at high tumor impurity without requiring purity estimates. The method has superior accuracy and sensitivity on impure samples compared to approaches based on either diploid genotype likelihoods or general allele-frequency tests.
Proper citation: Strelka (RRID:SCR_005109) Copy
http://www.cnio.es/ES/grupos/plantillas/presentacion.asp?grupo=50004308
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. The need to use human neoplastic tissue under ideal conditions is currently of particular importance due to the development molecular pathology techniques that allow large-scale studies of genetic expression that are also of clinical significance. The Tumour Bank Network (TBN), instigated and coordinated by the Molecular Pathology Programme (MMP) aims to respond to this need by the promoting of Tumour Banks in Spanish hospitals. This will be achieved through the application of homogeneous procedures for the collection, processing and storage of neoplastic and normal tissue samples in such a way as to make molecular studies possible, avoiding that avoid the intrinsic bias of multi-centre studies possible. These Hospital Tumour Banks are based within the Pathology Departments of the collaborating Hospitals, that are interconnected through a computer-based network. In this way, each Centre''s tissue remains in the Hospital itself, thereby playing a key role in the development of the welfare, teaching and research activities within the Hospital. At the same time, it represents a tool to encourage of multi-hospital cancer research and of cooperation between basic and clinical researchers, constituting important collaboration between biomedical disciplines. The design does not correspond to a Central Tumour Bank, but that of a cooperative and coordinated Network of Hospital Banks, based on simple, homogeneous and optimal tissue treatment protocols. This Network is promoted by the Centro Nacional de Investigaciones Oncologicas (CNIO), which thereby undertakes the work of coordinating the network, using and maintaining the database, adhering to quality control. The aim of the CNIO's TBN is to acquire neoplastic and control non-neoplastic material of all types of malignant neoplasias, in the form of tissue fixed in formalin and paraffin embedded, of samples that are unfixed or frozen according to conventional methods as set out in Annexe 1 and even, exceptionally as fresh tissue. When other types of samples are required to carry out a specific project, the central office of the TBN will draw up a protocol with the group leading the project for the collection and maintenance of the tissue and clinicopathological data required for the proposed research. These protocols will be disseminated among the Associated Hospitals in order to gather the previously agreed number cases. Basic data surrounding the processing and preservation conditions for each case will be sent to the central office of the Bank, which under no circumstances will reveal the identity of the patient. Any Spanish cancer research team will be able to request tissue from the Tissue Bank Network. Absolute priority will be afforded to projects whose principal researcher belongs to one of the Associated Centres of the TNB, to other institutions with special agreements concerning the exchange of samples, and to the CNIO's researchers.
Proper citation: Spanish National Tumour Bank Network (RRID:SCR_008707) Copy
http://www.capitalbiosciences.com/
Biological products including Cell Immortalization Products, Clinically Defined Human Tissue, cDNA ORF Clones, Premade Adenoviruses, Purified Proteins, Viral Expression Systems and others as well as services like Custom Recombinant Adenovirus Production, Custom Recombinant Lentivirus Production, Protein Detection and Quantification and Stable Cell Line Production for academic and governmental research institutes, pharmaceutical and biotechnology industry. Capital Biosciences offers most types of human tissues, normal and diseased, with extensive clinical history and follow up information. Standard specimen format: Snap-frozen(flash-frozen), Formalin fixed and paraffin embedded (FFPE) tissues, Blood and blood products, Bone marrow, Total RNA, Genomic DNA, Total Proteins, Primary cell cultures, Viable frozen tissue. Tumor tissue samples include: Bladder cancer, Glioblastoma, Medulloblastoma, Breast Carcinoma, Cervical Cancer, Colorectal Cancer, Endometrial Cancer, Esophageal Cancer, Head and Neck (H&N) Carcinoma, Hepatocellular Carcinoma (HCC), Hodgkin's lymphoma, Kidney, Renal Cell Carcinoma, Lung Cancer, Non-Small Cell (NCSLC), Lung Cancer, Small Cell (SCLC), Melanoma, Mesothelioma, non-Hodgkin's Lymphoma, Ovarian Adenocarcinoma, Pancreatic Cancer, Prostate Cancer, Stomach Cancer.
Proper citation: Capital Biosciences (RRID:SCR_004879) Copy
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
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
Statistical software to estimate tumor purity, ploidy and absolute copy numbers from next generation sequencing data.
Proper citation: AbsCN-seq (RRID:SCR_006409) Copy
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
http://sourceforge.net/projects/variantmaster/
Software program that extracts causative variants in familial and sporadic genetic diseases. The algorithm takes into account predicted variants (SNPs and indels) in affected individuals or tumor samples and utilizes the row (BAM) data to robustly estimate the conditional probability of segregation in a family, as well as the probability of it being de novo or somatic. In familial cases, various modes of inheritance are considered: X-linked, autosomal dominant, and recessive (homozygosity or compound heterozygosity). Moreover, it integrates phenotypes and genotypes, and employs Annovar to produce additional information as allelic frequencies in general population and damaging scores.
Proper citation: VariantMaster (RRID:SCR_000569) Copy
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
http://cran.r-project.org/web/packages/expands/
Software that characterizes coexisting subpopulations (SPs) in a tumor using copy number and allele frequencies derived from exome- or whole genome sequencing input data. The model amplifies the statistical power to detect coexisting genotypes, by fully exploiting run-specific tradeoffs between depth of coverage and breadth of coverage. ExPANdS predicts the number of clonal expansions, the size of the resulting SPs in the tumor bulk, the mutations specific to each SP and tumor purity. The main function runExPANdS provides the complete functionality needed to predict coexisting SPs from single nucleotide variations (SNVs) and associated copy numbers. The robustness of the subpopulation predictions by ExPANdS increases with the number of mutations provided. It is recommended that at least 200 mutations are used as an input to obtain stable results.
Proper citation: ExPANdS (RRID:SCR_005199) Copy
http://gmt.genome.wustl.edu/somatic-sniper/current/
Software program to identify single nucleotide positions that are different between tumor and normal (or, in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences. It outputs a file in a format very similar to Samtools consensus format. It uses the genotype likelihood model of MAQ (as implemented in Samtools) and then calculates the probability that the tumor and normal genotypes are different. This probability is reported as a somatic score. The somatic score is the Phred-scaled probability (between 0 to 255) that the Tumor and Normal genotypes are not different where 0 means there is no probability that the genotypes are different and 255 means there is a probability of 1 ? 10(255/-10) that the genotypes are different between tumor and normal. This is consistent with how the SAM format reports such probabilities. It is currently available as source code via github or as a Debian APT package.
Proper citation: SomaticSniper (RRID:SCR_005108) Copy
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